From 3374b48c406c0e7e4d90d72192a1e4dd1ec97407 Mon Sep 17 00:00:00 2001 From: Edison Florez Date: Thu, 24 Oct 2024 03:00:55 +0000 Subject: [PATCH 1/4] New Python Project Structure --- .../cesar_ang.py => example/01_basic_usage.py | 0 .../b2plypd3/log_files/geometry_log2xyz.sh | 85 ------------------ .../camb3lyp/log_files/geometry_log2xyz.sh | 85 ------------------ files_xyz/ccsd/geometry_log2xyz.sh | 85 ------------------ files_xyz/dirac/nonrel/geometry_out2xyz.sh | 77 ---------------- files_xyz/dirac/x2c/geometry_out2xyz.sh | 77 ---------------- files_xyz/hf/log_files/geometry_log2xyz.sh | 85 ------------------ .../lan/hf/log_files/geometry_log2xyz.sh | 85 ------------------ .../lan/mp2/log_files/geometry_log2xyz.sh | 85 ------------------ .../lan/pbe0/log_files/geometry_log2xyz.sh | 85 ------------------ files_xyz/pbe/log_files/geometry_log2xyz.sh | 85 ------------------ files_xyz/pbe0/log_files/geometry_log2xyz.sh | 85 ------------------ .../pbeqidh/log_files/geometry_log2xyz.sh | 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{files_xyz => old_files/files_xyz}/zora/sr/w6s13.xyz (100%) rename {files_xyz => old_files/files_xyz}/zora/sr/w6s14.xyz (100%) rename {files_xyz => old_files/files_xyz}/zora/sr/w6s15.xyz (100%) rename {files_xyz => old_files/files_xyz}/zora/sr/w6s16.xyz (100%) rename {files_xyz => old_files/files_xyz}/zora/sr/w6s17.xyz (100%) rename {files_xyz => old_files/files_xyz}/zora/sr/w6s18.xyz (100%) rename {files_xyz => old_files/files_xyz}/zora/sr/w6s19.xyz (100%) rename {files_xyz => old_files/files_xyz}/zora/sr/w6s2.xyz (100%) rename {files_xyz => old_files/files_xyz}/zora/sr/w6s3.xyz (100%) rename {files_xyz => old_files/files_xyz}/zora/sr/w6s4.xyz (100%) rename {files_xyz => old_files/files_xyz}/zora/sr/w6s5.xyz (100%) rename {files_xyz => old_files/files_xyz}/zora/sr/w6s6.xyz (100%) rename {files_xyz => old_files/files_xyz}/zora/sr/w6s7.xyz (100%) rename {files_xyz => old_files/files_xyz}/zora/sr/w6s8.xyz (100%) rename {files_xyz => old_files/files_xyz}/zora/sr/w6s9.xyz (100%) rename functions.py => old_files/functions.py (100%) rename main.py => old_files/main.py (100%) rename matrix_r.py => old_files/matrix_r.py (100%) rename {old_tools => old_files/old_tools}/Cesar_tools/DH_Angle.py (100%) create mode 100644 old_files/old_tools/Cesar_tools/cesar_ang.py rename {old_tools => old_files/old_tools}/andy_tools/coord/w2s1.xyz (100%) rename {old_tools => old_files/old_tools}/andy_tools/coord/w6s19.xyz (100%) rename {old_tools => old_files/old_tools}/andy_tools/coord/w6s23.xyz (100%) rename {old_tools => old_files/old_tools}/andy_tools/coord/w6s9.xyz (100%) rename {old_tools => old_files/old_tools}/andy_tools/cros.pyold (100%) rename {old_tools => old_files/old_tools}/andy_tools/crosvectsand0.py (100%) rename {old_tools => old_files/old_tools}/andy_tools/tools.py (100%) rename {old_tools => old_files/old_tools}/andy_tools/w1s1.xyz (100%) rename {old_tools => old_files/old_tools}/andy_tools/w3s2.xyz (100%) rename {old_tools => old_files/old_tools}/andy_tools/w6s23.xyz (100%) rename {old_tools => old_files/old_tools}/atoms_transfer.py (100%) rename {old_tools => old_files/old_tools}/blackbox1.py (100%) rename {old_tools => old_files/old_tools}/compare_xyz/compare_xyz.py (100%) rename {old_tools => old_files/old_tools}/compare_xyz/dihedral.py (100%) rename {old_tools => old_files/old_tools}/compare_xyz/w1s1-1c.xyz (100%) rename {old_tools => old_files/old_tools}/compare_xyz/w1s1-so.xyz (100%) rename {old_tools => old_files/old_tools}/compare_xyz/w1s1-sr.xyz (100%) rename {old_tools => old_files/old_tools}/compare_xyz/w2s1-1c.xyz (100%) rename {old_tools => old_files/old_tools}/compare_xyz/w2s1-so.xyz (100%) rename {old_tools => old_files/old_tools}/compare_xyz/w2s1-sr.xyz (100%) rename {old_tools => old_files/old_tools}/compare_xyz/w6s8.xyz (100%) rename {old_tools => old_files/old_tools}/compare_xyz/w6s9.xyz (100%) rename {old_tools => old_files/old_tools}/dihedral.py (100%) rename {old_tools => old_files/old_tools}/dihedral2.py (100%) rename {old_tools => old_files/old_tools}/doc_dihedral/dihedral_angle.pdf (100%) rename {old_tools => old_files/old_tools}/functions.py (100%) rename {old_tools => old_files/old_tools}/plot_rda.py (100%) rename {old_tools => old_files/old_tools}/radial_distribution_analisys.py (100%) rename {test_functions => old_files/test_functions}/blackbox_branch_edison.py (100%) rename {test_functions => old_files/test_functions}/blackbox_reading_files.py (100%) rename w1s1.xyz => old_files/w1s1.xyz (100%) rename w2s1.xyz => old_files/w2s1.xyz (100%) create mode 100644 pyproject.toml create mode 100644 src/__init__.py create mode 100644 src/core/__init__.py create mode 100644 src/utils/__init__.py create mode 100644 src/visualization/__init__.py create mode 100644 tests/__init__.py create mode 100644 tox.ini diff --git a/old_tools/Cesar_tools/cesar_ang.py b/example/01_basic_usage.py similarity index 100% rename from old_tools/Cesar_tools/cesar_ang.py rename to example/01_basic_usage.py diff --git a/files_xyz/b2plypd3/log_files/geometry_log2xyz.sh b/files_xyz/b2plypd3/log_files/geometry_log2xyz.sh deleted file mode 100755 index d0798d3..0000000 --- a/files_xyz/b2plypd3/log_files/geometry_log2xyz.sh +++ /dev/null @@ -1,85 +0,0 @@ -#!/bin/bash - -#---------------------------------------------------------- -# -# Creating XYZ file from Gaussian OUTPUT files '.log' -# -#---------------------------------------------------------- - -for file in $(ls *.log); -do - #- rename - gfile=$(echo $file | sed 's/.log//') - - echo "creating file ${gfile}.xyz from last geometry found in '$file'" - - # avoiding overwrite an exinting file - if [ -s "${gfile}.xyz" ]; then - mv ${gfile}.xyz ${gfile}.$(date +%F.%N) -# rm ${gfile}.xyz - echo "old file was renamed to: '${gile}.xyz.$(date +%F.%N)'" - fi - - #- number of atoms - natoms=$(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | wc -l) - chk=$(grep "Redundan" $file | wc -l ) - natoms=$( echo "scale=0; ($natoms/$chk) - 1" | bc) - - #- reading atom list - atomslist0=($(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | tail -$natoms)) - - # What was done? - comment="file '$file' at: ---'"$(grep "\#" $file | head -n 1 )"'---" - - # number of atoms - tot=$(echo "${#atomslist0[@]}") - - #saving coordinates - unset atomslist - for (( a=0; a<$tot; a++)); - do - atomslist+=($(echo "${atomslist0[a]}" | sed 's/,0,/,/')) - done - - # creating coordinates XYZ file - echo "$tot" >> ${gfile}.xyz - echo " $comment" >> ${gfile}.xyz - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.xyz - done -done - -echo -e "*** DONE\n" - - -####################################### -exit 0 - - - #- creating gaussian input file - echo "%chk=${gfile}.chk" >> ${gfile}.com - echo "%nproc=16" >> ${gfile}.com - echo "%mem=100gb" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "#p mp2=full gen pseudo=Read opt freq" >> ${gfile}.com - echo "" >> ${gfile}.com - echo " file: ${gfile} from a old opt at MP2/SDALL. Now we use MP2(full)/Def2-TZVPPD" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "2 1" >> ${gfile}.com - - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.com - done - - echo "" >> ${gfile}.com - cat def2-TZVPPD >> ${gfile}.com - - #- list to submmit jobs - echo " g16 < ${gfile}.com > ${gfile}.log" >> list.dat - - - diff --git a/files_xyz/camb3lyp/log_files/geometry_log2xyz.sh b/files_xyz/camb3lyp/log_files/geometry_log2xyz.sh deleted file mode 100755 index d0798d3..0000000 --- a/files_xyz/camb3lyp/log_files/geometry_log2xyz.sh +++ /dev/null @@ -1,85 +0,0 @@ -#!