From db61806b7f246a4fa3d5cdd78306a7c529c30d83 Mon Sep 17 00:00:00 2001 From: Victor Cano Gil Date: Sun, 23 Jul 2023 02:50:33 -0400 Subject: [PATCH 01/18] setup calculation functions --- src/Cclib.jl | 1 + src/calculation_methods.jl | 40 ++++++++++++++++++++++++++++++++++++++ src/functions.jl | 1 + test.jl | 8 ++++++++ 4 files changed, 50 insertions(+) create mode 100644 src/calculation_methods.jl create mode 100644 test.jl diff --git a/src/Cclib.jl b/src/Cclib.jl index 5d8cd5a..21bcbb4 100644 --- a/src/Cclib.jl +++ b/src/Cclib.jl @@ -5,6 +5,7 @@ using Logging include("functions.jl") include("config.jl") +include("calculation_methods.jl") const cclib = Ref{Py}() diff --git a/src/calculation_methods.jl b/src/calculation_methods.jl new file mode 100644 index 0000000..559a069 --- /dev/null +++ b/src/calculation_methods.jl @@ -0,0 +1,40 @@ +# +# Calculation methods for qchem outputs +# +export cspa + +function cspa(file::String) + #TODO: read in the original data using Julia's ccread + # and then append to that the analysis output + data = cclib[].io.ccread(file) + mol = cclib[].method.CSPA(data) + mol.calculate() + return mol +end + +function mpa(file::String) +end + +function lpa(file::String) +end + +function bpa(file::String) +end + +function getdensitymatrix(file::String) +end + +function mbo(file::String) +end + +function cda(file::String) +end + +function bader(file::String) +end + +function ddec6(file::String) +end + +function hpa(file::String) +end \ No newline at end of file diff --git a/src/functions.jl b/src/functions.jl index 8d3dac2..e454d6f 100644 --- a/src/functions.jl +++ b/src/functions.jl @@ -1,4 +1,5 @@ export ccread +export get_data function pyccread(file) data = cclib[].io.ccread(file) diff --git a/test.jl b/test.jl new file mode 100644 index 0000000..6b2a292 --- /dev/null +++ b/test.jl @@ -0,0 +1,8 @@ +using Cclib + +cclib = Cclib.cclib.x +cpsa = cclib.method.CSPA +mol = cclib.io.ccread("./test/data/uracil_two.xyz") + +a = cpsa(mol) +a.calculate() From c2342c6cd4f73eab209d553f79701e698e136e52 Mon Sep 17 00:00:00 2001 From: Victor Cano Gil Date: Sun, 23 Jul 2023 04:16:42 -0400 Subject: [PATCH 02/18] add calculation funcs, add docs --- docs/make.jl | 1 + docs/src/calculation.md | 3 +++ src/calculation_methods.jl | 22 +++++++++++++++++++++- test.jl | 8 ++++++-- 4 files changed, 31 insertions(+), 3 deletions(-) create mode 100644 docs/src/calculation.md diff --git a/docs/make.jl b/docs/make.jl index fbeaed8..79d5a8f 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -16,6 +16,7 @@ makedocs(; pages=[ "Home" => "index.md", "How to parse files" => "io.md", + "Additional Analyses" => "calculation.md" ], ) diff --git a/docs/src/calculation.md b/docs/src/calculation.md new file mode 100644 index 0000000..720601f --- /dev/null +++ b/docs/src/calculation.md @@ -0,0 +1,3 @@ +# Additional Analyses + +Cclib also allows to further analyse calculation outputs \ No newline at end of file diff --git a/src/calculation_methods.jl b/src/calculation_methods.jl index 559a069..0f00cdf 100644 --- a/src/calculation_methods.jl +++ b/src/calculation_methods.jl @@ -2,6 +2,17 @@ # Calculation methods for qchem outputs # export cspa +export mpa +export density +export lpa +export bpa +export density +export mbo +export cda +export bader +export ddec6 +export hpa + function cspa(file::String) #TODO: read in the original data using Julia's ccread @@ -21,10 +32,19 @@ end function bpa(file::String) end -function getdensitymatrix(file::String) +function density(file::String) + data = cclib[].io.ccread(file) + mol = cclib[].method.Density(data) + mol.calculate() + return pyconvert(Array{Float64}, mol.__dict__["density"]) end +#ToDo: check output dimensions? function mbo(file::String) + data = cclib[].io.ccread(file) + mol = cclib[].method.MBO(data) + mol.calculate() + return pyconvert(Array{Float64}, mol.__dict__["fragresults"]) end function cda(file::String) diff --git a/test.jl b/test.jl index 6b2a292..5786e40 100644 --- a/test.jl +++ b/test.jl @@ -2,7 +2,11 @@ using Cclib cclib = Cclib.cclib.x cpsa = cclib.method.CSPA -mol = cclib.io.ccread("./test/data/uracil_two.xyz") +lpa = cclib.method.LPA +bick = cclib.method.Bickelhaupt +density = cclib.method.Density +mol = cclib.io.ccread("./test/data/Trp_polar.fchk") -a = cpsa(mol) +a = lpa(mol) a.calculate() +a.__dict__.keys() \ No newline at end of file From 8bdfad835b34f6b1a871d021ac84e0e58df2e34d Mon Sep 17 00:00:00 2001 From: Victor Cano Gil Date: Sun, 23 Jul 2023 23:09:40 -0400 Subject: [PATCH 03/18] update cspa func --- src/calculation_methods.jl | 9 ++++++--- test.jl | 12 +++++++++--- 2 files changed, 15 insertions(+), 6 deletions(-) diff --git a/src/calculation_methods.jl b/src/calculation_methods.jl index 0f00cdf..e919689 100644 --- a/src/calculation_methods.jl +++ b/src/calculation_methods.jl @@ -13,14 +13,17 @@ export bader export ddec6 export hpa +expand(x) = pyconvert(Array{Float64}, x[0]) |> x -> reshape(x, (1, size(x)...)) function cspa(file::String) - #TODO: read in the original data using Julia's ccread - # and then append to that the analysis output + #TODO: implement the optional args from docs data = cclib[].io.ccread(file) mol = cclib[].method.CSPA(data) mol.calculate() - return mol + aoresults = mol.__dict__["aoresults"] |> expand + fragresults = mol.__dict__["fragresults"] |> expand + fragcharges = pyconvert(Array{Float64}, mol.__dict__["fragcharges"]) + return (aoresults, fragresults, fragcharges) end function mpa(file::String) diff --git a/test.jl b/test.jl index 5786e40..0baf92f 100644 --- a/test.jl +++ b/test.jl @@ -1,12 +1,18 @@ using Cclib +using PythonCall cclib = Cclib.cclib.x cpsa = cclib.method.CSPA lpa = cclib.method.LPA bick = cclib.method.Bickelhaupt density = cclib.method.Density -mol = cclib.io.ccread("./test/data/Trp_polar.fchk") +mol = cclib.io.ccread("./test/data/Trp_polar_tdhf.out") -a = lpa(mol) +a = cpsa(mol) a.calculate() -a.__dict__.keys() \ No newline at end of file +aoresults = a.__dict__["aoresults"] +fragresults = a.__dict__["fragresults"] +fragcharges = a.__dict__["fragcharges"] + +x = pyconvert(Array{Float64}, fragcharges) +reshape(x, (1, size(x)...)) From cbbc880bff8113a3e0c4f8f9558c0d693e47c7b9 Mon Sep 17 00:00:00 2001 From: Victor Cano Gil Date: Sun, 23 Jul 2023 23:18:51 -0400 Subject: [PATCH 04/18] add more calculation methods --- src/calculation_methods.jl | 23 ++++++++++++++++++++++- test.jl | 5 +++-- 2 files changed, 25 insertions(+), 3 deletions(-) diff --git a/src/calculation_methods.jl b/src/calculation_methods.jl index e919689..371a01c 100644 --- a/src/calculation_methods.jl +++ b/src/calculation_methods.jl @@ -23,16 +23,37 @@ function cspa(file::String) aoresults = mol.__dict__["aoresults"] |> expand fragresults = mol.__dict__["fragresults"] |> expand fragcharges = pyconvert(Array{Float64}, mol.__dict__["fragcharges"]) - return (aoresults, fragresults, fragcharges) + return aoresults, fragresults, fragcharges end function mpa(file::String) + data = cclib[].io.ccread(file) + mol = cclib[].method.MPA(data) + mol.calculate() + aoresults = mol.__dict__["aoresults"] |> expand + fragresults = mol.__dict__["fragresults"] |> expand + fragcharges = pyconvert(Array{Float64}, mol.__dict__["fragcharges"]) + return aoresults, fragresults, fragcharges end function lpa(file::String) + data = cclib[].io.ccread(file) + mol = cclib[].method.LPA(data) + mol.calculate() + aoresults = mol.__dict__["aoresults"] |> expand + fragresults = mol.__dict__["fragresults"] |> expand + fragcharges = pyconvert(Array{Float64}, mol.__dict__["fragcharges"]) + return aoresults, fragresults, fragcharges end function bpa(file::String) + data = cclib[].io.ccread(file) + mol = cclib[].method.Bickelhaupt(data) + mol.calculate() + aoresults = mol.__dict__["aoresults"] |> expand + fragresults = mol.__dict__["fragresults"] |> expand + fragcharges = pyconvert(Array{Float64}, mol.__dict__["fragcharges"]) + return aoresults, fragresults, fragcharges end function density(file::String) diff --git a/test.jl b/test.jl index 0baf92f..d61d4b1 100644 --- a/test.jl +++ b/test.jl @@ -6,10 +6,11 @@ cpsa = cclib.method.CSPA lpa = cclib.method.LPA bick = cclib.method.Bickelhaupt density = cclib.method.Density -mol = cclib.io.ccread("./test/data/Trp_polar_tdhf.out") +mol = cclib.io.ccread("./test/data/Trp_polar.fchk") -a = cpsa(mol) +a = lpa(mol) a.calculate() +a.__dict__.keys() aoresults = a.__dict__["aoresults"] fragresults = a.__dict__["fragresults"] fragcharges = a.__dict__["fragcharges"] From 2891823de5939579fc9f6cee874f06d0d7aa51d5 Mon Sep 17 00:00:00 2001 From: Victor Cano Gil Date: Sun, 23 Jul 2023 23:59:35 -0400 Subject: [PATCH 05/18] udpate doc page --- docs/src/calculation.md | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/docs/src/calculation.md b/docs/src/calculation.md index 720601f..8bc5e4e 100644 --- a/docs/src/calculation.md +++ b/docs/src/calculation.md @@ -1,3 +1,14 @@ # Additional Analyses -Cclib also allows to further analyse calculation outputs \ No newline at end of file +Cclib also allows to further analyse calculation ouputs. + +# C squared population analysis (CSPA) +# Mulliken population analysis (MPA) +# Löwdin Population Analysis +# Bickelhaupt Population Analysis +# Density Matrix calculation +# Mayer’s Bond Orders +# Charge Decomposition Analysis +# Bader’s QTAIM +# DDEC6 +# Hirshfeld Population Analysis \ No newline at end of file From 2e805da9a5b5d0a574c9128a9032c5dee40eb733 Mon Sep 17 00:00:00 2001 From: Victor Cano Gil Date: Thu, 27 Jul 2023 01:34:19 -0400 Subject: [PATCH 06/18] update cda function --- src/calculation_methods.jl | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/src/calculation_methods.jl b/src/calculation_methods.jl index 371a01c..7ec1bbc 100644 --- a/src/calculation_methods.jl +++ b/src/calculation_methods.jl @@ -71,7 +71,13 @@ function mbo(file::String) return pyconvert(Array{Float64}, mol.__dict__["fragresults"]) end -function cda(file::String) +function cda(mol::String, frag1::String, frag2::String) + mol = cclib[].io.ccread(mol) + frag1 = cclib[].io.ccread(frag1) + frag2 = cclib[].io.ccread(frag2) + cda = cclib[].method.MBO(mol) + cda.calculate() + return cda end function bader(file::String) From 7e22ffa80cd6aa31678ff18af7a7e10cc3391e5b Mon Sep 17 00:00:00 2001 From: Victor Cano Gil Date: Thu, 27 Jul 2023 20:49:03 -0400 Subject: [PATCH 07/18] add cda and test files --- test.jl | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/test.jl b/test.jl index d61d4b1..431d0d0 100644 --- a/test.jl +++ b/test.jl @@ -17,3 +17,12 @@ fragcharges = a.__dict__["fragcharges"] x = pyconvert(Array{Float64}, fragcharges) reshape(x, (1, size(x)...)) + + +a = cda( + "./test/data/calculation_methods/cda/BH3CO-sp.log", + "./test/data/calculation_methods/cda/BH3.log", + "./test/data/calculation_methods/cda/CO.log", +) +a.__dict__.keys() +z = a.__dict__["donations"] \ No newline at end of file From d0865b90b8d2aabd3579bb920bba705835d8822d Mon Sep 17 00:00:00 2001 From: Victor Cano Gil Date: Thu, 27 Jul 2023 20:49:24 -0400 Subject: [PATCH 08/18] add cda and test files --- Project.toml | 2 - src/calculation_methods.jl | 20 +- test/data/calculation_methods/cda/BH3.log | 645 +++ .../data/calculation_methods/cda/BH3CO-sp.log | 3619 +++++++++++++++++ test/data/calculation_methods/cda/CO.log | 836 ++++ .../calculation_methods/cda/water_mp2.out | 427 ++ 6 files changed, 5537 insertions(+), 12 deletions(-) create mode 100644 test/data/calculation_methods/cda/BH3.log create mode 100644 test/data/calculation_methods/cda/BH3CO-sp.log create mode 100644 test/data/calculation_methods/cda/CO.log create mode 100644 test/data/calculation_methods/cda/water_mp2.out diff --git a/Project.toml b/Project.toml index cc8d2f2..a0bd239 100644 --- a/Project.toml +++ b/Project.toml @@ -6,12 +6,10 @@ version = "0.2.0" [deps] CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab" Logging = "56ddb016-857b-54e1-b83d-db4d58db5568" -PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d" [compat] CondaPkg = "0.2" -PyCall = "1" PythonCall = "0.9" julia = "1" diff --git a/src/calculation_methods.jl b/src/calculation_methods.jl index 7ec1bbc..1ee6f8a 100644 --- a/src/calculation_methods.jl +++ b/src/calculation_methods.jl @@ -13,7 +13,8 @@ export bader export ddec6 export hpa -expand(x) = pyconvert(Array{Float64}, x[0]) |> x -> reshape(x, (1, size(x)...)) +# remake this function such that it's not (1, size(x)) but len(x), size(x) +expand(x) = pyconvert(Array{Float64}, x[0]) |> x -> reshape(length(x), (1, size(x)...)) function cspa(file::String) #TODO: implement the optional args from docs @@ -71,20 +72,19 @@ function mbo(file::String) return pyconvert(Array{Float64}, mol.__dict__["fragresults"]) end +#TODO Figure out the dimensions function cda(mol::String, frag1::String, frag2::String) mol = cclib[].io.ccread(mol) frag1 = cclib[].io.ccread(frag1) frag2 = cclib[].io.ccread(frag2) - cda = cclib[].method.MBO(mol) - cda.calculate() - return cda + mol = cclib[].method.CDA(mol) + mol.calculate([frag1, frag2]) + return mol + # donations = mol.__dict__["donations"] |> expand + # bdonations = mol.__dict__["bdonations"] |> expand + # repulsions = mol.__dict__["repulsions"] |> expand + # return donations, bdonations, repulsions end function bader(file::String) end - -function ddec6(file::String) -end - -function hpa(file::String) -end \ No newline at end of file diff --git a/test/data/calculation_methods/cda/BH3.log b/test/data/calculation_methods/cda/BH3.log new file mode 100644 index 0000000..29d7cef --- /dev/null +++ b/test/data/calculation_methods/cda/BH3.log @@ -0,0 +1,645 @@ + Entering Gaussian System, Link 0=g03 + Initial command: + //g03/l1.exe /home/adam/BH3CO/Gau-3612.inp -scrdir=/home/adam/BH3CO/ + Entering Link 1 = //g03/l1.exe PID= 3613. + + Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2004, Gaussian, Inc. + All Rights Reserved. + + This is the Gaussian(R) 03 program. It is based on the + the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.), + the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.), + the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.), + the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.), + the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.), + the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon + University), and the Gaussian 82(TM) system (copyright 1983, + Carnegie Mellon University). Gaussian is a federally registered + trademark of Gaussian, Inc. + + This software contains proprietary and confidential information, + including trade secrets, belonging to Gaussian, Inc. + + This software is provided under written license and may be + used, copied, transmitted, or stored only in accord with that + written license. + + The following legend is applicable only to US Government + contracts under FAR: + + RESTRICTED RIGHTS LEGEND + + Use, reproduction and disclosure by the US Government is + subject to restrictions as set forth in subparagraphs (a) + and (c) of the Commercial Computer Software - Restricted + Rights clause in FAR 52.227-19. + + Gaussian, Inc. + 340 Quinnipiac St., Bldg. 40, Wallingford CT 06492 + + + --------------------------------------------------------------- + Warning -- This program may not be used in any manner that + competes with the business of Gaussian, Inc. or will provide + assistance to any competitor of Gaussian, Inc. The licensee + of this program is prohibited from giving any competitor of + Gaussian, Inc. access to this program. By using this program, + the user acknowledges that Gaussian, Inc. is engaged in the + business of creating and licensing software in the field of + computational chemistry and represents and warrants to the + licensee that it is not a competitor of Gaussian, Inc. and that + it will not use this program in any manner prohibited above. + --------------------------------------------------------------- + + + Cite this work as: + Gaussian 03, Revision C.01, + M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, + M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, + K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, + V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, + G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, + R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, + H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, + C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, + A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, + K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, + V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, + O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, + J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, + J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, + I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, + C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, + B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, + Gaussian, Inc., Wallingford CT, 2004. + + ****************************************** + Gaussian 03: IA32L-G03RevC.01 3-Apr-2004 + 26-Jan-2006 + ****************************************** + %Mem=800MB + %NProcShared=2 + Will use up to 2 processors via shared memory. + %chk=bh3co + ----------------------------------------------------------- + #p gfinput iop(6/7=3) pop=full nosym density #HF/6-31G* #SP + ----------------------------------------------------------- + 1/30=1,38=1/1; + 2/15=1,17=6,18=5,40=1/2; + 3/5=1,6=6,7=1,11=9,16=1,24=10,25=1,30=1/1,2,3; + 4//1; + 5/5=2,32=1,38=5/2; + 6/7=3,22=-1,28=1/1; + 99/5=1,9=1/99; + Leave Link 1 at Thu Jan 26 17:16:48 2006, MaxMem= 104857600 cpu: 0.2 + (Enter //g03/l101.exe) + -------- + BH3CO sp + -------- + Symbolic Z-matrix: + Charge = 0 Multiplicity = 1 + B 0.06457 -0.0279 0.01364 + H 0.03117 -0.02317 1.21604 + H 1.16348 0.05251 -0.46818 + H -0.66779 -0.82424 -0.51225 + + Isotopes and Nuclear Properties: + + Atom 1 2 3 4 + IAtWgt= 11 1 1 1 + AtmWgt= 11.0093053 1.0078250 1.0078250 1.0078250 + IAtSpn= 3 1 1 1 + AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 + AtQMom= 4.0650000 0.0000000 0.0000000 0.0000000 + AtGFac= 2.6886370 2.7928460 2.7928460 2.7928460 + Leave Link 101 at Thu Jan 26 17:16:55 2006, MaxMem= 104857600 cpu: 0.1 + (Enter //g03/l202.exe) + Input orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 5 0 0.064567 -0.027896 0.013639 + 2 1 0 0.031167 -0.023173 1.216042 + 3 1 0 1.163475 0.052509 -0.468179 + 4 1 0 -0.667785 -0.824243 -0.512249 + --------------------------------------------------------------------- + Distance