diff --git a/INSTALL.txt b/INSTALL.txt new file mode 100644 index 0000000..9a1ab6e --- /dev/null +++ b/INSTALL.txt @@ -0,0 +1,9 @@ +* define $QUACK_ROOT +* ninja +* gfortran +* python3 +* libtool +* opam +* cmake +* wget + diff --git a/PyDuck b/PyDuck deleted file mode 100755 index 25016c9..0000000 --- a/PyDuck +++ /dev/null @@ -1,321 +0,0 @@ -#!/usr/bin/env python2 -import sys -from termcolor import colored -import shlex -from subprocess import Popen, PIPE -import itertools -import re -import numpy as np -import os -from shutil import copy2 -import matplotlib.pyplot as plt -import json -from math import * -from collections import OrderedDict -import csv -import argparse -def GetDuckDir(): - return os.path.dirname(os.path.realpath(__file__)) - -def nNucl(molbaselines): - return float(molbaselines[1].split()[0]) - -def isMononucle(molbaselines): - return nNucl(molbaselines)==1 - -def openfileindir(path,readwrite): - mydir=os.path.dirname(path) - if not os.path.exists(mydir) and mydir!="": - os.makedirs(mydir) - return open(path,readwrite) -def outfile(Outdic,item,index=None): - itemdata=Outdic[item] - if itemdata["Enabled"]: - fmt=itemdata["Format"] - if index is not None: - filename=fmt.format(index) - else: - filename=fmt - if "Parent" in Outdic: - path=os.path.join(Outdic["Parent"],filename) - else: - path=filename - return openfileindir(path,'w') - else: - return - -def runDuck(mol,basis,x,molbaselines,molbase,basisbase): - #gennerate molecule file - currdir=os.getcwd() - os.chdir(GetDuckDir()) - molname='.'.join([mol,str(x)]) - lstw=list() - for i,line in enumerate(molbaselines): - if i<3: - lstw.append(line) - else: - if isMononucle(molbaselines): - if i==3: - lstw.append(' '.join([str(x)]+line.split()[1:])) - else: - v=[float(abs(x))/float(2),float(-abs(x)/float(2))] - val=v[i-3] - lstw.append(' '.join([line.split()[0],'0.','0.',str(val)])) - junkfiles=list() - with open(molbase+molname,'w') as n: - junkfiles.append(n.name) - n.write(os.linesep.join(lstw)) - #Copy basis - basisfile=basisbase+'.'.join([mol,basis]) - newbasisfile=basisbase+'.'.join([molname,basis]) - copy2(basisfile,newbasisfile) - junkfiles.append(newbasisfile) - #start child process Goduck - cmd=" ".join(["./GoDuck",molname, basis]) - Duck=Popen(shlex.split(cmd),stdout=PIPE) - (DuckOut, DuckErr) = Duck.communicate() - excode=Duck.wait() - for junk in junkfiles: - os.remove(junk) - os.chdir(currdir) - return (excode,DuckOut,DuckErr) - -def addvalue(dic,key,x,y): - if key not in dic: - dic[key]=list() - dic[key].append(y) - print(key) - print(x,y) - -def main(mol): - #get basepath for files - molbase='examples/molecule.' - basisbase=molbase.replace('molecule','basis') - with open('PyOptions.json','r') as jfile: - options=json.loads(jfile.read()) - basis=str(options['Basis']) - #Get mehtod to analyse - methodsdic=options['Methods'] - #Get datas to analyse in this method - scandic=options['Scan'] - scan=np.arange(scandic['Start'],scandic['Stop']+scandic['Step'],scandic['Step']) - print(scan) - mymethods=dict() - alllabels=list() - for method,methoddatas in methodsdic.iteritems(): - if methoddatas['Enabled']: - mymethods[method]=methoddatas - for label,labeldatas in methoddatas['Labels'].iteritems(): - if type(labeldatas) is dict: - enabled=labeldatas['Enabled'] - else: - enabled=labeldatas - if enabled and label not in alllabels: - alllabels.append(label) - graphdic=dict() - errorconvstring="Convergence failed" - with open(os.path.join(GetDuckDir(),molbase+mol),'r') as b: - molbaselines=b.read().splitlines() - if isMononucle(molbaselines): - print('monoatomic system: variation of the nuclear