WIP: Address review

interfaces/BAGEL-SH/r.bagel-sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# You should't need to modify this file!
+# You should't need to modify this file.
 # Specification of CAS wavefunction is in file "bagel.inp"
 
 set -u
@@ -17,8 +17,8 @@ geom="../geom.dat.$ibead"
 read -t 2 -a nstate
 read -t 2 -a tocalc
 
-thresh="1.0e-8"   # default value is 1.0e-8 and shouldn't be modified. 
-                  # In the case of persisting convergence errors, see the "CHECK CHONVERGENCES" section bellow
+thresh_CASSCF="1.0e-8"
+thresh_CASPT2="1.0e-8"
 
 # Note that the actual filename is orbitals.archive
 ORBITAL_FILE=orbitals
@@ -28,16 +28,7 @@ file_exists $geom
 rm -f ../engrad.dat.$ibead ../nacm.dat ENERGY.out FORCE_*
 
 ### GENERATE BAGEL INPUT
-specify_molecule "$geom" "$input.json"
-
-if [[ -f "$ORBITAL_FILE.archive" ]]; then
-    # Load orbitals if the archive file exists
-    load_orbitals $ORBITAL_FILE $input.json
-else
-    # Calculate HF guess if the initial orbitals are not provided via the 'orbitals.archive' file
-    generate_hf_orbitals $input.json
-fi
-
+#
 # Determine for which state we need to calculate forces
 for ((ist=0; ist<nstate; ist++))
 do
@@ -51,53 +42,50 @@ do
   fi
 done
 
-cat >> $input.json << EOF
-  {
-    "title" : "forces",
-    "export" : true,
-    "grads" : [
-      {
-        "title": "force",
-        "target": $target_state
-      }
-    ],
-EOF
+function generate_input {
 
-# CAS section
-if [[ $method == "xms_caspt2" ]]; then
+input=$1
 
-    print_cas "caspt2" "$thresh" "$maxiter_CASSCF" $input.json
-    print_caspt2 "true" "$thresh" "$maxiter_CASPT2" "$input.json"
+specify_molecule "$geom" "$input"
 
-elif [[ $method == "ms_caspt2" ]]; then
+if [[ -f "$ORBITAL_FILE.archive" ]]; then
+    # Load orbitals if the archive file exists
+    load_orbitals $ORBITAL_FILE $input
+else
+    # Calculate HF guess if the initial orbitals are not provided via the 'orbitals.archive' file
+    generate_hf_orbitals $input
+fi
 
-    print_cas "caspt2" "$thresh" "$maxiter_CASSCF" $input.json
-    print_caspt2 "false" "$thresh" "$maxiter_CASPT2" "$input.json"
+print_forces "$target_state" "$input"
 
+# CAS section
+if [[ $method == "xms_caspt2" ]]; then
+    print_cas "caspt2" "$thresh_CASSCF" "$maxiter_CASSCF" "$input"
+    print_caspt2 "true" "$thresh_CASPT2" "$maxiter_CASPT2" "$input"
+elif [[ $method == "ms_caspt2" ]]; then
+    print_cas "caspt2" "$thresh_CASSCF" "$maxiter_CASSCF" "$input"
+    print_caspt2 "false" "$thresh_CASPT2" "$maxiter_CASPT2" "$input"
 elif [[ $method == "sa_casscf" ]]; then
-
-    print_cas "casscf" "$thresh" "$maxiter_CASSCF" "$input.json"
+    print_cas "casscf" "$thresh_CASSCF" "$maxiter_CASSCF" "$input"
     # Remove extra dangling comma
-    sed -i '$ s/,$//' "$input.json"
-
+    sed -i '$ s/,$//' "$input"
 else
-
     >&2 echo "ERROR: Unknown method ($method). Specify one of \"xms_caspt2\", \"ms_caspt2\" or \"sa_casscf\" in bagel.inp"
     exit 2
-
 fi
-
-echo -e "      }]\n  }," >> $input.json
-
-save_orbitals $ORBITAL_FILE $input.json
+echo -e "      }]\n  }," >> $input
+save_orbitals $ORBITAL_FILE $input
 
 if [[ ! -f "initial_orbitals.molden" ]];then
-    print_molden "initial_orbitals.molden" $input.json
+    print_molden "initial_orbitals.molden" $input
 else
-    print_molden "orbitals.molden" $input.json
+    print_molden "orbitals.molden" $input
 fi
 
-echo "]}" >> $input.json
+echo "]}" >> $input
+}
+
+generate_input $input.json
 ### END OF INPUT GENERATION 
 
 ### EXECUTE BAGEL
@@ -113,26 +101,25 @@ smith_error='EXCEPTION RAISED:  SMITH convergence not reached'
 if grep -q "$casscf_error" $input.out; then
     error=true
     savefile=$input.out.casscf_error.$timestep
-    >&2 echo "ERROR: CASSCF did not converge - let's set thresh=1.0e-7 and try again."
+    thresh_CASSCF="1.0e-7"
+    maxiter_CASSCF=600
+    >&2 echo "ERROR: CASSCF did not converge, trying again with thresh=$thresh_CASSCF and maxiter=$maxiter_CASSCF."
     >&2 echo "See file $savefile"
     cp $input.out $savefile
-    # TODO: This also changes thresh for CASPT2, is that a problem?
-    sed -i "s/\"thresh\": $thresh/\"thresh\": 1.0e-7/g" $input.json
-    sed -i "s/\"maxiter\": $maxiter_CASSCF/\"maxiter\": 600/" $input.json
-    # Run the job for the second time
+    generate_input "$input.json"
     exec_bagel $input.json $input.out
     returncode=$?
 fi
 
 if grep -q "$smith_error" $input.out; then
     error=true
     savefile=$input.out.caspt2_error.$timestep
-    >&2 echo "ERROR: CASPT2 did not convergence, trying again with looser thresh=1.0e-7 and more iterations."
+    thresh_CASPT2="1.0e-7"
+    maxiter_CASPT2=1000
+    >&2 echo "ERROR: CASPT2 did not converge, trying again with thresh=$thresh_CASPT2 and maxiter=$maxiter_CASPT2."
     >&2 echo "See file $savefile"
     cp $input.out $savefile
-    sed -i "s/\"thresh\": $thresh/\"thresh\": 1.0e-7/g" $input.json
-    sed -i "s/\"maxiter\": $maxiter_CASPT2/\"maxiter\": 1000/g" $input.json
-    # Run the job for the second time
+    generate_input "$input.json"
     exec_bagel $input.json $input.out
     returncode=$?
 fi