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marvinfriedemarvinfriede
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Fix ghost atom handling (#25)
The ghost atom handling did not work if the ghost atoms did not appear strictly after the regular coordinates.
1 parent 1d00e3b commit dc40a37

17 files changed

+816
-199
lines changed

‎.gitignore

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@@ -35,3 +35,8 @@
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/build*/
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/install*/
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/_*/
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# project-specific
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/scripts/old/*
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/scripts/*.h
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/scripts/*.cpp

‎include/dftd_ncoord.h

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@@ -200,4 +200,4 @@ extern inline double log_cn_cut(const double cn_max, const double cn);
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extern inline double dlog_cn_cut(const double cn_max, const double cn);
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}; // namespace dftd4
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} // namespace dftd4

‎include/dftd_parameters.h

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@@ -63,10 +63,10 @@ static const double zeff[119]{
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* These values are actually never used in the code. Only r4r2 is used.
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*/
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static const double r2r4[119]{
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0.0, // dummy
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8.0589, 3.4698, // H,He
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0.0, // dummy
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8.0589, 3.4698, // H,He
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29.0974, 14.8517, 11.8799, 7.8715, 5.5588, 4.7566, 3.8025,
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3.1036, // Li-Ne
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3.1036, // Li-Ne
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26.1552, 17.2304, 17.7210, 12.7442, 9.5361, 8.1652, 6.7463,
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5.6004, // Na-Ar
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29.2012, 22.3934, // K,Ca

‎scripts/README.md

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# Scripts
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Scripts for creating the ORCA source files. This mainly concatenates the corresponding files and adds headers and footers.