/bin/bash - -#---------------------------------------------------------- -# -# Creating XYZ file from Gaussian OUTPUT files '.log' -# -#---------------------------------------------------------- - -for file in $(ls *.log); -do - #- rename - gfile=$(echo $file | sed 's/.log//') - - echo "creating file ${gfile}.xyz from last geometry found in '$file'" - - # avoiding overwrite an exinting file - if [ -s "${gfile}.xyz" ]; then - mv ${gfile}.xyz ${gfile}.$(date +%F.%N) -# rm ${gfile}.xyz - echo "old file was renamed to: '${gile}.xyz.$(date +%F.%N)'" - fi - - #- number of atoms - natoms=$(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | wc -l) - chk=$(grep "Redundan" $file | wc -l ) - natoms=$( echo "scale=0; ($natoms/$chk) - 1" | bc) - - #- reading atom list - atomslist0=($(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | tail -$natoms)) - - # What was done? - comment="file '$file' at: ---'"$(grep "\#" $file | head -n 1 )"'---" - - # number of atoms - tot=$(echo "${#atomslist0[@]}") - - #saving coordinates - unset atomslist - for (( a=0; a<$tot; a++)); - do - atomslist+=($(echo "${atomslist0[a]}" | sed 's/,0,/,/')) - done - - # creating coordinates XYZ file - echo "$tot" >> ${gfile}.xyz - echo " $comment" >> ${gfile}.xyz - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.xyz - done -done - -echo -e "*** DONE\n" - - -####################################### -exit 0 - - - #- creating gaussian input file - echo "%chk=${gfile}.chk" >> ${gfile}.com - echo "%nproc=16" >> ${gfile}.com - echo "%mem=100gb" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "#p mp2=full gen pseudo=Read opt freq" >> ${gfile}.com - echo "" >> ${gfile}.com - echo " file: ${gfile} from a old opt at MP2/SDALL. Now we use MP2(full)/Def2-TZVPPD" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "2 1" >> ${gfile}.com - - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.com - done - - echo "" >> ${gfile}.com - cat def2-TZVPPD >> ${gfile}.com - - #- list to submmit jobs - echo " g16 < ${gfile}.com > ${gfile}.log" >> list.dat - - - diff --git a/files_xyz/ccsd/geometry_log2xyz.sh b/files_xyz/ccsd/geometry_log2xyz.sh deleted file mode 100755 index d0798d3..0000000 --- a/files_xyz/ccsd/geometry_log2xyz.sh +++ /dev/null @@ -1,85 +0,0 @@ -#!/bin/bash - -#---------------------------------------------------------- -# -# Creating XYZ file from Gaussian OUTPUT files '.log' -# -#---------------------------------------------------------- - -for file in $(ls *.log); -do - #- rename - gfile=$(echo $file | sed 's/.log//') - - echo "creating file ${gfile}.xyz from last geometry found in '$file'" - - # avoiding overwrite an exinting file - if [ -s "${gfile}.xyz" ]; then - mv ${gfile}.xyz ${gfile}.$(date +%F.%N) -# rm ${gfile}.xyz - echo "old file was renamed to: '${gile}.xyz.$(date +%F.%N)'" - fi - - #- number of atoms - natoms=$(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | wc -l) - chk=$(grep "Redundan" $file | wc -l ) - natoms=$( echo "scale=0; ($natoms/$chk) - 1" | bc) - - #- reading atom list - atomslist0=($(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | tail -$natoms)) - - # What was done? - comment="file '$file' at: ---'"$(grep "\#" $file | head -n 1 )"'---" - - # number of atoms - tot=$(echo "${#atomslist0[@]}") - - #saving coordinates - unset atomslist - for (( a=0; a<$tot; a++)); - do - atomslist+=($(echo "${atomslist0[a]}" | sed 's/,0,/,/')) - done - - # creating coordinates XYZ file - echo "$tot" >> ${gfile}.xyz - echo " $comment" >> ${gfile}.xyz - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.xyz - done -done - -echo -e "*** DONE\n" - - -####################################### -exit 0 - - - #- creating gaussian input file - echo "%chk=${gfile}.chk" >> ${gfile}.com - echo "%nproc=16" >> ${gfile}.com - echo "%mem=100gb" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "#p mp2=full gen pseudo=Read opt freq" >> ${gfile}.com - echo "" >> ${gfile}.com - echo " file: ${gfile} from a old opt at MP2/SDALL. Now we use MP2(full)/Def2-TZVPPD" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "2 1" >> ${gfile}.com - - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.com - done - - echo "" >> ${gfile}.com - cat def2-TZVPPD >> ${gfile}.com - - #- list to submmit jobs - echo " g16 < ${gfile}.com > ${gfile}.log" >> list.dat - - - diff --git a/files_xyz/dirac/nonrel/geometry_out2xyz.sh b/files_xyz/dirac/nonrel/geometry_out2xyz.sh deleted file mode 100755 index f678160..0000000 --- a/files_xyz/dirac/nonrel/geometry_out2xyz.sh +++ /dev/null @@ -1,77 +0,0 @@ -#!/bin/bash - -#---------------------------------------------------------- -# -# Creating XYZ file from Gaussian OUTPUT files '.log' -# -#---------------------------------------------------------- - -for file in $(ls *.out); -do - #- rename - gfile=$(echo $file | sed 's/.out//') - - echo "creating file ${gfile}.xyz from last geometry found in '$file'" - - # avoiding overwrite an exinting file - if [ -s "${gfile}.xyz" ]; then - mv ${gfile}.xyz ${gfile}.xyz.$(date +%F.%N) -# rm ${gfile}.xyz - echo "old file was renamed to: '${gile}.xyz.$(date +%F.