matrix (angstroms): + 1 2 3 4 + 1 B 0.000000 + 2 H 1.202876 0.000000 + 3 H 1.202586 2.030874 0.000000 + 4 H 1.202941 2.029098 2.030800 0.000000 + Symmetry turned off by external request. + Stoichiometry BH3 + Framework group C1[X(BH3)] + Deg. of freedom 6 + Full point group C1 NOp 1 + Rotational constants (GHZ): 224.8842512 224.4098725 121.6549033 + Leave Link 202 at Thu Jan 26 17:17:02 2006, MaxMem= 104857600 cpu: 0.3 + (Enter //g03/l301.exe) + Standard basis: 6-31G(d) (6D, 7F) + AO basis set in the form of general basis input: + 1 0 + S 6 1.00 0.000000000000 + 0.2068882250D+04 0.1866274590D-02 + 0.3106495700D+03 0.1425148170D-01 + 0.7068303300D+02 0.6955161850D-01 + 0.1986108030D+02 0.2325729330D+00 + 0.6299304840D+01 0.4670787120D+00 + 0.2127026970D+01 0.3634314400D+00 + SP 3 1.00 0.000000000000 + 0.4727971071D+01 -0.1303937974D+00 0.7459757992D-01 + 0.1190337736D+01 -0.1307889514D+00 0.3078466771D+00 + 0.3594116829D+00 0.1130944484D+01 0.7434568342D+00 + SP 1 1.00 0.000000000000 + 0.1267512469D+00 0.1000000000D+01 0.1000000000D+01 + D 1 1.00 0.000000000000 + 0.6000000000D+00 0.1000000000D+01 + **** + 2 0 + S 3 1.00 0.000000000000 + 0.1873113696D+02 0.3349460434D-01 + 0.2825394365D+01 0.2347269535D+00 + 0.6401216923D+00 0.8137573261D+00 + S 1 1.00 0.000000000000 + 0.1612777588D+00 0.1000000000D+01 + **** + 3 0 + S 3 1.00 0.000000000000 + 0.1873113696D+02 0.3349460434D-01 + 0.2825394365D+01 0.2347269535D+00 + 0.6401216923D+00 0.8137573261D+00 + S 1 1.00 0.000000000000 + 0.1612777588D+00 0.1000000000D+01 + **** + 4 0 + S 3 1.00 0.000000000000 + 0.1873113696D+02 0.3349460434D-01 + 0.2825394365D+01 0.2347269535D+00 + 0.6401216923D+00 0.8137573261D+00 + S 1 1.00 0.000000000000 + 0.1612777588D+00 0.1000000000D+01 + **** + + Integral buffers will be 262144 words long. + Raffenetti 1 integral format. + Two-electron integral symmetry is turned off. + 21 basis functions, 40 primitive gaussians, 21 cartesian basis functions + 4 alpha electrons 4 beta electrons + nuclear repulsion energy 7.3812487277 Hartrees. + IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 + ScaDFX= 1.000000 1.000000 1.000000 1.000000 + IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 + NAtoms= 4 NActive= 4 NUniq= 4 SFac= 1.00D+00 NAtFMM= 60 Big=F + Leave Link 301 at Thu Jan 26 17:17:06 2006, MaxMem= 104857600 cpu: 0.1 + (Enter //g03/l302.exe) + NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1 + NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0. + One-electron integrals computed using PRISM. + NBasis= 21 RedAO= T NBF= 21 + NBsUse= 21 1.00D-06 NBFU= 21 + Leave Link 302 at Thu Jan 26 17:17:09 2006, MaxMem= 104857600 cpu: 0.2 + (Enter //g03/l303.exe) + DipDrv: MaxL=1. + Leave Link 303 at Thu Jan 26 17:17:12 2006, MaxMem= 104857600 cpu: 0.0 + (Enter //g03/l401.exe) + Harris functional with IExCor= 205 diagonalized for initial guess. + ExpMin= 1.27D-01 ExpMax= 2.07D+03 ExpMxC= 3.11D+02 IAcc=1 IRadAn= 1 AccDes= 1.00D-06 + HarFok: IExCor= 205 AccDes= 1.00D-06 IRadAn= 1 IDoV=1 + ScaDFX= 1.000000 1.000000 1.000000 1.000000 + Harris En= -26.4560203302008 + Leave Link 401 at Thu Jan 26 17:17:14 2006, MaxMem= 104857600 cpu: 0.1 + (Enter //g03/l502.exe) + Warning! Cutoffs for single-point calculations used. + Closed shell SCF: + Requested convergence on RMS density matrix=1.00D-04 within 128 cycles. + Requested convergence on MAX density matrix=1.00D-02. + Requested convergence on energy=5.00D-05. + No special actions if energy rises. + Using DIIS extrapolation, IDIIS= 1040. + Two-electron integral symmetry not used. + Keep R1 integrals in memory in canonical form, NReq= 480643. + IEnd= 18750 IEndB= 18750 NGot= 104857600 MDV= 104829143 + LenX= 104829143 + Symmetry not used in FoFDir. + MinBra= 0 MaxBra= 2 Meth= 1. + IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. + + Cycle 1 Pass 1 IDiag 1: + E= -26.3356457813491 + DIIS: error= 5.28D-02 at cycle 1 NSaved= 1. + NSaved= 1 IEnMin= 1 EnMin= -26.3356457813491 IErMin= 1 ErrMin= 5.28D-02 + ErrMax= 5.28D-02 EMaxC= 1.00D-01 BMatC= 3.81D-02 BMatP= 3.81D-02 + IDIUse=3 WtCom= 4.72D-01 WtEn= 5.28D-01 + Coeff-Com: 0.100D+01 + Coeff-En: 0.100D+01 + Coeff: 0.100D+01 + Gap= 0.595 Goal= None Shift= 0.000 + GapD= 0.595 DampG=2.000 DampE=0.500 DampFc=1.0000 IDamp=-1. + RMSDP=9.37D-03 MaxDP=6.75D-02 OVMax= 7.61D-02 + + Cycle 2 Pass 1 IDiag 1: + E= -26.3717458701379 Delta-E= -0.036100088789 Rises=F Damp=F + DIIS: error= 8.49D-03 at cycle 2 NSaved= 2. + NSaved= 2 IEnMin= 2 EnMin= -26.3717458701379 IErMin= 2 ErrMin= 8.49D-03 + ErrMax= 8.49D-03 EMaxC= 1.00D-01 BMatC= 8.66D-04 BMatP= 3.81D-02 + IDIUse=3 WtCom= 9.15D-01 WtEn= 8.49D-02 + Coeff-Com: -0.110D-01 0.101D+01 + Coeff-En: 0.000D+00 0.100D+01 + Coeff: -0.101D-01 0.101D+01 + Gap= 0.559 Goal= None Shift= 0.000 + RMSDP=1.49D-03 MaxDP=1.20D-02 DE=-3.61D-02 OVMax= 9.97D-03 + + Cycle 3 Pass 1 IDiag 1: + E= -26.3723554098431 Delta-E= -0.000609539705 Rises=F Damp=F + DIIS: error= 7.01D-04 at cycle 3 NSaved= 3. + NSaved= 3 IEnMin= 3 EnMin= -26.3723554098431 IErMin= 3 ErrMin= 7.01D-04 + ErrMax= 7.01D-04 EMaxC= 1.00D-01 BMatC= 1.22D-05 BMatP= 8.66D-04 + IDIUse=3 WtCom= 9.93D-01 WtEn= 7.01D-03 + Coeff-Com: -0.856D-02 0.160D-01 0.993D+00 + Coeff-En: 0.000D+00 0.000D+00 0.100D+01 + Coeff: -0.850D-02 0.159D-01 0.993D+00 + Gap= 0.558 Goal= None Shift= 0.000 + RMSDP=2.58D-04 MaxDP=1.68D-03 DE=-6.10D-04 OVMax= 2.21D-03 + + Cycle 4 Pass 1 IDiag 1: + E= -26.3723828174690 Delta-E= -0.000027407626 Rises=F Damp=F + DIIS: error= 3.02D-04 at cycle 4 NSaved= 4. + NSaved= 4 IEnMin= 4 EnMin= -26.3723828174690 IErMin= 4 ErrMin= 3.02D-04 + ErrMax= 3.02D-04 EMaxC= 1.00D-01 BMatC= 9.67D-07 BMatP= 1.22D-05 + IDIUse=3 WtCom= 9.97D-01 WtEn= 3.02D-03 + Coeff-Com: 0.352D-02-0.237D-01-0.331D+00 0.135D+01 + Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.100D+01 + Coeff: 0.350D-02-0.236D-01-0.330D+00 0.135D+01 + Gap= 0.558 Goal= None Shift= 0.000 + RMSDP=1.09D-04 MaxDP=5.66D-04 DE=-2.74D-05 OVMax= 1.14D-03 + + Convergence on energy, delta-E=-2.74D-05 + SCF Done: E(RHF) = -26.3723828175 A.U. after 4 cycles + Convg = 0.1092D-03 -V/T = 2.0004 + S**2 = 0.0000 + KE= 2.636066735779D+01 PE=-7.528664364944D+01 EE= 1.517234474646D+01 + Leave Link 502 at Thu Jan 26 17:17:16 2006, MaxMem= 104857600 cpu: 0.1 + (Enter //g03/l601.exe) + Copying SCF densities to generalized density rwf, ISCF=0 IROHF=0. + + ********************************************************************** + + Population analysis using the SCF density. + + ********************************************************************** + + Alpha occ. eigenvalues -- -7.61630 -0.70186 -0.48652 -0.48608 + Alpha virt. eigenvalues -- 0.07187 0.30915 0.30950 0.32769 0.56964 + Alpha virt. eigenvalues -- 0.56980 0.64771 0.66727 1.15124 1.15206 + Alpha virt. eigenvalues -- 1.19122 1.49234 1.49247 1.77279 2.08048 + Alpha virt. eigenvalues -- 2.08149 3.75913 + Molecular Orbital Coefficients + 1 2 3 4 5 + O O O O V + EIGENVALUES -- -7.61630 -0.70186 -0.48652 -0.48608 0.07187 + 1 1 B 1S 0.99624 -0.18852 -0.00006 0.00000 -0.04818 + 2 2S 0.02363 0.30544 0.00014 0.00001 0.02313 + 3 2PX -0.00042 0.02043 0.33489 0.15094 -0.13976 + 4 2PY 0.00089 -0.04345 0.10357 0.16308 0.29598 + 5 2PZ -0.00024 0.01189 -0.20020 0.33687 -0.08067 + 6 3S -0.01151 0.24382 0.00000 -0.00001 0.34814 + 7 3PX -0.00007 -0.00227 0.12004 0.05421 -0.28602 + 8 3PY 0.00016 0.00485 0.03716 0.05858 0.60599 + 9 3PZ -0.00005 -0.00133 -0.07177 0.12099 -0.16520 + 10 4XX -0.00013 0.02586 0.02850 -0.01574 -0.00004 + 11 4YY -0.00073 0.00176 -0.00754 -0.01525 0.00578 + 12 4ZZ -0.00001 0.03042 -0.02096 0.03099 -0.00114 + 13 4XY 0.00042 0.01690 -0.00372 -0.01876 -0.00407 + 14 4XZ -0.00012 -0.00465 -0.02639 -0.01743 0.00112 + 15 4YZ 0.00024 0.00972 -0.01185 -0.01060 -0.00235 + 16 2 H 1S -0.00012 0.16084 -0.14364 0.22960 -0.03815 + 17 2S 0.00229 0.12543 -0.15872 0.25404 -0.08085 + 18 3 H 1S -0.00012 0.16088 0.27065 0.00956 -0.03824 + 19 2S 0.00229 0.12542 0.29916 0.01058 -0.08115 + 20 4 H 1S -0.00012 0.16082 -0.12707 -0.23918 -0.03815 + 21 2S 0.00230 0.12542 -0.14040 -0.26463 -0.08084 + 6 7 8 9 10 + V V V V V + EIGENVALUES -- 0.30915 0.30950 0.32769 0.56964 0.56980 + 1 1 B 1S -0.00003 0.00081 -0.15874 0.00000 0.00000 + 2 2S 0.00001 -0.00062 0.16571 -0.00176 -0.00030 + 3 2PX 0.07403 -0.16486 0.02399 -0.84053 -0.39269 + 4 2PY 0.08013 -0.05072 -0.05336 -0.25586 -0.41549 + 5 2PZ 0.16581 0.09810 0.01500 0.51683 -0.84433 + 6 3S 0.00072 -0.01446 2.82052 0.00214 0.00042 + 7 3PX 0.71276 -1.59237 0.25253 0.88927 0.41479 + 8 3PY 0.77151 -0.48984 -0.55979 0.27060 0.43879 + 9 3PZ 1.59660 0.94757 0.15716 -0.54669 0.89168 + 10 4XX 0.00995 0.01690 0.02576 -0.04108 0.02200 + 11 4YY 0.00883 -0.00445 0.03136 0.01036 0.02181 + 12 4ZZ -0.01877 -0.01277 0.02453 0.03040 -0.04385 + 13 4XY 0.01139 -0.00170 -0.00402 0.00480 0.02685 + 14 4XZ 0.01110 -0.01627 0.00102 0.03743 0.02552 + 15 4YZ 0.00594 -0.00773 -0.00234 0.01683 0.01523 + 16 2 H 1S -0.07622 -0.04706 -0.02042 0.13470 -0.20939 + 17 2S -1.60647 -0.99750 -1.42045 -0.10493 0.16419 + 18 3 H 1S -0.00307 0.08966 -0.01987 -0.24905 -0.01217 + 19 2S -0.06464 1.90345 -1.40440 0.19361 0.00943 + 20 4 H 1S 0.07924 -0.04179 -0.02041 0.11368 0.22143 + 21 2S 1.67022 -0.88575 -1.42056 -0.08847 -0.17367 + 11 12 13 14 15 + V V V V V + EIGENVALUES -- 0.64771 0.66727 1.15124 1.15206 1.19122 + 1 1 B 1S -0.03749 -0.04307 0.00001 -0.00024 0.04648 + 2 2S -0.54518 -1.51092 -0.00024 0.00688 -1.28524 + 3 2PX -0.45022 0.22218 -0.25787 0.57178 -0.10057 + 4 2PY 0.95507 -0.46809 -0.27817 0.17524 0.22123 + 5 2PZ -0.26047 0.12726 -0.57414 -0.34172 -0.06186 + 6 3S 1.24748 3.08179 0.00065 -0.01676 3.11587 + 7 3PX 0.45177 -0.03998 0.48410 -1.07437 0.19390 + 8 3PY -0.96165 0.07642 0.52221 -0.32930 -0.42751 + 9 3PZ 0.26280 -0.01957 1.07782 0.64209 0.11970 + 10 4XX -0.04819 -0.11163 -0.13712 -0.30652 0.04096 + 11 4YY 0.00880 -0.03569 -0.17925 0.09431 -0.22374 + 12 4ZZ -0.05909 -0.12620 0.31632 0.21290 0.09445 + 13 4XY -0.04005 -0.05344 -0.18908 0.06773 0.18782 + 14 4XZ 0.01094 0.01460 -0.14510 0.25498 -0.05003 + 15 4YZ -0.02304 -0.03070 -0.13550 0.08740 0.10819 + 16 2 H 1S -0.15826 -0.19679 0.70752 0.44027 0.63970 + 17 2S -0.20709 -0.58166 -1.40523 -0.87418 -1.32568 + 18 3 H 1S -0.15817 -0.19652 0.03028 -0.83767 0.63287 + 19 2S -0.20536 -0.57898 -0.06018 1.66497 -1.31216 + 20 4 H 1S -0.15829 -0.19684 -0.73753 0.38799 0.63970 + 21 2S -0.20718 -0.58178 1.46469 -0.77027 -1.32562 + 16 17 18 19 20 + V V V V V + EIGENVALUES -- 1.49234 1.49247 1.77279 2.08048 2.08149 + 1 1 B 1S 0.00001 0.00000 0.06813 0.00016 -0.00002 + 2 2S 0.00005 0.00000 -0.03298 -0.00096 0.00011 + 3 2PX 0.00416 0.00186 -0.02582 -0.27256 0.11455 + 4 2PY 0.00134 0.00203 0.05561 -0.08635 0.12891 + 5 2PZ -0.00250 0.00420 -0.01532 0.15429 0.27465 + 6 3S -0.00013 -0.00001 -0.58162 0.00033 -0.00003 + 7 3PX -0.01440 -0.00642 -0.04918 -0.17573 0.07352 + 8 3PY -0.00447 -0.00696 0.10667 -0.05584 0.08276 + 9 3PZ 0.00856 -0.01444 -0.02946 0.09954 0.17628 + 10 4XX 0.31210 0.44923 -0.21942 -0.79074 -0.37222 + 11 4YY -0.32661 -0.47413 0.70530 0.25886 -0.46508 + 12 4ZZ 0.01447 0.02489 -0.39825 0.53230 0.83726 + 13 4XY -0.60663 0.03730 -0.65132 0.19660 -0.48660 + 14 4XZ 0.28131 0.64153 0.17707 0.66863 -0.35338 + 15 4YZ 0.64544 -0.54968 -0.37468 0.23002 -0.35269 + 16 2 H 1S -0.00719 0.01175 0.43562 -0.45824 -0.77725 + 17 2S -0.00264 0.00418 0.03492 0.12494 0.21354 + 18 3 H 1S 0.01387 0.00046 0.43404 0.90364 -0.00954 + 19 2S 0.00500 0.00016 0.03459 -0.24706 0.00266 + 20 4 H 1S -0.00642 -0.01219 0.43577 -0.44187 0.78643 + 21 2S -0.00235 -0.00434 0.03492 0.12051 -0.21605 + 21 + V + EIGENVALUES -- 3.75913 + 1 1 B 1S -0.47185 + 2 2S 4.19665 + 3 2PX -0.01452 + 4 2PY 0.03080 + 5 2PZ -0.00841 + 6 3S 1.02910 + 7 3PX 0.04437 + 8 3PY -0.09524 + 9 3PZ 0.02616 + 10 4XX -2.11013 + 11 4YY -2.07342 + 12 4ZZ -2.11681 + 13 4XY -0.02556 + 14 4XZ 0.00718 + 15 4YZ -0.01467 + 16 2 H 1S 0.19006 + 17 2S -0.34786 + 18 3 H 1S 0.19034 + 19 2S -0.34756 + 20 4 H 1S 0.19002 + 21 2S -0.34786 + DENSITY MATRIX. + 1 2 3 4 5 + 1 1 B 1S 2.05608 + 2 2S -0.06809 0.18771 + 3 2PX -0.00859 0.01256 0.27071 + 4 2PY 0.01815 -0.02647 0.11682 0.07842 + 5 2PZ -0.00494 0.00720 -0.03191 0.06737 0.30740 + 6 3S -0.11486 0.14840 0.00997 -0.02121 0.00579 + 7 3PX 0.00070 -0.00135 0.09668 0.04274 -0.01159 + 8 3PY -0.00152 0.00298 0.04277 0.02638 0.02470 + 9 3PZ 0.00042 -0.00083 -0.01160 0.02471 0.11022 + 10 4XX -0.01000 0.01580 0.01539 -0.00148 -0.02140 + 11 4YY -0.00212 0.00104 -0.00959 -0.00669 -0.00722 + 12 4ZZ -0.01149 0.01857 -0.00344 0.00312 0.03000 + 13 4XY -0.00553 0.01034 -0.00747 -0.00836 -0.01075 + 14 4XZ 0.00152 -0.00285 -0.02313 -0.01075 -0.00129 + 15 4YZ -0.00318 0.00594 -0.01074 -0.00675 -0.00216 + 16 2 H 1S -0.06086 0.09821 -0.02032 0.03115 0.21603 + 17 2S -0.04270 0.07669 -0.02449 0.03909 0.23769 + 18 3 H 1S -0.06092 0.09835 0.19074 0.04520 -0.09810 + 19 2S -0.04276 0.07681 0.20869 0.05452 -0.10967 + 20 4 H 1S -0.06085 0.09820 -0.15074 -0.11831 -0.10644 + 21 2S -0.04270 0.07668 -0.16880 -0.12629 -0.11910 + 6 7 8 9 10 + 6 3S 0.11916 + 7 3PX -0.00111 0.03471 + 8 3PY 0.00236 0.01525 0.00967 + 9 3PZ -0.00065 -0.00411 0.00883 0.03959 + 10 4XX 0.01261 0.00502 0.00052 -0.00797 0.00346 + 11 4YY 0.00087 -0.00347 -0.00233 -0.00261 0.00014 + 12 4ZZ 0.01483 -0.00181 0.00237 0.01043 -0.00060 + 13 4XY 0.00823 -0.00300 -0.00231 -0.00405 0.00125 + 14 4XZ -0.00226 -0.00820 -0.00405 -0.00042 -0.00120 + 15 4YZ 0.00473 -0.00404 -0.00203 -0.00089 0.00016 + 16 2 H 1S 0.07843 -0.01032 0.01779 0.07575 -0.00710 + 17 2S 0.06110 -0.01113 0.01919 0.08392 -0.01056 + 18 3 H 1S 0.07846 0.06529 0.02279 -0.03697 0.02344 + 19 2S 0.06111 0.07240 0.02469 -0.04072 0.02320 + 20 4 H 1S 0.07843 -0.05717 -0.03590 -0.04006 0.00861 + 21 2S 0.06111 -0.06297 -0.04022 -0.04422 0.00682 + 11 12 13 14 15 + 11 4YY 0.00059 + 12 4ZZ -0.00052 0.00465 + 13 4XY 0.00069 0.00002 0.00130 + 14 4XZ 0.00091 -0.00026 0.00069 0.00204 + 15 4YZ 0.00054 0.00043 0.00081 0.00090 0.00069 + 16 2 H 1S -0.00427 0.03004 -0.00211 -0.00192 0.00166 + 17 2S -0.00492 0.03003 -0.00411 -0.00165 0.00082 + 18 3 H 1S -0.00381 -0.00097 0.00307 -0.01611 -0.00349 + 19 2S -0.00440 -0.00426 0.00162 -0.01732 -0.00487 + 20 4 H 1S 0.00978 0.00028 0.01536 0.01355 0.01120 + 21 2S 0.01063 -0.00289 0.01522 0.01547 0.01137 + 16 17 18 19 20 + 16 2 H 1S 0.19843 + 17 2S 0.20260 0.21093 + 18 3 H 1S -0.02161 -0.04070 0.19845 + 19 2S -0.04074 -0.05811 0.20249 0.21069 + 20 4 H 1S -0.02159 -0.04084 -0.02161 -0.04075 0.19843 + 21 2S -0.04084 -0.05842 -0.04070 -0.05813 0.20261 + 21 + 21 2S 0.21095 + Full Mulliken population analysis: + 1 2 3 4 5 + 1 1 B 1S 2.05608 + 2 2S -0.01517 0.18771 + 3 2PX 0.00000 0.00000 0.27071 + 4 2PY 0.00000 0.00000 0.00000 0.07842 + 5 2PZ 0.00000 0.00000 0.00000 0.00000 0.30740 + 6 3S -0.02282 0.12581 0.00000 0.00000 0.00000 + 7 3PX 0.00000 0.00000 0.06029 0.00000 0.00000 + 8 3PY 0.00000 0.00000 0.00000 0.01645 0.00000 + 9 3PZ 0.00000 0.00000 0.00000 0.00000 0.06874 + 10 4XX -0.00091 0.01142 0.00000 0.00000 0.00000 + 11 4YY -0.00019 0.00075 0.00000 0.00000 0.00000 + 12 4ZZ -0.00105 0.01343 0.00000 0.00000 0.00000 + 13 4XY 0.00000 0.00000 0.00000 0.00000 0.00000 + 14 4XZ 0.00000 0.00000 0.00000 0.00000 0.00000 + 15 4YZ 0.00000 0.00000 0.00000 0.00000 0.00000 + 16 2 H 1S -0.00172 0.02702 0.00022 0.00005 0.08568 + 17 2S -0.00453 0.03993 0.00025 0.00006 0.08600 + 18 3 H 1S -0.00172 0.02707 0.06919 0.00120 0.01560 + 19 2S -0.00454 0.04000 0.06903 0.00132 0.01591 + 20 4 H 1S -0.00172 0.02701 0.03641 0.03107 0.01846 + 21 2S -0.00453 0.03992 0.03720 0.03026 0.01885 + 6 7 8 9 10 + 6 3S 0.11916 + 7 3PX 0.00000 0.03471 + 8 3PY 0.00000 0.00000 0.00967 + 9 3PZ 0.00000 0.00000 0.00000 0.03959 + 10 4XX 0.00795 0.00000 0.00000 0.00000 0.00346 + 11 4YY 0.00055 0.00000 0.00000 0.00000 0.00005 + 12 4ZZ 0.00935 0.00000 0.00000 0.00000 -0.00020 + 13 4XY 0.00000 0.00000 0.00000 0.00000 0.00000 + 14 4XZ 0.00000 0.00000 0.00000 0.00000 0.00000 + 15 4YZ 0.00000 0.00000 0.00000 0.00000 0.00000 + 16 2 H 1S 0.02628 0.00013 0.00003 0.03479 -0.00067 + 17 2S 0.04189 0.00019 0.00005 0.05212 -0.00368 + 18 3 H 1S 0.02630 0.02741 0.00070 0.00681 0.00953 + 19 2S 0.04190 0.04110 0.00103 0.01013 0.01048 + 20 4 H 1S 0.02628 0.01599 0.01092 0.00805 0.00200 + 21 2S 0.04189 0.02382 0.01654 0.01201 0.00269 + 11 12 13 14 15 + 11 4YY 0.00059 + 12 4ZZ -0.00017 0.00465 + 13 4XY 0.00000 0.00000 0.00130 + 14 4XZ 0.00000 0.00000 0.00000 0.00204 + 15 4YZ 0.00000 0.00000 0.00000 0.00000 0.00069 + 16 2 H 1S -0.00040 0.01406 0.00000 0.00003 0.00000 + 17 2S -0.00171 0.01416 0.00000 0.00001 0.00000 + 18 3 H 1S -0.00037 -0.00015 0.00012 0.00382 0.00006 + 19 2S -0.00154 -0.00157 0.00002 0.00135 0.00003 + 20 4 H 1S 0.00252 0.00005 0.00401 0.00234 0.00210 + 21 2S 0.00428 -0.00107 0.00131 0.00088 0.00070 + 16 17 18 19 20 + 16 2 H 1S 0.19843 + 17 2S 0.13337 0.21093 + 18 3 H 1S -0.00013 -0.00388 0.19845 + 19 2S -0.00389 -0.01772 0.13330 0.21069 + 20 4 H 1S -0.00013 -0.00391 -0.00013 -0.00389 0.19843 + 21 2S -0.00391 -0.01785 -0.00388 -0.01773 0.13337 + 21 + 21 2S 0.21095 + Gross orbital populations: + 1 + 1 1 B 1S 1.99717 + 2 2S 0.52489 + 3 2PX 0.54329 + 4 2PY 0.15883 + 5 2PZ 0.61665 + 6 3S 0.44455 + 7 3PX 0.20365 + 8 3PY 0.05539 + 9 3PZ 0.23224 + 10 4XX 0.04211 + 11 4YY 0.00435 + 12 4ZZ 0.05148 + 13 4XY 0.00676 + 14 4XZ 0.01048 + 15 4YZ 0.00359 + 16 2 H 1S 0.50926 + 17 2S 0.52565 + 18 3 H 1S 0.50931 + 19 2S 0.52542 + 20 4 H 1S 0.50924 + 21 2S 0.52569 + Condensed to atoms (all electrons): + 1 2 3 4 + 1 B 3.664708 0.410241 0.410236 0.410238 + 2 H 0.410241 0.676096 -0.025621 -0.025801 + 3 H 0.410236 -0.025621 0.675742 -0.025631 + 4 H 0.410238 -0.025801 -0.025631 0.676130 + Mulliken atomic charges: + 1 + 1 B 0.104577 + 2 H -0.034915 + 3 H -0.034726 + 4 H -0.034936 + Sum of Mulliken charges= 0.00000 + Atomic charges with hydrogens summed into heavy atoms: + 1 + 1 B 0.000000 + 2 H 0.000000 + 3 H 0.000000 + 4 H 0.000000 + Sum of Mulliken charges= 0.00000 + Electronic spatial extent (au): = 35.3134 + Charge= 0.0000 electrons + Dipole moment (field-independent basis, Debye): + X= -0.2979 Y= 0.6348 Z= -0.1736 Tot= 0.7224 + Quadrupole moment (field-independent basis, Debye-Ang): + XX= -9.0945 YY= -7.5847 ZZ= -9.3518 + XY= -0.8672 XZ= 0.2329 YZ= -0.5165 + Traceless Quadrupole moment (field-independent basis, Debye-Ang): + XX= -0.4175 YY= 1.0923 ZZ= -0.6748 + XY= -0.8672 XZ= 0.2329 YZ= -0.5165 + Octapole moment (field-independent basis, Debye-Ang**2): + XXX= -2.9281 YYY= 3.2175 ZZZ= -1.1685 XYY= -0.8820 + XXY= 0.9821 XXZ= -0.2098 XZZ= -0.9509 YZZ= 1.0252 + YYZ= -0.3234 XYZ= 0.0325 + Hexadecapole moment (field-independent basis, Debye-Ang**3): + XXXX= -21.4973 YYYY= -11.8724 ZZZZ= -22.7465 XXXY= -2.6658 + XXXZ= 0.5758 YYYX= -2.6008 YYYZ= -1.5484 ZZZX= 0.7261 + ZZZY= -1.6768 XXYY= -5.5717 XXZZ= -7.4803 YYZZ= -5.8723 + XXYZ= -0.4757 YYXZ= 0.3439 ZZXY= -0.8681 + N-N= 7.381248727730D+00 E-N=-7.528676373606D+01 KE= 2.636066735779D+01 + Orbital energies and kinetic energies (alpha): + 1 2 + 1 O -7.61630 10.90178 + 2 O -0.70186 0.85369 + 3 O -0.48652 0.71248 + 4 O -0.48608 0.71238 + 5 V 0.07187 0.52619 + 6 V 0.30915 0.55943 + 7 V 0.30950 0.55941 + 8 V 0.32769 0.85035 + 9 V 0.56964 1.33357 + 10 V 0.56980 1.33412 + 11 V 0.64771 1.54114 + 12 V 0.66727 1.24746 + 13 V 1.15124 2.15988 + 14 V 1.15206 2.16149 + 15 V 1.19122 2.32068 + 16 V 1.49234 2.10004 + 17 V 1.49247 2.10004 + 18 V 1.77279 2.52161 + 19 V 2.08048 2.97362 + 20 V 2.08149 2.97472 + 21 V 3.75913 7.76513 + Total kinetic energy from orbitals= 2.636066735779D+01 + No NMR shielding tensors so no spin-rotation constants. + Leave Link 601 at Thu Jan 26 17:17:19 2006, MaxMem= 104857600 cpu: 0.2 + (Enter //g03/l9999.exe) + + Test job not archived. + 1\1\GINC-KOH18\SP\RHF\6-31G(d)\B1H3\ADAM\26-Jan-2006\0\\#P GFINPUT IOP + (6/7=3) POP=FULL NOSYM DENSITY #HF/6-31G* #SP\\BH3CO sp\\0,1\B,0,0.064 + 567,-0.027896,0.013639\H,0,0.031167,-0.023173,1.216042\H,0,1.163475,0. + 052509,-0.468179\H,0,-0.667785,-0.824243,-0.512249\\Version=IA32L-G03R + evC.01\HF=-26.3723828\RMSD=1.092e-04\Dipole=-0.1171996,0.2497466,-0.06 + 82855\PG=C01 [X(B1H3)]\\@ + + + NOTHING PUZZLES ME MORE THAN TIME AND SPACE; AND YET NOTHING TROUBLES ME LESS + -- CHARLES LAMB (1810) + Job cpu time: 0 days 0 hours 0 minutes 18.4 seconds. + File lengths (MBytes): RWF= 11 Int= 0 D2E= 0 Chk= 7 Scr= 1 + Normal termination of Gaussian 03 at Thu Jan 26 17:17:22 2006. diff --git a/test/data/calculation_methods/cda/BH3CO-sp.log b/test/data/calculation_methods/cda/BH3CO-sp.log new file mode 100644 index 0000000..a5a44e8 --- /dev/null +++ b/test/data/calculation_methods/cda/BH3CO-sp.log @@ -0,0 +1,3619 @@ + Entering Gaussian System, Link 0=g03 + Initial command: + //g03/l1.exe /home/adam/BH3CO/Gau-5330.inp -scrdir=/home/adam/BH3CO/ + Entering Link 1 = //g03/l1.exe PID= 5331. + + Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2004, Gaussian, Inc. + All Rights Reserved. + + This is the Gaussian(R) 03 program. It is based on the + the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.), + the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.), + the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.), + the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.), + the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.), + the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon + University), and the Gaussian 82(TM) system (copyright 1983, + Carnegie Mellon University). Gaussian is a federally registered + trademark of Gaussian, Inc. + + This software contains proprietary and confidential information, + including trade secrets, belonging to Gaussian, Inc. + + This software is provided under written license and may be + used, copied, transmitted, or stored only in accord with that + written license. + + The following legend is applicable only to US Government + contracts under FAR: + + RESTRICTED RIGHTS LEGEND + + Use, reproduction and disclosure by the US Government is + subject to restrictions as set forth in subparagraphs (a) + and (c) of the Commercial Computer Software - Restricted + Rights clause in FAR 52.227-19. + + Gaussian, Inc. + 340 Quinnipiac St., Bldg. 40, Wallingford CT 06492 + + + --------------------------------------------------------------- + Warning -- This program may not be used in any manner that + competes with the business of Gaussian, Inc. or will provide + assistance to any competitor of Gaussian, Inc. The licensee + of this program is prohibited from giving any competitor of + Gaussian, Inc. access to this program. By using this program, + the user acknowledges that Gaussian, Inc. is engaged in the + business of creating and licensing software in the field of + computational chemistry and represents and warrants to the + licensee that it is not a competitor of Gaussian, Inc. and that + it will not use this program in any manner prohibited above. + --------------------------------------------------------------- + + + Cite this work as: + Gaussian 03, Revision C.01, + M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, + M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, + K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, + V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, + G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, + R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, + H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, + C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, + A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, + K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, + V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, + O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, + J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, + J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, + I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, + C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, + B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, + Gaussian, Inc., Wallingford CT, 2004. + + ****************************************** + Gaussian 03: IA32L-G03RevC.01 3-Apr-2004 + 26-Jan-2006 + ****************************************** + %Mem=800MB + %NProcShared=2 + Will use up to 2 processors via shared memory. + %chk=bh3co + ---------------------------------------------------------------------- + #p gfinput iop(6/7=3) iop(3/33=1) iop(3/36=-1) #HF/6-31G* pop=full den + sity nosym #SP + ---------------------------------------------------------------------- + 1/30=1,38=1/1; + 2/15=1,17=6,18=5,40=1/2; + 3/5=1,6=6,7=1,11=9,16=1,24=10,25=1,30=1,33=1,36=-1/1,2,3; + 4//1; + 5/5=2,32=1,38=5/2; + 6/7=3,22=-1,28=1/1; + 99/5=1,9=1/99; + Leave Link 1 at Thu Jan 26 17:17:11 2006, MaxMem= 104857600 cpu: 0.4 + (Enter //g03/l101.exe) + -------- + BH3CO sp + -------- + Symbolic Z-matrix: + Charge = 0 Multiplicity = 1 + B 0.06457 -0.0279 0.01364 + H 0.03117 -0.02317 1.21604 + H 1.16348 0.05251 -0.46818 + H -0.66779 -0.82424 -0.51225 + C -0.61187 1.40183 -0.37553 + O -1.07258 2.37408 -0.64075 + + Isotopes and Nuclear Properties: + + Atom 1 2 3 4 5 6 + IAtWgt= 11 1 1 1 12 16 + AtmWgt= 11.0093053 1.0078250 1.0078250 1.0078250 12.0000000 15.9949146 + IAtSpn= 3 1 1 1 0 0 + AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 + AtQMom= 4.0650000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 + AtGFac= 2.6886370 2.7928460 2.7928460 2.7928460 0.0000000 0.0000000 + Leave Link 101 at Thu Jan 26 17:17:13 2006, MaxMem= 104857600 cpu: 0.1 + (Enter //g03/l202.exe) + Input orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 5 0 0.064567 -0.027896 0.013639 + 2 1 0 0.031167 -0.023173 1.216042 + 3 1 0 1.163475 0.052509 -0.468179 + 4 1 0 -0.667785 -0.824243 -0.512249 + 5 6 0 -0.611870 1.401829 -0.375526 + 6 8 0 -1.072579 2.374082 -0.640747 + --------------------------------------------------------------------- + Distance matrix (angstroms): + 1 2 3 4 5 + 1 B 0.000000 + 2 H 1.202876 0.000000 + 3 H 1.202586 2.030874 0.000000 + 4 H 1.202941 2.029098 2.030800 0.000000 + 5 C 1.628843 2.230967 2.231838 2.230968 0.000000 + 6 O 2.736936 3.226880 3.227912 3.226399 1.108093 + 6 + 6 O 0.000000 + Symmetry turned off by external request. + Stoichiometry CH3BO + Framework group C1[X(CH3BO)] + Deg. of freedom 12 + Full point group C1 NOp 1 + Rotational constants (GHZ): 121.6548511 8.2876598 8.2870144 + Leave Link 202 at Thu Jan 26 17:17:17 2006, MaxMem= 104857600 cpu: 0.1 + (Enter //g03/l301.exe) + Standard basis: 6-31G(d) (6D, 7F) + Coordinates in L301: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 5 0 0.064567 -0.027896 0.013639 + 2 1 0 0.031167 -0.023173 1.216042 + 3 1 0 1.163475 0.052509 -0.468179 + 4 1 0 -0.667785 -0.824243 -0.512249 + 5 6 0 -0.611870 1.401829 -0.375526 + 6 8 0 -1.072579 2.374082 -0.640747 + --------------------------------------------------------------------- + AO basis set in the form of general basis input: + 1 0 + S 6 1.00 0.000000000000 + 0.2068882250D+04 0.1866274590D-02 + 0.3106495700D+03 0.1425148170D-01 + 0.7068303300D+02 0.6955161850D-01 + 0.1986108030D+02 0.2325729330D+00 + 0.6299304840D+01 0.4670787120D+00 + 0.2127026970D+01 0.3634314400D+00 + SP 3 1.00 0.000000000000 + 0.4727971071D+01 -0.1303937974D+00 0.7459757992D-01 + 0.1190337736D+01 -0.1307889514D+00 0.3078466771D+00 + 0.3594116829D+00 0.1130944484D+01 0.7434568342D+00 + SP 1 1.00 0.000000000000 + 0.1267512469D+00 0.1000000000D+01 0.1000000000D+01 + D 1 1.00 0.000000000000 + 0.6000000000D+00 0.1000000000D+01 + **** + 2 0 + S 3 1.00 0.000000000000 + 0.1873113696D+02 0.3349460434D-01 + 0.2825394365D+01 0.2347269535D+00 + 0.6401216923D+00 0.8137573261D+00 + S 1 1.00 0.000000000000 + 0.1612777588D+00 0.1000000000D+01 + **** + 3 0 + S 3 1.00 0.000000000000 + 0.1873113696D+02 0.3349460434D-01 + 0.2825394365D+01 0.2347269535D+00 + 0.6401216923D+00 0.8137573261D+00 + S 1 1.00 0.000000000000 + 0.1612777588D+00 0.1000000000D+01 + **** + 4 0 + S 3 1.00 0.000000000000 + 0.1873113696D+02 0.3349460434D-01 + 0.2825394365D+01 0.2347269535D+00 + 0.6401216923D+00 0.8137573261D+00 + S 1 1.00 0.000000000000 + 0.1612777588D+00 0.1000000000D+01 + **** + 5 0 + S 6 1.00 0.000000000000 + 0.3047524880D+04 0.1834737132D-02 + 0.4573695180D+03 0.1403732281D-01 + 0.1039486850D+03 0.6884262226D-01 + 0.2921015530D+02 0.2321844432D+00 + 0.9286662960D+01 0.4679413484D+00 + 0.3163926960D+01 0.3623119853D+00 + SP 3 1.00 0.000000000000 + 0.7868272350D+01 -0.1193324198D+00 0.6899906659D-01 + 0.1881288540D+01 -0.1608541517D+00 0.3164239610D+00 + 0.5442492580D+00 0.1143456438D+01 0.7443082909D+00 + SP 1 1.00 0.000000000000 + 0.1687144782D+00 0.1000000000D+01 0.1000000000D+01 + D 1 1.00 0.000000000000 + 0.8000000000D+00 0.1000000000D+01 + **** + 6 0 + S 6 1.00 0.000000000000 + 0.5484671660D+04 0.1831074430D-02 + 0.8252349460D+03 0.1395017220D-01 + 0.1880469580D+03 0.6844507810D-01 + 0.5296450000D+02 0.2327143360D+00 + 0.1689757040D+02 0.4701928980D+00 + 0.5799635340D+01 0.3585208530D+00 + SP 3 1.00 0.000000000000 + 0.1553961625D+02 -0.1107775495D+00 0.7087426823D-01 + 0.3599933586D+01 -0.1480262627D+00 0.3397528391D+00 + 0.1013761750D+01 0.1130767015D+01 0.7271585773D+00 + SP 1 1.00 0.000000000000 + 0.2700058226D+00 0.1000000000D+01 0.1000000000D+01 + D 1 1.00 0.000000000000 + 0.8000000000D+00 0.1000000000D+01 + **** + + LdAtmC: AtmChg= 5.000000 1.000000 1.000000 1.000000 6.000000 + LdAtmC: AtmChg= 8.000000 + AtZEff= -2.7500000 -1.0000000 -1.0000000 -1.0000000 -3.6000000 -5.6000000 + Integral buffers will be 262144 words long. + Raffenetti 1 integral format. + Two-electron integral symmetry is turned off. + 51 basis functions, 96 primitive gaussians, 51 cartesian basis functions + 11 alpha electrons 11 beta electrons + nuclear repulsion energy 55.9887222516 Hartrees. + IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 + ScaDFX= 1.000000 1.000000 1.000000 1.000000 + IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 + NAtoms= 6 NActive= 6 NUniq= 6 SFac= 1.00D+00 NAtFMM= 60 Big=F + Leave Link 301 at Thu Jan 26 17:17:20 2006, MaxMem= 104857600 cpu: 0.1 + (Enter //g03/l302.exe) + NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1 + NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0. + One-electron integrals computed using PRISM. + Entering OneElI... + Calculate overlap and kinetic energy integrals + NBasis = 51 MinDer = 0 MaxDer = 0 + Requested accuracy = 0.1000D-12 + PrsmSu: NPrtUS= 1 ThrOK=F + PRISM was handed 104826643 working-precision words and 171 shell-pairs + *** Overlap *** + 1 2 3 4 5 + 1 0.100000D+01 + 2 0.222815D+00 0.100000D+01 + 3 0.000000D+00 0.000000D+00 0.100000D+01 + 4 0.000000D+00 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0.000000D+00-0.532261D-01 + 6 + 1 0.000000D+00 + 2 0.249800D-04 + 3-0.423105D-04 + 4 0.893719D-04 + 5-0.243481D-04 + 6 0.510030D-02 + 7-0.780400D-02 + 8 0.164843D-01 + 9-0.449092D-02 + 10 0.000000D+00 + 11 0.148467D-05 + 12 0.000000D+00 + 13-0.121741D-05 + 14 0.000000D+00 + 15 0.000000D+00 + 16 0.000000D+00 + 17 0.450925D-03 + 18 0.000000D+00 + 19 0.449198D-03 + 20 0.000000D+00 + 21 0.451731D-03 + 22 0.000000D+00 + 23 0.474379D-01 + 24-0.399320D-01 + 25 0.842701D-01 + 26-0.229881D-01 + 27 0.895348D-01 + 28-0.640359D-01 + 29 0.135138D+00 + 30-0.368642D-01 + 31 0.252947D-01 + 32 0.112651D+00 + 33 0.838287D-02 + 34-0.924578D-01 + 35 0.252216D-01 + 36-0.532261D-01 + 37 0.118438D+02 + 38-0.794473D-01 + 39 0.000000D+00 + 40 0.000000D+00 + 41 0.000000D+00 + 42 0.266956D+00 + 43 0.000000D+00 + 44 0.000000D+00 + 45 0.000000D+00 + 46 0.000000D+00 + 47 0.000000D+00 + 48 0.000000D+00 + 49 0.000000D+00 + 50 0.000000D+00 + 51 0.000000D+00 + Leave Link 303 at Thu Jan 26 17:17:26 2006, MaxMem= 104857600 cpu: 0.0 + (Enter //g03/l401.exe) + Harris functional with IExCor= 205 diagonalized for initial guess. + ExpMin= 1.27D-01 ExpMax= 5.48D+03 ExpMxC= 8.25D+02 IAcc=1 IRadAn= 1 AccDes= 1.00D-06 + HarFok: IExCor= 205 AccDes= 1.00D-06 IRadAn= 1 IDoV=1 + ScaDFX= 1.000000 1.000000 1.000000 1.000000 + Harris En= -139.295009497094 + Leave Link 401 at Thu Jan 26 17:17:29 2006, MaxMem= 104857600 cpu: 0.3 + (Enter //g03/l502.exe) + Warning! Cutoffs for single-point calculations used. + Closed shell SCF: + Requested convergence on RMS density matrix=1.00D-04 within 128 cycles. + Requested convergence on MAX density matrix=1.00D-02. + Requested convergence on energy=5.00D-05. + No special actions if energy rises. + Using DIIS extrapolation, IDIIS= 1040. + Two-electron integral symmetry not used. + Keep R1 integrals in memory in canonical form, NReq= 1404848. + IEnd= 26080 IEndB= 26080 NGot= 104857600 MDV= 103970998 + LenX= 103970998 + Symmetry not used in FoFDir. + MinBra= 0 MaxBra= 2 Meth= 1. + IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. + + Cycle 1 Pass 1 IDiag 1: + E= -139.003674398715 + DIIS: error= 5.22D-02 at cycle 1 NSaved= 1. + NSaved= 1 IEnMin= 1 EnMin= -139.003674398715 IErMin= 1 ErrMin= 5.22D-02 + ErrMax= 5.22D-02 EMaxC= 1.00D-01 BMatC= 1.78D-01 BMatP= 1.78D-01 + IDIUse=3 WtCom= 4.78D-01 WtEn= 5.22D-01 + Coeff-Com: 0.100D+01 + Coeff-En: 0.100D+01 + Coeff: 0.100D+01 + Gap= 0.509 Goal= None Shift= 0.000 + GapD= 0.509 DampG=2.000 DampE=0.500 DampFc=1.0000 IDamp=-1. + RMSDP=8.34D-03 MaxDP=1.11D-01 OVMax= 1.28D-01 + + Cycle 2 Pass 1 IDiag 1: + E= -139.133780549689 Delta-E= -0.130106150975 Rises=F Damp=F + DIIS: error= 1.19D-02 at cycle 2 NSaved= 2. + NSaved= 2 IEnMin= 2 EnMin= -139.133780549689 IErMin= 2 ErrMin= 1.19D-02 + ErrMax= 1.19D-02 EMaxC= 1.00D-01 BMatC= 7.59D-03 BMatP= 1.78D-01 + IDIUse=3 WtCom= 8.81D-01 WtEn= 1.19D-01 + Coeff-Com: 0.819D-01 0.918D+00 + Coeff-En: 0.000D+00 0.100D+01 + Coeff: 0.721D-01 0.928D+00 + Gap= 0.592 Goal= None Shift= 0.000 + RMSDP=1.85D-03 MaxDP=2.37D-02 DE=-1.30D-01 OVMax= 3.31D-02 + + Cycle 3 Pass 1 IDiag 1: + E= -139.141759097974 Delta-E= -0.007978548284 Rises=F Damp=F + DIIS: error= 2.33D-03 at cycle 3 NSaved= 3. + NSaved= 3 IEnMin= 3 EnMin= -139.141759097974 IErMin= 3 ErrMin= 2.33D-03 + ErrMax= 2.33D-03 EMaxC= 1.00D-01 BMatC= 4.90D-04 BMatP= 7.59D-03 + IDIUse=3 WtCom= 9.77D-01 WtEn= 2.33D-02 + Coeff-Com: -0.209D-01 0.107D+00 0.914D+00 + Coeff-En: 0.000D+00 0.000D+00 0.100D+01 + Coeff: -0.204D-01 0.105D+00 0.916D+00 + Gap= 0.582 Goal= None Shift= 0.000 + RMSDP=5.53D-04 MaxDP=6.53D-03 DE=-7.98D-03 OVMax= 9.35D-03 + + Cycle 4 Pass 1 IDiag 1: + E= -139.142303648709 Delta-E= -0.000544550735 Rises=F Damp=F + DIIS: error= 1.03D-03 at cycle 4 NSaved= 4. + NSaved= 4 IEnMin= 4 EnMin= -139.142303648709 IErMin= 4 ErrMin= 1.03D-03 + ErrMax= 1.03D-03 EMaxC= 1.00D-01 BMatC= 6.85D-05 BMatP= 4.90D-04 + IDIUse=3 WtCom= 9.90D-01 WtEn= 1.03D-02 + Coeff-Com: -0.700D-02 0.322D-02 0.237D+00 0.767D+00 + Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.100D+01 + Coeff: -0.693D-02 0.319D-02 0.235D+00 0.769D+00 + Gap= 0.582 Goal= None Shift= 0.000 + RMSDP=1.67D-04 MaxDP=2.18D-03 DE=-5.45D-04 OVMax= 3.27D-03 + + Cycle 5 Pass 1 IDiag 1: + E= -139.142387763875 Delta-E= -0.000084115166 Rises=F Damp=F + DIIS: error= 3.76D-04 at cycle 5 NSaved= 5. + NSaved= 5 IEnMin= 5 EnMin= -139.142387763875 IErMin= 5 ErrMin= 3.76D-04 + ErrMax= 3.76D-04 EMaxC= 1.00D-01 BMatC= 1.33D-05 BMatP= 6.85D-05 + IDIUse=3 WtCom= 9.96D-01 WtEn= 3.76D-03 + Coeff-Com: 0.294D-02-0.193D-01-0.179D+00 0.137D+00 0.106D+01 + Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.100D+01 + Coeff: 0.293D-02-0.192D-01-0.178D+00 0.136D+00 0.106D+01 + Gap= 0.584 Goal= None Shift= 0.000 + RMSDP=1.33D-04 MaxDP=1.58D-03 DE=-8.41D-05 OVMax= 2.11D-03 + + Cycle 6 Pass 1 IDiag 1: + E= -139.142410953335 Delta-E= -0.000023189461 Rises=F Damp=F + DIIS: error= 7.84D-05 at cycle 6 NSaved= 6. + NSaved= 6 IEnMin= 6 EnMin= -139.142410953335 IErMin= 6 ErrMin= 7.84D-05 + ErrMax= 7.84D-05 EMaxC= 1.00D-01 BMatC= 2.94D-07 BMatP= 1.33D-05 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: 0.684D-03-0.270D-02-0.340D-01-0.331D-01 0.841D-01 0.985D+00 + Coeff: 0.684D-03-0.270D-02-0.340D-01-0.331D-01 0.841D-01 0.985D+00 + Gap= 0.583 Goal= None Shift= 0.000 + RMSDP=2.59D-05 MaxDP=3.55D-04 DE=-2.32D-05 OVMax= 5.39D-04 + + SCF Done: E(RHF) = -139.142410953 A.U. after 6 cycles + Convg = 0.2588D-04 -V/T = 2.0019 + S**2 = 0.0000 + KE= 1.388757376541D+02 PE=-4.373466502895D+02 EE= 1.033397794304D+02 + Leave Link 502 at Thu Jan 26 17:17:33 2006, MaxMem= 104857600 cpu: 0.7 + (Enter //g03/l601.exe) + Copying SCF densities to generalized density rwf, ISCF=0 IROHF=0. + + ********************************************************************** + + Population analysis using the SCF density. + + ********************************************************************** + + Alpha occ. eigenvalues -- -20.73284 -11.44012 -7.55950 -1.59082 -0.88263 + Alpha occ. eigenvalues -- -0.79509 -0.70208 -0.70207 -0.55502 -0.46757 + Alpha occ. eigenvalues -- -0.46719 + Alpha virt. eigenvalues -- 0.11613 0.11615 0.27722 0.30175 0.34596 + Alpha virt. eigenvalues -- 0.34643 0.39349 0.60155 0.60162 0.72699 + Alpha virt. eigenvalues -- 0.72707 0.73220 0.87060 0.96122 1.09400 + Alpha virt. eigenvalues -- 1.14585 1.14640 1.19829 1.19851 1.24168 + Alpha virt. eigenvalues -- 1.42563 1.49528 1.49542 1.67330 1.67331 + Alpha 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50 4XZ 0.00000 0.00000 0.00000 0.00000 0.00080 + 51 4YZ 0.00000 0.00000 0.00000 0.00000 0.00000 + 51 + 51 4YZ 0.00280 + Gross orbital populations: + 1 + 1 1 B 1S 1.99714 + 2 2S 0.46407 + 3 2PX 0.56399 + 4 2PY 0.40390 + 5 2PZ 0.59436 + 6 3S 0.35371 + 7 3PX 0.22595 + 8 3PY 0.10204 + 9 3PZ 0.24974 + 10 4XX 0.03843 + 11 4YY 0.02001 + 12 4ZZ 0.04639 + 13 4XY 0.01483 + 14 4XZ 0.01141 + 15 4YZ 0.00661 + 16 2 H 1S 0.50221 + 17 2S 0.54362 + 18 3 H 1S 0.50229 + 19 2S 0.54336 + 20 4 H 1S 0.50218 + 21 2S 0.54361 + 22 5 C 1S 1.99811 + 23 2S 0.80825 + 24 2PX 0.45370 + 25 2PY 0.76258 + 26 2PZ 0.39387 + 27 3S 0.61718 + 28 3PX 0.14876 + 29 3PY 0.07858 + 30 3PZ 0.16237 + 31 4XX -0.00548 + 32 4YY 0.03758 + 33 4ZZ -0.01584 + 34 4XY 0.02267 + 35 4XZ 0.00647 + 36 4YZ 0.02344 + 37 6 O 1S 1.99569 + 38 2S 0.93276 + 39 2PX 0.92590 + 40 2PY 0.99431 + 41 2PZ 0.91270 + 42 3S 0.90414 + 43 3PX 0.55181 + 44 3PY 0.43256 + 45 3PZ 0.57493 + 46 4XX 0.00673 + 47 4YY 0.01721 + 48 4ZZ 0.00342 + 49 4XY 0.01075 + 50 4XZ 0.00333 + 51 4YZ 0.01169 + Condensed to atoms (all electrons): + 1 2 3 4 5 6 + 1 B 3.649835 0.405590 0.405671 0.405617 0.251183 -0.025336 + 2 H 0.405590 0.692841 -0.015305 -0.015494 -0.021950 0.000152 + 3 H 0.405671 -0.015305 0.692397 -0.015324 -0.021935 0.000153 + 4 H 0.405617 -0.015494 -0.015324 0.692803 -0.021953 0.000144 + 5 C 0.251183 -0.021950 -0.021935 -0.021953 4.634861 0.672039 + 6 O -0.025336 0.000152 0.000153 0.000144 0.672039 7.630758 + Mulliken atomic charges: + 1 + 1 B -0.092560 + 2 H -0.045835 + 3 H -0.045658 + 4 H -0.045793 + 5 C 0.507755 + 6 O -0.277910 + Sum of Mulliken charges= 0.00000 + Atomic charges with hydrogens summed into heavy atoms: + 1 + 1 B -0.229846 + 2 H 0.000000 + 3 H 0.000000 + 4 H 0.000000 + 5 C 0.507755 + 6 O -0.277910 + Sum of Mulliken charges= 0.00000 + N-N= 5.598872225161D+01 E-N=-4.373492044832D+02 KE= 1.388757376541D+02 + Orbital energies and kinetic energies (alpha): + 1 2 + 1 O -20.73284 29.14687 + 2 O -11.44012 16.01541 + 3 O -7.55950 10.89617 + 4 O -1.59082 2.89938 + 5 O -0.88263 2.00080 + 6 O -0.79509 1.91200 + 7 O -0.70208 1.95599 + 8 O -0.70207 1.95590 + 9 O -0.55502 1.15058 + 10 O -0.46757 0.75242 + 11 O -0.46719 0.75237 + 12 V 0.11613 1.57751 + 13 V 0.11615 1.57742 + 14 V 0.27722 0.69812 + 15 V 0.30175 1.32565 + 16 V 0.34596 0.70699 + 17 V 0.34643 0.70739 + 18 V 0.39349 1.02461 + 19 V 0.60155 1.40959 + 20 V 0.60162 1.40980 + 21 V 0.72699 2.00579 + 22 V 0.72707 2.00553 + 23 V 0.73220 2.22361 + 24 V 0.87060 1.54278 + 25 V 0.96122 2.35702 + 26 V 1.09400 2.84417 + 27 V 1.14585 2.47114 + 28 V 1.14640 2.47913 + 29 V 1.19829 3.15688 + 30 V 1.19851 3.15000 + 31 V 1.24168 2.47009 + 32 V 1.42563 3.15263 + 33 V 1.49528 2.23581 + 34 V 1.49542 2.23602 + 35 V 1.67330 2.59180 + 36 V 1.67331 2.59184 + 37 V 1.77108 2.72864 + 38 V 1.98854 3.11157 + 39 V 1.98881 3.11166 + 40 V 2.09032 2.95516 + 41 V 2.09097 2.95562 + 42 V 2.12209 3.38408 + 43 V 2.24775 3.13820 + 44 V 2.24809 3.13865 + 45 V 2.97828 4.04478 + 46 V 2.97830 4.04476 + 47 V 3.17544 5.26576 + 48 V 3.41546 6.11555 + 49 V 3.89616 8.14366 + 50 V 4.40878 10.28894 + 51 V 4.77280 11.10594 + Total kinetic energy from orbitals= 1.388757376541D+02 + No NMR shielding tensors so no spin-rotation constants. + Leave Link 601 at Thu Jan 26 17:17:37 2006, MaxMem= 104857600 cpu: 0.5 + (Enter //g03/l9999.exe) + + Test job not archived. + 1\1\GINC-KOH01\SP\RHF\6-31G(d)\C1H3B1O1\ADAM\26-Jan-2006\0\\#P GFINPUT + IOP(6/7=3) IOP(3/33=1) IOP(3/36=-1) #HF/6-31G* POP=FULL DENSITY NOSYM + #SP\\BH3CO sp\\0,1\B,0,0.064567,-0.027896,0.013639\H,0,0.031167,-0.02 + 3173,1.216042\H,0,1.163475,0.052509,-0.468179\H,0,-0.667785,-0.824243, + -0.512249\C,0,-0.61187,1.401829,-0.375526\O,0,-1.072579,2.374082,-0.64 + 0747\\Version=IA32L-G03RevC.01\HF=-139.142411\RMSD=2.588e-05\PG=C01 [X + (C1H3B1O1)]\\@ + + + FAULTILY FAULTLESS, ICILY REGULAR, SPLENDIDLY NULL... + MAUDE BY TENNYSON + Job cpu time: 0 days 0 hours 0 minutes 25.7 seconds. + File lengths (MBytes): RWF= 11 Int= 0 D2E= 0 Chk= 7 Scr= 1 + Normal termination of Gaussian 03 at Thu Jan 26 17:17:40 2006. diff --git a/test/data/calculation_methods/cda/CO.log b/test/data/calculation_methods/cda/CO.log new file mode 100644 index 0000000..cf87d6f --- /dev/null +++ b/test/data/calculation_methods/cda/CO.log @@ -0,0 +1,836 @@ + Entering Gaussian System, Link 0=g03 + Initial command: + //g03/l1.exe /home/adam/BH3CO/Gau-3679.inp -scrdir=/home/adam/BH3CO/ + Entering Link 1 = //g03/l1.exe PID= 3680. + + Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2004, Gaussian, Inc. + All Rights Reserved. + + This is the Gaussian(R) 03 program. It is based on the + the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.), + the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.), + the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.), + the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.), + the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.), + the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon + University), and the Gaussian 82(TM) system (copyright 1983, + Carnegie Mellon University). Gaussian is a federally registered + trademark of Gaussian, Inc. + + This software contains proprietary and confidential information, + including trade secrets, belonging to Gaussian, Inc. + + This software is provided under written license and may be + used, copied, transmitted, or stored only in accord with that + written license. + + The following legend is applicable only to US Government + contracts under FAR: + + RESTRICTED RIGHTS LEGEND + + Use, reproduction and disclosure by the US Government is + subject to restrictions as set forth in subparagraphs (a) + and (c) of the Commercial Computer Software - Restricted + Rights clause in FAR 52.227-19. + + Gaussian, Inc. + 340 Quinnipiac St., Bldg. 40, Wallingford CT 06492 + + + --------------------------------------------------------------- + Warning -- This program may not be used in any manner that + competes with the business of Gaussian, Inc. or will provide + assistance to any competitor of Gaussian, Inc. The licensee + of this program is prohibited from giving any competitor of + Gaussian, Inc. access to this program. By using this program, + the user acknowledges that Gaussian, Inc. is engaged in the + business of creating and licensing software in the field of + computational chemistry and represents and warrants to the + licensee that it is not a competitor of Gaussian, Inc. and that + it will not use this program in any manner prohibited above. + --------------------------------------------------------------- + + + Cite this work as: + Gaussian 03, Revision C.01, + M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, + M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, + K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, + V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, + G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, + R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, + H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, + C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, + A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, + K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, + V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, + O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, + J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, + J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, + I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, + C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, + B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, + Gaussian, Inc., Wallingford CT, 2004. + + ****************************************** + Gaussian 03: IA32L-G03RevC.01 3-Apr-2004 + 26-Jan-2006 + ****************************************** + %Mem=800MB + %NProcShared=2 + Will use up to 2 processors via shared memory. + %chk=co + ----------------------------------------------------------- + #p gfinput iop(6/7=3) #HF/6-31G* pop=full density nosym #SP + ----------------------------------------------------------- + 1/30=1,38=1/1; + 2/15=1,17=6,18=5,40=1/2; + 3/5=1,6=6,7=1,11=9,16=1,24=10,25=1,30=1/1,2,3; + 4//1; + 5/5=2,32=1,38=5/2; + 6/7=3,22=-1,28=1/1; + 99/5=1,9=1/99; + Leave Link 1 at Thu Jan 26 17:17:25 2006, MaxMem= 104857600 cpu: 0.1 + (Enter //g03/l101.exe) + ----- + CO sp + ----- + Symbolic Z-matrix: + Charge = 0 Multiplicity = 1 + C -0.61187 1.40183 -0.37553 + O -1.07258 2.37408 -0.64075 + + Isotopes and Nuclear Properties: + + Atom 1 2 + IAtWgt= 12 16 + AtmWgt= 12.0000000 15.9949146 + IAtSpn= 0 0 + AtZEff= 0.0000000 0.0000000 + AtQMom= 0.0000000 0.0000000 + AtGFac= 0.0000000 0.0000000 + Leave Link 101 at Thu Jan 26 17:17:27 2006, MaxMem= 104857600 cpu: 0.1 + (Enter //g03/l202.exe) + Input orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 6 0 -0.611870 1.401829 -0.375526 + 2 8 0 -1.072579 2.374082 -0.640747 + --------------------------------------------------------------------- + Symmetry turned off by external request. + Stoichiometry CO + Framework group C*V[C*(CO)] + Deg. of freedom 1 + Full point group C*V NOp 4 + Rotational constants (GHZ): 0.0000000 60.0316775 60.0316775 + Leave Link 202 at Thu Jan 26 17:17:31 2006, MaxMem= 104857600 cpu: 0.1 + (Enter //g03/l301.exe) + Standard basis: 6-31G(d) (6D, 7F) + AO basis set in the form of general basis input: + 1 0 + S 6 1.00 0.000000000000 + 0.3047524880D+04 0.1834737132D-02 + 0.4573695180D+03 0.1403732281D-01 + 0.1039486850D+03 0.6884262226D-01 + 0.2921015530D+02 0.2321844432D+00 + 0.9286662960D+01 0.4679413484D+00 + 0.3163926960D+01 0.3623119853D+00 + SP 3 1.00 0.000000000000 + 0.7868272350D+01 -0.1193324198D+00 0.6899906659D-01 + 0.1881288540D+01 -0.1608541517D+00 0.3164239610D+00 + 0.5442492580D+00 0.1143456438D+01 0.7443082909D+00 + SP 1 1.00 0.000000000000 + 0.1687144782D+00 0.1000000000D+01 0.1000000000D+01 + D 1 1.00 0.000000000000 + 0.8000000000D+00 0.1000000000D+01 + **** + 2 0 + S 6 1.00 0.000000000000 + 0.5484671660D+04 0.1831074430D-02 + 0.8252349460D+03 0.1395017220D-01 + 0.1880469580D+03 0.6844507810D-01 + 0.5296450000D+02 0.2327143360D+00 + 0.1689757040D+02 0.4701928980D+00 + 0.5799635340D+01 0.3585208530D+00 + SP 3 1.00 0.000000000000 + 0.1553961625D+02 -0.1107775495D+00 0.7087426823D-01 + 0.3599933586D+01 -0.1480262627D+00 0.3397528391D+00 + 0.1013761750D+01 0.1130767015D+01 0.7271585773D+00 + SP 1 1.00 0.000000000000 + 0.2700058226D+00 0.1000000000D+01 0.1000000000D+01 + D 1 1.00 0.000000000000 + 0.8000000000D+00 0.1000000000D+01 + **** + + Integral buffers will be 262144 words long. + Raffenetti 1 integral format. + Two-electron integral symmetry is turned off. + 30 basis functions, 56 primitive gaussians, 30 cartesian basis functions + 7 alpha electrons 7 beta electrons + nuclear repulsion energy 22.9227132816 Hartrees. + IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 + ScaDFX= 1.000000 1.000000 1.000000 1.000000 + IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 + NAtoms= 2 NActive= 2 NUniq= 2 SFac= 1.00D+00 NAtFMM= 60 Big=F + Leave Link 301 at Thu Jan 26 17:17:33 2006, MaxMem= 104857600 cpu: 0.0 + (Enter //g03/l302.exe) + NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1 + NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0. + One-electron integrals computed using PRISM. + NBasis= 30 RedAO= T NBF= 30 + NBsUse= 30 1.00D-06 NBFU= 30 + Leave Link 302 at Thu Jan 26 17:17:36 2006, MaxMem= 104857600 cpu: 0.2 + (Enter //g03/l303.exe) + DipDrv: MaxL=1. + Leave Link 303 at Thu Jan 26 17:17:38 2006, MaxMem= 104857600 cpu: 0.0 + (Enter //g03/l401.exe) + Harris functional with IExCor= 205 diagonalized for initial guess. + ExpMin= 1.69D-01 ExpMax= 5.48D+03 ExpMxC= 8.25D+02 IAcc=1 IRadAn= 1 AccDes= 1.00D-06 + HarFok: IExCor= 205 AccDes= 1.00D-06 IRadAn= 1 IDoV=1 + ScaDFX= 1.000000 1.000000 1.000000 1.000000 + Harris En= -112.711026565856 + Leave Link 401 at Thu Jan 26 17:17:40 2006, MaxMem= 104857600 cpu: 0.1 + (Enter //g03/l502.exe) + Warning! Cutoffs for single-point calculations used. + Closed shell SCF: + Requested convergence on RMS density matrix=1.00D-04 within 128 cycles. + Requested convergence on MAX density matrix=1.00D-02. + Requested convergence on energy=5.00D-05. + No special actions if energy rises. + Using DIIS extrapolation, IDIIS= 1040. + Two-electron integral symmetry not used. + Keep R1 integrals in memory in canonical form, NReq= 573106. + IEnd= 20332 IEndB= 20332 NGot= 104857600 MDV= 104746480 + LenX= 104746480 + Symmetry not used in FoFDir. + MinBra= 0 MaxBra= 2 Meth= 1. + IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. + + Cycle 1 Pass 1 IDiag 1: + E= -112.702769626322 + DIIS: error= 5.82D-02 at cycle 1 NSaved= 1. + NSaved= 1 IEnMin= 1 EnMin= -112.702769626322 IErMin= 1 ErrMin= 5.82D-02 + ErrMax= 5.82D-02 EMaxC= 1.00D-01 BMatC= 8.97D-02 BMatP= 8.97D-02 + IDIUse=3 WtCom= 4.18D-01 WtEn= 5.82D-01 + Coeff-Com: 0.100D+01 + Coeff-En: 0.100D+01 + Coeff: 0.100D+01 + Gap= 0.744 Goal= None Shift= 0.000 + GapD= 0.744 DampG=2.000 DampE=0.500 DampFc=1.0000 IDamp=-1. + RMSDP=6.66D-03 MaxDP=5.69D-02 OVMax= 5.84D-02 + + Cycle 2 Pass 1 IDiag 1: + E= -112.733498505708 Delta-E= -0.030728879386 Rises=F Damp=F + DIIS: error= 1.22D-02 at cycle 2 NSaved= 2. + NSaved= 2 IEnMin= 2 EnMin= -112.733498505708 IErMin= 2 ErrMin= 1.22D-02 + ErrMax= 1.22D-02 EMaxC= 1.00D-01 BMatC= 6.30D-03 BMatP= 8.97D-02 + IDIUse=3 WtCom= 8.78D-01 WtEn= 1.22D-01 + Coeff-Com: 0.915D-01 0.908D+00 + Coeff-En: 0.000D+00 0.100D+01 + Coeff: 0.803D-01 0.920D+00 + Gap= 0.707 Goal= None Shift= 0.000 + RMSDP=2.08D-03 MaxDP=2.39D-02 DE=-3.07D-02 OVMax= 3.19D-02 + + Cycle 3 Pass 1 IDiag 1: + E= -112.736062178291 Delta-E= -0.002563672583 Rises=F Damp=F + DIIS: error= 8.31D-03 at cycle 3 NSaved= 3. + NSaved= 3 IEnMin= 3 EnMin= -112.736062178291 IErMin= 3 ErrMin= 8.31D-03 + ErrMax= 8.31D-03 EMaxC= 1.00D-01 BMatC= 2.57D-03 BMatP= 6.30D-03 + IDIUse=3 WtCom= 9.17D-01 WtEn= 8.31D-02 + Coeff-Com: -0.286D-01 0.377D+00 0.652D+00 + Coeff-En: 0.000D+00 0.219D+00 0.781D+00 + Coeff: -0.263D-01 0.364D+00 0.662D+00 + Gap= 0.716 Goal= None Shift= 0.000 + RMSDP=1.05D-03 MaxDP=1.34D-02 DE=-2.56D-03 OVMax= 1.24D-02 + + Cycle 4 Pass 1 IDiag 1: + E= -112.737763191064 Delta-E= -0.001701012774 Rises=F Damp=F + DIIS: error= 9.63D-04 at cycle 4 NSaved= 4. + NSaved= 4 IEnMin= 4 EnMin= -112.737763191064 IErMin= 4 ErrMin= 9.63D-04 + ErrMax= 9.63D-04 EMaxC= 1.00D-01 BMatC= 1.58D-05 BMatP= 2.57D-03 + IDIUse=3 WtCom= 9.90D-01 WtEn= 9.63D-03 + Coeff-Com: -0.269D-02 0.327D-02 0.616D-01 0.938D+00 + Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.100D+01 + Coeff: -0.267D-02 0.324D-02 0.610D-01 0.938D+00 + Gap= 0.715 Goal= None Shift= 0.000 + RMSDP=1.49D-04 MaxDP=1.81D-03 DE=-1.70D-03 OVMax= 1.91D-03 + + Cycle 5 Pass 1 IDiag 1: + E= -112.737784595398 Delta-E= -0.000021404334 Rises=F Damp=F + DIIS: error= 2.27D-04 at cycle 5 NSaved= 5. + NSaved= 5 IEnMin= 5 EnMin= -112.737784595398 IErMin= 5 ErrMin= 2.27D-04 + ErrMax= 2.27D-04 EMaxC= 1.00D-01 BMatC= 1.65D-06 BMatP= 1.58D-05 + IDIUse=3 WtCom= 9.98D-01 WtEn= 2.27D-03 + Coeff-Com: 0.194D-02-0.211D-01-0.635D-01-0.153D+00 0.124D+01 + Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.100D+01 + Coeff: 0.193D-02-0.211D-01-0.633D-01-0.153D+00 0.124D+01 + Gap= 0.716 Goal= None Shift= 0.000 + RMSDP=1.05D-04 MaxDP=1.96D-03 DE=-2.14D-05 OVMax= 7.45D-04 + + Convergence on energy, delta-E=-2.14D-05 + SCF Done: E(RHF) = -112.737784595 A.U. after 5 cycles + Convg = 0.1048D-03 -V/T = 2.0021 + S**2 = 0.0000 + KE= 1.125000028499D+02 PE=-3.114447849909D+02 EE= 6.328428426407D+01 + Leave Link 502 at Thu Jan 26 17:17:43 2006, MaxMem= 104857600 cpu: 0.1 + (Enter //g03/l601.exe) + Copying SCF densities to generalized density rwf, ISCF=0 IROHF=0. + + ********************************************************************** + + Population analysis using the SCF density. + + ********************************************************************** + + Alpha occ. eigenvalues -- -20.67505 -11.35282 -1.53343 -0.79832 -0.64184 + Alpha occ. eigenvalues -- -0.64184 -0.54516 + Alpha virt. eigenvalues -- 0.17045 0.17045 0.40970 0.73343 0.73343 + Alpha virt. eigenvalues -- 0.76008 0.99714 1.12937 1.20654 1.20654 + Alpha virt. eigenvalues -- 1.61738 1.74272 1.74272 1.86240 1.86240 + Alpha virt. eigenvalues -- 2.27370 2.27370 2.81915 2.97559 2.97559 + Alpha virt. eigenvalues -- 3.39033 4.11902 4.30900 + Molecular Orbital Coefficients + 1 2 3 4 5 + O O O O O + EIGENVALUES -- -20.67505 -11.35282 -1.53343 -0.79832 -0.64184 + 1 1 C 1S -0.00001 0.99591 -0.11723 0.12686 0.00000 + 2 2S -0.00004 0.02574 0.21868 -0.28116 0.00000 + 3 2PX 0.00024 -0.00183 -0.08967 0.05261 0.20552 + 4 2PY -0.00050 0.00387 0.18923 -0.11102 0.04382 + 5 2PZ 0.00014 -0.00106 -0.05162 0.03028 -0.19637 + 6 3S -0.00103 -0.00156 0.04259 -0.16879 0.00000 + 7 3PX 0.00026 -0.00035 0.00608 -0.01033 0.08062 + 8 3PY -0.00055 0.00073 -0.01283 0.02181 0.01719 + 9 3PZ 0.00015 -0.00020 0.00350 -0.00595 -0.07703 + 10 4XX -0.00008 -0.00221 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0.04257 0.04332 0.05312 0.01436 + 20 2PZ -0.00020 0.00317 0.00322 0.01436 0.02799 + 21 3S 0.00154 -0.03753 0.00398 0.01772 0.00132 + 22 3PX -0.00115 0.00832 0.03307 0.03034 0.00226 + 23 3PY -0.00512 0.03707 0.03034 0.00973 0.01005 + 24 3PZ -0.00038 0.00276 0.00226 0.01005 0.05637 + 25 4XX 0.00000 -0.00008 0.00019 0.00150 0.00011 + 26 4YY -0.00078 0.00494 0.00603 0.00220 0.00200 + 27 4ZZ 0.00002 -0.00055 -0.00013 -0.00059 0.00025 + 28 4XY -0.00044 0.00164 0.00098 0.00348 0.00068 + 29 4XZ -0.00003 0.00012 0.00007 0.00068 0.00085 + 30 4YZ -0.00015 0.00054 0.00068 0.00115 0.00380 + 6 7 8 9 10 + 6 3S 0.81951 + 7 3PX 0.00000 0.03005 + 8 3PY 0.00000 0.00000 0.04592 + 9 3PZ 0.00000 0.00000 0.00000 0.02698 + 10 4XX -0.00144 0.00000 0.00000 0.00000 0.00240 + 11 4YY -0.01789 0.00000 0.00000 0.00000 -0.00085 + 12 4ZZ 0.00174 0.00000 0.00000 0.00000 0.00020 + 13 4XY 0.00000 0.00000 0.00000 0.00000 0.00000 + 14 4XZ 0.00000 0.00000 0.00000 0.00000 0.00000 + 15 4YZ 0.00000 0.00000 0.00000 0.00000 0.00000 + 16 2 O 1S 0.00215 -0.00010 -0.00044 -0.00003 0.00005 + 17 2S -0.03252 0.00105 0.00469 0.00035 -0.00085 + 18 2PX -0.00308 0.01313 0.00524 0.00039 0.00123 + 19 2PY -0.01373 0.00524 -0.00002 0.00174 0.00023 + 20 2PZ -0.00102 0.00039 0.00174 0.01892 0.00002 + 21 3S -0.07903 0.00177 0.00790 0.00059 -0.00025 + 22 3PX -0.00757 0.03153 0.00819 0.00061 -0.00194 + 23 3PY -0.03370 0.00819 -0.00087 0.00271 