Merge pull request #87 from wszhang/develop

edit code part of README.md; change name test.0.dat to orb_matrix.0.dat

Author: dyzheng

doc/generate-basis.md

@@ -4,7 +4,7 @@
 
 In ABACUS, the atomic orbital bases are generated using a scheme developed in the [paper](https://iopscience.iop.org/article/10.1088/0953-8984/22/44/445501). We provide a script named “generate_orbital.sh” under the directory tools/ to generate the atomic orbitals bases. In order to run this script, an ORBITAL_INPUT file is required.
 
-An example of this ORBITAL_INPUT file can be found in $ABACUS/tools/SIAB/2_Generate:
+An example of this ORBITAL_INPUT file can be found in $ABACUS/tools/SIAB/SimulatedAnnealing/example_N:
 ```
 #1.exe_dir
 #----------------------------------------------------------------------------
@@ -101,7 +101,7 @@ The ORBITAL_INPUT file contains 5 parts :
     This part gives the bond lengths of the reference systems (dimer or trimer). Generally, the bond lengths are chosen to distribute on both sides of the equilibrium value. For example, for N dimer we use (in Å):
      - Dis 1.0 1.1 1.5 2.0 3.0
 
-    It means we take 5 reference systems (dimer), and the bond lengths are 1.0 1.1 1.5 2.0 3.0 angstrom, respectively. Every element has reference systems with different bond lengths, which could be found in file $ABACUS/tools/SIAB/2_Generate/DIS.txt.
+    It means we take 5 reference systems (dimer), and the bond lengths are 1.0 1.1 1.5 2.0 3.0 angstrom, respectively. Every element has reference systems with different bond lengths, which could be found in file $ABACUS/tools/SIAB/DIS.txt.
 4. orbital generation
 
     The main parameters for orbital generation
@@ -142,7 +142,7 @@ The ORBITAL_INPUT file contains 5 parts :
 
         the accept rise of spillage when optimizing the kinetic energy
         
-After preparing the ORBITAL_INPUT file, one just needs to run the script and wait for the results. The results will be written into several output files under the directory $element.id_element/$Rcut/, for example 07_N/6/.
+After preparing the ORBITAL_INPUT file, one just needs to run the script "$PATH_TO/generate_orbital.sh ORBITAL_INPUT" and wait for the results. The results will be written into several output files under the directory $element.id_element/$Rcut/, for example 07_N/6/.
 
 Some output files listed here are useful.
 - ORBITAL_RESULTS.txt
@@ -160,4 +160,4 @@ For some elements, you can download the reference ORBITAL_INPUT files and pseudo
 A file README is also given and you can decide the parameters with it as a reference.
 In most cases, you just need to modify the parameters in Section 1, 2. Section 4 may be
 partially modified if you need higher precision orbitals. The users are not encouraged to change
-the settings in sections 5, unless you are very familiar with the code generating algorithms.
+the settings in sections 5, unless you are very familiar with the code generating algorithms.

source/src_io/numerical_basis.cpp

@@ -67,7 +67,7 @@ void Numerical_Basis::output_overlap( const ModuleBase::ComplexMatrix *psi)
         std::ofstream ofs;
         std::stringstream ss;
         // the parameter 'winput::spillage_outdir' is read from INPUTw.