%N)'" - fi - - #- number of atoms - natoms=$(sed -n "/Final geometry (angstrom)/,/Iter Energy Change/p" $file | sed '/Iter Energy Change/d' | sed '/^$/d' | wc -l) - natoms=$( echo "scale=0; ($natoms) - 2" | bc) - - #- reading atom list - atomslist=($(sed -n "/Final geometry (angstrom)/,/Iter Energy Change/p" $file | sed '/Iter Energy Change/d' | sed '/^$/d' | tail -$natoms)) - - # What was done? - comment="file: '$file'" - - # number of atoms - tot=$(echo "scale=0; ${#atomslist[@]}" | bc) - tot2=$(echo "scale=0; ${#atomslist[@]}/4" | bc) - - # creating coordinates XYZ file - echo "$tot2" >> ${gfile}.xyz - echo " $comment" >> ${gfile}.xyz - for ((j=0; j<$tot; j+=4)); - do - printf "%-3s %14s %14s %14s\n" "${atomslist[j]}" "${atomslist[j+1]}" "${atomslist[j+2]}" "${atomslist[j+3]}" >> ${gfile}.xyz - done -done - -echo -e "*** DONE\n" - - -####################################### -exit 0 - - - #- creating gaussian input file - echo "%chk=${gfile}.chk" >> ${gfile}.com - echo "%nproc=16" >> ${gfile}.com - echo "%mem=100gb" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "#p mp2=full gen pseudo=Read opt freq" >> ${gfile}.com - echo "" >> ${gfile}.com - echo " file: ${gfile} from a old opt at MP2/SDALL. Now we use MP2(full)/Def2-TZVPPD" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "2 1" >> ${gfile}.com - - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.com - done - - echo "" >> ${gfile}.com - cat def2-TZVPPD >> ${gfile}.com - - #- list to submmit jobs - echo " g16 < ${gfile}.com > ${gfile}.log" >> list.dat - - - diff --git a/files_xyz/dirac/x2c/geometry_out2xyz.sh b/files_xyz/dirac/x2c/geometry_out2xyz.sh deleted file mode 100755 index f678160..0000000 --- a/files_xyz/dirac/x2c/geometry_out2xyz.sh +++ /dev/null @@ -1,77 +0,0 @@ -#!/bin/bash - -#---------------------------------------------------------- -# -# Creating XYZ file from Gaussian OUTPUT files '.log' -# -#---------------------------------------------------------- - -for file in $(ls *.out); -do - #- rename - gfile=$(echo $file | sed 's/.out//') - - echo "creating file ${gfile}.xyz from last geometry found in '$file'" - - # avoiding overwrite an exinting file - if [ -s "${gfile}.xyz" ]; then - mv ${gfile}.xyz ${gfile}.xyz.$(date +%F.%N) -# rm ${gfile}.xyz - echo "old file was renamed to: '${gile}.xyz.$(date +%F.%N)'" - fi - - #- number of atoms - natoms=$(sed -n "/Final geometry (angstrom)/,/Iter Energy Change/p" $file | sed '/Iter Energy Change/d' | sed '/^$/d' | wc -l) - natoms=$( echo "scale=0; ($natoms) - 2" | bc) - - #- reading atom list - atomslist=($(sed -n "/Final geometry (angstrom)/,/Iter Energy Change/p" $file | sed '/Iter Energy Change/d' | sed '/^$/d' | tail -$natoms)) - - # What was done? - comment="file: '$file'" - - # number of atoms - tot=$(echo "scale=0; ${#atomslist[@]}" | bc) - tot2=$(echo "scale=0; ${#atomslist[@]}/4" | bc) - - # creating coordinates XYZ file - echo "$tot2" >> ${gfile}.xyz - echo " $comment" >> ${gfile}.xyz - for ((j=0; j<$tot; j+=4)); - do - printf "%-3s %14s %14s %14s\n" "${atomslist[j]}" "${atomslist[j+1]}" "${atomslist[j+2]}" "${atomslist[j+3]}" >> ${gfile}.xyz - done -done - -echo -e "*** DONE\n" - - -####################################### -exit 0 - - - #- creating gaussian input file - echo "%chk=${gfile}.chk" >> ${gfile}.com - echo "%nproc=16" >> ${gfile}.com - echo "%mem=100gb" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "#p mp2=full gen pseudo=Read opt freq" >> ${gfile}.com - echo "" >> ${gfile}.com - echo " file: ${gfile} from a old opt at MP2/SDALL. Now we use MP2(full)/Def2-TZVPPD" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "2 1" >> ${gfile}.com - - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.com - done - - echo "" >> ${gfile}.com - cat def2-TZVPPD >> ${gfile}.com - - #- list to submmit jobs - echo " g16 < ${gfile}.com > ${gfile}.log" >> list.dat - - - diff --git a/files_xyz/hf/log_files/geometry_log2xyz.sh b/files_xyz/hf/log_files/geometry_log2xyz.sh deleted file mode 100755 index d0798d3..0000000 --- a/files_xyz/hf/log_files/geometry_log2xyz.sh +++ /dev/null @@ -1,85 +0,0 @@ -#!/bin/bash - -#---------------------------------------------------------- -# -# Creating XYZ file from Gaussian OUTPUT files '.log' -# -#---------------------------------------------------------- - -for file in $(ls *.log); -do - #- rename - gfile=$(echo $file | sed 's/.log//') - - echo "creating file ${gfile}.xyz from last geometry found in '$file'" - - # avoiding overwrite an exinting file - if [ -s "${gfile}.xyz" ]; then - mv ${gfile}.xyz ${gfile}.$(date +%F.%N) -# rm ${gfile}.xyz - echo "old file was renamed to: '${gile}.xyz.$(date +%F.%N)'" - fi - - #- number of atoms - natoms=$(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | wc -l) - chk=$(grep "Redundan" $file | wc -l ) - natoms=$( echo "scale=0; ($natoms/$chk) - 1" | bc) - - #- reading atom list - atomslist0=($(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | tail -$natoms)) - - # What was done? - comment="file '$file' at: ---'"$(grep "\#" $file | head -n 1 )"'---" - - # number of atoms - tot=$(echo "${#atomslist0[@]}") - - #saving coordinates - unset atomslist - for (( a=0; a<$tot; a++)); - do - atomslist+=($(echo "${atomslist0[a]}" | sed 's/,0,/,/')) - done - - # creating coordinates XYZ file - echo "$tot" >> ${gfile}.xyz - echo " $comment" >> ${gfile}.xyz - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.xyz - done -done - -echo -e "*** DONE\n" - - -####################################### -exit 0 - - - #- creating gaussian input file - echo "%chk=${gfile}.chk" >> ${gfile}.com - echo "%nproc=16" >> ${gfile}.com - echo "%mem=100gb" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "#p mp2=full gen pseudo=Read opt freq" >> ${gfile}.com - echo "" >> ${gfile}.com - echo " file: ${gfile} from a old opt at MP2/SDALL. Now we use MP2(full)/Def2-TZVPPD" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "2 1" >> ${gfile}.com - - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.com - done - - echo "" >> ${gfile}.com - cat def2-TZVPPD >> ${gfile}.com - - #- list to submmit jobs - echo " g16 < ${gfile}.com > ${gfile}.log" >> list.dat - - - diff --git a/files_xyz/lan/hf/log_files/geometry_log2xyz.sh b/files_xyz/lan/hf/log_files/geometry_log2xyz.sh deleted file mode 100755 index d0798d3..0000000 --- a/files_xyz/lan/hf/log_files/geometry_log2xyz.sh +++ /dev/null @@ -1,85 +0,0 @@ -#!/bin/bash - -#---------------------------------------------------------- -# -# Creating XYZ file from Gaussian OUTPUT files '.log' -# -#---------------------------------------------------------- - -for file in $(ls *.log); -do - #- rename - gfile=$(echo $file | sed 's/.log//') - - echo "creating file ${gfile}.xyz from last geometry found in '$file'" - - # avoiding overwrite an exinting file - if [ -s "${gfile}.xyz" ]; then - mv ${gfile}.xyz ${gfile}.$(date +%F.%N) -# rm ${gfile}.xyz - echo "old file was renamed to: '${gile}.xyz.$(date +%F.