Merge pull request #847 from tang070205/master

For abacus change the virial information in the second line to the stress information

tools/abacus2xyz/multipleFrames-abacus2nep-exyz.sh

@@ -2,15 +2,13 @@
 ### HOW TO USE #################################################################################
 ### SYNTAX: ./multipleFrames-abacus2nep-exyz.sh dire_name
 ###     NOTE: 1).'dire_name' is the directory containing running_md.log and MD_dump file.
-### Email: yanzhowang@gmail.com if any questions
-### Modified by Yuwen Zhang
-### Modified by Shunda Chen
-### Modified by Zihan Yan
+### Email: tang070205@proton.me if any questions
+### Modified by Yuwen Zhang, Shunda Chen, Zihan Yan
 ### Modified by Benrui Tang
 ################################################################################################
 #--- DEFAULT ASSIGNMENTS ---------------------------------------------------------------------
 isol_ener=0     # Shifted energy, specify the value?
-viri_logi=0     # Logical value for virial, true=1, false=0
+stress_logi=0     # Logical value for virial, true=1, false=0
 #--------------------------------------------------------------------------------------------
 read_dire=$1
 if [ -z "$read_dire" ]; then
@@ -24,12 +22,11 @@ rm -rf $writ_dire; mkdir $writ_dire
 configuration=$(pwd | awk -F'/' '{print $(NF-2)"/"$(NF-1)"/"$NF}')
 syst_numb_atom=$(grep "TOTAL ATOM NUMBER" running_md.log |awk '{print $5}')
 ener_values=($(grep 'etot' running_md.log |awk '{print $4}'))
-if [[ $viri_logi -eq 1 ]]; then
+if [[ $stress_logi -eq 1 ]]; then
     mdstep_lines=($(grep -n 'MDSTEP' MD_dump | awk -F: '{print $1+12+'$syst_numb_atom'}'))
 else
     mdstep_lines=($(grep -n 'MDSTEP' MD_dump | awk -F: '{print $1+9+'$syst_numb_atom'}'))
 fi
-conversion_value=$(grep "Volume (A^3)" running_md.log |awk '{print $4/1602.1766208}')
 N_counts=$(( ${#mdstep_lines[@]} - 1 ))
 
 
@@ -41,9 +38,9 @@ for ((i=1; i<${#mdstep_lines[@]}; i++)); do
     sed -n "${start_line},${end_line}p" MD_dump > temp.file
     echo "$syst_numb_atom" >> "$writ_dire/$writ_file"
     latt=$(grep -A 3 "LATTICE_VECTORS" temp.file | tail -n 3 | awk '{for (i = 1; i <= NF; i++) {printf "%.8f ", $i}}' |xargs)
-    if [[ $viri_logi -eq 1 ]]; then
-        viri=$(grep -A 3 "VIRIAL (kbar)" temp.file | tail -n 3 | awk '{for (i = 1; i <= NF; i++) {printf "%.8f ", $i * '$conversion_value'}}' |xargs)
-        echo "Config_type=$configuration Weight=1.0 Lattice=\"$latt\" Energy=$ener Virial=\"$viri\" pbc=\"T T T\" Properties=species:S:1:pos:R:3:forces:R:3" >> "$writ_dire/$writ_file"
+    if [[ $stress_logi -eq 1 ]]; then
+        stress=$(grep -A 3 "VIRIAL (kbar)" temp.file | tail -n 3 | awk '{for (i = 1; i <= NF; i++) {printf "%.8f ", $i * 0.1}}' |xargs)
+        echo "Config_type=$configuration Weight=1.0 Lattice=\"$latt\" Energy=$ener Stress=\"$stress\" pbc=\"T T T\" Properties=species:S:1:pos:R:3:forces:R:3" >> "$writ_dire/$writ_file"
     else
         echo "Config_type=$configuration Weight=1.0 Lattice=\"$latt\" Energy=$ener Properties=species:S:1:pos:R:3:forces:R:3 pbc=\"T T T\"" >> "$writ_dire/$writ_file"
     fi

tools/abacus2xyz/singleFrame-abacus2nep-exyz.sh

@@ -3,13 +3,12 @@
 ### SYNTAX: ./singleFrame-abacus2nep-exyz.sh dire_name   
 ###     NOTE: 1).'dire_name' is the directory containing running_scf.logs
 ### Email: tang070205@proton.me if have questions
-### Modified by Yanzhou Wang 
-### Modified by Shunda Chen 
+### Modified by Yanzhou Wang Shunda Chen 
 ### Modified by Benrui Tang
 ################################################################################################
 #--- DEFAULT ASSIGNMENTSts ---------------------------------------------------------------------
 isol_ener=0     # Shifted energy, specify the value?
-viri_logi=1     # Logical value for virial, true=1, false=0
+stress_logi=1     # Logical value for virial, true=1, false=0
 #--------------------------------------------------------------------------------------------
 read_dire=$1
 if [ -z $read_dire ]; then
@@ -28,11 +27,10 @@ do
              echo $syst_numb_atom >> $writ_dire/$writ_file
              latt=$(grep -A 3 "Lattice vectors" $i | tail -n 3 | sed 's/+//g' | awk '{ for (i=1; i<=NF; i++) printf "%.8f ", $i}')
              ener=$(grep "FINAL_ETOT_IS" $i | awk '{printf "%.6f\n", $2 - '$syst_numb_atom' * '$isol_ener'}')
-             if [ $viri_logi -eq 1 ]
+             if [ $stress_logi -eq 1 ]
              then
-                   conversion_value=$(grep "Volume (A^3)" $i |awk '{print $4/1602.1766208}')
-                   viri=$(grep -A 4 "TOTAL-STRESS" $i | tail -n 3 | awk '{for (i = 1; i <= NF; i++) {printf "%.8f ", $i * '$conversion_value'}}' |xargs)
-                   echo Energy=$ener Lattice=\"$latt\" Virial=\"$viri\" "Config_type=$configuration Weight=1.0 Properties=species:S:1:pos:R:3:forces:R:3" >> $writ_dire/$writ_file
+                   stress=$(grep -A 4 "TOTAL-STRESS" $i | tail -n 3 | awk '{for (i = 1; i <= NF; i++) {printf "%.8f ", $i * 0.1}}' |xargs)
+                   echo Energy=$ener Lattice=\"$latt\" Stress=\"$stress\" "Config_type=$configuration Weight=1.0 Properties=species:S:1:pos:R:3:forces:R:3" >> $writ_dire/$writ_file
              else
                    echo Energy=$ener Lattice=\"$latt\" "Config_type=$configuration Weight=1.0 Properties=species:S:1:pos:R:3:forces:R:3" >> $writ_dire/$writ_file
              fi