0.00174 + 24 3PZ -0.00251 0.00061 0.00271 0.04287 0.00013 + 25 4XX 0.00028 -0.00072 0.00096 0.00007 -0.00021 + 26 4YY -0.00107 0.00138 -0.00074 0.00046 0.00029 + 27 4ZZ 0.00050 0.00002 0.00010 -0.00026 0.00003 + 28 4XY -0.00013 0.00060 -0.00001 0.00004 0.00011 + 29 4XZ -0.00001 0.00004 0.00004 0.00023 0.00001 + 30 4YZ -0.00004 0.00004 0.00000 0.00103 0.00002 + 11 12 13 14 15 + 11 4YY 0.00501 + 12 4ZZ -0.00067 0.00186 + 13 4XY 0.00000 0.00000 0.00416 + 14 4XZ 0.00000 0.00000 0.00000 0.00103 + 15 4YZ 0.00000 0.00000 0.00000 0.00000 0.00369 + 16 2 O 1S -0.00078 0.00004 -0.00056 -0.00004 -0.00018 + 17 2S 0.00719 -0.00110 0.00420 0.00031 0.00139 + 18 2PX 0.00927 -0.00040 0.00107 0.00008 0.00143 + 19 2PY 0.00134 -0.00176 0.00838 0.00143 0.00278 + 20 2PZ 0.00307 0.00091 0.00143 0.00134 0.00597 + 21 3S 0.00522 -0.00099 0.00101 0.00008 0.00034 + 22 3PX 0.00698 -0.00052 0.00243 0.00018 0.00039 + 23 3PY -0.00038 -0.00231 0.00080 0.00039 0.00026 + 24 3PZ 0.00231 -0.00064 0.00039 0.00123 0.00546 + 25 4XX 0.00053 0.00002 0.00008 0.00001 0.00006 + 26 4YY -0.00019 -0.00016 0.00062 0.00019 0.00021 + 27 4ZZ 0.00006 -0.00006 -0.00001 0.00002 0.00009 + 28 4XY 0.00051 -0.00008 0.00006 0.00000 0.00015 + 29 4XZ 0.00017 0.00002 0.00000 -0.00004 0.00017 + 30 4YZ 0.00017 0.00010 0.00015 0.00017 0.00052 + 16 17 18 19 20 + 16 2 O 1S 2.08328 + 17 2S -0.04537 0.53470 + 18 2PX 0.00000 0.00000 0.63090 + 19 2PY 0.00000 0.00000 0.00000 0.67695 + 20 2PZ 0.00000 0.00000 0.00000 0.00000 0.62198 + 21 3S -0.03598 0.39464 0.00000 0.00000 0.00000 + 22 3PX 0.00000 0.00000 0.19859 0.00000 0.00000 + 23 3PY 0.00000 0.00000 0.00000 0.17725 0.00000 + 24 3PZ 0.00000 0.00000 0.00000 0.00000 0.20272 + 25 4XX -0.00033 0.00198 0.00000 0.00000 0.00000 + 26 4YY -0.00033 0.00328 0.00000 0.00000 0.00000 + 27 4ZZ -0.00033 0.00173 0.00000 0.00000 0.00000 + 28 4XY 0.00000 0.00000 0.00000 0.00000 0.00000 + 29 4XZ 0.00000 0.00000 0.00000 0.00000 0.00000 + 30 4YZ 0.00000 0.00000 0.00000 0.00000 0.00000 + 21 22 23 24 25 + 21 3S 0.56265 + 22 3PX 0.00000 0.25229 + 23 3PY 0.00000 0.00000 0.19140 + 24 3PZ 0.00000 0.00000 0.00000 0.26408 + 25 4XX 0.00314 0.00000 0.00000 0.00000 0.00156 + 26 4YY -0.00169 0.00000 0.00000 0.00000 -0.00048 + 27 4ZZ 0.00408 0.00000 0.00000 0.00000 0.00000 + 28 4XY 0.00000 0.00000 0.00000 0.00000 0.00000 + 29 4XZ 0.00000 0.00000 0.00000 0.00000 0.00000 + 30 4YZ 0.00000 0.00000 0.00000 0.00000 0.00000 + 26 27 28 29 30 + 26 4YY 0.00308 + 27 4ZZ -0.00026 0.00074 + 28 4XY 0.00000 0.00000 0.00213 + 29 4XZ 0.00000 0.00000 0.00000 0.00071 + 30 4YZ 0.00000 0.00000 0.00000 0.00000 0.00248 + Gross orbital populations: + 1 + 1 1 C 1S 1.99789 + 2 2S 0.81493 + 3 2PX 0.41294 + 4 2PY 0.73201 + 5 2PZ 0.35117 + 6 3S 0.96068 + 7 3PX 0.13651 + 8 3PY 0.14043 + 9 3PZ 0.13575 + 10 4XX -0.00600 + 11 4YY 0.02043 + 12 4ZZ -0.01194 + 13 4XY 0.02422 + 14 4XZ 0.00636 + 15 4YZ 0.02270 + 16 2 O 1S 1.99568 + 17 2S 0.93789 + 18 2PX 0.92295 + 19 2PY 1.01046 + 20 2PZ 0.90600 + 21 3S 0.85049 + 22 3PX 0.56399 + 23 3PY 0.42754 + 24 3PZ 0.59041 + 25 4XX 0.00867 + 26 4YY 0.01895 + 27 4ZZ 0.00546 + 28 4XY 0.00971 + 29 4XZ 0.00303 + 30 4YZ 0.01066 + Condensed to atoms (all electrons): + 1 2 + 1 C 5.110376 0.627725 + 2 O 0.627725 7.634175 + Mulliken atomic charges: + 1 + 1 C 0.261900 + 2 O -0.261900 + Sum of Mulliken charges= 0.00000 + Atomic charges with hydrogens summed into heavy atoms: + 1 + 1 C 0.261900 + 2 O -0.261900 + Sum of Mulliken charges= 0.00000 + Electronic spatial extent (au): = 283.1969 + Charge= 0.0000 electrons + Dipole moment (field-independent basis, Debye): + X= 0.0985 Y= -0.2079 Z= 0.0567 Tot= 0.2370 + Quadrupole moment (field-independent basis, Debye-Ang): + XX= -10.4253 YY= -12.3800 ZZ= -10.0584 + XY= 1.1772 XZ= -0.3205 YZ= 0.6826 + Traceless Quadrupole moment (field-independent basis, Debye-Ang): + XX= 0.5293 YY= -1.4254 ZZ= 0.8961 + XY= 1.1772 XZ= -0.3205 YZ= 0.6826 + Octapole moment (field-independent basis, Debye-Ang**2): + XXX= 25.8304 YYY= -65.9660 ZZZ= 15.1841 XYY= 13.0278 + XXY= -20.7431 XXZ= 5.5868 XZZ= 8.6231 YZZ= -19.3098 + YYZ= 7.7881 XYZ= -1.2888 + Hexadecapole moment (field-independent basis, Debye-Ang**3): + XXXX= -54.5798 YYYY= -265.4053 ZZZZ= -24.3810 XXXY= 53.6591 + XXXZ= -14.4600 YYYX= 65.0294 YYYZ= 38.9721 ZZZX= -13.9350 + ZZZY= 31.0866 XXYY= -54.4184 XXZZ= -13.3843 YYZZ= -45.3298 + XXYZ= 11.9281 YYXZ= -8.4355 ZZXY= 17.9400 + N-N= 2.292271328161D+01 E-N=-3.114449472987D+02 KE= 1.125000028499D+02 + Orbital energies and kinetic energies (alpha): + 1 2 + 1 O -20.67505 29.14627 + 2 O -11.35282 16.01570 + 3 O -1.53343 2.89309 + 4 O -0.79832 2.64642 + 5 O -0.64184 1.98798 + 6 O -0.64184 1.98798 + 7 O -0.54516 1.57256 + 8 V 0.17045 1.46945 + 9 V 0.17045 1.46945 + 10 V 0.40970 1.00616 + 11 V 0.73343 2.12181 + 12 V 0.73343 2.12181 + 13 V 0.76008 1.86433 + 14 V 0.99714 2.12578 + 15 V 1.12937 3.89936 + 16 V 1.20654 3.51871 + 17 V 1.20654 3.51871 + 18 V 1.61738 2.60444 + 19 V 1.74272 2.59467 + 20 V 1.74272 2.59467 + 21 V 1.86240 2.99897 + 22 V 1.86240 2.99897 + 23 V 2.27370 3.09201 + 24 V 2.27370 3.09201 + 25 V 2.81915 4.93367 + 26 V 2.97559 3.94865 + 27 V 2.97559 3.94865 + 28 V 3.39033 5.67960 + 29 V 4.11902 10.50236 + 30 V 4.30900 9.72819 + Total kinetic energy from orbitals= 1.125000028499D+02 + No NMR shielding tensors so no spin-rotation constants. + Leave Link 601 at Thu Jan 26 17:17:45 2006, MaxMem= 104857600 cpu: 0.2 + (Enter //g03/l9999.exe) + + Test job not archived. + 1\1\GINC-KOH18\SP\RHF\6-31G(d)\C1O1\ADAM\26-Jan-2006\0\\#P GFINPUT IOP + (6/7=3) #HF/6-31G* POP=FULL DENSITY NOSYM #SP\\CO sp\\0,1\C,0,-0.61187 + ,1.401829,-0.375526\O,0,-1.072579,2.374082,-0.640747\\Version=IA32L-G0 + 3RevC.01\HF=-112.7377846\RMSD=1.048e-04\Dipole=0.0387677,-0.0818124,0. + 0223177\PG=C*V [C*(C1O1)]\\@ + + + A MAN SHOULD NEVER BE ASHAMED TO OWN HE HAS BEEN IN THE WRONG + WHICH IS BUT SAYING IN OTHER WORDS, + THAT HE IS WISER TODAY THAN HE WAS YESTERDAY. + + -- JONATHAN SWIFT + Job cpu time: 0 days 0 hours 0 minutes 17.7 seconds. + File lengths (MBytes): RWF= 11 Int= 0 D2E= 0 Chk= 7 Scr= 1 + Normal termination of Gaussian 03 at Thu Jan 26 17:17:48 2006. diff --git a/test/data/calculation_methods/cda/water_mp2.out b/test/data/calculation_methods/cda/water_mp2.out new file mode 100644 index 0000000..2ee4a6f --- /dev/null +++ b/test/data/calculation_methods/cda/water_mp2.out @@ -0,0 +1,427 @@ + + ----------------------------------------------------------------------- + Psi4: An Open-Source Ab Initio Electronic Structure Package + Psi4 1.2.1 release + + Git: Rev {HEAD} 406f4de + + + R. M. Parrish, L. A. Burns, D. G. A. Smith, A. C. Simmonett, + A. E. DePrince III, E. G. Hohenstein, U. Bozkaya, A. Yu. Sokolov, + R. Di Remigio, R. M. Richard, J. F. Gonthier, A. M. James, + H. R. McAlexander, A. Kumar, M. Saitow, X. Wang, B. P. Pritchard, + P. Verma, H. F. Schaefer III, K. Patkowski, R. A. King, E. F. Valeev, + F. A. Evangelista, J. M. Turney, T. D. Crawford, and C. D. Sherrill, + J. Chem. Theory Comput. 13(7) pp 3185--3197 (2017). + (doi: 10.1021/acs.jctc.7b00174) + + + Additional Contributions by + P. Kraus, H. Kruse, M. H. Lechner, M. C. Schieber, and R. A. Shaw + + ----------------------------------------------------------------------- + + + Psi4 started on: Wednesday, 15 July 2020 02:57PM + + Process ID: 959791 + Host: homesvr + PSIDATADIR: /home/minsikcho/anaconda3/envs/p4env/share/psi4 + Memory: 500.0 MiB + Threads: 1 + + ==> Input File <== + +-------------------------------------------------------------------------- +molecule water { +0 1 +O +H 1 0.99 +H 1 0.99 2 106.0 +} + +set { + basis sto-3g + print_basis true + print_mos true + cubeprop_tasks ['orbitals', 'density'] + cubic_grid_spacing [0.5, 0.5, 0.5] + cubic_grid_overage [3, 1.5, 2.4] +} + +mp2_e, scf_wfn = energy('mp2', return_wfn=True) +cubeprop(scf_wfn) + + +-------------------------------------------------------------------------- + SCF Algorithm Type (re)set to DF. + +*** tstart() called on homesvr +*** at Wed Jul 15 14:57:37 2020 + + => Loading Basis Set <= + + Name: STO-3G + Role: ORBITAL + Keyword: BASIS + atoms 1 entry O line 81 file /home/minsikcho/anaconda3/envs/p4env/share/psi4/basis/sto-3g.gbs + atoms 2-3 entry H line 19 file /home/minsikcho/anaconda3/envs/p4env/share/psi4/basis/sto-3g.gbs + + + --------------------------------------------------------- + SCF + by Justin Turney, Rob Parrish, Andy Simmonett + and Daniel Smith + RHF Reference + 1 Threads, 500 MiB Core + --------------------------------------------------------- + + ==> Geometry <== + + Molecular point group: c2v + Full point group: C2v + + Geometry (in Angstrom), charge = 0, multiplicity = 1: + + Center X Y Z Mass + ------------ ----------------- ----------------- ----------------- ----------------- + O 0.000000000000 0.000000000000 -0.066678531529 15.994914619560 + H 0.000000000000 -0.790649154947 0.529118341392 1.007825032070 + H 0.000000000000 0.790649154947 0.529118341392 1.007825032070 + + Running in c2v symmetry. + + Rotational constants: A = 26.52958 B = 13.37869 C = 8.89367 [cm^-1] + Rotational constants: A = 795336.70122 B = 401083.16849 C = 266625.59877 [MHz] + Nuclear repulsion = 8.887006225878341 + + Charge = 0 + Multiplicity = 1 + Electrons = 10 + Nalpha = 5 + Nbeta = 5 + + ==> Algorithm <== + + SCF Algorithm Type is DF. + DIIS enabled. + MOM disabled. + Fractional occupation disabled. + Guess Type is SAD. + Energy threshold = 1.00e-08 + Density threshold = 1.00e-08 + Integral threshold = 0.00e+00 + + ==> Primary Basis <== + + Basis Set: STO-3G + Blend: STO-3G + Number of shells: 5 + Number of basis function: 7 + Number of Cartesian functions: 7 + Spherical Harmonics?: true + Max angular momentum: 1 + + => Loading Basis Set <= + + Name: (STO-3G AUX) + Role: JKFIT + Keyword: DF_BASIS_SCF + atoms 1 entry O line 323 file /home/minsikcho/anaconda3/envs/p4env/share/psi4/basis/def2-svp-jkfit.gbs + atoms 2-3 entry H line 23 file /home/minsikcho/anaconda3/envs/p4env/share/psi4/basis/def2-svp-jkfit.gbs + + -AO BASIS SET INFORMATION: + Name = STO-3G + Blend = STO-3G + Total number of shells = 5 + Number of primitives = 15 + Number of AO = 7 + Number of SO = 7 + Maximum AM = 1 + Spherical Harmonics = TRUE + + -Contraction Scheme: + Atom Type All Primitives // Shells: + ------ ------ -------------------------- + 1 O 6s 3p // 2s 1p + 2 H 3s // 1s + 3 H 3s // 1s + + ==> AO Basis Functions <== + + [ STO-3G ] + spherical + **** + O 1 + S 3 1.00 + 130.70932000 0.15432897 + 23.80886100 0.53532814 + 6.44360830 0.44463454 + S 3 1.00 + 5.03315130 -0.09996723 + 1.16959610 0.39951283 + 0.38038900 0.70011547 + P 3 1.00 + 5.03315130 0.15591627 + 1.16959610 0.60768372 + 0.38038900 0.39195739 + **** + H 2 + S 3 1.00 + 3.42525091 0.15432897 + 0.62391373 0.53532814 + 0.16885540 0.44463454 + **** + + ==> Pre-Iterations <== + + ------------------------------------------------------- + Irrep Nso Nmo Nalpha Nbeta Ndocc Nsocc + ------------------------------------------------------- + A1 4 4 0 0 0 0 + A2 0 0 0 0 0 0 + B1 1 1 0 0 0 0 + B2 2 2 0 0 0 0 + ------------------------------------------------------- + Total 7 7 5 5 5 0 + ------------------------------------------------------- + + ==> Integral Setup <== + + DFHelper Memory: AOs need 0.000 [GiB]; user supplied 0.366 [GiB]. Using in-core AOs. + + ==> MemDFJK: Density-Fitted J/K Matrices <== + + J tasked: Yes + K tasked: Yes + wK tasked: No + OpenMP threads: 1 + Memory (MB): 375 + Algorithm: Core + Schwarz Cutoff: 1E-12 + Mask sparsity (%): 0.0000 + Fitting Condition: 1E-12 + + => Auxiliary Basis Set <= + + Basis Set: (STO-3G AUX) + Blend: DEF2-SVP-JKFIT + Number of shells: 37 + Number of basis function: 113 + Number of Cartesian functions: 133 + Spherical Harmonics?: true + Max angular momentum: 4 + + Minimum eigenvalue in the overlap matrix is 3.6393052139E-01. + Using Symmetric Orthogonalization. + + SCF Guess: Superposition of Atomic Densities via on-the-fly atomic UHF. + + ==> Iterations <== + + Total Energy Delta E RMS |[F,P]| + + @DF-RHF iter 0: -74.71460191108939 -7.47146e+01 3.03940e-01 + @DF-RHF iter 1: -74.91600325470347 -2.01401e-01 5.09813e-02 + @DF-RHF iter 2: -74.96229021097456 -4.62870e-02 9.16895e-03 DIIS + @DF-RHF iter 3: -74.96398815218649 -1.69794e-03 3.56711e-03 DIIS + @DF-RHF iter 4: -74.96441461354455 -4.26461e-04 3.22682e-04 DIIS + @DF-RHF iter 5: -74.96441710793660 -2.49439e-06 3.57733e-05 DIIS + @DF-RHF iter 6: -74.96441713216285 -2.42263e-08 1.11484e-06 DIIS + @DF-RHF iter 7: -74.96441713218326 -2.04068e-11 4.76814e-10 DIIS + + ==> Post-Iterations <== + + Orbital Energies [Eh] + --------------------- + + Doubly Occupied: + + 1A1 -20.243976 2A1 -1.250662 1B2 -0.603166 + 3A1 -0.445470 1B1 -0.388215 + + Virtual: + + 4A1 0.570772 2B2 0.708631 + + Final Occupation by Irrep: + A1 A2 B1 B2 + DOCC [ 3, 0, 1, 1 ] + + Energy converged. + + @DF-RHF Final Energy: -74.96441713218326 + + => Energetics <= + + Nuclear Repulsion Energy = 8.8870062258783413 + One-Electron Energy = -121.8398687190952501 + Two-Electron Energy = 37.9884453610336408 + Total Energy = -74.9644171321832715 + + + +Properties will be evaluated at 0.000000, 0.000000, 0.000000 [a0] + +Properties computed using the SCF density matrix + + Nuclear Dipole Moment: [e a0] + X: 0.0000 Y: 0.0000 Z: 0.9917 + + Electronic Dipole Moment: [e a0] + X: 0.0000 Y: 0.0000 Z: -0.3335 + + Dipole Moment: [e a0] + X: 0.0000 Y: 0.0000 Z: 0.6583 Total: 0.6583 + + Dipole Moment: [D] + X: 0.0000 Y: 0.0000 Z: 1.6732 Total: 1.6732 + + + ==> Molecular Orbitals <== + + 1 2 3 4 5 + + 1 O1 s0 0.9942034 0.2342174 0.0000000 0.1004582 0.0000000 + 2 O1 s0 0.0259139 -0.8458846 0.0000000 -0.5214075 0.0000000 + 3 O1 p0 0.0039930 -0.1170354 0.0000000 0.7742484 0.0000000 + 4 O1 p+1 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 + 5 O1 p-1 0.0000000 0.0000000 0.6032830 0.0000000 0.0000000 + 6 H2 s0 -0.0056268 -0.1564492 -0.4463951 0.2890869 0.0000000 + 7 H3 s0 -0.0056268 -0.1564492 0.4463951 0.2890869 0.0000000 + + Ene -20.2439758 -1.2506624 -0.6031659 -0.4454697 -0.3882152 + Sym A1 A1 B2 A1 B1 + Occ 2 2 2 2 2 + + + 6 7 + + 1 O1 s0 0.1283482 0.0000000 + 2 O1 s0 -0.8325149 0.0000000 + 3 O1 p0 -0.7326476 0.0000000 + 4 O1 p+1 0.0000000 0.0000000 + 5 O1 p-1 0.0000000 0.9764982 + 6 H2 s0 0.7757921 0.8089054 + 7 H3 s0 0.7757921 -0.8089054 + + Ene 0.5707720 0.7086314 + Sym A1 B2 + Occ 0 0 + + +*** tstop() called on homesvr at Wed Jul 15 14:57:38 2020 +Module time: + user time = 0.43 seconds = 0.01 minutes + system time = 0.01 seconds = 0.00 minutes + total time = 1 seconds = 0.02 minutes +Total time: + user time = 0.43 seconds = 0.01 minutes + system time = 0.01 seconds = 0.00 minutes + total time = 1 seconds = 0.02 minutes + +*** tstart() called on homesvr +*** at Wed Jul 15 14:57:38 2020 + + + //>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>// + // DFMP2 // + //<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< Loading Basis Set <= + + Name: (STO-3G AUX) + Role: RIFIT + Keyword: DF_BASIS_MP2 + atoms 1 entry O line 406 file /home/minsikcho/anaconda3/envs/p4env/share/psi4/basis/def2-qzvpp-ri.gbs + atoms 2-3 entry H line 24 file /home/minsikcho/anaconda3/envs/p4env/share/psi4/basis/def2-qzvpp-ri.gbs + + -------------------------------------------------------- + DF-MP2 + 2nd-Order Density-Fitted Moller-Plesset Theory + RMP2 Wavefunction, 1 Threads + + Rob Parrish, Justin Turney, Andy Simmonett, + Ed Hohenstein, and C. David Sherrill + -------------------------------------------------------- + + => Auxiliary Basis Set <= + + Basis Set: (STO-3G AUX) + Blend: DEF2-QZVPP-RI + Number of shells: 65 + Number of basis function: 253 + Number of Cartesian functions: 333 + Spherical Harmonics?: true + Max angular momentum: 5 + + -------------------------------------------------------- + NBF = 7, NAUX = 253 + -------------------------------------------------------- + CLASS FOCC OCC AOCC AVIR VIR FVIR + PAIRS 0 5 5 2 2 0 + -------------------------------------------------------- + + ----------------------------------------------------------- + ==================> DF-MP2 Energies <==================== + ----------------------------------------------------------- + Reference Energy = -74.9644171321832573 [Eh] + Singles Energy = -0.0000000000000000 [Eh] + Same-Spin Energy = -0.0021865372482756 [Eh] + Opposite-Spin Energy = -0.0358629201406502 [Eh] + Correlation Energy = -0.0380494573889258 [Eh] + Total Energy = -75.0024665895721796 [Eh] + ----------------------------------------------------------- + ================> DF-SCS-MP2 Energies <================== + ----------------------------------------------------------- + SCS Same-Spin Scale = 0.3333333333333333 [-] + SCS Opposite-Spin Scale = 1.2000000000000000 [-] + SCS Same-Spin Energy = -0.0007288457494252 [Eh] + SCS Opposite-Spin Energy = -0.0430355041687802 [Eh] + SCS Correlation Energy = -0.0437643499182054 [Eh] + SCS Total Energy = -75.0081814821014632 [Eh] + ----------------------------------------------------------- + + +*** tstop() called on homesvr at Wed Jul 15 14:57:38 2020 +Module time: + user time = 0.13 seconds = 0.00 minutes + system time = 0.00 seconds = 0.00 minutes + total time = 0 seconds = 0.00 minutes +Total time: + user time = 0.56 seconds = 0.01 minutes + system time = 0.01 seconds = 0.00 minutes + total time = 1 seconds = 0.02 minutes + ==> One Electron Grid Properties (v2.0) <== + + ==> CubicScalarGrid <== + + Filepath = . + Total Points = 2197 + XYZ Blocking = 10 + X Points = 13 + Y Points = 13 + Z Points = 13 + X Spacing = 5.000E-01 + Y Spacing = 5.000E-01 + Z Spacing = 5.000E-01 + X Minimum = -3.000E+00 + Y Minimum = -3.000E+00 + Z Minimum = -2.563E+00 + X Maximum = 3.000E+00 + Y Maximum = 3.000E+00 + Z Maximum = 3.437E+00 + + Basis Set: STO-3G + Blend: STO-3G + Number of shells: 5 + Number of basis function: 7 + Number of Cartesian functions: 7 + Spherical Harmonics?: true + Max angular momentum: 1 + + + Psi4 stopped on: Wednesday, 15 July 2020 02:57PM + Psi4 wall time for execution: 0:00:00.60 + +*** Psi4 exiting successfully. Buy a developer a beer! From 10ed13f1453c6008d69ea8cda22fc9465e3c8705 Mon Sep 17 00:00:00 2001 From: Victor Cano Gil Date: Mon, 31 Jul 2023 18:54:44 -0400 Subject: [PATCH 09/18] add docs to some functions --- src/calculation_methods.jl | 54 +++++++++++++++++++++++++++++++++----- test.jl | 7 +++-- 2 files changed, 52 insertions(+), 9 deletions(-) diff --git a/src/calculation_methods.jl b/src/calculation_methods.jl index 1ee6f8a..79d9737 100644 --- a/src/calculation_methods.jl +++ b/src/calculation_methods.jl @@ -13,9 +13,23 @@ export bader export ddec6 export hpa -# remake this function such that it's not (1, size(x)) but len(x), size(x) -expand(x) = pyconvert(Array{Float64}, x[0]) |> x -> reshape(length(x), (1, size(x)...)) +# dimensions of some outputs are NxMxK, however python return dimension N as a list +# which needs to be adjusted +function expand(x) + N = length(x) + x = pyconvert(Array{Float64}, x[0]) + return reshape(x, (N, size(x)...)) +end + +""" + cspa(file::String) +C-Squared Population Analysis (CSPA) +# Arguments +- `file::String`: Cclib-supported output file +# Returns +tuple (aoresults, fragresults, fragcharges) +""" function cspa(file::String) #TODO: implement the optional args from docs data = cclib[].io.ccread(file) @@ -27,6 +41,15 @@ function cspa(file::String) return aoresults, fragresults, fragcharges end +""" + mpa(file::String) + +Mulliken Population Analysis +# Arguments +- `file::String`: Cclib-supported output file +# Returns +tuple (aoresults, fragresults, fragcharges) +""" function mpa(file::String) data = cclib[].io.ccread(file) mol = cclib[].method.MPA(data) @@ -37,6 +60,15 @@ function mpa(file::String) return aoresults, fragresults, fragcharges end +""" + mpa(file::String) + +Lowdin Population Analysis +# Arguments +- `file::String`: Cclib-supported output file +# Returns +tuple (aoresults, fragresults, fragcharges) +""" function lpa(file::String) data = cclib[].io.ccread(file) mol = cclib[].method.LPA(data) @@ -47,6 +79,15 @@ function lpa(file::String) return aoresults, fragresults, fragcharges end +""" + bpa(file::String) + +Bickelhaupt Population Analysis +# Arguments +- `file::String`: Cclib-supported output file +# Returns +tuple (aoresults, fragresults, fragcharges) +""" function bpa(file::String) data = cclib[].io.ccread(file) mol = cclib[].method.Bickelhaupt(data) @@ -79,11 +120,10 @@ function cda(mol::String, frag1::String, frag2::String) frag2 = cclib[].io.ccread(frag2) mol = cclib[].method.CDA(mol) mol.calculate([frag1, frag2]) - return mol - # donations = mol.