%N)'" - fi - - #- number of atoms - natoms=$(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | wc -l) - chk=$(grep "Redundan" $file | wc -l ) - natoms=$( echo "scale=0; ($natoms/$chk) - 1" | bc) - - #- reading atom list - atomslist0=($(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | tail -$natoms)) - - # What was done? - comment="file '$file' at: ---'"$(grep "\#" $file | head -n 1 )"'---" - - # number of atoms - tot=$(echo "${#atomslist0[@]}") - - #saving coordinates - unset atomslist - for (( a=0; a<$tot; a++)); - do - atomslist+=($(echo "${atomslist0[a]}" | sed 's/,0,/,/')) - done - - # creating coordinates XYZ file - echo "$tot" >> ${gfile}.xyz - echo " $comment" >> ${gfile}.xyz - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.xyz - done -done - -echo -e "*** DONE\n" - - -####################################### -exit 0 - - - #- creating gaussian input file - echo "%chk=${gfile}.chk" >> ${gfile}.com - echo "%nproc=16" >> ${gfile}.com - echo "%mem=100gb" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "#p mp2=full gen pseudo=Read opt freq" >> ${gfile}.com - echo "" >> ${gfile}.com - echo " file: ${gfile} from a old opt at MP2/SDALL. Now we use MP2(full)/Def2-TZVPPD" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "2 1" >> ${gfile}.com - - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.com - done - - echo "" >> ${gfile}.com - cat def2-TZVPPD >> ${gfile}.com - - #- list to submmit jobs - echo " g16 < ${gfile}.com > ${gfile}.log" >> list.dat - - - diff --git a/files_xyz/lan/mp2/log_files/geometry_log2xyz.sh b/files_xyz/lan/mp2/log_files/geometry_log2xyz.sh deleted file mode 100755 index d0798d3..0000000 --- a/files_xyz/lan/mp2/log_files/geometry_log2xyz.sh +++ /dev/null @@ -1,85 +0,0 @@ -#!/bin/bash - -#---------------------------------------------------------- -# -# Creating XYZ file from Gaussian OUTPUT files '.log' -# -#---------------------------------------------------------- - -for file in $(ls *.log); -do - #- rename - gfile=$(echo $file | sed 's/.log//') - - echo "creating file ${gfile}.xyz from last geometry found in '$file'" - - # avoiding overwrite an exinting file - if [ -s "${gfile}.xyz" ]; then - mv ${gfile}.xyz ${gfile}.$(date +%F.%N) -# rm ${gfile}.xyz - echo "old file was renamed to: '${gile}.xyz.$(date +%F.%N)'" - fi - - #- number of atoms - natoms=$(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | wc -l) - chk=$(grep "Redundan" $file | wc -l ) - natoms=$( echo "scale=0; ($natoms/$chk) - 1" | bc) - - #- reading atom list - atomslist0=($(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | tail -$natoms)) - - # What was done? - comment="file '$file' at: ---'"$(grep "\#" $file | head -n 1 )"'---" - - # number of atoms - tot=$(echo "${#atomslist0[@]}") - - #saving coordinates - unset atomslist - for (( a=0; a<$tot; a++)); - do - atomslist+=($(echo "${atomslist0[a]}" | sed 's/,0,/,/')) - done - - # creating coordinates XYZ file - echo "$tot" >> ${gfile}.xyz - echo " $comment" >> ${gfile}.xyz - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.xyz - done -done - -echo -e "*** DONE\n" - - -####################################### -exit 0 - - - #- creating gaussian input file - echo "%chk=${gfile}.chk" >> ${gfile}.com - echo "%nproc=16" >> ${gfile}.com - echo "%mem=100gb" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "#p mp2=full gen pseudo=Read opt freq" >> ${gfile}.com - echo "" >> ${gfile}.com - echo " file: ${gfile} from a old opt at MP2/SDALL. Now we use MP2(full)/Def2-TZVPPD" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "2 1" >> ${gfile}.com - - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.com - done - - echo "" >> ${gfile}.com - cat def2-TZVPPD >> ${gfile}.com - - #- list to submmit jobs - echo " g16 < ${gfile}.com > ${gfile}.log" >> list.dat - - - diff --git a/files_xyz/lan/pbe0/log_files/geometry_log2xyz.sh b/files_xyz/lan/pbe0/log_files/geometry_log2xyz.sh deleted file mode 100755 index d0798d3..0000000 --- a/files_xyz/lan/pbe0/log_files/geometry_log2xyz.sh +++ /dev/null @@ -1,85 +0,0 @@ -#!/bin/bash - -#---------------------------------------------------------- -# -# Creating XYZ file from Gaussian OUTPUT files '.log' -# -#---------------------------------------------------------- - -for file in $(ls *.log); -do - #- rename - gfile=$(echo $file | sed 's/.log//') - - echo "creating file ${gfile}.xyz from last geometry found in '$file'" - - # avoiding overwrite an exinting file - if [ -s "${gfile}.xyz" ]; then - mv ${gfile}.xyz ${gfile}.$(date +%F.%N) -# rm ${gfile}.xyz - echo "old file was renamed to: '${gile}.xyz.$(date +%F.%N)'" - fi - - #- number of atoms - natoms=$(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | wc -l) - chk=$(grep "Redundan" $file | wc -l ) - natoms=$( echo "scale=0; ($natoms/$chk) - 1" | bc) - - #- reading atom list - atomslist0=($(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | tail -$natoms)) - - # What was done? - comment="file '$file' at: ---'"$(grep "\#" $file | head -n 1 )"'---" - - # number of atoms - tot=$(echo "${#atomslist0[@]}") - - #saving coordinates - unset atomslist - for (( a=0; a<$tot; a++)); - do - atomslist+=($(echo "${atomslist0[a]}" | sed 's/,0,/,/')) - done - - # creating coordinates XYZ file - echo "$tot" >> ${gfile}.xyz - echo " $comment" >> ${gfile}.xyz - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.xyz - done -done - -echo -e "*** DONE\n" - - -####################################### -exit 0 - - - #- creating gaussian input file - echo "%chk=${gfile}.chk" >> ${gfile}.com - echo "%nproc=16" >> ${gfile}.com - echo "%mem=100gb" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "#p mp2=full gen pseudo=Read opt freq" >> ${gfile}.com - echo "" >> ${gfile}.com - echo " file: ${gfile} from a old opt at MP2/SDALL. Now we use MP2(full)/Def2-TZVPPD" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "2 1" >> ${gfile}.com - - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.com - done - - echo "" >> ${gfile}.com - cat def2-TZVPPD >> ${gfile}.com - - #- list to submmit jobs - echo " g16 < ${gfile}.com > ${gfile}.log" >> list.dat - - - diff --git a/files_xyz/pbe/log_files/geometry_log2xyz.sh b/files_xyz/pbe/log_files/geometry_log2xyz.sh deleted file mode 100755 index d0798d3..0000000 --- a/files_xyz/pbe/log_files/geometry_log2xyz.sh +++ /dev/null @@ -1,85 +0,0 @@ -#!/bin/bash - -#---------------------------------------------------------- -# -# Creating XYZ file from Gaussian OUTPUT files '.log' -# -#---------------------------------------------------------- - -for file in $(ls *.log); -do - #- rename - gfile=$(echo $file | sed 's/.log//') - - echo "creating file ${gfile}.xyz from last geometry found in '$file'" - - # avoiding overwrite an exinting file - if [ -s "${gfile}.xyz" ]; then - mv ${gfile}.xyz ${gfile}.$(date +%F.%N) -# rm ${gfile}.xyz - echo "old file was renamed to: '${gile}.xyz.$(date +%F.