Merge pull request #104 from efposadac/moreEasyIssues

Adding options to add custom potentials and particles. Also setting t…

bin/lowdin

@@ -204,6 +204,9 @@ if [ $extFile="lowdin" ]; then
                         else if(toupper($i)==toupper("m")){
 				printf("\tInputParticle_mass = %s\n",toupper($(i+2)) )
 			}
+                        else if(toupper($i)==toupper("eta")){
+				printf("\tInputParticle_eta = %s\n",toupper($(i+2)) )
+			}
                         else if(toupper($i)==toupper("omega")){
 				printf("\tInputParticle_omega = %s\n",toupper($(i+2)) )
 			}
@@ -381,10 +384,10 @@ if [ $extFile="lowdin" ]; then
 	' | $SED "s/,/./g" >> $nameFile.aux
 
 	###########################################
-	# Check custom basis sets in the input
+	# Check custom basis sets/potentials in the input
 	###########################################
 
-	BASIS_NAMES=(`gawk '($1~/BASIS/){print toupper($2)}' $nameFile`)
+	BASIS_NAMES=(`gawk '($1~/^BASIS$/){print toupper($2)}' $nameFile`)
 	if [ ${#BASIS_NAMES[@]} -gt "0" ]
 	then
 	    for BASIS_NAME in ${BASIS_NAMES[@]}				 
@@ -401,6 +404,23 @@ if [ $extFile="lowdin" ]; then
      	    done
 	fi
 
+	POTENTIALS_NAMES=(`gawk '($1~/^POTENTIAL$/){print toupper($2)}' $nameFile`)
+	if [ ${#POTENTIALS_NAMES[@]} -gt "0" ]
+	then
+	    for POTENTIALS_NAME in ${POTENTIALS_NAMES[@]}				 
+	    do
+		if [ -e $LOWDIN_DATA/basis/$POTENTIALS_NAME ]
+		then
+		    echo "## ERROR: ## The custom potential file already exists in " $LOWDIN_DATA/potentials/$POTENTIALS_NAME		    
+		    echo "Modify the POTENTIALS block in your input and select a different name"
+		    exit 1
+		fi
+		gawk '($1~/^POTENTIAL$/ && toupper($2)~/^'$POTENTIALS_NAME'$/){flag=1; next}
+		      ($0~/END/){flag=0};
+		      (flag==1){print toupper($0)}' $nameFile > $POTENTIALS_NAME.$PID
+     	    done
+	fi
+
 
 	###########################################
 	# Exec lowdin.x
@@ -421,6 +441,7 @@ if [ $extFile="lowdin" ]; then
 
 	cp $nameFile*.vec $LOWDIN_SCRATCH/$nameFile &> /dev/null
 	cp $nameFile*.plainvec $LOWDIN_SCRATCH/$nameFile &> /dev/null
+	cp $nameFile*.fchk $LOWDIN_SCRATCH/$nameFile &> /dev/null
 	cp $nameFile*.val $LOWDIN_SCRATCH/$nameFile &> /dev/null
 	cp $nameFile*.dens $LOWDIN_SCRATCH/$nameFile &> /dev/null
 	cp $nameFile*.sup $LOWDIN_SCRATCH/$nameFile &> /dev/null
@@ -432,20 +453,24 @@ if [ $extFile="lowdin" ]; then
 	mv $nameFile*.over $LOWDIN_SCRATCH/$nameFile &> /dev/null
 	mv $nameFile*.kin $LOWDIN_SCRATCH/$nameFile &> /dev/null
 	mv $nameFile*.coeff $LOWDIN_SCRATCH/$nameFile &> /dev/null		
-	#PID to avoid basis duplicates in simultaneous calculations
+	cp $nameFile*.gms.bs $LOWDIN_SCRATCH/$nameFile &> /dev/null
+
+	#PID to avoid basis/potentials duplicates in simultaneous calculations
 	if [ ${#BASIS_NAMES[@]} -gt "0" ]
 	then
 	    for BASIS_NAME in ${BASIS_NAMES[@]}				 
 	    do
 		mv $BASIS_NAME.$PID $LOWDIN_SCRATCH/$nameFile/$BASIS_NAME &> /dev/null		
      	    done
 	fi
-
-	if [ -e  $nameFile.gms.bs ]
+	if [ ${#POTENTIALS_NAMES[@]} -gt "0" ]
 	then
-	    cp $nameFile.gms.bs $LOWDIN_SCRATCH/$nameFile
+	    for POTENTIALS_NAME in ${POTENTIALS_NAMES[@]}				 
+	    do
+		mv $POTENTIALS_NAME.$PID $LOWDIN_SCRATCH/$nameFile/$POTENTIALS_NAME &> /dev/null		
+     	    done
 	fi
-
+	
 	# setting default number of cores for OpenMP
 
 	if [ -z "$OMP_NUM_THREADS" ]; then
@@ -515,6 +540,7 @@ if [ $extFile="lowdin" ]; then
 	mv $LOWDIN_SCRATCH/$nameFile/$nameFile*.47 $currentPath &> 2
 	mv $LOWDIN_SCRATCH/$nameFile/*.vec $currentPath &> 2
 	mv $LOWDIN_SCRATCH/$nameFile/*.plainvec $currentPath &> 2
+	mv $LOWDIN_SCRATCH/$nameFile/*.fchk $currentPath &> 2
 	# mv $LOWDIN_SCRATCH/$nameFile/*.val $currentPath &> 2
         mv $LOWDIN_SCRATCH/$nameFile/*.NOCI.coords $currentPath &> 2
         mv $LOWDIN_SCRATCH/$nameFile/*.NOCI.s* $currentPath &> 2