__dict__["donations"] |> expand - # bdonations = mol.__dict__["bdonations"] |> expand - # repulsions = mol.__dict__["repulsions"] |> expand - # return donations, bdonations, repulsions + donations = mol.__dict__["donations"] |> expand + bdonations = mol.__dict__["bdonations"] |> expand + repulsions = mol.__dict__["repulsions"] |> expand + return donations, bdonations, repulsions end function bader(file::String) diff --git a/test.jl b/test.jl index 431d0d0..9ec1452 100644 --- a/test.jl +++ b/test.jl @@ -15,8 +15,10 @@ aoresults = a.__dict__["aoresults"] fragresults = a.__dict__["fragresults"] fragcharges = a.__dict__["fragcharges"] -x = pyconvert(Array{Float64}, fragcharges) -reshape(x, (1, size(x)...)) +# x = pyconvert(Array{Float64}, fragcharges) +# reshape(x, (1, size(x)...)) + +b = mpa("./test/data/Trp_polar.fchk") a = cda( @@ -25,4 +27,5 @@ a = cda( "./test/data/calculation_methods/cda/CO.log", ) a.__dict__.keys() +a.__dict__["repulsions"] z = a.__dict__["donations"] \ No newline at end of file From baf2e109638147a17153be6036ee82c3c7867d43 Mon Sep 17 00:00:00 2001 From: Victor Cano Gil Date: Thu, 3 Aug 2023 18:50:38 -0400 Subject: [PATCH 10/18] update funcs --- src/calculation_methods.jl | 62 ++- .../calculation_methods/bader/water_mp2.out | 427 ++++++++++++++++++ 2 files changed, 481 insertions(+), 8 deletions(-) create mode 100644 test/data/calculation_methods/bader/water_mp2.out diff --git a/src/calculation_methods.jl b/src/calculation_methods.jl index 79d9737..ceee5ce 100644 --- a/src/calculation_methods.jl +++ b/src/calculation_methods.jl @@ -13,8 +13,7 @@ export bader export ddec6 export hpa -# dimensions of some outputs are NxMxK, however python return dimension N as a list -# which needs to be adjusted +# dimensions of some outputs are NxMxK, however python return dimension N as a list, not an array function expand(x) N = length(x) x = pyconvert(Array{Float64}, x[0]) @@ -28,7 +27,7 @@ C-Squared Population Analysis (CSPA) # Arguments - `file::String`: Cclib-supported output file # Returns -tuple (aoresults, fragresults, fragcharges) +Tuple (aoresults, fragresults, fragcharges) """ function cspa(file::String) #TODO: implement the optional args from docs @@ -48,7 +47,7 @@ Mulliken Population Analysis # Arguments - `file::String`: Cclib-supported output file # Returns -tuple (aoresults, fragresults, fragcharges) +Tuple (aoresults, fragresults, fragcharges) """ function mpa(file::String) data = cclib[].io.ccread(file) @@ -61,13 +60,13 @@ function mpa(file::String) end """ - mpa(file::String) + lpa(file::String) Lowdin Population Analysis # Arguments - `file::String`: Cclib-supported output file # Returns -tuple (aoresults, fragresults, fragcharges) +Tuple (aoresults, fragresults, fragcharges) """ function lpa(file::String) data = cclib[].io.ccread(file) @@ -86,7 +85,7 @@ Bickelhaupt Population Analysis # Arguments - `file::String`: Cclib-supported output file # Returns -tuple (aoresults, fragresults, fragcharges) +Tuple (aoresults, fragresults, fragcharges) """ function bpa(file::String) data = cclib[].io.ccread(file) @@ -98,6 +97,15 @@ function bpa(file::String) return aoresults, fragresults, fragcharges end +""" + density(file::String) + +Density matrix calculation +# Arguments +- `file::String`: Cclib-supported output file +# Returns +Density Matrix +""" function density(file::String) data = cclib[].io.ccread(file) mol = cclib[].method.Density(data) @@ -106,6 +114,16 @@ function density(file::String) end #ToDo: check output dimensions? +""" + mbo(file::String) + +Calculate Mayer's bond orders +# Arguments +- `file::String`: Cclib-supported output file +# Returns +Array of rank 3. The first axis is for contributions of each spin to the MBO, +while the second and third correspond to the indices of the atoms. +""" function mbo(file::String) data = cclib[].io.ccread(file) mol = cclib[].method.MBO(data) @@ -114,6 +132,15 @@ function mbo(file::String) end #TODO Figure out the dimensions +""" + cda(file::String) + +Charge decomposition analysis +# Arguments +- `file::String`: Cclib-supported output file +# Returns +Tuple (donations, backdonations, repulsions) +""" function cda(mol::String, frag1::String, frag2::String) mol = cclib[].io.ccread(mol) frag1 = cclib[].io.ccread(frag1) @@ -126,5 +153,24 @@ function cda(mol::String, frag1::String, frag2::String) return donations, bdonations, repulsions end -function bader(file::String) +""" + bader(file::String) + +Bader's QTAIM charges calculation +# Arguments +- `file::String`: Cclib-supported output file +# Returns +Tuple (donations, backdonations, repulsions) +""" +function bader(file::String, vol::Vector{Vector}) + data = cclib[].io.ccread(file) + vol = pytuple(pytuple(i) for i in vol) + vol = cclib[].method.Volume(vol...) + mol = cclib[].method.Bader(data, vol) + mol.calculate() + return mol + # aoresults = mol.__dict__["aoresults"] |> expand + # fragresults = mol.__dict__["fragresults"] |> expand + # fragcharges = pyconvert(Array{Float64}, mol.__dict__["fragcharges"]) + # return aoresults, fragresults, fragcharges end diff --git a/test/data/calculation_methods/bader/water_mp2.out b/test/data/calculation_methods/bader/water_mp2.out new file mode 100644 index 0000000..2ee4a6f --- /dev/null +++ b/test/data/calculation_methods/bader/water_mp2.out @@ -0,0 +1,427 @@ + + ----------------------------------------------------------------------- + Psi4: An Open-Source Ab Initio Electronic Structure Package + Psi4 1.2.1 release + + Git: Rev {HEAD} 406f4de + + + R. M. Parrish, L. A. Burns, D. G. A. Smith, A. C. Simmonett, + A. E. DePrince III, E. G. Hohenstein, U. Bozkaya, A. Yu. Sokolov, + R. Di Remigio, R. M. Richard, J. F. Gonthier, A. M. James, + H. R. McAlexander, A. Kumar, M. Saitow, X. Wang, B. P. Pritchard, + P. Verma, H. F. Schaefer III, K. Patkowski, R. A. King, E. F. Valeev, + F. A. Evangelista, J. M. Turney, T. D. Crawford, and C. D. Sherrill, + J. Chem. Theory Comput. 13(7) pp 3185--3197 (2017). + (doi: 10.1021/acs.jctc.7b00174) + + + Additional Contributions by + P. Kraus, H. Kruse, M. H. Lechner, M. C. Schieber, and R. A. Shaw + + ----------------------------------------------------------------------- + + + Psi4 started on: Wednesday, 15 July 2020 02:57PM + + Process ID: 959791 + Host: homesvr + PSIDATADIR: /home/minsikcho/anaconda3/envs/p4env/share/psi4 + Memory: 500.0 MiB + Threads: 1 + + ==> Input File <== + +-------------------------------------------------------------------------- +molecule water { +0 1 +O +H 1 0.99 +H 1 0.99 2 106.0 +} + +set { + basis sto-3g + print_basis true + print_mos true + cubeprop_tasks ['orbitals', 'density'] + cubic_grid_spacing [0.5, 0.5, 0.5] + cubic_grid_overage [3, 1.5, 2.4] +} + +mp2_e, scf_wfn = energy('mp2', return_wfn=True) +cubeprop(scf_wfn) + + +-------------------------------------------------------------------------- + SCF Algorithm Type (re)set to DF. + +*** tstart() called on homesvr +*** at Wed Jul 15 14:57:37 2020 + + => Loading Basis Set <= + + Name: STO-3G + Role: ORBITAL + Keyword: BASIS + atoms 1 entry O line 81 file /home/minsikcho/anaconda3/envs/p4env/share/psi4/basis/sto-3g.gbs + atoms 2-3 entry H line 19 file /home/minsikcho/anaconda3/envs/p4env/share/psi4/basis/sto-3g.gbs + + + --------------------------------------------------------- + SCF + by Justin Turney, Rob Parrish, Andy Simmonett + and Daniel Smith + RHF Reference + 1 Threads, 500 MiB Core + --------------------------------------------------------- + + ==> Geometry <== + + Molecular point group: c2v + Full point group: C2v + + Geometry (in Angstrom), charge = 0, multiplicity = 1: + + Center X Y Z Mass + ------------ ----------------- ----------------- ----------------- ----------------- + O 0.000000000000 0.000000000000 -0.066678531529 15.994914619560 + H 0.000000000000 -0.790649154947 0.529118341392 1.007825032070 + H 0.000000000000 0.790649154947 0.529118341392 1.007825032070 + + Running in c2v symmetry. + + Rotational constants: A = 26.52958 B = 13.37869 C = 8.89367 [cm^-1] + Rotational constants: A = 795336.70122 B = 401083.16849 C = 266625.59877 [MHz] + Nuclear repulsion = 8.887006225878341 + + Charge = 0 + Multiplicity = 1 + Electrons = 10 + Nalpha = 5 + Nbeta = 5 + + ==> Algorithm <== + + SCF Algorithm Type is DF. + DIIS enabled. + MOM disabled. + Fractional occupation disabled. + Guess Type is SAD. + Energy threshold = 1.00e-08 + Density threshold = 1.00e-08 + Integral threshold = 0.00e+00 + + ==> Primary Basis <== + + Basis Set: STO-3G + Blend: STO-3G + Number of shells: 5 + Number of basis function: 7 + Number of Cartesian functions: 7 + Spherical Harmonics?: true + Max angular momentum: 1 + + => Loading Basis Set <= + + Name: (STO-3G AUX) + Role: JKFIT + Keyword: DF_BASIS_SCF + atoms 1 entry O line 323 file /home/minsikcho/anaconda3/envs/p4env/share/psi4/basis/def2-svp-jkfit.gbs + atoms 2-3 entry H line 23 file /home/minsikcho/anaconda3/envs/p4env/share/psi4/basis/def2-svp-jkfit.gbs + + -AO BASIS SET INFORMATION: + Name = STO-3G + Blend = STO-3G + Total number of shells = 5 + Number of primitives = 15 + Number of AO = 7 + Number of SO = 7 + Maximum AM = 1 + Spherical Harmonics = TRUE + + -Contraction Scheme: + Atom Type All Primitives // Shells: + ------ ------ -------------------------- + 1 O 6s 3p // 2s 1p + 2 H 3s // 1s + 3 H 3s // 1s + + ==> AO Basis Functions <== + + [ STO-3G ] + spherical + **** + O 1 + S 3 1.00 + 130.70932000 0.15432897 + 23.80886100 0.53532814 + 6.44360830 0.44463454 + S 3 1.00 + 5.03315130 -0.09996723 + 1.16959610 0.39951283 + 0.38038900 0.70011547 + P 3 1.00 + 5.03315130 0.15591627 + 1.16959610 0.60768372 + 0.38038900 0.39195739 + **** + H 2 + S 3 1.00 + 3.42525091 0.15432897 + 0.62391373 0.53532814 + 0.16885540 0.44463454 + **** + + ==> Pre-Iterations <== + + ------------------------------------------------------- + Irrep Nso Nmo Nalpha Nbeta Ndocc Nsocc + ------------------------------------------------------- + A1 4 4 0 0 0 0 + A2 0 0 0 0 0 0 + B1 1 1 0 0 0 0 + B2 2 2 0 0 0 0 + ------------------------------------------------------- + Total 7 7 5 5 5 0 + ------------------------------------------------------- + + ==> Integral Setup <== + + DFHelper Memory: AOs need 0.000 [GiB]; user supplied 0.366 [GiB]. Using in-core AOs. + + ==> MemDFJK: Density-Fitted J/K Matrices <== + + J tasked: Yes + K tasked: Yes + wK tasked: No + OpenMP threads: 1 + Memory (MB): 375 + Algorithm: Core + Schwarz Cutoff: 1E-12 + Mask sparsity (%): 0.0000 + Fitting Condition: 1E-12 + + => Auxiliary Basis Set <= + + Basis Set: (STO-3G AUX) + Blend: DEF2-SVP-JKFIT + Number of shells: 37 + Number of basis function: 113 + Number of Cartesian functions: 133 + Spherical Harmonics?: true + Max angular momentum: 4 + + Minimum eigenvalue in the overlap matrix is 3.6393052139E-01. + Using Symmetric Orthogonalization. + + SCF Guess: Superposition of Atomic Densities via on-the-fly atomic UHF. + + ==> Iterations <== + + Total Energy Delta E RMS |[F,P]| + + @DF-RHF iter 0: -74.71460191108939 -7.47146e+01 3.03940e-01 + @DF-RHF iter 1: -74.91600325470347 -2.01401e-01 5.09813e-02 + @DF-RHF iter 2: -74.96229021097456 -4.62870e-02 9.16895e-03 DIIS + @DF-RHF iter 3: -74.96398815218649 -1.69794e-03 3.56711e-03 DIIS + @DF-RHF iter 4: -74.96441461354455 -4.26461e-04 3.22682e-04 DIIS + @DF-RHF iter 5: -74.96441710793660 -2.49439e-06 3.57733e-05 DIIS + @DF-RHF iter 6: -74.96441713216285 -2.42263e-08 1.11484e-06 DIIS + @DF-RHF iter 7: -74.96441713218326 -2.04068e-11 4.76814e-10 DIIS + + ==> Post-Iterations <== + + Orbital Energies [Eh] + --------------------- + + Doubly Occupied: + + 1A1 -20.243976 2A1 -1.250662 1B2 -0.603166 + 3A1 -0.445470 1B1 -0.388215 + + Virtual: + + 4A1 0.570772 2B2 0.708631 + + Final Occupation by Irrep: + A1 A2 B1 B2 + DOCC [ 3, 0, 1, 1 ] + + Energy converged. + + @DF-RHF Final Energy: -74.96441713218326 + + => Energetics <= + + Nuclear Repulsion Energy = 8.8870062258783413 + One-Electron Energy = -121.8398687190952501 + Two-Electron Energy = 37.9884453610336408 + Total Energy = -74.9644171321832715 + + + +Properties will be evaluated at 0.000000, 0.000000, 0.000000 [a0] + +Properties computed using the SCF density matrix + + Nuclear Dipole Moment: [e a0] + X: 0.0000 Y: 0.0000 Z: 0.9917 + + Electronic Dipole Moment: [e a0] + X: 0.0000 Y: 0.0000 Z: -0.3335 + + Dipole Moment: [e a0] + X: 0.0000 Y: 0.0000 Z: 0.6583 Total: 0.6583 + + Dipole Moment: [D] + X: 0.0000 Y: 0.0000 Z: 1.6732 Total: 1.6732 + + + ==> Molecular Orbitals <== + + 1 2 3 4 5 + + 1 O1 s0 0.9942034 0.2342174 0.0000000 0.1004582 0.0000000 + 2 O1 s0 0.0259139 -0.8458846 0.0000000 -0.5214075 0.0000000 + 3 O1 p0 0.0039930 -0.1170354 0.0000000 0.7742484 0.0000000 + 4 O1 p+1 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 + 5 O1 p-1 0.0000000 0.0000000 0.6032830 0.0000000 0.0000000 + 6 H2 s0 -0.0056268 -0.1564492 -0.4463951 0.2890869 0.0000000 + 7 H3 s0 -0.0056268 -0.1564492 0.4463951 0.2890869 0.0000000 + + Ene -20.2439758 -1.2506624 -0.6031659 -0.4454697 -0.3882152 + Sym A1 A1 B2 A1 B1 + Occ 2 2 2 2 2 + + + 6 7 + + 1 O1 s0 0.1283482 0.0000000 + 2 O1 s0 -0.8325149 0.0000000 + 3 O1 p0 -0.7326476 0.0000000 + 4 O1 p+1 0.0000000 0.0000000 + 5 O1 p-1 0.0000000 0.9764982 + 6 H2 s0 0.7757921 0.8089054 + 7 H3 s0 0.7757921 -0.8089054 + + Ene 0.5707720 0.7086314 + Sym A1 B2 + Occ 0 0 + + +*** tstop() called on homesvr at Wed Jul 15 14:57:38 2020 +Module time: + user time = 0.43 seconds = 0.01 minutes + system time = 0.01 seconds = 0.00 minutes + total time = 1 seconds = 0.02 minutes +Total time: + user time = 0.43 seconds = 0.01 minutes + system time = 0.01 seconds = 0.00 minutes + total time = 1 seconds = 0.02 minutes + +*** tstart() called on homesvr +*** at Wed Jul 15 14:57:38 2020 + + + //>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>// + // DFMP2 // + //<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< Loading Basis Set <= + + Name: (STO-3G AUX) + Role: RIFIT + Keyword: DF_BASIS_MP2 + atoms 1 entry O line 406 file /home/minsikcho/anaconda3/envs/p4env/share/psi4/basis/def2-qzvpp-ri.gbs + atoms 2-3 entry H line 24 file /home/minsikcho/anaconda3/envs/p4env/share/psi4/basis/def2-qzvpp-ri.gbs + + -------------------------------------------------------- + DF-MP2 + 2nd-Order Density-Fitted Moller-Plesset Theory + RMP2 Wavefunction, 1 Threads + + Rob Parrish, Justin Turney, Andy Simmonett, + Ed Hohenstein, and C. David Sherrill + -------------------------------------------------------- + + => Auxiliary Basis Set <= + + Basis Set: (STO-3G AUX) + Blend: DEF2-QZVPP-RI + Number of shells: 65 + Number of basis function: 253 + Number of Cartesian functions: 333 + Spherical Harmonics?: true + Max angular momentum: 5 + + -------------------------------------------------------- + NBF = 7, NAUX = 253 + -------------------------------------------------------- + CLASS FOCC OCC AOCC AVIR VIR FVIR + PAIRS 0 5 5 2 2 0 + -------------------------------------------------------- + + ----------------------------------------------------------- + ==================> DF-MP2 Energies <==================== + ----------------------------------------------------------- + Reference Energy = -74.9644171321832573 [Eh] + Singles Energy = -0.0000000000000000 [Eh] + Same-Spin Energy = -0.0021865372482756 [Eh] + Opposite-Spin Energy = -0.0358629201406502 [Eh] + Correlation Energy = -0.0380494573889258 [Eh] + Total Energy = -75.0024665895721796 [Eh] + ----------------------------------------------------------- + ================> DF-SCS-MP2 Energies <================== + ----------------------------------------------------------- + SCS Same-Spin Scale = 0.3333333333333333 [-] + SCS Opposite-Spin Scale = 1.2000000000000000 [-] + SCS Same-Spin Energy = -0.0007288457494252 [Eh] + SCS Opposite-Spin Energy = -0.0430355041687802 [Eh] + SCS Correlation Energy = -0.0437643499182054 [Eh] + SCS Total Energy = -75.0081814821014632 [Eh] + ----------------------------------------------------------- + + +*** tstop() called on homesvr at Wed Jul 15 14:57:38 2020 +Module time: + user time = 0.13 seconds = 0.00 minutes + system time = 0.00 seconds = 0.00 minutes + total time = 0 seconds = 0.00 minutes +Total time: + user time = 0.56 seconds = 0.01 minutes + system time = 0.01 seconds = 0.00 minutes + total time = 1 seconds = 0.02 minutes + ==> One Electron Grid Properties (v2.0) <== + + ==> CubicScalarGrid <== + + Filepath = . + Total Points = 2197 + XYZ Blocking = 10 + X Points = 13 + Y Points = 13 + Z Points = 13 + X Spacing = 5.000E-01 + Y Spacing = 5.000E-01 + Z Spacing = 5.000E-01 + X Minimum = -3.000E+00 + Y Minimum = -3.000E+00 + Z Minimum = -2.563E+00 + X Maximum = 3.000E+00 + Y Maximum = 3.000E+00 + Z Maximum = 3.437E+00 + + Basis Set: STO-3G + Blend: STO-3G + Number of shells: 5 + Number of basis function: 7 + Number of Cartesian functions: 7 + Spherical Harmonics?: true + Max angular momentum: 1 + + + Psi4 stopped on: Wednesday, 15 July 2020 02:57PM + Psi4 wall time for execution: 0:00:00.60 + +*** Psi4 exiting successfully. Buy a developer a beer! From 918dc7dcc853c6352d44ac4efe13ae8fbdd54508 Mon Sep 17 00:00:00 2001 From: Victor Cano Gil Date: Sat, 5 Aug 2023 01:48:17 -0400 Subject: [PATCH 11/18] update calculation docs --- docs/src/calculation.md | 79 +++- src/calculation_methods.jl | 79 ++-- .../calculation_methods/cda/water_mp2.out | 427 ------------------ 3 files changed, 123 insertions(+), 462 deletions(-) delete mode 100644 test/data/calculation_methods/cda/water_mp2.out diff --git a/docs/src/calculation.md b/docs/src/calculation.md index 8bc5e4e..c85de2e 100644 --- a/docs/src/calculation.md +++ b/docs/src/calculation.md @@ -3,12 +3,83 @@ Cclib also allows to further analyse calculation ouputs. # C squared population analysis (CSPA) +**CSPA** can be used to determine and interpret the electron density of a molecule. The contribution of the a-th atomic orbital to the i-th molecular orbital can be written in terms of the molecular orbital coefficients: +$$\Phi_{ai} = \frac{c^2_{ai}}{\sum_k c^2_{ki}}$$ +```Julia +# Example calculation files can be found in the test folder of the main branch. +julia> using Cclib +julia> aoresults, fragresults, fragcharges = cspa("./Trp_polar.fchk") +``` + +* ``aoresults``: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that ``aoresults[1][46][1]`` gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, +* ``fragresults``: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1][24][5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) +* ``fragcharges``: a vector with the number of (partial) electrons in each fragment, so that ``fragcharges[3]`` gives the number of electrons in the 3rd fragment. + # Mulliken population analysis (MPA) +MPA can be used to determine and interpret the electron density of a molecule. The contribution of the a-th atomic orbital to the i-th molecular orbital in this method is written in terms of the molecular orbital coefficients, c, and the overlap matrix, S: +$$\Phi_{ai} = \sum_b c_{ai} c_{bi} S_{ab}$$ +```Julia +julia> using Cclib +julia> aoresults, fragresults, fragcharges = mpa("./Trp_polar.fchk") +``` + +* ``aoresults``: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that ``aoresults[1][46][1]`` gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, +* ``fragresults``: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1][24][5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) +* ``fragcharges``: a vector with the number of (partial) electrons in each fragment, so that ``fragcharges[3]`` gives the number of electrons in the 3rd fragment. + # Löwdin Population Analysis +```Julia +julia> using Cclib +julia> aoresults, fragresults, fragcharges = lpa("./Trp_polar.fchk") +``` + +* ``aoresults``: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that ``aoresults[1][46][1]`` gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, +* ``fragresults``: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1][24][5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) +* ``fragcharges``: a vector with the number of (partial) electrons in each fragment, so that ``fragcharges[3]`` gives the number of electrons in the 3rd fragment. + # Bickelhaupt Population Analysis +The Bickelhaupt class available from cclib.method performs Bickelhaupt population analysis that has been proposed in *Organometallics* 1996, 15, 13, 2923–2931. [doi:10.1021/om950966x](https://pubs.acs.org/doi/abs/10.1021/om950966x) + +The contribution of the a-th atomic orbital to the i-th molecular orbital in this method is written in terms of the molecular orbital coefficients, c, and the overlap matrix, S: + +$$\Phi_{ai,\alpha} = \sum_b w_{ab,\alpha} c_{ai,\alpha} c_{bi,\alpha} S_{ab}$$ + +where the weights :math:`w_{ab}` that are applied on the Mulliken atomic orbital contributions are defined as following when the coefficients of the molecular orbitals are substituted into equation 11 in the original article. + +$$w_{ab,\alpha} = 2 \frac{\sum_k c_{ak,\alpha}^2}{\sum_i c_{ai,\alpha}^2 + \sum_j c_{bj,\alpha}^2}$$ + +In case of unrestricted calculations, $\alpha$ charges and $\beta$ charges are each determined to obtain total charge. In restricted calculations, $\alpha$ subscript can be ignored since the coefficients are equivalent for both spin orbitals. + +The weights are introduced to replace the somewhat arbitrary partitioning of off-diagonal charges in the Mulliken population analysis, which divides the off-diagonal charges identically to both atoms. Bickelhaupt population analysis instead divides the off-diagonal elements based on the relative magnitude of diagonal elements. +```Julia +julia> using Cclib +julia> aoresults, fragresults, fragcharges = bpa("./Trp_polar.fchk") +``` +* ``aoresults``: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that ``aoresults[1][46][1]`` gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, +* ``fragresults``: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1][24][5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) +* ``fragcharges``: a vector with the number of (partial) electrons in each fragment, so that ``fragcharges[3]`` gives the number of electrons in the 3rd fragment. + # Density Matrix calculation -# Mayer’s Bond Orders +Calculates the electron density matrix +```Julia +julia> using Cclib +julia> result = density("./Trp_polar.fchk") +``` +Returns an array with three axes. The first axis is for the spin contributions, the second and the third axes for the density matrix, which follows standard definition. +# Mayer’s Bond Orders (MBO) +Calculates Mayer's bond orders +```Julia +julia> using Cclib +julia> result = mbo("./Trp_polar.fchk") +``` +Returns an array with three axes. The first axis is for contributions of each spin to the MBO, while the second and the third correspond to the indices of the atoms. # Charge Decomposition Analysis -# Bader’s QTAIM -# DDEC6 -# Hirshfeld Population Analysis \ No newline at end of file +The Charge Decomposition Analysis (CDA) as developed by Gernot Frenking et al. is used to study the donor-acceptor interactions of a molecule in terms of two user-specified fragments. +```Julia +julia> using Cclib +julia> donations, bdonations, repulsions = cda("BH3CO-sp.log", "BH3.log", "CO.log") +``` +Returns donations, bdonations (back donations), and repulsions attributes. +These attributes are simply lists of 1-dimensional arrays corresponding to the restricted or alpha/beta molecular orbitals of the entire molecule. + + diff --git a/src/calculation_methods.jl b/src/calculation_methods.jl index ceee5ce..8d470ed 100644 --- a/src/calculation_methods.jl +++ b/src/calculation_methods.jl @@ -10,8 +10,6 @@ export density export mbo export cda export bader -export ddec6 -export hpa # dimensions of some outputs are NxMxK, however python return dimension N as a list, not an array function expand(x) @@ -27,7 +25,10 @@ C-Squared Population Analysis (CSPA) # Arguments - `file::String`: Cclib-supported output file # Returns -Tuple (aoresults, fragresults, fragcharges) +Tuple with 3 elements: +- `aoresults`: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that ``aoresults[1][46][1]`` gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, +- `fragresults`: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1][24][5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) +- `fragcharges`: a vector with the number of (partial) electrons in each fragment, so that ``fragcharges[3]`` gives the number of electrons in the 3rd fragment. """ function cspa(file::String) #TODO: implement the optional args from docs @@ -47,7 +48,10 @@ Mulliken Population Analysis # Arguments - `file::String`: Cclib-supported output file # Returns -Tuple (aoresults, fragresults, fragcharges) +Tuple with 3 elements: +- `aoresults`: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that ``aoresults[1][46][1]`` gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, +- `fragresults`: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1][24][5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) +- `fragcharges`: a vector with the number of (partial) electrons in each fragment, so that ``fragcharges[3]`` gives the number of electrons in the 3rd fragment. """ function mpa(file::String) data = cclib[].io.ccread(file) @@ -66,7 +70,10 @@ Lowdin Population Analysis # Arguments - `file::String`: Cclib-supported output file # Returns -Tuple (aoresults, fragresults, fragcharges) +Tuple with 3 elements: +- `aoresults`: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that ``aoresults[1][46][1]`` gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, +- `fragresults`: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1][24][5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) +- `fragcharges`: a vector with the number of (partial) electrons in each fragment, so that ``fragcharges[3]`` gives the number of electrons in the 3rd fragment. """ function lpa(file::String) data = cclib[].io.ccread(file) @@ -85,7 +92,10 @@ Bickelhaupt Population Analysis # Arguments - `file::String`: Cclib-supported output file # Returns -Tuple (aoresults, fragresults, fragcharges) +Tuple with 3 elements: +- `aoresults`: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that ``aoresults[1][46][1]`` gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, +- `fragresults`: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1][24][5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) +- `fragcharges`: a vector with the number of (partial) electrons in each fragment, so that ``fragcharges[3]`` gives the number of electrons in the 3rd fragment. """ function bpa(file::String) data = cclib[].io.ccread(file) @@ -104,7 +114,8 @@ Density matrix calculation # Arguments - `file::String`: Cclib-supported output file # Returns -Density Matrix +- An array with three axes. The first axis is for the spin contributions, +the second and the third axes for the density matrix, which follows standard definition. """ function density(file::String) data = cclib[].io.ccread(file) @@ -121,7 +132,7 @@ Calculate Mayer's bond orders # Arguments - `file::String`: Cclib-supported output file # Returns -Array of rank 3. The first axis is for contributions of each spin to the MBO, +- An array with three axes. The first axis is for contributions of each spin to the MBO, while the second and third correspond to the indices of the atoms. """ function mbo(file::String) @@ -137,9 +148,13 @@ end Charge decomposition analysis # Arguments -- `file::String`: Cclib-supported output file +- `mol::String`: Cclib-supported output file +- `frag1::String`: Cclib-supported output file +- `frag2::String`: Cclib-supported output file # Returns -Tuple (donations, backdonations, repulsions) +- Tuple (donations, backdonations, repulsions) +donations, bdonations (back donations), and repulsions attributes. +These attributes are simply lists of 1-dimensional arrays corresponding to the restricted or alpha/beta molecular orbitals of the entire molecule. """ function cda(mol::String, frag1::String, frag2::String) mol = cclib[].io.ccread(mol) @@ -153,24 +168,26 @@ function cda(mol::String, frag1::String, frag2::String) return donations, bdonations, repulsions end -""" - bader(file::String) - -Bader's QTAIM charges calculation -# Arguments -- `file::String`: Cclib-supported output file -# Returns -Tuple (donations, backdonations, repulsions) -""" -function bader(file::String, vol::Vector{Vector}) - data = cclib[].io.ccread(file) - vol = pytuple(pytuple(i) for i in vol) - vol = cclib[].method.Volume(vol...) - mol = cclib[].method.Bader(data, vol) - mol.calculate() - return mol - # aoresults = mol.__dict__["aoresults"] |> expand - # fragresults = mol.__dict__["fragresults"] |> expand - # fragcharges = pyconvert(Array{Float64}, mol.__dict__["fragcharges"]) - # return aoresults, fragresults, fragcharges -end +# TODO: this requires PyQuante which doens't seem to work +# when trying to install it into a conda env +# """ +# bader(file::string) + +# bader's qtaim charges calculation +# # arguments +# - `file::string`: cclib-supported output file +# # returns +# tuple (donations, backdonations, repulsions) +# """ +# function bader(file::string, vol::vector{vector{float64}}) +# data = cclib[].io.ccread(file) +# vol = pytuple(pytuple(i) for i in vol) +# vol = cclib[].method.volume(vol...) +# mol = cclib[].method.bader(data, vol) +# mol.calculate() +# return mol +# # aoresults = mol.__dict__["aoresults"] |> expand +# # fragresults = mol.__dict__["fragresults"] |> expand +# # fragcharges = pyconvert(array{float64}, mol.__dict__["fragcharges"]) +# # return aoresults, fragresults, fragcharges +# end diff --git a/test/data/calculation_methods/cda/water_mp2.out b/test/data/calculation_methods/cda/water_mp2.out deleted file mode 100644 index 2ee4a6f..0000000 --- a/test/data/calculation_methods/cda/water_mp2.out +++ /dev/null @@ -1,427 +0,0 @@ - - ----------------------------------------------------------------------- - Psi4: An Open-Source Ab Initio Electronic Structure Package - Psi4 1.2.1 release - - Git: Rev {HEAD} 406f4de - - - R. M. Parrish, L. A. Burns, D. G. A. Smith, A. C. Simmonett, - A. E. DePrince III, E. G. Hohenstein, U. Bozkaya, A. Yu. Sokolov, - R. Di Remigio, R. M. Richard, J. F. Gonthier, A. M. James, - H. R. McAlexander, A. Kumar, M. Saitow, X. Wang, B. P. Pritchard, - P. Verma, H. F. Schaefer III, K. Patkowski, R. A. King, E. F. Valeev, - F. A. Evangelista, J. M. Turney, T. D. Crawford, and C. D. Sherrill, - J. Chem. Theory Comput. 13(7) pp 3185--3197 (2017). - (doi: 10.1021/acs.jctc.7b00174) - - - Additional Contributions by - P. Kraus, H. Kruse, M. H. Lechner, M. C. Schieber, and R. A. Shaw - - ----------------------------------------------------------------------- - - - Psi4 started on: Wednesday, 15 July 2020 02:57PM - - Process ID: 959791 - Host: homesvr - PSIDATADIR: /home/minsikcho/anaconda3/envs/p4env/share/psi4 - Memory: 500.0 MiB - Threads: 1 - - ==> Input File <== - --------------------------------------------------------------------------- -molecule water { -0 1 -O -H 1 0.99 -H 1 0.99 2 106.0 -} - -set { - basis sto-3g - print_basis true - print_mos true - cubeprop_tasks ['orbitals', 'density'] - cubic_grid_spacing [0.5, 0.5, 0.5] - cubic_grid_overage [3, 1.5, 2.4] -} - -mp2_e, scf_wfn = energy('mp2', return_wfn=True) -cubeprop(scf_wfn) - - --------------------------------------------------------------------------- - SCF Algorithm Type (re)set to DF. - -*** tstart() called on homesvr -*** at Wed Jul 15 14:57:37 2020 - - => Loading Basis Set <= - - Name: STO-3G - Role: ORBITAL - Keyword: BASIS - atoms 1 entry O line 81 file /home/minsikcho/anaconda3/envs/p4env/share/psi4/basis/sto-3g.gbs - atoms 2-3 entry H line 19 file /home/minsikcho/anaconda3/envs/p4env/share/psi4/basis/sto-3g.gbs - - - --------------------------------------------------------- - SCF - by Justin Turney, Rob Parrish, Andy Simmonett - and Daniel Smith - RHF Reference - 1 Threads, 500 MiB Core - --------------------------------------------------------- - - ==> Geometry <== - - Molecular point group: c2v - Full point group: C2v - - Geometry (in Angstrom), charge = 0, multiplicity = 1: - - Center X Y Z Mass - ------------ ----------------- ----------------- ----------------- ----------------- - O 0.000000000000 0.000000000000 -0.066678531529 15.994914619560 - H 0.000000000000 -0.790649154947 0.529118341392 1.007825032070 - H 0.000000000000 0.790649154947 0.529118341392 1.007825032070 - - Running in c2v symmetry. - - Rotational constants: A = 26.52958 B = 13.37869 C = 8.89367 [cm^-1] - Rotational constants: A = 795336.70122 B = 401083.16849 C = 266625.59877 [MHz] - Nuclear repulsion = 8.887006225878341 - - Charge = 0 - Multiplicity = 1 - Electrons = 10 - Nalpha = 5 - Nbeta = 5 - - ==> Algorithm <== - - SCF Algorithm Type is DF. - DIIS enabled. - MOM disabled. - Fractional occupation disabled. - Guess Type is SAD. - Energy threshold = 1.00e-08 - Density threshold = 1.00e-08 - Integral threshold = 0.00e+00 - - ==> Primary Basis <== - - Basis Set: STO-3G - Blend: STO-3G - Number of shells: 5 - Number of basis function: 7 - Number of Cartesian functions: 7 - Spherical Harmonics?: true - Max angular momentum: 1 - - => Loading Basis Set <= - - Name: (STO-3G AUX) - Role: JKFIT - Keyword: DF_BASIS_SCF - atoms 1 entry O line 323 file /home/minsikcho/anaconda3/envs/p4env/share/psi4/basis/def2-svp-jkfit.gbs - atoms 2-3 entry H line 23 file /home/minsikcho/anaconda3/envs/p4env/share/psi4/basis/def2-svp-jkfit.gbs - - -AO BASIS SET INFORMATION: - Name = STO-3G - Blend = STO-3G - Total number of shells = 5 - Number of primitives = 15 - Number of AO = 7 - Number of SO = 7 - Maximum AM = 1 - Spherical Harmonics = TRUE - - -Contraction Scheme: - Atom Type All Primitives // Shells: - ------ ------ -------------------------- - 1 O 6s 3p // 2s 1p - 2 H 3s // 1s - 3 H 3s // 1s - - ==> AO Basis Functions <== - - [ STO-3G ] - spherical - **** - O 1 - S 3 1.00 - 130.70932000 0.15432897 - 23.80886100 0.53532814 - 6.44360830 0.44463454 - S 3 1.00 - 5.03315130 -0.09996723 - 1.16959610 0.39951283 - 0.38038900 0.70011547 - P 3 1.00 - 5.03315130 0.15591627 - 1.16959610 0.60768372 - 0.38038900 0.39195739 - **** - H 2 - S 3 1.00 - 3.42525091 0.15432897 - 0.62391373 0.53532814 - 0.16885540 0.44463454 - **** - - ==> Pre-Iterations <== - - ------------------------------------------------------- - Irrep Nso Nmo Nalpha Nbeta Ndocc Nsocc - ------------------------------------------------------- - A1 4 4 0 0 0 0 - A2 0 0 0 0 0 0 - B1 1 1 0 0 0 0 - B2 2 2 0 0 0 0 - ------------------------------------------------------- - Total 7 7 5 5 5 0 - ------------------------------------------------------- - - ==> Integral Setup <== - - DFHelper Memory: AOs need 0.000 [GiB]; user supplied 0.366 [GiB]. Using in-core AOs. - - ==> MemDFJK: Density-Fitted J/K Matrices <== - - J tasked: Yes - K tasked: Yes - wK tasked: No - OpenMP threads: 1 - Memory (MB): 375 - Algorithm: Core - Schwarz Cutoff: 1E-12 - Mask sparsity (%): 0.0000 - Fitting