%N)'" - fi - - #- number of atoms - natoms=$(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | wc -l) - chk=$(grep "Redundan" $file | wc -l ) - natoms=$( echo "scale=0; ($natoms/$chk) - 1" | bc) - - #- reading atom list - atomslist0=($(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | tail -$natoms)) - - # What was done? - comment="file '$file' at: ---'"$(grep "\#" $file | head -n 1 )"'---" - - # number of atoms - tot=$(echo "${#atomslist0[@]}") - - #saving coordinates - unset atomslist - for (( a=0; a<$tot; a++)); - do - atomslist+=($(echo "${atomslist0[a]}" | sed 's/,0,/,/')) - done - - # creating coordinates XYZ file - echo "$tot" >> ${gfile}.xyz - echo " $comment" >> ${gfile}.xyz - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.xyz - done -done - -echo -e "*** DONE\n" - - -####################################### -exit 0 - - - #- creating gaussian input file - echo "%chk=${gfile}.chk" >> ${gfile}.com - echo "%nproc=16" >> ${gfile}.com - echo "%mem=100gb" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "#p mp2=full gen pseudo=Read opt freq" >> ${gfile}.com - echo "" >> ${gfile}.com - echo " file: ${gfile} from a old opt at MP2/SDALL. Now we use MP2(full)/Def2-TZVPPD" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "2 1" >> ${gfile}.com - - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.com - done - - echo "" >> ${gfile}.com - cat def2-TZVPPD >> ${gfile}.com - - #- list to submmit jobs - echo " g16 < ${gfile}.com > ${gfile}.log" >> list.dat - - - diff --git a/files_xyz/pbe0/log_files/geometry_log2xyz.sh b/files_xyz/pbe0/log_files/geometry_log2xyz.sh deleted file mode 100755 index d0798d3..0000000 --- a/files_xyz/pbe0/log_files/geometry_log2xyz.sh +++ /dev/null @@ -1,85 +0,0 @@ -#!/bin/bash - -#---------------------------------------------------------- -# -# Creating XYZ file from Gaussian OUTPUT files '.log' -# -#---------------------------------------------------------- - -for file in $(ls *.log); -do - #- rename - gfile=$(echo $file | sed 's/.log//') - - echo "creating file ${gfile}.xyz from last geometry found in '$file'" - - # avoiding overwrite an exinting file - if [ -s "${gfile}.xyz" ]; then - mv ${gfile}.xyz ${gfile}.$(date +%F.%N) -# rm ${gfile}.xyz - echo "old file was renamed to: '${gile}.xyz.$(date +%F.%N)'" - fi - - #- number of atoms - natoms=$(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | wc -l) - chk=$(grep "Redundan" $file | wc -l ) - natoms=$( echo "scale=0; ($natoms/$chk) - 1" | bc) - - #- reading atom list - atomslist0=($(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | tail -$natoms)) - - # What was done? - comment="file '$file' at: ---'"$(grep "\#" $file | head -n 1 )"'---" - - # number of atoms - tot=$(echo "${#atomslist0[@]}") - - #saving coordinates - unset atomslist - for (( a=0; a<$tot; a++)); - do - atomslist+=($(echo "${atomslist0[a]}" | sed 's/,0,/,/')) - done - - # creating coordinates XYZ file - echo "$tot" >> ${gfile}.xyz - echo " $comment" >> ${gfile}.xyz - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.xyz - done -done - -echo -e "*** DONE\n" - - -####################################### -exit 0 - - - #- creating gaussian input file - echo "%chk=${gfile}.chk" >> ${gfile}.com - echo "%nproc=16" >> ${gfile}.com - echo "%mem=100gb" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "#p mp2=full gen pseudo=Read opt freq" >> ${gfile}.com - echo "" >> ${gfile}.com - echo " file: ${gfile} from a old opt at MP2/SDALL. Now we use MP2(full)/Def2-TZVPPD" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "2 1" >> ${gfile}.com - - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.com - done - - echo "" >> ${gfile}.com - cat def2-TZVPPD >> ${gfile}.com - - #- list to submmit jobs - echo " g16 < ${gfile}.com > ${gfile}.log" >> list.dat - - - diff --git a/files_xyz/pbeqidh/log_files/geometry_log2xyz.sh b/files_xyz/pbeqidh/log_files/geometry_log2xyz.sh deleted file mode 100755 index d0798d3..0000000 --- a/files_xyz/pbeqidh/log_files/geometry_log2xyz.sh +++ /dev/null @@ -1,85 +0,0 @@ -#!/bin/bash - -#---------------------------------------------------------- -# -# Creating XYZ file from Gaussian OUTPUT files '.log' -# -#---------------------------------------------------------- - -for file in $(ls *.log); -do - #- rename - gfile=$(echo $file | sed 's/.log//') - - echo "creating file ${gfile}.xyz from last geometry found in '$file'" - - # avoiding overwrite an exinting file - if [ -s "${gfile}.xyz" ]; then - mv ${gfile}.xyz ${gfile}.$(date +%F.%N) -# rm ${gfile}.xyz - echo "old file was renamed to: '${gile}.xyz.$(date +%F.%N)'" - fi - - #- number of atoms - natoms=$(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | wc -l) - chk=$(grep "Redundan" $file | wc -l ) - natoms=$( echo "scale=0; ($natoms/$chk) - 1" | bc) - - #- reading atom list - atomslist0=($(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | tail -$natoms)) - - # What was done? - comment="file '$file' at: ---'"$(grep "\#" $file | head -n 1 )"'---" - - # number of atoms - tot=$(echo "${#atomslist0[@]}") - - #saving coordinates - unset atomslist - for (( a=0; a<$tot; a++)); - do - atomslist+=($(echo "${atomslist0[a]}" | sed 's/,0,/,/')) - done - - # creating coordinates XYZ file - echo "$tot" >> ${gfile}.xyz - echo " $comment" >> ${gfile}.xyz - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.xyz - done -done - -echo -e "*** DONE\n" - - -####################################### -exit 0 - - - #- creating gaussian input file - echo "%chk=${gfile}.chk" >> ${gfile}.com - echo "%nproc=16" >> ${gfile}.com - echo "%mem=100gb" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "#p mp2=full gen pseudo=Read opt freq" >> ${gfile}.com - echo "" >> ${gfile}.com - echo " file: ${gfile} from a old opt at MP2/SDALL. Now we use MP2(full)/Def2-TZVPPD" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "2 1" >> ${gfile}.com - - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.com - done - - echo "" >> ${gfile}.com - cat def2-TZVPPD >> ${gfile}.com - - #- list to submmit jobs - echo " g16 < ${gfile}.com > ${gfile}.log" >> list.dat - - - diff --git a/files_xyz/sdd/hf/log_files/geometry_log2xyz.sh b/files_xyz/sdd/hf/log_files/geometry_log2xyz.sh deleted file mode 100755 index d0798d3..0000000 --- a/files_xyz/sdd/hf/log_files/geometry_log2xyz.sh +++ /dev/null @@ -1,85 +0,0 @@ -#!/bin/bash - -#---------------------------------------------------------- -# -# Creating XYZ file from Gaussian OUTPUT files '.log' -# -#---------------------------------------------------------- - -for file in $(ls *.log); -do - #- rename - gfile=$(echo $file | sed 's/.log//') - - echo "creating file ${gfile}.xyz from last geometry found in '$file'" - - # avoiding overwrite an exinting file - if [ -s "${gfile}.xyz" ]; then - mv ${gfile}.xyz ${gfile}.$(date +%F.%N) -# rm ${gfile}.xyz - echo "old file was renamed to: '${gile}.xyz.$(date +%F.