-        ss << winput::spillage_outdir << "/" << GlobalC::ucell.latName << "." << derivative_order << ".dat";
+        ss << winput::spillage_outdir << "/" <<  "orb_matrix." << derivative_order << ".dat";
         if (GlobalV::MY_RANK==0)
         {
             ofs.open(ss.str().c_str());

tools/SIAB/SimulatedAnnealing/example_N/DIS.txt renamed to tools/SIAB/DIS.txt

@@ -169,6 +169,12 @@ maxL=`grep -E "^\s*maxL" $InputFile | awk -F "maxL" '{print $0}' | awk '{print $
 # (0.x.x) check info (include Level) for each STRU 
 nSTRU=`grep -E "^\s*BLSTRU" $InputFile | wc -l`
 #nSTRU=`grep -o "^\s*ListSTRU\s*[^#]*" W/ORBITAL_INPUT_DZP |wc -w |awk '{print $1-1}'`
+if [[ "$nSTRU" == "0" ]] ; then 
+    nSTRU=`grep -E "^\s*Dis" $InputFile | wc -l`
+    if [ "$nSTRU" != "1" ]; then  
+        echo "error: input file has more than one line for Dis argument, please use the BLSTRU* "
+    fi
+fi
 echo "          nSTRU = $nSTRU"
 #
 LevelBegin[0]=0
@@ -180,23 +186,27 @@ for((iSTRU=1;iSTRU<=$nSTRU;iSTRU++))
 do
     ListSTRU[iSTRU]=`grep -E "^\s*ListSTRU " $InputFile |awk -F "ListSTRU" '{print $0}' \\
                 |awk -v iSTRU=$iSTRU '{print $(iSTRU+1) }'`
+    ListSTRU[iSTRU]=${ListSTRU[iSTRU]:-dimer}
     echo "        STRU[$iSTRU] = ${ListSTRU[iSTRU]}"
 
 
-    info[iSTRU]=`grep -E "^\s*BLSTRU$iSTRU" $InputFile | awk -F "BLSTRU$iSTRU" '{print $2}'`
-    BL_number[iSTRU]=`echo "${info[iSTRU]}" | awk '// {print NF}'`
-
+    BLSTRU[iSTRU]=`grep -E "^\s*BLSTRU$iSTRU" $InputFile | awk -F "BLSTRU$iSTRU" '{print $2}'`
+    if [[ -z "${BLSTRU[iSTRU]}" ]] && [[ "$iSTRU=1" ]] ; then 
+        BLSTRU[iSTRU]=`grep -E "^\s*Dis" $InputFile | awk -F "Dis" '{print $2}'`
+    fi
+    BL_number[iSTRU]=`echo "${BLSTRU[iSTRU]}" | awk '// {print NF}'`
     # (0.1.11) calculate the number of different dimers or trimers.
-    #info=`grep "Dis1" $InputFile | awk -F "Dis1" '{print $2}'`
-    #BL_number=`echo "$info" | awk '// {print NF}'`
-    echo "   BL_number[$iSTRU] = ${BL_number[iSTRU]}, info[$iSTRU] =" ${info[iSTRU]}
+    #BLSTRU=`grep "Dis1" $InputFile | awk -F "Dis1" '{print $2}'`
+    #BL_number=`echo "$BLSTRU" | awk '// {print NF}'`
+    echo "   BL_number[$iSTRU] = ${BL_number[iSTRU]}"
+    echo "      BLSTRU[$iSTRU] ="  ${BLSTRU[iSTRU]} "  :Bond Length for each STRU"
 
     EndLevel[iSTRU]=`grep -E "^\s*Level" $InputFile |awk -F "Level" '{print $0}' \\
                 |awk -v iSTRU=$iSTRU '{print $(iSTRU+1) }'`
     echo "    EndLevel[$iSTRU] = ${EndLevel[iSTRU]}"
     BeginLevel[iSTRU]=`grep -E "^\s*BeginLevel" $InputFile |awk -F "BeginLevel" '{print $0}' \\
                 |awk -v iSTRU=$iSTRU '{print $(iSTRU+1) }'`
-    echo "  BeginLevel[$iSTRU] = ${BeginLevel[iSTRU]}"
+    echo "  BeginLevel[$iSTRU] = ${BeginLevel[iSTRU]:-auto/default}"
 
     # (0.1.4)get the nbands
     nbands[iSTRU]=`grep -E "^\s*nbands" $InputFile | awk -F "nbands" '{print $0}' \\
@@ -211,7 +221,7 @@ do
     RestartSTRU[iSTRU]=`grep -E "^\s*RestartSTRU" $InputFile \\
                     | awk -F "$RestartSTRU" '{print $0}' \\
                     | awk -v iSTRU=$iSTRU '{print $(iSTRU+1) }'`
-    echo " RestartSTRU[$iSTRU] = ${RestartSTRU[iSTRU]}"
+    echo " RestartSTRU[$iSTRU] = ${RestartSTRU[iSTRU]:-auto/default}"