charge') - else: - print('polyatomic system: variation is on the distance') - for x in scan: - (DuckExit,DuckOut,DuckErr)=runDuck(mol,basis,x,molbaselines,molbase,basisbase) - #print DuckOut on file or not - if "Outputs" in options: - outdat=options["Outputs"] - if 'DuckOutput' in outdat: - outopt=outdat["DuckOutput"] - if outopt['Enabled']: - if outopt['Multiple']: - duckoutf=outfile(outopt,"DuckOutput",x) - else: - if x==scan[0]: - duckoutf=outfile(outdat,"DuckOutput") - duckoutf.write('Z' if isMononucle(molbaselines) else 'Distance'+' '+str(x)+os.linesep+os.linesep) - duckoutf.write(DuckOut) - if outopt['Multiple']: - duckoutf.close() - print("GoDuk exit code " + str(DuckExit)) - if DuckExit !=0: - #if GoDuck is not happy - print(DuckErr) - sys.exit(-1) - #get all data for the method - for method,methoddatas in mymethods.iteritems(): - isnan=False - if '{0}' in method: - if "index" in methoddatas: - methodheaders=[method.format(str(x)) for x in methoddatas['Index']] - else: - try: - print(method) - reglist=re.findall('(\d+)'.join([re.escape(s) for s in method.split('{0}')]),DuckOut) - print(reglist) - final=max([(int(i[0]) if type(i) is tuple else int(i)) for i in reglist]) - print(final) - methodheaders=[method.format(str(final))] - except: - isnan=True - methodheaders=[None] - method=method.replace('{0}','') - else: - methodheaders=list([method]) - for methodheader in methodheaders: - if len(methodheaders)!=1: - method=methodheader - lbldic=methoddatas['Labels'] - print(methodheader) - if methodheader is None: - methodtxt='' - else: - it=itertools.dropwhile(lambda line: methodheader + ' calculation' not in line , DuckOut.splitlines()) - it=itertools.takewhile(lambda line: 'Total CPU time for ' not in line, it) - methodtxt=os.linesep.join(it) - if errorconvstring in methodtxt: - print(colored(' '.join([method, errorconvstring, '!!!!!']),'red')) - isnan=True - if methodtxt=='': - print(colored('No data' +os.linesep+ 'RHF scf not converged or method not enabled','red')) - isnan=True - #find the expected values - for label,labeldatas in lbldic.iteritems(): - if type(labeldatas) is dict: - indexed=('Index' in labeldatas) - enabled=labeldatas['Enabled'] - graph=labeldatas['Graph'] if 'Graph' in labeldatas else 1 - else: - enabled=labeldatas - graph=1 - indexed=False - if enabled: - if graph not in graphdic: - graphdic[graph]=OrderedDict() - y=graphdic[graph] - if not indexed: - v=np.nan - print(method) - print(label) - if not isnan: - try: - m=re.search('\s+'.join([re.escape(w) for w in label.split()]) + "\s+(?:"+re.escape("(eV):")+"\s+)?(?:=\s+)?(-?\d+.?\d*)",methodtxt) - v=m.group(1) - except: - v=np.nan - addvalue(y,(method,label),x,v) - else: - startindex=-1 - columnindex=-1 - linedtxt=methodtxt.split(os.linesep) - for n,line in enumerate(linedtxt): - if all(x in line for x in ['|',' '+label+' ','#']): - startindex=n+2 - columnindex=[s.strip() for s in line.split('|')].index(label) - break - with open(os.path.join(GetDuckDir(),'input','molecule'),'r') as molfile: - molfile.readline() - line=molfile.readline() - nel=int(line.split()[1]) - print(nel) - HOMO=int(nel/2) - HO=HOMO - LUMO=HOMO+1 - BV=LUMO - for i in labeldatas['Index']: - v=np.nan - if type(i) is str or type(i) is unicode: - ival=eval(i) - if type(ival) is not int: - print('Index '+ str(i) + 'must be integer') - sys.exit(-2) - else: - ival=i - v=np.nan - if not isnan: - try: - if startindex!=-1 and columnindex!