‎scripts/make-qcdftd4.sh

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#!/bin/bash
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INCLUDE="../include"
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SRC="../src"
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cat > qcdftd4param.h << 'EOT'
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/*
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* This is the DFT-D4 equivalent of copyc6, since this is an *empirical*
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* dispersion correction we can hardly avoid having this big, scary blob
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* of data lying around somewhere.
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*
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* Files like this are usually computer generated so avoid modifying it,
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* but have the appropriate tool generate it from dftd4.
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*
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* Responsible for this mess:
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* Sebastian Ehlert <[email protected]> (SAW190521)
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*
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* Update/Fix for parameters from periodic extension by:
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* Marvin Friede <[email protected]> (MF161222)
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*
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* Extension for Fr, Ra and Actinides by:
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* Marvin Friede <[email protected]> (MF121223)
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*/
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#ifndef QCDFTD4PARAM_H
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#define QCDFTD4PARAM_H
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EOT
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sed -n '/namespace/,$p' "${INCLUDE}/dftd_parameters.h" >> qcdftd4param.h
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# Append the Footer:
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printf "\n#endif // QCDFTD4PARAM_H\n" >> qcdftd4param.h
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##################################################################
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##################################################################
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dosed(){
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sed -n '/namespace dftd4 {/,/} \/\/ namespace dftd4/p' $1 | \
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sed '/namespace dftd4 {/d; /} \/\/ namespace dftd4/d' | \
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awk '/./,EOF' > $2
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}
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dosed "${INCLUDE}/dftd_cutoff.h" cutoff.txt
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dosed "${INCLUDE}/dftd_model.h" model.txt
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dosed "${INCLUDE}/dftd_dispersion.h" dispersion.txt
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dosed "${INCLUDE}/damping/dftd_rational.h" rational.txt
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dosed "${INCLUDE}/damping/dftd_atm.h" atm.txt
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cat > qcdftd4.h << 'EOT'
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/*
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* D4(EEQ)-ATM implementation
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*
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* Sebastian Ehlert <[email protected]> (SAW190521)
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* Marvin Friede <[email protected]> (MF161222)
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*/
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#ifndef __QCDFTD4_H
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#define __QCDFTD4_H
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#include "qcinpdat.h" // TGeomInput class
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#include "qcmat1.h" // TRVector and TRMatrix class
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namespace dftd4 {
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EOT
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######
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cat >> qcdftd4.h << 'EOT'
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/* --------------------------------------------------------------------------
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Cutoff (dftd_cutoff.h)
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https://github.com/dftd4/cpp-d4/blob/main/include/dftd_cutoff.h
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-------------------------------------------------------------------------- */
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EOT
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cat cutoff.txt >> qcdftd4.h
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rm cutoff.txt
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######
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cat >> qcdftd4.h << 'EOT'
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/* --------------------------------------------------------------------------
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D4 model (dftd_model.h)
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https://github.com/dftd4/cpp-d4/blob/main/include/dftd_model.h
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-------------------------------------------------------------------------- */
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EOT
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cat model.txt >> qcdftd4.h
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rm model.txt
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######
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cat >> qcdftd4.h << 'EOT'
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/* --------------------------------------------------------------------------
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Dispersion (dftd_dispersion.h)
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https://github.com/dftd4/cpp-d4/blob/main/include/dftd_dispersion.h
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-------------------------------------------------------------------------- */
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EOT
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cat dispersion.txt >> qcdftd4.h
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rm dispersion.txt
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######
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cat >> qcdftd4.h << 'EOT'
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/* --------------------------------------------------------------------------
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Dispersion (damping/dftd_rational.h)
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https://github.com/dftd4/cpp-d4/blob/main/include/damping/dftd_rational.h
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-------------------------------------------------------------------------- */
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EOT
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cat rational.txt >> qcdftd4.h
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rm rational.txt
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######
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cat >> qcdftd4.h << 'EOT'
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/* --------------------------------------------------------------------------
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Dispersion (damping/dftd_atm.h)
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https://github.com/dftd4/cpp-d4/blob/main/include/damping/dftd_atm.h
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-------------------------------------------------------------------------- */
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EOT
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cat atm.txt >> qcdftd4.h
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rm atm.txt
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######
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cat >> qcdftd4.h << 'EOT'
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} // namespace dftd4
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/* --------------------------------------------------------------------------------------
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// Calculates the EEQ charges according to the D4 paper
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// https://doi.org/10.1063/1.5090222
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// Bernardo de Souza, 14/09/2023
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-------------------------------------------------------------------------------------- */
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int CalcEEQCharges(TRMatrix &XYZ, TIVector &ATNO, int NAtoms, int totalcharge, TRVector &q, bool printerror=true);
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#endif // __QCDFTD4_H
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EOT
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##################################################################
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##################################################################
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dosed "${SRC}/dftd_cutoff.cpp" cutoff.txt
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dosed "${SRC}/dftd_model.cpp" model.txt
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dosed "${SRC}/dftd_dispersion.cpp" dispersion.txt
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dosed "${SRC}/damping/dftd_rational.cpp" rational.txt
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dosed "${SRC}/damping/dftd_atm.cpp" atm.txt
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cat > qcdftd4.cpp << 'EOT'
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/*
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* D4(EEQ)-ATM implementation
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*
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* Sebastian Ehlert <[email protected]> (SAW190521)
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* Marvin Friede <[email protected]> (MF161222)
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*/
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#include <cmath>
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#include <limits>
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#include "qcinpdat.h" // TGeomInput class
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#include "qcmat2.h" // BLAS routines
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#include "qcmath.h" // TVector and TMatrix class
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// we cannot avoid one big, scary parameter file...
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#include "qcdftd4param.h"
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#include "qceeq.h"
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#include "qcncoord.h"
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// always include self
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#include "qcdftd4.h"
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/* --------------------------------------------------------------------------------------
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// Calculates the EEQ charges according to the D4 paper
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// https://doi.org/10.1063/1.5090222
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// Bernardo de Souza, 14/09/2023
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-------------------------------------------------------------------------------------- */
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int CalcEEQCharges(TRMatrix &XYZ, TIVector &ATNO, int NAtoms, int totalcharge, TRVector &q, bool printerror){
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// initialize the charges to zero
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q.Init();
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// check atomic numbers to guarantee we have all parameters
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// ghost atoms (ATNO=0) will have no charge
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for (int i=0;i<NAtoms;i++)
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if (ATNO(i)>86){
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if (printerror) printMessage("Atomic number %d detected. EEQ charges can not be calculated.\n",ATNO(i));
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return 1;
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}
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TGeomInput molecule;
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molecule.NAtoms=NAtoms;
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molecule.CC.CopyMat(XYZ);
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molecule.ATNO.CopyVec(ATNO);
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TIVector Index(NAtoms);
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for (int i=0;i<NAtoms;i++) Index(i)=i;
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TRMatrix dist;
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dist.NewMatrix(NAtoms, NAtoms);
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dftd4::calc_distances(molecule, Index, dist);
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TRMatrix dqdr;
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return dftd4::get_charges(molecule, Index, dist, totalcharge, 25, q, dqdr, false);
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}
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namespace dftd4 {
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EOT
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######
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cat >> qcdftd4.cpp << 'EOT'
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/* --------------------------------------------------------------------------
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Cutoff (dftd_cutoff.cpp)
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https://github.com/dftd4/cpp-d4/blob/main/src/dftd_cutoff.cpp
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-------------------------------------------------------------------------- */
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EOT
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cat cutoff.txt >> qcdftd4.cpp
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rm cutoff.txt
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######
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cat >> qcdftd4.cpp << 'EOT'
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/* --------------------------------------------------------------------------
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D4 model (dftd_model.cpp)
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https://github.com/dftd4/cpp-d4/blob/main/src/dftd_model.cpp
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-------------------------------------------------------------------------- */
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EOT
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cat model.txt >> qcdftd4.cpp
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rm model.txt
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######
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cat >> qcdftd4.cpp << 'EOT'
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/* --------------------------------------------------------------------------
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Dispersion (dftd_dispersion.cpp)
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https://github.com/dftd4/cpp-d4/blob/main/src/dftd_dispersion.cpp
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-------------------------------------------------------------------------- */
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EOT
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cat dispersion.txt >> qcdftd4.cpp
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rm dispersion.txt
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######
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cat >> qcdftd4.cpp << 'EOT'
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/* --------------------------------------------------------------------------
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Dispersion (damping/dftd_rational.cpp)
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https://github.com/dftd4/cpp-d4/blob/main/src/damping/dftd_rational.cpp
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-------------------------------------------------------------------------- */
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EOT
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cat rational.txt >> qcdftd4.cpp
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rm rational.txt
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######
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cat >> qcdftd4.cpp << 'EOT'
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/* --------------------------------------------------------------------------
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Dispersion (damping/dftd_atm.cpp)
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https://github.com/dftd4/cpp-d4/blob/main/src/damping/dftd_atm.cpp
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-------------------------------------------------------------------------- */
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EOT
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cat atm.txt >> qcdftd4.cpp
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rm atm.txt
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######
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cat >> qcdftd4.cpp << 'EOT'
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} // namespace dftd4
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EOT
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##########################################################################
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sed -i "s/TMolecule/TGeomInput/" *.h
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sed -i "s/TMolecule/TGeomInput/" *.cpp