     #if [ ! -n "${RestartSTRU[iSTRU]}" ]; then
     #    RestartSTRU[iSTRU]=0
     #    echo " set RestartSTRU[$iSTRU]=0 "
@@ -231,8 +241,6 @@ if [ "$nSTRU" == "1" ]; then
     SkipSTRU[1]=0 
 fi
 
-#exit 0
-
 # (0.1.8)get the level
 #Level=`grep "Level" $InputFile | awk -F "level" '{print $0}' | awk '{print $2}'`
 #echo "__Level=$Level"
@@ -493,7 +501,7 @@ do
 	    do
 
 	        # (1.4.2.0) calculate the Bond Length for iSTRU
-	        BL=`echo "${info[iSTRU]}" | awk '{print $'$count'}' ` 
+	        BL=`echo "${BLSTRU[iSTRU]}" | awk '{print $'$count'}' ` 
             dis1=$(echo "scale=5;$BL * 0.86603 "|bc)
             dis2=$(echo "scale=5;$BL * 0.5     "|bc)
 	        dis3=$(echo "scale=5;$BL * 0.81649 "|bc)
@@ -690,7 +698,7 @@ EOF
 count_files=1
 while [ $count_files -le ${BL_number[iSTRU]} ]
 do
-    BL=`echo "${info[iSTRU]}" | awk '{print $'$count_files'}' ` 
+    BL=`echo "${BLSTRU[iSTRU]}" | awk '{print $'$count_files'}' ` 
     cat >> INPUT << EOF
 ../OUT.$element-$rcut-$BL/orb_matrix.0.dat
 EOF
@@ -829,13 +837,13 @@ EOF
 count_files=1
 while [ $count_files -lt ${BL_number[iSTRU]} ]
 do
-    BL=`echo "${info[iSTRU]}" | awk '{print $'$count_files'}' ` 
+    BL=`echo "${BLSTRU[iSTRU]}" | awk '{print $'$count_files'}' ` 
     cat >> INPUT << EOF
             "../OUT.$element-$rcut-$BL/orb_matrix.0.dat",
 EOF
     let count_files++
 done
-BL=`echo "${info[iSTRU]}" | awk '{print $'$count_files'}' ` 
+BL=`echo "${BLSTRU[iSTRU]}" | awk '{print $'$count_files'}' ` 
 cat >> INPUT << EOF
             "../OUT.$element-$rcut-$BL/orb_matrix.0.dat"
         ],
@@ -847,13 +855,13 @@ EOF
 count_files=1
 while [ $count_files -lt ${BL_number[iSTRU]} ]
 do
-    BL=`echo "${info[iSTRU]}" | awk '{print $'$count_files'}' ` 
+    BL=`echo "${BLSTRU[iSTRU]}" | awk '{print $'$count_files'}' ` 
     cat >> INPUT << EOF
             "../OUT.$element-$rcut-$BL/orb_matrix.1.dat",
 EOF
     let count_files++
 done
-BL=`echo "${info[iSTRU]}" | awk '{print $'$count_files'}' ` 
+BL=`echo "${BLSTRU[iSTRU]}" | awk '{print $'$count_files'}' ` 
 cat >> INPUT << EOF
             "../OUT.$element-$rcut-$BL/orb_matrix.1.dat"
             ]
@@ -1047,13 +1055,13 @@ EOF
 count_files=1
 while [ $count_files -lt ${BL_number[iSTRU]} ]
 do
-    BL=`echo "${info[iSTRU]}" | awk '{print $'$count_files'}' ` 
+    BL=`echo "${BLSTRU[iSTRU]}" | awk '{print $'$count_files'}' ` 
     cat >> INPUT << EOF
         "../OUT.$element-$rcut-$BL/orb_matrix.0.dat",
 EOF
     let count_files++
 done
-    BL=`echo "${info[iSTRU]}" | awk '{print $'$count_files'}' ` 
+    BL=`echo "${BLSTRU[iSTRU]}" | awk '{print $'$count_files'}' ` 
 cat >> INPUT << EOF
         "../OUT.$element-$rcut-$BL/orb_matrix.0.dat"
     ],

tools/SIAB/Generate_Orbital_AllInOne.sh

@@ -1,39 +1,57 @@
 # SIAB Package Description
 
 
-(S)ystematically
-(I)mprovable
-(A)tomic orbital
-(B)asis generator based on spillage formula
+**S**ystematically
+
+**I**mprovable
+
+**A**tomic orbital
+
+**B**asis generator based on spillage formula
 
 
 # HOW TO USE SIAB
 
-The optimization can choose three minimization methods: 'Simulated Annealing', 'PyTorch Gradient' and 'PyTorch Gradient whit dpsi'. 
