to make doc/generate-basis.md consistent with the new generate_orbital.sh/Generate_Orbital_AllInOne.sh

Author: wszhang

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.

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

@@ -1,14 +1,18 @@
 #!/bin/bash
 # author mohan 
 # edit by Pengfei Li 2013-6-4
+# edit by Wenshuai Zhang 2016-11-30
 #-----------------------------------------------------------------
 #
 # (0.0) fixed  parameters 
 #
 #-----------------------------------------------------------------
 mass=1                                         #not used yet.
 lat0=20                                        #in a.u
-cpu_num=1         
+cpu_num=8         
+export OMP_NUM_THREADS=1
+#hostfpath="/home/nic/wszhang/eclipse_project/mesia_dft/error_estimates_for_DFT/cif2cellroot/0abacus_lcao/myhosts"
+#hostfpath="/home/nic/wszhang/eclipse_project/mesia_dft/delta_test/delta_dft/cifs2deltaDFT/myhosts"
 #-----------------------------------------------------------------
 #
 # (0.1) input parameters
@@ -170,11 +174,16 @@ do
 	# (1.4.2.0) calculate the distance of dimers
 	dis=`echo "$info" | awk '{print $'$count'}' ` 
         dis1=$(echo "scale=5;$dis * 0.86603 "|bc)
-        dis2=$(echo "scale=5;$dis * 0.5 "|bc)
+        dis2=$(echo "scale=5;$dis * 0.5     "|bc)
+	dis3=$(echo "scale=5;$dis * 0.81649 "|bc)
+	dis4=$(echo "scale=5;$dis * 0.28867 "|bc)
         echo "dis=$dis"
+
+
 # (1.4.2.1) get the" structures"
 if ( test $element = Na -o $element = Li -o $element = K -o $element = Ca )
 then
+echo "use trimer"
 na=3
 cat > $name.stru << EOF
 ATOMIC_SPECIES
@@ -195,7 +204,32 @@ $element //Element Label
 0.0     $dis1   $dis2   0   0   0
 EOF
 
+#elif ( test $element = Mn -o $element = Fe ) 
+#then
+#echo "use tetramer"
+#na=4
+#cat > $name.stru << EOF
+#ATOMIC_SPECIES
+#$element $mass $pseudofile
+#LATTICE_CONSTANT
+#$lat0  // add lattice constant(a.u.)
+#LATTICE_VECTORS
+#1 0 0
+#0 1 0
+#0 0 1
+#ATOMIC_POSITIONS
+#Cartesian_angstrom  //Cartesian or Direct coordinate.
+#$element //Element Label
+#0.0     //starting magnetism
+#4       //number of atoms
+#0.0     0.0     0.0     0   0   0  // crystal coor.
+#0.0     0.0     $dis    0   0   0 
+#0.0     $dis1   $dis2   0   0   0 
+#$dis3   $dis4   $dis2   0   0   0 
+#EOF
+
 else
+echo "use dimer"
 na=2
 cat > $name.stru << EOF
 ATOMIC_SPECIES
@@ -263,7 +297,7 @@ symmetry            0
 nbands             	$nbands 
 
 ecutwfc             $ecut
-dr2                 1.0e-7  // about iteration
+dr2                 2.0e-8  // about iteration
 niter               1000
 
 smearing            gauss
@@ -290,9 +324,10 @@ let count++
 #-------------
 #mpiexec -np $cpu_num -machinefile node_openmpi $EXE_pw
 #mpiexec -np $1 -machinefile $EXE_pw
-#mpirun -np 4 $EXE_pw
+mpirun -np $cpu_num $EXE_pw
+#mpirun -np $cpu_num -hostfile $hostfpath  $EXE_pw
 
-$EXE_pw 
+#$EXE_pw 
 
 #mpiexec -n 12  -machinefile $PBS_NODEFILE $EXE_pw >> Log.txt
 # end (1.4.2), dimer distace cicle
@@ -343,12 +378,12 @@ cat >> INPUT << EOF
 $Start_tem_S              // Start temparature for spillage
 0.8                 // Cooling rate
 $Step_S                   // Number of temperatures(spillage)
-500                // Number of steps per temparature
+600                // Number of steps per temparature
 
 $Start_tem_K              // start temperature for kinetic energy
 0.8                 // Cooling rate
 $Step_K                  // Number of temperatures(kinetical)
-500                // Number of steps per temparature
+600                // Number of steps per temparature
 
 $Delta_kappa        // Delta kappa
 50                  // Selectly output information
@@ -416,7 +451,8 @@ cat >> INPUT << EOF
 EOF
 
 #mpiexec -n 1 -machinefile $PBS_NODEFILE $EXE_orbital >> Log.txt
-$EXE_orbital
+$EXE_orbital 
+#mpirun -np cpu_num $EXE_orbital
 
 # (1.4.3.5)
 cd ..
@@ -431,3 +467,4 @@ cd ..
 done
 # end targets cicle
 
+unset OMP_NUM_THREADS

tools/SIAB/SimulatedAnnealing/backup_old_version/2_Generate/generate_orbital.sh

@@ -12,7 +12,7 @@ ref_bands   5                  # reference bands
 nbands      8                 # num of bands for calculate ( > reference bands)  
 Ecut        50                # cutoff energy (in Ry)
 Rcut        6                # cutoff radius (in a.u.)
-Pseudo_dir  ../ 
+Pseudo_dir  ./ 
 Pseudo      N_ONCV_PBE-1.0.upf
 sigma       0.01          # energy range for gauss smearing (in Ry)
 #--------------------------------------------------------------------------------

tools/SIAB/SimulatedAnnealing/example_N/ORBITAL_INPUT

@@ -1,4 +1,5 @@
 http://abacus.ustc.edu.cn/manual_411.html can be a reference to generate orbitals.
 
 First, change some parameter in ORBITAL_INPUT, for EXE_pw, EXE_orbital and Pseudo_dir, you'd better use the absolute path;
-Second, run the script: ./generate_orbital.sh
+
+Second, run the script: ../../../generate_orbital.sh ORBITAL_INPUT