%N)'" - fi - - #- number of atoms - natoms=$(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | wc -l) - chk=$(grep "Redundan" $file | wc -l ) - natoms=$( echo "scale=0; ($natoms/$chk) - 1" | bc) - - #- reading atom list - atomslist0=($(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | tail -$natoms)) - - # What was done? - comment="file '$file' at: ---'"$(grep "\#" $file | head -n 1 )"'---" - - # number of atoms - tot=$(echo "${#atomslist0[@]}") - - #saving coordinates - unset atomslist - for (( a=0; a<$tot; a++)); - do - atomslist+=($(echo "${atomslist0[a]}" | sed 's/,0,/,/')) - done - - # creating coordinates XYZ file - echo "$tot" >> ${gfile}.xyz - echo " $comment" >> ${gfile}.xyz - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.xyz - done -done - -echo -e "*** DONE\n" - - -####################################### -exit 0 - - - #- creating gaussian input file - echo "%chk=${gfile}.chk" >> ${gfile}.com - echo "%nproc=16" >> ${gfile}.com - echo "%mem=100gb" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "#p mp2=full gen pseudo=Read opt freq" >> ${gfile}.com - echo "" >> ${gfile}.com - echo " file: ${gfile} from a old opt at MP2/SDALL. Now we use MP2(full)/Def2-TZVPPD" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "2 1" >> ${gfile}.com - - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.com - done - - echo "" >> ${gfile}.com - cat def2-TZVPPD >> ${gfile}.com - - #- list to submmit jobs - echo " g16 < ${gfile}.com > ${gfile}.log" >> list.dat - - - diff --git a/files_xyz/sdd/mp2/log_files/geometry_log2xyz.sh b/files_xyz/sdd/mp2/log_files/geometry_log2xyz.sh deleted file mode 100755 index d0798d3..0000000 --- a/files_xyz/sdd/mp2/log_files/geometry_log2xyz.sh +++ /dev/null @@ -1,85 +0,0 @@ -#!/bin/bash - -#---------------------------------------------------------- -# -# Creating XYZ file from Gaussian OUTPUT files '.log' -# -#---------------------------------------------------------- - -for file in $(ls *.log); -do - #- rename - gfile=$(echo $file | sed 's/.log//') - - echo "creating file ${gfile}.xyz from last geometry found in '$file'" - - # avoiding overwrite an exinting file - if [ -s "${gfile}.xyz" ]; then - mv ${gfile}.xyz ${gfile}.$(date +%F.%N) -# rm ${gfile}.xyz - echo "old file was renamed to: '${gile}.xyz.$(date +%F.%N)'" - fi - - #- number of atoms - natoms=$(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | wc -l) - chk=$(grep "Redundan" $file | wc -l ) - natoms=$( echo "scale=0; ($natoms/$chk) - 1" | bc) - - #- reading atom list - atomslist0=($(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | tail -$natoms)) - - # What was done? - comment="file '$file' at: ---'"$(grep "\#" $file | head -n 1 )"'---" - - # number of atoms - tot=$(echo "${#atomslist0[@]}") - - #saving coordinates - unset atomslist - for (( a=0; a<$tot; a++)); - do - atomslist+=($(echo "${atomslist0[a]}" | sed 's/,0,/,/')) - done - - # creating coordinates XYZ file - echo "$tot" >> ${gfile}.xyz - echo " $comment" >> ${gfile}.xyz - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.xyz - done -done - -echo -e "*** DONE\n" - - -####################################### -exit 0 - - - #- creating gaussian input file - echo "%chk=${gfile}.chk" >> ${gfile}.com - echo "%nproc=16" >> ${gfile}.com - echo "%mem=100gb" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "#p mp2=full gen pseudo=Read opt freq" >> ${gfile}.com - echo "" >> ${gfile}.com - echo " file: ${gfile} from a old opt at MP2/SDALL. Now we use MP2(full)/Def2-TZVPPD" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "2 1" >> ${gfile}.com - - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.com - done - - echo "" >> ${gfile}.com - cat def2-TZVPPD >> ${gfile}.com - - #- list to submmit jobs - echo " g16 < ${gfile}.com > ${gfile}.log" >> list.dat - - - diff --git a/files_xyz/sdd/pbe0/log_files/geometry_log2xyz.sh b/files_xyz/sdd/pbe0/log_files/geometry_log2xyz.sh deleted file mode 100755 index d0798d3..0000000 --- a/files_xyz/sdd/pbe0/log_files/geometry_log2xyz.sh +++ /dev/null @@ -1,85 +0,0 @@ -#!/bin/bash - -#---------------------------------------------------------- -# -# Creating XYZ file from Gaussian OUTPUT files '.log' -# -#---------------------------------------------------------- - -for file in $(ls *.log); -do - #- rename - gfile=$(echo $file | sed 's/.log//') - - echo "creating file ${gfile}.xyz from last geometry found in '$file'" - - # avoiding overwrite an exinting file - if [ -s "${gfile}.xyz" ]; then - mv ${gfile}.xyz ${gfile}.$(date +%F.%N) -# rm ${gfile}.xyz - echo "old file was renamed to: '${gile}.xyz.$(date +%F.%N)'" - fi - - #- number of atoms - natoms=$(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | wc -l) - chk=$(grep "Redundan" $file | wc -l ) - natoms=$( echo "scale=0; ($natoms/$chk) - 1" | bc) - - #- reading atom list - atomslist0=($(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | tail -$natoms)) - - # What was done? - comment="file '$file' at: ---'"$(grep "\#" $file | head -n 1 )"'---" - - # number of atoms - tot=$(echo "${#atomslist0[@]}") - - #saving coordinates - unset atomslist - for (( a=0; a<$tot; a++)); - do - atomslist+=($(echo "${atomslist0[a]}" | sed 's/,0,/,/')) - done - - # creating coordinates XYZ file - echo "$tot" >> ${gfile}.xyz - echo " $comment" >> ${gfile}.xyz - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.xyz - done -done - -echo -e "*** DONE\n" - - -####################################### -exit 0 - - - #- creating gaussian input file - echo "%chk=${gfile}.chk" >> ${gfile}.com - echo "%nproc=16" >> ${gfile}.com - echo "%mem=100gb" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "#p mp2=full gen pseudo=Read opt freq" >> ${gfile}.com - echo "" >> ${gfile}.com - echo " file: ${gfile} from a old opt at MP2/SDALL. Now we use MP2(full)/Def2-TZVPPD" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "2 1" >> ${gfile}.com - - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.com - done - - echo "" >> ${gfile}.com - cat def2-TZVPPD >> ${gfile}.com - - #- list to submmit jobs - echo " g16 < ${gfile}.com > ${gfile}.log" >> list.dat - - - diff --git a/files_xyz/uhf/log_files/geometry_log2xyz.sh b/files_xyz/uhf/log_files/geometry_log2xyz.sh deleted file mode 100755 index d0798d3..0000000 --- a/files_xyz/uhf/log_files/geometry_log2xyz.sh +++ /dev/null @@ -1,85 +0,0 @@ -#!/bin/bash - -#---------------------------------------------------------- -# -# Creating XYZ file from Gaussian OUTPUT files '.log' -# -#---------------------------------------------------------- - -for file in $(ls *.log); -do - #- rename - gfile=$(echo $file | sed 's/.log//') - - echo "creating file ${gfile}.xyz from last geometry found in '$file'" - - # avoiding overwrite an exinting file - if [ -s "${gfile}.xyz" ]; then - mv ${gfile}.xyz ${gfile}.$(date +%F.%N) -# rm ${gfile}.xyz - echo "old file was renamed to: '${gile}.xyz.$(date +%F.