=-1: - line=linedtxt[startindex+ival-1] - v=float(line.split('|')[columnindex].split()[0]) - print(method) - print(label) - print(i) - else: - v=np.nan - except: - v=np.nan - key=(method,label,i) - addvalue(y,key,x,v) - tpl=(x,scan.tolist().index(x)+1,len(y[key])) - print(tpl) - if tpl[1]-tpl[2]: - sys.exit() - #define graph grid - maxgraph=max(graphdic.keys()) - maxrow=int(round(sqrt(maxgraph))) - maxcol=int(ceil(float(maxgraph)/float(maxrow))) - #define label ls - for graph,y in graphdic.iteritems(): - datas=list() - datas.append(["#x"]+scan.tolist()) - if len(y.keys())!=0: - plt.subplot(maxrow,maxcol,graph) - plt.xlabel('Z' if isMononucle(molbaselines) else 'Distance '+mol) - ylbls=list([basis]) - for i in range(0,2): - lst=list(set([key[i] for key in y.keys()])) - if len(lst)==1: - ylbls.append(lst[0]) - plt.ylabel(' '.join(ylbls)) - print('Legend') - print(list(y.keys())) - for key,values in y.iteritems(): - legend=list() - for el in key[0:2]: - if el not in ylbls: - legend.append(el) - if len(key)>2: - legend.append(str(key[2])) - #plot curves - lbl=' '.join(legend) - plt.plot(scan,y[key],'-o',label=lbl) - #print("min",x[y.index(min(y))]/2) - #generate legends - plt.legend() - dataout=False - if "Outputs" in options: - outputs=options['Outputs'] - if "DataOutput" in outputs: - DataOutput=outputs['DataOutput'] - dataout=DataOutput['Enabled'] - if dataout: - fmtlegendf='{0}({1})' - datas.append([fmtlegendf.format("y",lbl)]+y[key]) - if dataout: - csvdatas=zip(*datas) - with outfile(outputs,"DataOutput",graph) as csvf: - writer = csv.writer(csvf, delimiter=' ') - writer.writerow(['#']+ylbls) - writer.writerows(csvdatas) - #show graph - if "Outputs" in options: - outputs=options['Outputs'] - if "FigureOutput" in outputs: - figout=outputs["FigureOutput"] - if figout["Enabled"]: - plt.savefig(figout['Path']) - plt.show() -if __name__ == '__main__': - parser=argparse.ArgumentParser() - parser.add_argument("mol",nargs='?', help="molecule to compute",type=str) - parser.add_argument("-c,--copy", help="Copy sample option file",action="store_true",dest="copy") - args = parser.parse_args() - if len(sys.argv)==1: - parser.print_help() - else: - if args.copy: - copy2(os.path.join(GetDuckDir(),"PyOptions.template.json"),"PyOptions.json") - if args.mol is not None: - os.system("vim PyOptions.json") - if args.mol is not None: - main(args.mol) diff --git a/PyOptions.json b/PyOptions.json deleted file mode 100644 index 055b3aa..0000000 --- a/PyOptions.json +++ /dev/null @@ -1,145 +0,0 @@ -{ - "Scan": { - "Start":1.8, - "Stop":1.9, - "Step":0.1 - }, - "Basis":"VDZ", - "Outputs": { - "DataOutput": { - "Enabled":true, - "Format":"Duck{0}.dat" - }, - "DuckOutput": { - "Enabled":true, - "Multiple":false, - "Format":"DuckOut.out" - }, - "FigureOutput":{ - "Enabled":false, - "Path":"Figure.png" - } - }, - "Methods": { - "RHF":{ - "Enabled": true, - "Labels": { - "One-electron energy":false, - "Kinetic energy":false, - "Potential energy":false, - "Two-electron energy":false, - "Coulomb energy":false, - "Exchange energy":false, - "Electronic energy":false, - "Nuclear repulsion":false, - "Hartree-Fock energy":true, - "HF HOMO energy":false, - "HF LUMO energy":false, - "HF HOMO-LUMO gap":false - } - }, - "One-shot G0W0": { - "Enabled": true, - "Labels": { - "G0W0 HOMO energy":true, - "G0W0 LUMO energy":true, - "G0W0 HOMO-LUMO gap":false, - "G0W0 total energy":false, - "RPA correlation energy" :false, - "Z": { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":1 - }, - "Sigma_c (eV)" : { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":2 - }, - "e_QP (eV)" : { - "Enabled":true, - "Index":["HOMO","LUMO+1","LUMO+2"], - "Graph":3 - }, - "e_HF (eV)" : { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":4 - } - } - }, - "Self-consistent evG{0}W{0}": { - "Enabled":false, - "Labels": { - "evGW