Condition: 1E-12 - - => Auxiliary Basis Set <= - - Basis Set: (STO-3G AUX) - Blend: DEF2-SVP-JKFIT - Number of shells: 37 - Number of basis function: 113 - Number of Cartesian functions: 133 - Spherical Harmonics?: true - Max angular momentum: 4 - - Minimum eigenvalue in the overlap matrix is 3.6393052139E-01. - Using Symmetric Orthogonalization. - - SCF Guess: Superposition of Atomic Densities via on-the-fly atomic UHF. - - ==> Iterations <== - - Total Energy Delta E RMS |[F,P]| - - @DF-RHF iter 0: -74.71460191108939 -7.47146e+01 3.03940e-01 - @DF-RHF iter 1: -74.91600325470347 -2.01401e-01 5.09813e-02 - @DF-RHF iter 2: -74.96229021097456 -4.62870e-02 9.16895e-03 DIIS - @DF-RHF iter 3: -74.96398815218649 -1.69794e-03 3.56711e-03 DIIS - @DF-RHF iter 4: -74.96441461354455 -4.26461e-04 3.22682e-04 DIIS - @DF-RHF iter 5: -74.96441710793660 -2.49439e-06 3.57733e-05 DIIS - @DF-RHF iter 6: -74.96441713216285 -2.42263e-08 1.11484e-06 DIIS - @DF-RHF iter 7: -74.96441713218326 -2.04068e-11 4.76814e-10 DIIS - - ==> Post-Iterations <== - - Orbital Energies [Eh] - --------------------- - - Doubly Occupied: - - 1A1 -20.243976 2A1 -1.250662 1B2 -0.603166 - 3A1 -0.445470 1B1 -0.388215 - - Virtual: - - 4A1 0.570772 2B2 0.708631 - - Final Occupation by Irrep: - A1 A2 B1 B2 - DOCC [ 3, 0, 1, 1 ] - - Energy converged. - - @DF-RHF Final Energy: -74.96441713218326 - - => Energetics <= - - Nuclear Repulsion Energy = 8.8870062258783413 - One-Electron Energy = -121.8398687190952501 - Two-Electron Energy = 37.9884453610336408 - Total Energy = -74.9644171321832715 - - - -Properties will be evaluated at 0.000000, 0.000000, 0.000000 [a0] - -Properties computed using the SCF density matrix - - Nuclear Dipole Moment: [e a0] - X: 0.0000 Y: 0.0000 Z: 0.9917 - - Electronic Dipole Moment: [e a0] - X: 0.0000 Y: 0.0000 Z: -0.3335 - - Dipole Moment: [e a0] - X: 0.0000 Y: 0.0000 Z: 0.6583 Total: 0.6583 - - Dipole Moment: [D] - X: 0.0000 Y: 0.0000 Z: 1.6732 Total: 1.6732 - - - ==> Molecular Orbitals <== - - 1 2 3 4 5 - - 1 O1 s0 0.9942034 0.2342174 0.0000000 0.1004582 0.0000000 - 2 O1 s0 0.0259139 -0.8458846 0.0000000 -0.5214075 0.0000000 - 3 O1 p0 0.0039930 -0.1170354 0.0000000 0.7742484 0.0000000 - 4 O1 p+1 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 - 5 O1 p-1 0.0000000 0.0000000 0.6032830 0.0000000 0.0000000 - 6 H2 s0 -0.0056268 -0.1564492 -0.4463951 0.2890869 0.0000000 - 7 H3 s0 -0.0056268 -0.1564492 0.4463951 0.2890869 0.0000000 - - Ene -20.2439758 -1.2506624 -0.6031659 -0.4454697 -0.3882152 - Sym A1 A1 B2 A1 B1 - Occ 2 2 2 2 2 - - - 6 7 - - 1 O1 s0 0.1283482 0.0000000 - 2 O1 s0 -0.8325149 0.0000000 - 3 O1 p0 -0.7326476 0.0000000 - 4 O1 p+1 0.0000000 0.0000000 - 5 O1 p-1 0.0000000 0.9764982 - 6 H2 s0 0.7757921 0.8089054 - 7 H3 s0 0.7757921 -0.8089054 - - Ene 0.5707720 0.7086314 - Sym A1 B2 - Occ 0 0 - - -*** tstop() called on homesvr at Wed Jul 15 14:57:38 2020 -Module time: - user time = 0.43 seconds = 0.01 minutes - system time = 0.01 seconds = 0.00 minutes - total time = 1 seconds = 0.02 minutes -Total time: - user time = 0.43 seconds = 0.01 minutes - system time = 0.01 seconds = 0.00 minutes - total time = 1 seconds = 0.02 minutes - -*** tstart() called on homesvr -*** at Wed Jul 15 14:57:38 2020 - - - //>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>// - // DFMP2 // - //<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< Loading Basis Set <= - - Name: (STO-3G AUX) - Role: RIFIT - Keyword: DF_BASIS_MP2 - atoms 1 entry O line 406 file /home/minsikcho/anaconda3/envs/p4env/share/psi4/basis/def2-qzvpp-ri.gbs - atoms 2-3 entry H line 24 file /home/minsikcho/anaconda3/envs/p4env/share/psi4/basis/def2-qzvpp-ri.gbs - - -------------------------------------------------------- - DF-MP2 - 2nd-Order Density-Fitted Moller-Plesset Theory - RMP2 Wavefunction, 1 Threads - - Rob Parrish, Justin Turney, Andy Simmonett, - Ed Hohenstein, and C. David Sherrill - -------------------------------------------------------- - - => Auxiliary Basis Set <= - - Basis Set: (STO-3G AUX) - Blend: DEF2-QZVPP-RI - Number of shells: 65 - Number of basis function: 253 - Number of Cartesian functions: 333 - Spherical Harmonics?: true - Max angular momentum: 5 - - -------------------------------------------------------- - NBF = 7, NAUX = 253 - -------------------------------------------------------- - CLASS FOCC OCC AOCC AVIR VIR FVIR - PAIRS 0 5 5 2 2 0 - -------------------------------------------------------- - - ----------------------------------------------------------- - ==================> DF-MP2 Energies <==================== - ----------------------------------------------------------- - Reference Energy = -74.9644171321832573 [Eh] - Singles Energy = -0.0000000000000000 [Eh] - Same-Spin Energy = -0.0021865372482756 [Eh] - Opposite-Spin Energy = -0.0358629201406502 [Eh] - Correlation Energy = -0.0380494573889258 [Eh] - Total Energy = -75.0024665895721796 [Eh] - ----------------------------------------------------------- - ================> DF-SCS-MP2 Energies <================== - ----------------------------------------------------------- - SCS Same-Spin Scale = 0.3333333333333333 [-] - SCS Opposite-Spin Scale = 1.2000000000000000 [-] - SCS Same-Spin Energy = -0.0007288457494252 [Eh] - SCS Opposite-Spin Energy = -0.0430355041687802 [Eh] - SCS Correlation Energy = -0.0437643499182054 [Eh] - SCS Total Energy = -75.0081814821014632 [Eh] - ----------------------------------------------------------- - - -*** tstop() called on homesvr at Wed Jul 15 14:57:38 2020 -Module time: - user time = 0.13 seconds = 0.00 minutes - system time = 0.00 seconds = 0.00 minutes - total time = 0 seconds = 0.00 minutes -Total time: - user time = 0.56 seconds = 0.01 minutes - system time = 0.01 seconds = 0.00 minutes - total time = 1 seconds = 0.02 minutes - ==> One Electron Grid Properties (v2.0) <== - - ==> CubicScalarGrid <== - - Filepath = . - Total Points = 2197 - XYZ Blocking = 10 - X Points = 13 - Y Points = 13 - Z Points = 13 - X Spacing = 5.000E-01 - Y Spacing = 5.000E-01 - Z Spacing = 5.000E-01 - X Minimum = -3.000E+00 - Y Minimum = -3.000E+00 - Z Minimum = -2.563E+00 - X Maximum = 3.000E+00 - Y Maximum = 3.000E+00 - Z Maximum = 3.437E+00 - - Basis Set: STO-3G - Blend: STO-3G - Number of shells: 5 - Number of basis function: 7 - Number of Cartesian functions: 7 - Spherical Harmonics?: true - Max angular momentum: 1 - - - Psi4 stopped on: Wednesday, 15 July 2020 02:57PM - Psi4 wall time for execution: 0:00:00.60 - -*** Psi4 exiting successfully. Buy a developer a beer! From 0467f35ad14b3e1a5538b58961653f2a139847d3 Mon Sep 17 00:00:00 2001 From: Victor Cano Gil Date: Sat, 5 Aug 2023 01:52:41 -0400 Subject: [PATCH 12/18] update docstrings --- src/calculation_methods.jl | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/calculation_methods.jl b/src/calculation_methods.jl index 8d470ed..ecea86c 100644 --- a/src/calculation_methods.jl +++ b/src/calculation_methods.jl @@ -124,7 +124,6 @@ function density(file::String) return pyconvert(Array{Float64}, mol.__dict__["density"]) end -#ToDo: check output dimensions? """ mbo(file::String) @@ -142,7 +141,6 @@ function mbo(file::String) return pyconvert(Array{Float64}, mol.__dict__["fragresults"]) end -#TODO Figure out the dimensions """ cda(file::String) From e8b46844cc40e6e33e391758f91ccca9f25a18cb Mon Sep 17 00:00:00 2001 From: Victor Cano Gil Date: Sat, 5 Aug 2023 02:39:40 -0400 Subject: [PATCH 13/18] write tests --- test/runtests.jl | 50 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/test/runtests.jl b/test/runtests.jl index 75b44db..a4add7c 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -7,6 +7,10 @@ using AtomsBase @testset "Cclib.jl" begin test_file = "./data/uracil_two.xyz" + + # + # Test parsing and reading + # test_ccdata = ccread(test_file) # Check that input is read correctly @@ -23,11 +27,57 @@ using AtomsBase @test isnothing(ccread("./data/invalid_file.txt")) @test isnothing(ccread("./data/")) + # # Check AtomsBase Integration + # test_atom_objects = get_atom_objects(test_file) @test atomic_number(test_atom_objects[1]) == 7 @test atomic_symbol(test_atom_objects[1]) == :N @test atomic_number(test_atom_objects[6]) == 6 @test atomic_symbol(test_atom_objects[6]) == :C + # + # Check calculation methods + # + + # populations, density, and mbo + test_calc_file = "./data/Trp_polar.fchk" + pop_funcs = [cspa, mpa, lpa, bpa] + for func in pop_funcs + aoresults, fragresults, fragcharges = func(test_calc_file) + @test size(aoresults) == (1, 87, 87) + @test typeof(aoresults) == Array{Float64, 3} + + @test size(fragresults) == (1, 87, 27) + @test typeof(fragresults) == Array{Float64, 3} + + @test size(fragcharges) == (27,) + @test typeof(fragcharges) == Array{Float64, 1} + end + + test_density = density(test_calc_file) + @test size(test_density) == (1, 87, 87) + @test typeof(test_density) == Array{Float64, 3} + + test_mbo = mbo(test_calc_file) + @test size(test_mbo) == (1, 27, 27) + @test typeof(test_mbo) == Array{Float64, 3} + + # cda + test_attrs = ( + "./data/calculation_methods/cda/BH3CO-sp.log", + "./data/calculation_methods/cda/BH3.log", + "./data/calculation_methods/cda/CO.log" + ) + donations, bdonations, repulsions = cda(test_attrs...) + @test size(donations) == (1, 51) + @test typeof(donations) == Matrix{Float64} + + @test size(bdonations) == (1, 51) + @test typeof(bdonations) == Matrix{Float64} + + @test size(repulsions) == (1, 51) + @test typeof(repulsions) == Matrix{Float64} + + end From 777e6f34d99fc432880f2ae5dbb3213177d10d95 Mon Sep 17 00:00:00 2001 From: Victor Cano Gil Date: Sat, 5 Aug 2023 02:44:50 -0400 Subject: [PATCH 14/18] remove junk --- src/functions.jl | 1 - test.jl | 31 ------------------------------- 2 files changed, 32 deletions(-) delete mode 100644 test.jl diff --git a/src/functions.jl b/src/functions.jl index 78c9135..43394b0 100644 --- a/src/functions.jl +++ b/src/functions.jl @@ -3,7 +3,6 @@ # export ccread -export get_data function pyccread(file) data = cclib[].io.ccread(file) diff --git a/test.jl b/test.jl deleted file mode 100644 index 9ec1452..0000000 --- a/test.jl +++ /dev/null @@ -1,31 +0,0 @@ -using Cclib -using PythonCall - -cclib = Cclib.cclib.x -cpsa = cclib.method.CSPA -lpa = cclib.method.LPA -bick = cclib.method.Bickelhaupt -density = cclib.method.Density -mol = cclib.io.ccread("./test/data/Trp_polar.fchk") - -a = lpa(mol) -a.calculate() -a.__dict__.keys() -aoresults = a.__dict__["aoresults"] -fragresults = a.__dict__["fragresults"] -fragcharges = a.__dict__["fragcharges"] - -# x = pyconvert(Array{Float64}, fragcharges) -# reshape(x, (1, size(x)...)) - -b = mpa("./test/data/Trp_polar.fchk") - - -a = cda( - "./test/data/calculation_methods/cda/BH3CO-sp.log", - "./test/data/calculation_methods/cda/BH3.log", - "./test/data/calculation_methods/cda/CO.log", -) -a.__dict__.keys() -a.__dict__["repulsions"] -z = a.__dict__["donations"] \ No newline at end of file From 4ab01216c02c0e51522e218732db0a0027f389f9 Mon Sep 17 00:00:00 2001 From: Victor Cano Gil Date: Sat, 5 Aug 2023 02:55:17 -0400 Subject: [PATCH 15/18] fix make doc --- docs/make.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/make.jl b/docs/make.jl index 7869318..9dc2833 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -16,7 +16,7 @@ makedocs(; pages=[ "Home" => "index.md", "How to parse files" => "io.md", - "Additional Analyses" => "calculation.md" + "Additional Analyses" => "calculation.md", "AtomsBase Integration" => "atombase.md" ], ) From d8481736f7ea377a97b78e660ea2b0376e58f2f9 Mon Sep 17 00:00:00 2001 From: Victor Cano Gil Date: Sat, 5 Aug 2023 03:14:47 -0400 Subject: [PATCH 16/18] fix doc typo --- docs/src/calculation.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/src/calculation.md b/docs/src/calculation.md index c85de2e..cd3ef95 100644 --- a/docs/src/calculation.md +++ b/docs/src/calculation.md @@ -44,7 +44,7 @@ The contribution of the a-th atomic orbital to the i-th molecular orbital in thi $$\Phi_{ai,\alpha} = \sum_b w_{ab,\alpha} c_{ai,\alpha} c_{bi,\alpha} S_{ab}$$ -where the weights :math:`w_{ab}` that are applied on the Mulliken atomic orbital contributions are defined as following when the coefficients of the molecular orbitals are substituted into equation 11 in the original article. +where the weights $w_{ab}$ that are applied on the Mulliken atomic orbital contributions are defined as following when the coefficients of the molecular orbitals are substituted into equation 11 in the original article. $$w_{ab,\alpha} = 2 \frac{\sum_k c_{ak,\alpha}^2}{\sum_i c_{ai,\alpha}^2 + \sum_j c_{bj,\alpha}^2}$$ From 386c30b6143bea95fdd855a793f05a60335ce442 Mon Sep 17 00:00:00 2001 From: Victor Cano Gil Date: Sat, 5 Aug 2023 03:21:34 -0400 Subject: [PATCH 17/18] fix indexing in docs --- docs/src/calculation.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/src/calculation.md b/docs/src/calculation.md index cd3ef95..a530efc 100644 --- a/docs/src/calculation.md +++ b/docs/src/calculation.md @@ -11,8 +11,8 @@ julia> using Cclib julia> aoresults, fragresults, fragcharges = cspa("./Trp_polar.fchk") ``` -* ``aoresults``: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that ``aoresults[1][46][1]`` gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, -* ``fragresults``: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1][24][5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) +* ``aoresults``: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that ``aoresults[1, 46, 1]`` gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, +* ``fragresults``: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1, 24, 5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) * ``fragcharges``: a vector with the number of (partial) electrons in each fragment, so that ``fragcharges[3]`` gives the number of electrons in the 3rd fragment. # Mulliken population analysis (MPA) @@ -23,8 +23,8 @@ julia> using Cclib julia> aoresults, fragresults, fragcharges = mpa("./Trp_polar.fchk") ``` -* ``aoresults``: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that ``aoresults[1][46][1]`` gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, -* ``fragresults``: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1][24][5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) +* ``aoresults``: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that ``aoresults[1, 46, 1]`` gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, +* ``fragresults``: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1, 24, 5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) * ``fragcharges``: a vector with the number of (partial) electrons in each fragment, so that ``fragcharges[3]`` gives the number of electrons in the 3rd fragment. # Löwdin Population Analysis @@ -33,8 +33,8 @@ julia> using Cclib julia> aoresults, fragresults, fragcharges = lpa("./Trp_polar.fchk") ``` -* ``aoresults``: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that ``aoresults[1][46][1]`` gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, -* ``fragresults``: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1][24][5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) +* ``aoresults``: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that ``aoresults[1, 46, 1]`` gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, +* ``fragresults``: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1, 24, 5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) * ``fragcharges``: a vector with the number of (partial) electrons in each fragment, so that ``fragcharges[3]`` gives the number of electrons in the 3rd fragment. # Bickelhaupt Population Analysis @@ -55,8 +55,8 @@ The weights are introduced to replace the somewhat arbitrary partitioning of off julia> using Cclib julia> aoresults, fragresults, fragcharges = bpa("./Trp_polar.fchk") ``` -* ``aoresults``: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that ``aoresults[1][46][1]`` gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, -* ``fragresults``: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1][24][5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) +* ``aoresults``: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that ``aoresults[1, 46, 1]`` gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, +* ``fragresults``: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1, 24, 5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) * ``fragcharges``: a vector with the number of (partial) electrons in each fragment, so that ``fragcharges[3]`` gives the number of electrons in the 3rd fragment. # Density Matrix calculation From ae198e7873be62423ffd716772e5502e75808087 Mon Sep 17 00:00:00 2001 From: Victor Cano Gil Date: Mon, 7 Aug 2023 13:30:07 -0400 Subject: [PATCH 18/18] address comments --- src/calculation_methods.jl | 2 +- test/runtests.jl | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/calculation_methods.jl b/src/calculation_methods.jl index ecea86c..6d53cda 100644 --- a/src/calculation_methods.jl +++ b/src/calculation_methods.jl @@ -177,7 +177,7 @@ end # # returns # tuple (donations, backdonations, repulsions) # """ -# function bader(file::string, vol::vector{vector{float64}}) +# function bader(file::String, vol::Vector{Vector{Float64}}) # data = cclib[].io.ccread(file) # vol = pytuple(pytuple(i) for i in vol) # vol = cclib[].method.volume(vol...) diff --git a/test/runtests.jl b/test/runtests.jl index a4add7c..eaf6b28 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -45,14 +45,14 @@ using AtomsBase pop_funcs = [cspa, mpa, lpa, bpa] for func in pop_funcs aoresults, fragresults, fragcharges = func(test_calc_file) - @test size(aoresults) == (1, 87, 87) @test typeof(aoresults) == Array{Float64, 3} + @test size(aoresults) == (1, 87, 87) - @test size(fragresults) == (1, 87, 27) @test typeof(fragresults) == Array{Float64, 3} + @test size(fragresults) == (1, 87, 27) - @test size(fragcharges) == (27,) @test typeof(fragcharges) == Array{Float64, 1} + @test size(fragcharges) == (27,) end test_density = density(test_calc_file) @@ -70,14 +70,14 @@ using AtomsBase "./data/calculation_methods/cda/CO.log" ) donations, bdonations, repulsions = cda(test_attrs...) - @test size(donations) == (1, 51) @test typeof(donations) == Matrix{Float64} + @test size(donations) == (1, 51) - @test size(bdonations) == (1, 51) @test typeof(bdonations) == Matrix{Float64} + @test size(bdonations) == (1, 51) - @test size(repulsions) == (1, 51) @test typeof(repulsions) == Matrix{Float64} + @test size(repulsions) == (1, 51) end