%N)'" - fi - - #- number of atoms - natoms=$(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | wc -l) - chk=$(grep "Redundan" $file | wc -l ) - natoms=$( echo "scale=0; ($natoms/$chk) - 1" | bc) - - #- reading atom list - atomslist0=($(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | tail -$natoms)) - - # What was done? - comment="file '$file' at: ---'"$(grep "\#" $file | head -n 1 )"'---" - - # number of atoms - tot=$(echo "${#atomslist0[@]}") - - #saving coordinates - unset atomslist - for (( a=0; a<$tot; a++)); - do - atomslist+=($(echo "${atomslist0[a]}" | sed 's/,0,/,/')) - done - - # creating coordinates XYZ file - echo "$tot" >> ${gfile}.xyz - echo " $comment" >> ${gfile}.xyz - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.xyz - done -done - -echo -e "*** DONE\n" - - -####################################### -exit 0 - - - #- creating gaussian input file - echo "%chk=${gfile}.chk" >> ${gfile}.com - echo "%nproc=16" >> ${gfile}.com - echo "%mem=100gb" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "#p mp2=full gen pseudo=Read opt freq" >> ${gfile}.com - echo "" >> ${gfile}.com - echo " file: ${gfile} from a old opt at MP2/SDALL. Now we use MP2(full)/Def2-TZVPPD" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "2 1" >> ${gfile}.com - - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.com - done - - echo "" >> ${gfile}.com - cat def2-TZVPPD >> ${gfile}.com - - #- list to submmit jobs - echo " g16 < ${gfile}.com > ${gfile}.log" >> list.dat - - - diff --git a/files_xyz/wb97xd_grimmeD2/log_files/geometry_log2xyz.sh b/files_xyz/wb97xd_grimmeD2/log_files/geometry_log2xyz.sh deleted file mode 100755 index d0798d3..0000000 --- a/files_xyz/wb97xd_grimmeD2/log_files/geometry_log2xyz.sh +++ /dev/null @@ -1,85 +0,0 @@ -#!/bin/bash - -#---------------------------------------------------------- -# -# Creating XYZ file from Gaussian OUTPUT files '.log' -# -#---------------------------------------------------------- - -for file in $(ls *.log); -do - #- rename - gfile=$(echo $file | sed 's/.log//') - - echo "creating file ${gfile}.xyz from last geometry found in '$file'" - - # avoiding overwrite an exinting file - if [ -s "${gfile}.xyz" ]; then - mv ${gfile}.xyz ${gfile}.$(date +%F.%N) -# rm ${gfile}.xyz - echo "old file was renamed to: '${gile}.xyz.$(date +%F.%N)'" - fi - - #- number of atoms - natoms=$(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | wc -l) - chk=$(grep "Redundan" $file | wc -l ) - natoms=$( echo "scale=0; ($natoms/$chk) - 1" | bc) - - #- reading atom list - atomslist0=($(sed -n "/Redundant/,/Recover/p" $file | sed '/Recover/d' | tail -$natoms)) - - # What was done? - comment="file '$file' at: ---'"$(grep "\#" $file | head -n 1 )"'---" - - # number of atoms - tot=$(echo "${#atomslist0[@]}") - - #saving coordinates - unset atomslist - for (( a=0; a<$tot; a++)); - do - atomslist+=($(echo "${atomslist0[a]}" | sed 's/,0,/,/')) - done - - # creating coordinates XYZ file - echo "$tot" >> ${gfile}.xyz - echo " $comment" >> ${gfile}.xyz - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.xyz - done -done - -echo -e "*** DONE\n" - - -####################################### -exit 0 - - - #- creating gaussian input file - echo "%chk=${gfile}.chk" >> ${gfile}.com - echo "%nproc=16" >> ${gfile}.com - echo "%mem=100gb" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "#p mp2=full gen pseudo=Read opt freq" >> ${gfile}.com - echo "" >> ${gfile}.com - echo " file: ${gfile} from a old opt at MP2/SDALL. Now we use MP2(full)/Def2-TZVPPD" >> ${gfile}.com - echo "" >> ${gfile}.com - echo "2 1" >> ${gfile}.com - - for ((j=0; j<$tot; j++)); - do - coord=($( echo ${atomslist[j]} | sed 's/,/ /g' )) - printf "%-3s %14s %14s %14s\n" "${coord[0]}" "${coord[1]}" "${coord[2]}" "${coord[3]}" >> ${gfile}.com - done - - echo "" >> ${gfile}.com - cat def2-TZVPPD >> ${gfile}.com - - #- list to submmit jobs - echo " g16 < ${gfile}.com > ${gfile}.log" >> list.dat - - - diff --git a/2020-10-14-Note-11-34.pdf b/old_files/2020-10-14-Note-11-34.pdf similarity index 100% rename from 2020-10-14-Note-11-34.pdf rename to old_files/2020-10-14-Note-11-34.pdf diff --git a/files_xyz/b2plypd3/ada_O-Hg-O.dat b/old_files/files_xyz/b2plypd3/ada_O-Hg-O.dat similarity index 100% rename from files_xyz/b2plypd3/ada_O-Hg-O.dat rename to old_files/files_xyz/b2plypd3/ada_O-Hg-O.dat diff --git a/files_xyz/b2plypd3/dada_Hg-O-H-H.dat b/old_files/files_xyz/b2plypd3/dada_Hg-O-H-H.dat similarity index 100% rename from files_xyz/b2plypd3/dada_Hg-O-H-H.dat rename to old_files/files_xyz/b2plypd3/dada_Hg-O-H-H.dat diff --git a/files_xyz/b2plypd3/rda_H-H.dat b/old_files/files_xyz/b2plypd3/rda_H-H.dat similarity index 100% rename from files_xyz/b2plypd3/rda_H-H.dat rename to old_files/files_xyz/b2plypd3/rda_H-H.dat diff --git a/files_xyz/b2plypd3/rda_Hg-H.dat b/old_files/files_xyz/b2plypd3/rda_Hg-H.dat similarity index 100% rename from files_xyz/b2plypd3/rda_Hg-H.dat rename to old_files/files_xyz/b2plypd3/rda_Hg-H.dat diff --git a/files_xyz/b2plypd3/rda_Hg-O.dat b/old_files/files_xyz/b2plypd3/rda_Hg-O.dat similarity index 100% rename from files_xyz/b2plypd3/rda_Hg-O.dat rename to old_files/files_xyz/b2plypd3/rda_Hg-O.dat diff --git a/files_xyz/b2plypd3/rda_O-H.dat b/old_files/files_xyz/b2plypd3/rda_O-H.dat similarity index 100% rename from files_xyz/b2plypd3/rda_O-H.dat rename to old_files/files_xyz/b2plypd3/rda_O-H.dat diff --git a/files_xyz/b2plypd3/rda_O-O.dat b/old_files/files_xyz/b2plypd3/rda_O-O.dat similarity index 100% rename from files_xyz/b2plypd3/rda_O-O.dat rename to old_files/files_xyz/b2plypd3/rda_O-O.dat diff --git a/files_xyz/b2plypd3/transfer_O-H-O.dat b/old_files/files_xyz/b2plypd3/transfer_O-H-O.dat similarity index 100% rename from files_xyz/b2plypd3/transfer_O-H-O.dat rename to old_files/files_xyz/b2plypd3/transfer_O-H-O.dat diff --git a/files_xyz/b2plypd3/w1s1.xyz b/old_files/files_xyz/b2plypd3/w1s1.xyz similarity index 100% rename from files_xyz/b2plypd3/w1s1.xyz rename to old_files/files_xyz/b2plypd3/w1s1.xyz diff --git a/files_xyz/b2plypd3/w2s1.xyz b/old_files/files_xyz/b2plypd3/w2s1.xyz similarity index 100% rename from files_xyz/b2plypd3/w2s1.xyz rename to old_files/files_xyz/b2plypd3/w2s1.xyz diff --git a/files_xyz/b2plypd3/w3s1.xyz b/old_files/files_xyz/b2plypd3/w3s1.xyz similarity index 100% rename from files_xyz/b2plypd3/w3s1.xyz rename to old_files/files_xyz/b2plypd3/w3s1.xyz diff --git a/files_xyz/b2plypd3/w3s2.xyz b/old_files/files_xyz/b2plypd3/w3s2.xyz similarity index 100% rename from files_xyz/b2plypd3/w3s2.xyz rename to old_files/files_xyz/b2plypd3/w3s2.xyz diff --git a/files_xyz/b2plypd3/w3s3.xyz b/old_files/files_xyz/b2plypd3/w3s3.xyz similarity index 100% rename from files_xyz/b2plypd3/w3s3.xyz rename to old_files/files_xyz/b2plypd3/w3s3.xyz diff --git a/files_xyz/b2plypd3/w4s1.xyz b/old_files/files_xyz/b2plypd3/w4s1.xyz similarity index 100% rename from