Docs: add the readme and running scripts for example (#207)

* Docs: add the readme and running scripts for example/matrix_hs

* Docs: add the readme and running scripts for examples/md

* Flow: dflow abacus examples (#1364)

* example: dflow compensating_charge

* example: dflow dipole_correction

* example: update README

* example: dflow electric_field

* example: dflow implicit_solvation_model

* example: dflow deepks example

* example: dflow dft_plus_u example

* example: dflow force example

* example: dflow hse example

* example: dflow vdw examples

* example: dflow stress example

* examples: dflow smearing example

* example: dflow relax example

* example: dflow sdft

Co-authored-by: root <pxlppq007@163.com>
Co-authored-by: hongriTianqi <hongriTianqi@users.noreply.github.com>

Author: 3 people

examples/README

@@ -9,3 +9,21 @@ use the interfaces between ABACUS and some extenal softwares.
 
 The examples interface_XXXX show the using of interface of ABACUS and XXXX
 
+Except for interface examples, a bash script `runall.sh` is required for each example
+directory to be accessed by `dflow_run.py`. Each example directory may contains several
+examples for different systems or input settings, where a bash script `run.sh` is
+required to run the specific example. The `SETENV` is read by `run.sh` to get the 
+executable directory of abacus (`ABACUS_PATH`), number of processes (`ABACUS_NPROCS`) and 
+number of threads (`ABACUS_THREADS`).
+
+How to run dflow_run.py:
+
+- `python3 dflow_run.py --find 1`:
+   find all directories where `runall.sh` has been prepared.
+
+- `python3 dflow_run.py --run 1`:
+   submmit dflow jobs.
+
+- `python3 dflow_run.py --post 1` 
+   checkout the status of jobs.
+

examples/compensating_charge/Pt-slab/INPUT

@@ -1,5 +1,5 @@
 INPUT_PARAMETERS
-pseudo_dir	  ./
+pseudo_dir        ../../../tests/PP_ORB
 ntype		  1
 dft_functional    pbe
 symmetry	  0

examples/compensating_charge/Pt-slab/run.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+ABACUS_PATH=$(awk -F "=" '$1=="ABACUS_PATH"{print $2}' ../../SETENV)
+ABACUS_NPROCS=$(awk -F "=" '$1=="ABACUS_NPROCS"{print $2}' ../../SETENV)
+ABACUS_THREADS=$(awk -F "=" '$1=="ABACUS_THREADS"{print $2}' ../../SETENV)
+
+OMP_NUM_THREADS=${ABACUS_THREADS} mpirun -np ${ABACUS_NPROCS} ${ABACUS_PATH} | tee scf.output

…mples/compensating_charge/Pt-slab/README examples/compensating_charge/READMEexamples/compensating_charge/Pt-slab/README renamed to examples/compensating_charge/README examples/compensating_charge/Pt-slab/README renamed to examples/compensating_charge/README

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+for ii in *
+do
+	if [ -d $ii ];then
+		cd ${ii}
+		echo "RUN: ${ii}"
+		bash run.sh
+		cd ..
+	fi
+done

examples/compensating_charge/runall.sh

@@ -0,0 +1,18 @@
+/*******************************************************************************/
+/
+/ These are the examples of ABACUS program.
+/
+/*******************************************************************************/
+
+Here are two examples:
+
+1. Generate projectors (a series of bessel functions) for DeePKS. \
+A file named `jle.orb` will be generated which contains the projectors.
+
+   - see pw_H2O
+
+2. A scf calculation with a trained DeePKS model loaded. A few .npy files will \
+be generated which are for DeePKS training only. The total energy and \
+force will be output in a way as a normal SCF job does. 
+
+   - see lcao_H2O

examples/deepks/README

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+ABACUS_PATH=$(awk -F "=" '$1=="ABACUS_PATH"{print $2}' ../../SETENV)
+ABACUS_NPROCS=$(awk -F "=" '$1=="ABACUS_NPROCS"{print $2}' ../../SETENV)
+ABACUS_THREADS=$(awk -F "=" '$1=="ABACUS_THREADS"{print $2}' ../../SETENV)
+
+OMP_NUM_THREADS=${ABACUS_THREADS} mpirun -np ${ABACUS_NPROCS} ${ABACUS_PATH} | tee scf.output

examples/deepks/lcao_H2O/run.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+ABACUS_PATH=$(awk -F "=" '$1=="ABACUS_PATH"{print $2}' ../../SETENV)
+ABACUS_NPROCS=$(awk -F "=" '$1=="ABACUS_NPROCS"{print $2}' ../../SETENV)
+ABACUS_THREADS=$(awk -F "=" '$1=="ABACUS_THREADS"{print $2}' ../../SETENV)
+
+OMP_NUM_THREADS=${ABACUS_THREADS} mpirun -np ${ABACUS_NPROCS} ${ABACUS_PATH} | tee scf.output

examples/deepks/pw_H2O/run.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+for ii in *
+do
+	if [ -d $ii ];then
+		cd ${ii}
+		echo "RUN: ${ii}"
+		bash run.sh
+		cd ..
+	fi
+done

examples/deepks/runall.sh

@@ -3,6 +3,9 @@ suffix    NiO
 ntype    2
 nbands    40
 
+pseudo_dir ../../../tests/PP_ORB
+orbital_dir ../../../tests/PP_ORB
+
 calculation    scf
 ecutwfc    100
 scf_thr    1.0e-6