‎scripts/make-qcdftd4param.sh

+34
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@@ -0,0 +1,34 @@
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#!/bin/bash
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INCLUDE="../include"
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5+
cat > qcdftd4param.h << 'EOT'
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/*
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* This is the DFT-D4 equivalent of copyc6, since this is an *empirical*
8+
* dispersion correction we can hardly avoid having this big, scary blob
9+
* of data lying around somewhere.
10+
*
11+
* Files like this are usually computer generated so avoid modifying it,
12+
* but have the appropriate tool generate it from dftd4.
13+
*
14+
* Responsible for this mess:
15+
* Sebastian Ehlert <[email protected]> (SAW190521)
16+
*
17+
* Update/Fix for parameters from periodic extension by:
18+
* Marvin Friede <[email protected]> (MF161222)
19+
*
20+
* Extension for Fr, Ra and Actinides by:
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* Marvin Friede <[email protected]> (MF121223)
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*/
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#ifndef QCDFTD4PARAM_H
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#define QCDFTD4PARAM_H
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EOT
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sed -n '/namespace/,$p' "${INCLUDE}/dftd_parameters.h" >> qcdftd4param.h
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printf "\n#endif // QCDFTD4PARAM_H\n" >> qcdftd4param.h
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sed -i "s/TMolecule/TGeomInput/" qcdftd4param.h

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