files_xyz/b2plypd3/w4s1.xyz rename to old_files/files_xyz/b2plypd3/w4s1.xyz diff --git a/files_xyz/b2plypd3/w4s2.xyz b/old_files/files_xyz/b2plypd3/w4s2.xyz similarity index 100% rename from files_xyz/b2plypd3/w4s2.xyz rename to old_files/files_xyz/b2plypd3/w4s2.xyz diff --git a/files_xyz/b2plypd3/w4s3.xyz b/old_files/files_xyz/b2plypd3/w4s3.xyz similarity index 100% rename from files_xyz/b2plypd3/w4s3.xyz rename to old_files/files_xyz/b2plypd3/w4s3.xyz diff --git a/files_xyz/b2plypd3/w4s4.xyz b/old_files/files_xyz/b2plypd3/w4s4.xyz similarity index 100% rename from files_xyz/b2plypd3/w4s4.xyz rename to old_files/files_xyz/b2plypd3/w4s4.xyz diff --git a/files_xyz/b2plypd3/w5s1.xyz b/old_files/files_xyz/b2plypd3/w5s1.xyz similarity index 100% rename from files_xyz/b2plypd3/w5s1.xyz rename to old_files/files_xyz/b2plypd3/w5s1.xyz diff --git a/files_xyz/b2plypd3/w5s10.xyz b/old_files/files_xyz/b2plypd3/w5s10.xyz similarity index 100% rename from files_xyz/b2plypd3/w5s10.xyz rename to old_files/files_xyz/b2plypd3/w5s10.xyz diff --git a/files_xyz/b2plypd3/w5s2.xyz b/old_files/files_xyz/b2plypd3/w5s2.xyz similarity index 100% rename from files_xyz/b2plypd3/w5s2.xyz rename to old_files/files_xyz/b2plypd3/w5s2.xyz diff --git a/files_xyz/b2plypd3/w5s3.xyz b/old_files/files_xyz/b2plypd3/w5s3.xyz similarity index 100% rename from files_xyz/b2plypd3/w5s3.xyz rename to old_files/files_xyz/b2plypd3/w5s3.xyz diff --git a/files_xyz/b2plypd3/w5s4.xyz b/old_files/files_xyz/b2plypd3/w5s4.xyz similarity index 100% rename from files_xyz/b2plypd3/w5s4.xyz rename to 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file mode 100644 index 0000000..e69de29 diff --git a/src/__init__.py b/src/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/core/__init__.py b/src/core/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/utils/__init__.py b/src/utils/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/visualization/__init__.py b/src/visualization/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tox.ini b/tox.ini new file mode 100644 index 0000000..e69de29 From f108bdf0b439ef18ebd76f48c08e9121d0363633 Mon Sep 17 00:00:00 2001 From: Edison Florez Date: Thu, 24 Oct 2024 03:04:48 +0000 Subject: [PATCH 2/4] Deleted VScode local setting --- .vscode/settings.json | 4 ---- 1 file changed, 4 deletions(-) delete mode 100644 .vscode/settings.json diff --git a/.vscode/settings.json b/.vscode/settings.json deleted file mode 100644 index 1c1edce..0000000 --- a/.vscode/settings.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "python.pythonPath": "/usr/local/bin/python3.8", - "python.linting.enabled": false -} \ No newline at end of file From 20db8d06ae61814dc74d97edc6430fd5c27444f7 Mon Sep 17 00:00:00 2001 From: Edison Florez Date: Thu, 24 Oct 2024 03:20:48 +0000 Subject: [PATCH 3/4] Git ignoring .`vscode` folder --- .gitignore | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/.gitignore b/.gitignore index 2e75a6a..ce25556 100644 --- a/.gitignore +++ b/.gitignore @@ -3,12 +3,12 @@ *.out *.tgz - # xyz -#*.xyz +#*.xyz # - IDE files/dir -*.vscode/ +.vscode/* +*.vscode/* # bash script to transfor output files to XYZ *geometry*.sh @@ -18,8 +18,6 @@ *org_files/ # local files/directories -.vscode/ -*.vscode/ # Byte-compiled / optimized / DLL files __pycache__/ From 5b09750e9777091c357c8aadf8acefe2c2376086 Mon Sep 17 00:00:00 2001 From: Edison Florez Date: Thu, 24 Oct 2024 03:47:48 +0000 Subject: [PATCH 4/4] ci: implement comprehensive GitHub Actions workflows - Add main CI workflow for multi-platform testing - Test on Ubuntu, Windows, and macOS - Support Python 3.8-3.11 - Include coverage reporting via codecov - Add code quality workflow - Black for code formatting - isort for import sorting - flake8 for linting - mypy for type checking - Add documentation workflow - Automated Sphinx docs building - Deploy to GitHub Pages - RTD theme integration - Configure concurrency settings - Group by git ref - Cancel in-progress for non-master branches - Add dependency management - Automated pip updates - Dev dependencies installation - Test requirements handling Resolves #12 https://github.com/e-florez/pyCC/issues/12 --- .github/workflows/python-package.yml | 97 ++++++++++++++++++++-------- 1 file changed, 70 insertions(+), 27 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 850cce8..eebf1cd 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -1,40 +1,83 @@ -# This workflow will install Python dependencies, run tests and lint with a variety of Python versions -# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python - -name: Python package +name: Python Cluster Compare (pyCC) on: push: - branches: [ "master" ] + branches: + # - "*" # matches every branch that doesn't contain a '/' + # - "*/*" # matches every branch containing a single '/' + - "**" # matches every branch + # - "!main" # excludes master pull_request: - branches: [ "master" ] + branches: ["main"] + +concurrency: + group: ${{ github.ref }} + cancel-in-progress: ${{ github.ref != 'refs/heads/master' }} jobs: build: - runs-on: ubuntu-latest strategy: fail-fast: false matrix: - python-version: ["3.8", "3.9", "3.10"] + python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] steps: - - uses: actions/checkout@v3 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v3 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - python -m pip install flake8 pytest - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - name: Test with pytest - run: | - pytest + - uses: actions/checkout@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - name: Display Python version + run: python -c "import sys; print(sys.version)" + shell: bash + + # - name: Install dependencies + # run: | + # python -m pip install --upgrade pip + # # pip install .[dev] + # pip install poetry + # poetry install + # shell: bash + + # - name: Lint with ruff + # run: | + # poetry run ruff check . + # shell: bash + + # # continue-on-error: true + + # - name: Lint with mypy + # run: | + # poetry run mypy . + # shell: bash + + # # continue-on-error: true + + # - name: Build documentation + # run: | + # poetry run sphinx-build -b html docs/source docs/_build/html + # shell: bash + + # - name: Deploy to GitHub Pages + # uses: peaceiris/actions-gh-pages@v3 + # if: github.ref == 'refs/heads/main' + # with: + # github_token: ${{ secrets.GITHUB_TOKEN }} + # publish_dir: ./docs/_build/html + + # - name: Test with pytest + # run: | + # python -m pip install pytest + # python -m pip install pytest-cov + # poetry run pytest -v -x + # shell: bash + + # - name: Test Coverage + # run: | + # python -m pip install coverage + # poetry run coverage report + # poetry run coverage html + # shell: bash \ No newline at end of file