HOMO energy":false, - "evGW LUMO energy":false, - "evGW HOMO-LUMO gap":false, - "evGW total energy":false, - "RPA correlation energy" :false, - "Z": { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":1 - }, - "Sigma_c (eV)" : { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":2 - }, - "e_QP (eV)" : { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":3 - }, - "e_HF (eV)" : { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":4 - } - } - }, - "Self-consistent qsG{0}W{0}": { - "Enabled": false, - "Labels": { - "qsGW HOMO energy":false, - "qsGW LUMO energy":false, - "qsGW HOMO-LUMO gap":false, - "qsGW total energy":false, - "qsGW exchange energy":false, - "qsGW correlation energy":false, - "RPA correlation energy":{ - "Enabled":false, - "Graph":2 - }, - "Z": { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":4 - }, - "e_QP-e_HF (eV)" : { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":5 - }, - "e_QP (eV)" : { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":6 - } - } - }, - "MP2": { - "Enabled": false, - "Labels": { - "MP2 correlation energy": { - "Enabled":true, - "Graph":4 - }, - "Direct part":false, - "Exchange part":false, - "MP2 total energy":true, - "MP2 energy":false - } - } - } -} diff --git a/PyOptions.template.json b/PyOptions.template.json deleted file mode 100644 index 055b3aa..0000000 --- a/PyOptions.template.json +++ /dev/null @@ -1,145 +0,0 @@ -{ - "Scan": { - "Start":1.8, - "Stop":1.9, - "Step":0.1 - }, - "Basis":"VDZ", - "Outputs": { - "DataOutput": { - "Enabled":true, - "Format":"Duck{0}.dat" - }, - "DuckOutput": { - "Enabled":true, - "Multiple":false, - "Format":"DuckOut.out" - }, - "FigureOutput":{ - "Enabled":false, - "Path":"Figure.png" - } - }, - "Methods": { - "RHF":{ - "Enabled": true, - "Labels": { - "One-electron energy":false, - "Kinetic energy":false, - "Potential energy":false, - "Two-electron energy":false, - "Coulomb energy":false, - "Exchange energy":false, - "Electronic energy":false, - "Nuclear repulsion":false, - "Hartree-Fock energy":true, - "HF HOMO energy":false, - "HF LUMO energy":false, - "HF HOMO-LUMO gap":false - } - }, - "One-shot G0W0": { - "Enabled": true, - "Labels": { - "G0W0 HOMO energy":true, - "G0W0 LUMO energy":true, - "G0W0 HOMO-LUMO gap":false, - "G0W0 total energy":false, - "RPA correlation energy" :false, - "Z": { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":1 - }, - "Sigma_c (eV)" : { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":2 - }, - "e_QP (eV)" : { - "Enabled":true, - "Index":["HOMO","LUMO+1","LUMO+2"], - "Graph":3 - }, - "e_HF (eV)" : { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":4 - } - } - }, - "Self-consistent evG{0}W{0}": { - "Enabled":false, - "Labels": { - "evGW HOMO energy":false, - "evGW LUMO energy":false, - "evGW HOMO-LUMO gap":false, - "evGW total energy":false, - "RPA correlation energy" :false, - "Z": { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":1 - }, - "Sigma_c (eV)" : { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":2 - }, - "e_QP (eV)" : { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":3 - }, - "e_HF (eV)" : { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":4 - } - } - }, - "Self-consistent qsG{0}W{0}": { - "Enabled": false, - "Labels": { - "qsGW HOMO energy":false, - "qsGW LUMO energy":false, - "qsGW HOMO-LUMO gap":false, - "qsGW total energy":false, - "qsGW exchange energy":false, - "qsGW correlation energy":false, - "RPA correlation energy":{ - "Enabled":false, - "Graph":2 - }, - "Z": { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":4 - }, - "e_QP-e_HF (eV)" : { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":5 - }, - "e_QP (eV)" : { - "Enabled":true, - "Index":["HOMO","LUMO","LUMO+1","LUMO+2"], - "Graph":6 - } - } - }, - "MP2": { - "Enabled": false, - "Labels": { - "MP2 correlation energy": { - "Enabled":true, - "Graph":4 - }, - "Direct part":false, - "Exchange part":false, - "MP2 total energy":true, - "MP2 energy":false - } - } - } -} diff --git a/examples/basis.BH2.aug-cc-pvtz b/examples/basis.BH2.aug-cc-pvtz new file mode 100644 index 0000000..fc3caa4 --- /dev/null +++ b/examples/basis.BH2.aug-cc-pvtz @@ -0,0 +1,87 @@ +1 14 +S 8 + 1 5473.0000000 0.0005550 + 2 820.9000000 0.0042910 + 3 186.8000000 0.0219490 + 4 52.8300000 0.0844410 + 5 17.0800000 0.2385570 + 6 5.9990000 0.4350720 + 7 2.2080000 0.3419550 + 8 0.2415000 -0.0095450 +S 8 + 1 5473.0000000 -0.0001120 + 2 820.9000000 -0.0008680 + 3 186.8000000 -0.0044840 + 4 52.8300000 -0.0176830 + 5 17.0800000 -0.0536390 + 6 5.9990000 -0.1190050 + 7 2.2080000 -0.1658240 + 8 0.2415000 0.5959810 +S 1 + 1 0.5879000 1.0000000 +S 1 + 1 0.0861000 1.0000000 +S 1 + 1 0.0291400 1.0000000 +P 3 + 1 12.0500000 0.0131180 + 2 2.6130000 0.0798960 + 3 0.7475000 0.2772750 +P 1 + 1 0.2385000 1.0000000 +P 1 + 1 0.0769800 1.0000000 +P 1 + 1 0.0209600 1.0000000 +D 1 + 1 0.6610000 1.0000000 +D 1 + 1 0.1990000 1.0000000 +D 1 + 1 0.0604000 1.0000000 +F 1 + 1 0.4900000 1.0000000 +F 1 + 1 0.1630000 1.0000000 +2 9 +S 3 + 1 33.8700000 0.0060680 + 2 5.0950000 0.0453080 + 3 1.1590000 0.2028220 +S 1 + 1 0.3258000 1.0000000 +S 1 + 1 0.1027000 1.0000000 +S 1 + 1 0.0252600 1.0000000 +P 1 + 1 1.4070000 1.0000000 +P 1 + 1 0.3880000 1.0000000 +P 1 + 1 0.1020000 1.0000000 +D 1 + 1 1.0570000 1.0000000 +D 1 + 1 0.2470000 1.0000000 +3 9 +S 3 + 1 33.8700000 0.0060680 + 2 5.0950000 0.0453080 + 3 1.1590000 0.2028220 +S 1 + 1 0.3258000 1.0000000 +S 1 + 1 0.1027000 1.0000000 +S 1 + 1 0.0252600 1.0000000 +P 1 + 1 1.4070000 1.0000000 +P 1 + 1 0.3880000 1.0000000 +P 1 + 1 0.1020000 1.0000000 +D 1 + 1 1.0570000 1.0000000 +D 1 + 1 0.2470000 1.0000000 diff --git a/examples/basis.BeF.aug-cc-pvtz b/examples/basis.BeF.aug-cc-pvtz new file mode 100644 index 0000000..7f2fa1b --- /dev/null +++ b/examples/basis.BeF.aug-cc-pvtz @@ -0,0 +1,106 @@ +1 14 +S 11 +1 6.863000E+03 2.360000E-04 +2 1.030000E+03 1.826000E-03 +3 2.347000E+02 9.452000E-03 +4 6.656000E+01 3.795700E-02 +5 2.169000E+01 1.199650E-01 +6 7.734000E+00 2.821620E-01 +7 2.916000E+00 4.274040E-01 +8 1.130000E+00 2.662780E-01 +9 2.577000E-01 1.819300E-02 +10 1.101000E-01 -7.275000E-03 +11 4.409000E-02 1.903000E-03 +S 11 +1 6.863000E+03 -4.300000E-05 +2 1.030000E+03 -3.330000E-04 +3 2.347000E+02 -1.736000E-03 +4 6.656000E+01 -7.012000E-03 +5 2.169000E+01 -2.312600E-02 +6 7.734000E+00 -5.813800E-02 +7 2.916000E+00 -1.145560E-01 +8 1.130000E+00 -1.359080E-01 +9 2.577000E-01 2.280260E-01 +10 1.101000E-01 5.774410E-01 +11 4.409000E-02 3.178730E-01 +S 1 +1 2.577000E-01 1.000000E+00 +S 1 +1 4.409000E-02 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6 12.5400000 0.4335010 + 7 4.6440000 0.3474720 + 8 0.5118000 -0.0085080 +S 8 + 1 11420.0000000 -0.0001150 + 2 1712.0000000 -0.0008950 + 3 389.3000000 -0.0046240 + 4 110.0000000 -0.0185280 + 5 35.5700000 -0.0573390 + 6 12.5400000 -0.1320760 + 7 4.6440000 -0.1725100 + 8 0.5118000 0.5999440 +S 1 + 1 1.2930000 1.0000000 +S 1 + 1 0.1787000 1.0000000 +S 1 + 1 0.0576000 1.0000000 +P 3 + 1 26.6300000 0.0146700 + 2 5.9480000 0.0917640 + 3 1.7420000 0.2986830 +P 1 + 1 0.5550000 1.0000000 +P 1 + 1 0.1725000 1.0000000 +P 1 + 1 0.0491000 1.0000000 +D 1 + 1 1.6540000 1.0000000 +D 1 + 1 0.4690000 1.0000000 +D 1 + 1 0.1510000 1.0000000 +F 1 + 1 1.0930000 1.0000000 +F 1 + 1 0.3640000 1.0000000 +2 14 +S 8 + 1 15330.0000000 0.0005080 + 2 2299.0000000 0.0039290 + 3 522.4000000 0.0202430 + 4 147.3000000 0.0791810 + 5 47.5500000 0.2306870 + 6 16.7600000 0.4331180 + 7 6.2070000 0.3502600 + 8 0.6882000 -0.0081540 +S 8 + 1 15330.0000000 -0.0001150 + 2 2299.0000000 -0.0008950 + 3 522.4000000 -0.0046360 + 4 147.3000000 -0.0187240 + 5 47.5500000 -0.0584630 + 6 16.7600000 -0.1364630 + 7 6.2070000 -0.1757400 + 8 0.6882000 0.6034180 +S 1 + 1 1.7520000 1.0000000 +S 1 + 1 0.2384000 1.0000000 +S 1 + 1 0.0737600 1.0000000 +P 3 + 1 34.4600000 0.0159280 + 2 7.7490000 0.0997400 + 3 2.2800000 0.3104920 +P 1 + 1 0.7156000 1.0000000 +P 1 + 1 0.2140000 1.0000000 +P 1 + 1 0.0597400 1.0000000 +D 1 + 1 2.3140000 1.0000000 +D 1 + 1 0.6450000 1.0000000 +D 1 + 1 0.2140000 1.0000000 +F 1 + 1 1.4280000 1.0000000 +F 1 + 1 0.5000000 1.0000000 + diff --git a/examples/basis.OH.aug-cc-pvtz b/examples/basis.OH.aug-cc-pvtz new file mode 100644 index 0000000..562a831 --- /dev/null +++ b/examples/basis.OH.aug-cc-pvtz @@ -0,0 +1,112 @@ +1 9 +S 3 + 1 33.8700000 0.0060680 + 2 5.0950000 0.0453080 + 3 1.1590000 0.2028220 +S 1 + 1 0.3258000 1.0000000 +S 1 + 1 0.1027000 1.0000000 +S 1 + 1 0.0252600 1.0000000 +P 1 + 1 1.4070000 1.0000000 +P 1 + 1 0.3880000 1.0000000 +P 1 + 1 0.1020000 1.0000000 +D 1 + 1 1.0570000 1.0000000 +D 1 + 1 0.2470000 1.0000000 +2 14 +S 8 + 1 8236.0000000 0.0005310 + 2 1235.0000000 0.0041080 + 3 280.8000000 0.0210870 + 4 79.2700000 0.0818530 + 5 25.5900000 0.2348170 + 6 8.9970000 0.4344010 + 7 3.3190000 0.3461290 + 8 0.3643000 -0.0089830 +S 8 + 1 8236.0000000 -0.0001130 + 2 1235.0000000 -0.0008780 + 3 280.8000000 -0.0045400 + 4 79.2700000 -0.0181330 + 5 25.5900000 -0.0557600 + 6 8.9970000 -0.1268950 + 7 3.3190000 -0.1703520 + 8 0.3643000 0.5986840 +S 1 + 1 0.9059000 1.0000000 +S 1 + 1 0.1285000 1.0000000 +S 1 + 1 0.0440200 1.0000000 +P 3 + 1 18.7100000 0.0140310 + 2 4.1330000 0.0868660 + 3 1.2000000 0.2902160 +P 1 + 1 0.3827000 1.0000000 +P 1 + 1 0.1209000 1.0000000 +P 1 + 1 0.0356900 1.0000000 +D 1 + 1 1.0970000 1.0000000 +D 1 + 1 0.3180000 1.0000000 +D 1 + 1 0.1000000 1.0000000 +F 1 + 1 0.7610000 1.0000000 +F 1 + 1 0.2680000 1.0000000 +3 14 +S 8 + 1 15330.0000000 0.0005080 + 2 2299.0000000 0.0039290 + 3 522.4000000 0.0202430 + 4 147.3000000 0.0791810 + 5 47.5500000 0.2306870 + 6 16.7600000 0.4331180 + 7 6.2070000 0.3502600 + 8 0.6882000 -0.0081540 +S 8 + 1 15330.0000000 -0.0001150 + 2 2299.0000000 -0.0008950 + 3 522.4000000 -0.0046360 + 4 147.3000000 -0.0187240 + 5 47.5500000 -0.0584630 + 6 16.7600000 -0.1364630 + 7 6.2070000 -0.1757400 + 8 0.6882000 0.6034180 +S 1 + 1 1.7520000 1.0000000 +S 1 + 1 0.2384000 1.0000000 +S 1 + 1 0.0737600 1.0000000 +P 3 + 1 34.4600000 0.0159280 + 2 7.7490000 0.0997400 + 3 2.2800000 0.3104920 +P 1 + 1 0.7156000 1.0000000 +P 1 + 1 0.2140000 1.0000000 +P 1 + 1 0.0597400 1.0000000 +D 1 + 1 2.3140000 1.0000000 +D 1 + 1 0.6450000 1.0000000 +D 1 + 1 0.2140000 1.0000000 +F 1 + 1 1.4280000 1.0000000 +F 1 + 1 0.5000000 1.0000000 + diff --git a/examples/molecule.BH2 b/examples/molecule.BH2 new file mode 100644 index 0000000..28c7bbc --- /dev/null +++ b/examples/molecule.BH2 @@ -0,0 +1,6 @@ +# nAt nEla nElb nCore nRyd + 3 4 3 0 0 +# Znuc x y z +B 0.00000000 0.00000000 0.14984923 +H 0.00000000 2.01119016 -0.81846345 +H 0.00000000 -2.01119016 -0.81846345 diff --git a/examples/molecule.BeF b/examples/molecule.BeF new file mode 100644 index 0000000..00a2c17 --- /dev/null +++ b/examples/molecule.BeF @@ -0,0 +1,5 @@ +# nAt nEla nElb nCore nRyd + 2 7 6 0 0 +# Znuc x y z +Be 0.00000000 0.00000000 -1.77936990 +F 