+The optimization can choose one of the three minimization methods:
+
+- Simulated Annealing (**SA**),
+- PyTorch Gradient (**PTG**),
+- PyTorch Gradient with dpsi (**PTG_dpsi**).
+
+The executable files for the three methods are:
+
+- ./SimulatedAnnealing/source/SIA_s.exe, 
+- ./PyTorchGradient/source/main.py, 
+- ../opt_orb_pytorch_dpsi/main.py, 
+
+respectively.
 
-The executable files for three methods are './SimulatedAnnealing/source/SIA_s.exe', './PyTorchGradient/source/main.py', '../opt_orb_pytorch_dpsi/main.py', respectively.
 
+##  1. Write input file
 
-##  (1) write input file
-Firstly, write the input file, such as "ORBITAL_INPUT_DZP" in example-directories, for script 'Generate_Orbital_AllInOne.sh'.
-Both approachs, 'PyTorch Gradient' and 'Simulated Annealing', work with one bash script and use the same input file.
-Please use the absolute path for each each file and directory.
+Firstly, write the input file, such as **ORBITAL_INPUT_DZP** in example-directories, for script **Generate_Orbital_AllInOne.sh**.
+All three approachs work with the same bash script and use the same input file.
+Please use **absolute path** for each file/directory in input file.
 
 
-##  (2) set up dependence env
-Then, we set up the dependence env for ABACUS and SIAB, such as:
-'''
-module load hpcx/2.9.0/hpcx-intel-2019.update5 mkl/2019.update5 elpa/2019.05.002/hpcx-intel-2019.update5
-'''
-Especially for SIAB with 'PyTorch Gradient' approach, we need pytorch v1.1.0.
+##  2. Set up dependence environment
 
+Secondly, we set up the dependence environment for ABACUS and SIAB, such as:
+
+```bash
+$ module load hpcx/2.9.0/hpcx-intel-2019.update5 mkl/2019.update5 elpa/2019.05.002/hpcx-intel-2019.update5
+```
+
+Especially for SIAB with **PyTorch Gradient** approach, we need pytorch v1.1.0.
+
+
+### How to install pytorch:
 
-### how to install pytorch:
 Take the HanHai20@USTC system for example:
 
-''' bash
-$ module load gcc/7.5.0min      #:optional, larger version gcc may not be necessary.
-$ module load anaconda3
+```bash
+$ module load gcc/7.5.0min      #optional, maybe unnecessary.
+$ module load anaconda3_nompi
 $ module list
 Currently Loaded Modulefiles:
   1) elpa/2019.05.002/hpcx-intel-2019.update5   4) hpcx/2.9.0/hpcx-intel-2019.update5         7) libxc/4.3.4/hpcx-intel-2019.update5
@@ -43,22 +61,23 @@ $ python3 -V
 Python 3.7.4
 
 $ conda create -n pytorch110 python=3.7
-$ source activate pytorch110  #or: conda activate pytorch110
+$ source activate pytorch110    #or: conda activate pytorch110
 $ conda install pytorch torchvision torchaudio cpuonly -c pytorch
-$ source deactivate  #or: conda deactivate
+$ source deactivate             #or: conda deactivate
 
 $ source activate pytorch110  #or: conda activate pytorch110
 $ pip3 install --user scipy numpy
 $ pip3 install --user torch_optimizer
-'''
+```
+
 
+## 3. Run generation
 
-## (3) run generation
-Finally, 'cd' into an example folder, and run command like this:
+Finally, `cd` into an example folder, and run command like this:
 
-''' bash
-../Generate_Orbital_AllInOne.sh ORBITAL_INPUT_DZP
-# or
-bsub -q idle -n 8 -oo running.log ../Generate_Orbital_AllInOne.sh ORBITAL_INPUT_DZP
-'''
+```bash
+$ ../Generate_Orbital_AllInOne.sh ORBITAL_INPUT_DZP
+ or
+$ bsub -q idle -n 8 -oo running.log ../Generate_Orbital_AllInOne.sh ORBITAL_INPUT_DZP
+```