lib/basis/PSX-DZ

@@ -1,5 +1,53 @@
-O-POSITRON E+ (5S) BASIS TYPE: 3
-# (5S)-[5S]
+O-POSITRON E+ (5S3P2D) BASIS TYPE: 3
+# (5S3P2D)-[5S3P2D]
+10
+1 0 1
+.0189693659 1.0
+1 0 1
+.05186863351164733038 1.0
+1 0 1
+.14182630861506996771 1.0
+1 0 1
+.38780088183468771642 1.0
+1 0 1
+1.06037818667291718709 1.0
+1 1 1
+.0590955656 1.0
+1 1 1
+.16127967470846848928 1.0
+1 1 1
+.44015372744092004227 1.0
+1 2 1
+.11654481880000000000 1.0
+1 2 1
+.31287113568838127412 1.0
+
+O-POSITRON E+A (5S3P2D) BASIS TYPE: 3
+# (5S3P2D)-[5S3P2D]
+10
+1 0 1
+.0189693659 1.0
+1 0 1
+.05186863351164733038 1.0
+1 0 1
+.14182630861506996771 1.0
+1 0 1
+.38780088183468771642 1.0
+1 0 1
+1.06037818667291718709 1.0
+1 1 1
+.0590955656 1.0
+1 1 1
+.16127967470846848928 1.0
+1 1 1
+.44015372744092004227 1.0
+1 2 1
+.11654481880000000000 1.0
+1 2 1
+.31287113568838127412 1.0
+
+O-POSITRON E+B (5S3P2D) BASIS TYPE: 3
+# (5S3P2D)-[5S3P2D]
 10
 1 0 1
 .0189693659 1.0

lib/dataBases/constantsOfCoupling.lib

@@ -4525,19 +4525,3 @@
 	LAMBDA = 2.0
 	PARTICLESFRACTION = 0.5
 /
-&SPECIE
-	NAME = "HA-TIP"
-	SYMBOL = "X0.5+"
-	KAPPA = -1.0
-	ETA = 1.0
-	LAMBDA = 1.0
-	PARTICLESFRACTION = 1
-/
-&SPECIE
-	NAME = "HB-TIP"
-	SYMBOL = "Y0.5+"
-	KAPPA = -1.0
-	ETA = 1.0
-	LAMBDA = 1.0
-	PARTICLESFRACTION = 1
-/

lib/dataBases/elementalParticles.lib

@@ -171,71 +171,47 @@
 	SYMBOL = "HEA3"
 	CATEGORY = "LEPTON"
 	CHARGE = 1
-	MASS = 5494.892576965
+	MASS = 5495.8851
 	SPIN = 0.5
 /
 &PARTICLE
 	NAME = "HE-ATOM2"
 	SYMBOL = "HEB3"
 	CATEGORY = "LEPTON"
 	CHARGE = 1
-	MASS = 5494.892576965
+	MASS = 5495.8851
 	SPIN = 0.5
 /
 &PARTICLE
 	NAME = "HE-ATOM"
 	SYMBOL = "HES3"
 	CATEGORY = "LEPTON"
 	CHARGE = 1
-	MASS = 5494.892576965
+	MASS = 5495.8851
 	SPIN = 0.5
 /
 &PARTICLE
 	NAME = "HE-ATOM1"
 	SYMBOL = "HEA4"
 	CATEGORY = "LEPTON"
 	CHARGE = 1
-	MASS = 7292.327967297
+	MASS = 7294.2994
 	SPIN = 0.5
 /
 &PARTICLE
 	NAME = "HE-ATOM2"
 	SYMBOL = "HEB4"
 	CATEGORY = "LEPTON"
 	CHARGE = 1
-	MASS = 7292.327967297
+	MASS = 7294.2994
 	SPIN = 0.5
 /
 &PARTICLE
 	NAME = "HE-ATOM"
 	SYMBOL = "HES4"
 	CATEGORY = "LEPTON"
 	CHARGE = 1
-	MASS = 7292.327967297
-	SPIN = 0.5
-/
-&PARTICLE
-	NAME = "HA-TIP"
-	SYMBOL = "X0.5+"
-	CATEGORY = "LEPTON"
-	CHARGE = 0.5564
-	MASS = 1836.15267247
-	SPIN = 0.5
-/
-&PARTICLE
-	NAME = "HB-TIP"
-	SYMBOL = "Y0.5+"
-	CATEGORY = "LEPTON"
-	CHARGE = 0.5564
-	MASS = 1836.15267247
-	SPIN = -0.5
-/
-&PARTICLE
-	NAME = "M-TIP"
-	SYMBOL = "X1.1-"
-	CATEGORY = "LEPTON"
-	CHARGE = -1.1128
-	MASS = 1836.15267247
+	MASS = 7294.2994
 	SPIN = 0.5
 /
 &PARTICLE