0.00000000 0.00000000 0.79083149 diff --git a/examples/molecule.BeH b/examples/molecule.BeH new file mode 100644 index 0000000..1fabf3c --- /dev/null +++ b/examples/molecule.BeH @@ -0,0 +1,5 @@ +# nAt nEla nElb nCore nRyd + 2 3 2 0 0 +# Znuc x y z +Be 0.00000000 0.00000000 0.25103976 +H 0.00000000 0.00000000 -2.24485003 diff --git a/examples/molecule.C2H3 b/examples/molecule.C2H3 new file mode 100644 index 0000000..a7e4add --- /dev/null +++ b/examples/molecule.C2H3 @@ -0,0 +1,8 @@ +# nAt nEla nElb nCore nRyd + 5 8 7 0 0 +# Znuc x y z +C 0.00000000 1.16769663 -0.04303146 +C 0.00000000 -1.29945364 0.15810072 +H 0.00000000 2.38429609 1.59801822 +H 0.00000000 2.08759130 -1.87998309 +H 0.00000000 -2.90307925 -1.08814513 diff --git a/examples/molecule.C3H5 b/examples/molecule.C3H5 new file mode 100644 index 0000000..6f647cd --- /dev/null +++ b/examples/molecule.C3H5 @@ -0,0 +1,11 @@ +# nAt nEla nElb nCore nRyd + 8 12 11 0 0 +# Znuc x y z +C 0.00000000 0.00000000 0.83050732 +C 0.00000000 2.30981224 -0.38722841 +C 0.00000000 -2.30981224 -0.38722841 +H 0.00000000 0.00000000 2.87547067 +H 0.00000000 4.06036949 0.65560561 +H 0.00000000 -4.06036949 0.65560561 +H 0.00000000 2.41059890 -2.42703281 +H 0.00000000 -2.41059890 -2.42703281 diff --git a/examples/molecule.CH2NO2 b/examples/molecule.CH2NO2 new file mode 100644 index 0000000..25410a4 --- /dev/null +++ b/examples/molecule.CH2NO2 @@ -0,0 +1,9 @@ +# nAt nEla nElb nCore nRyd + 6 16 15 0 0 +# Znuc x y z +C 0.00000000 0.00000000 -2.58417104 +N 0.00000000 0.00000000 0.08692471 +O 0.00000000 -2.06715629 1.15098225 +O 0.00000000 2.06715629 1.15098225 +H 0.00000000 1.81656349 -3.48616378 +H 0.00000000 -1.81656349 -3.48616378 diff --git a/examples/molecule.CH3 b/examples/molecule.CH3 new file mode 100644 index 0000000..74e33ab --- /dev/null +++ b/examples/molecule.CH3 @@ -0,0 +1,7 @@ +# nAt nEla nElb nCore nRyd + 4 5 4 0 0 +# Znuc x y z +C 0.00000000 0.00000000 0.00000000 +H 0.00000000 0.00000000 2.03379507 +H 0.00000000 1.76131924 -1.01689753 +H 0.00000000 -1.76131924 -1.01689753 diff --git a/examples/molecule.CN b/examples/molecule.CN new file mode 100644 index 0000000..ce3c676 --- /dev/null +++ b/examples/molecule.CN @@ -0,0 +1,5 @@ +# nAt nEla nElb nCore nRyd + 2 7 6 0 0 +# Znuc x y z +C 0.00000000 0.00000000 -1.18953886 +N 0.00000000 0.00000000 1.01938091 diff --git a/examples/molecule.CNO b/examples/molecule.CNO new file mode 100644 index 0000000..980ba52 --- /dev/null +++ b/examples/molecule.CNO @@ -0,0 +1,6 @@ +# nAt nEla nElb nCore nRyd + 3 11 10 0 0 +# Znuc x y z +C 0.00000000 0.00000000 -2.50680714 +N 0.00000000 0.00000000 -0.22402176 +O 0.00000000 0.00000000 2.07682752 diff --git a/examples/molecule.CO+ b/examples/molecule.CO+ new file mode 100644 index 0000000..54161a9 --- /dev/null +++ b/examples/molecule.CO+ @@ -0,0 +1,5 @@ +# nAt nEla nElb nCore nRyd + 2 7 6 0 0 +# Znuc x y z +C 0.00000000 0.00000000 -1.20324172 +O 0.00000000 0.00000000 0.90271821 diff --git a/examples/molecule.CON b/examples/molecule.CON new file mode 100644 index 0000000..f0f1c37 --- /dev/null +++ b/examples/molecule.CON @@ -0,0 +1,6 @@ +# nAt nEla nElb nCore nRyd + 3 11 10 0 0 +# Znuc x y z +C 0.00000000 0.00000000 -2.44062558 +O 0.00000000 0.00000000 -0.20455596 +N 0.00000000 0.00000000 2.32515818 diff --git a/examples/molecule.F2BO b/examples/molecule.F2BO new file mode 100644 index 0000000..5b1a618 --- /dev/null +++ b/examples/molecule.F2BO @@ -0,0 +1,7 @@ +# nAt nEla nElb nCore nRyd + 4 16 15 0 0 +# Znuc x y z +O 0.00000000 0.00000000 2.65260017 +B 0.00000000 0.00000000 0.07681654 +F 0.00000000 2.16433924 -1.13888019 +F 0.00000000 -2.16433924 -1.13888019 diff --git a/examples/molecule.F2BS b/examples/molecule.F2BS new file mode 100644 index 0000000..c820968 --- /dev/null +++ b/examples/molecule.F2BS @@ -0,0 +1,7 @@ +# nAt nEla nElb nCore nRyd + 4 20 19 0 0 +# Znuc x y z +S 0.00000000 0.00000000 2.64960984 +B 0.00000000 0.00000000 -0.74406239 +F 0.00000000 2.14169276 -2.01390354 +F 0.00000000 -2.14169276 -2.01390354 diff --git a/examples/molecule.H2BO b/examples/molecule.H2BO new file mode 100644 index 0000000..9d27cfc --- /dev/null +++ b/examples/molecule.H2BO @@ -0,0 +1,7 @@ +# nAt nEla nElb nCore nRyd + 4 8 7 0 0 +# Znuc x y z +O 0.00000000 0.00000000 1.17360276 +B 0.00000000 0.00000000 -1.27133435 +H 0.00000000 1.98370787 -2.36904602 +H 0.00000000 -1.98370787 -2.36904602 diff --git a/examples/molecule.H2PO b/examples/molecule.H2PO new file mode 100644 index 0000000..44981a4 --- /dev/null +++ b/examples/molecule.H2PO @@ -0,0 +1,7 @@ +# nAt nEla nElb nCore nRyd + 4 13 12 0 0 +# Znuc x y z +P 0.00000000 0.87766783 -0.10010856 +O 0.00000000 -1.95912323 0.05701315 +H 2.08101554 2.05955113 1.08591181 +H -2.08101554 2.05955113 1.08591181 diff --git a/examples/molecule.H2PS b/examples/molecule.H2PS new file mode 100644 index 0000000..55430fd --- /dev/null +++ b/examples/molecule.H2PS @@ -0,0 +1,7 @@ +# nAt nEla nElb nCore nRyd + 4 17 16 0 0 +# Znuc x y z +P 0.00000000 1.81994516 -0.10769248 +S 0.00000000 -1.93707861 0.02086846 +H 2.03762554 2.75934101 1.32385757 +H -2.03762554 2.75934101 1.32385757 diff --git a/examples/molecule.HCO b/examples/molecule.HCO new file mode 100644 index 0000000..5bd7b29 --- /dev/null +++ b/examples/molecule.HCO @@ -0,0 +1,6 @@ +# nAt nEla nElb nCore nRyd + 3 8 7 0 0 +# Znuc x y z +H 0.00000000 -2.55038496 1.39798104 +C 0.00000000 -1.17300976 -0.19046167 +O 0.00000000 1.04073447 0.05480615 diff --git a/examples/molecule.HOC b/examples/molecule.HOC new file mode 100644 index 0000000..ed213c5 --- /dev/null +++ b/examples/molecule.HOC @@ -0,0 +1,3 @@ +H 0.00000000 1.82002973 1.50851586 +O 0.00000000 0.96467865 -0.12887834 +C 0.00000000 -1.43868535 0.04508983 diff --git a/examples/molecule.NCO b/examples/molecule.NCO new file mode 100644 index 0000000..e328afb --- /dev/null +++ b/examples/molecule.NCO @@ -0,0 +1,6 @@ +# nAt nEla nElb nCore nRyd + 3 11 10 0 0 +# Znuc x y z +N 0.00000000 0.00000000 -2.39343558 +C 0.00000000 0.00000000 -0.07238136 +O 0.00000000 0.00000000 2.14968523 diff --git a/examples/molecule.NH2 b/examples/molecule.NH2 new file mode 100644 index 0000000..7bfe3af --- /dev/null +++ b/examples/molecule.NH2 @@ -0,0 +1,6 @@ +# nAt nEla nElb nCore nRyd + 3 5 4 0 0 +# Znuc x y z +N 0.00000000 0.00000000 0.15111603 +H 0.00000000 1.51574744 -1.04982949 +H 0.00000000 -1.51574744 -1.04982949 diff --git a/examples/molecule.NO b/examples/molecule.NO new file mode 100644 index 0000000..886dd95 --- /dev/null +++ b/examples/molecule.NO @@ -0,0 +1,5 @@ +# nAt nEla nElb nCore nRyd + 2 8 7 0 0 +# Znuc x y z +N 0.00000000 0.00000000 -1.15775086 +O 0.00000000 0.00000000 1.01357658 diff --git a/examples/molecule.OH b/examples/molecule.OH new file mode 100644 index 0000000..1dc1c66 --- /dev/null +++ b/examples/molecule.OH @@ -0,0 +1,5 @@ +# nAt nEla nElb nCore nRyd + 2 5 4 0 0 +# Znuc x y z +O 0.00000000 0.00000000 -0.10864763 +H 0.00000000 0.00000000 1.72431679 diff --git a/examples/molecule.PH2 b/examples/molecule.PH2 new file mode 100644 index 0000000..fa86d63 --- /dev/null +++ b/examples/molecule.PH2 @@ -0,0 +1,6 @@ +# nAt nEla nElb nCore nRyd + 3 9 8 0 0 +# Znuc x y z +P 0.00000000 0.00000000 0.11427641 +H 0.00000000 1.91899987 -1.75604411 +H 0.00000000 -1.91899987 -1.75604411