import os import sys import olex import olx import olex_core import gui import shutil import time import math import subprocess from olexFunctions import OV from utilities import run_with_bitmap try: from_outside = False p_path = os.path.dirname(os.path.abspath(__file__)) except: from_outside = True p_path = os.path.dirname(os.path.abspath("__file__")) class wfn_Job(object): origin_folder = " " is_copied_back = False date = None input_fn = None log_fn = None fchk_fn = None completed = None full_dir = None exe_fn = None oftware = None def __init__(self, parent, name, _dir, software=None): self.parent = parent self.status = 0 self.name = name full_dir = '.' self.full_dir = full_dir if _dir != '': self.full_dir = _dir full_dir = _dir self.software = software if not os.path.exists(full_dir): return self.date = os.path.getctime(full_dir) self.log_fn = os.path.join(full_dir, name) + ".log" self.fchk_fn = os.path.join(full_dir, name) + ".fchk" self.completed = os.path.exists(self.fchk_fn) try: os.mkdir(self.full_dir) except: pass tries = 0 while not os.path.exists(self.full_dir) and tries < 5: try: os.mkdir(self.full_dir) break except: time.sleep(0.1) tries += 1 pass time.sleep(0.1) self.origin_folder = OV.FilePath() def write_xyz_file(self): coordinates_fn = os.path.join(self.full_dir, self.name) + ".xyz" olx.Kill("$Q") olx.File(coordinates_fn,p=10) def write_input(self, xyz=True, basis=None, method=None, relativistic=None, charge=None, mult=None, strategy=None, conv=None, part=None, damp=None): if self.software == "ORCA": self.write_orca_input(xyz, basis, method, relativistic, charge, mult, strategy, conv, part) elif self.software == "ORCA 5.0" or self.software == "ORCA 6.0": embedding = OV.GetParam('snum.NoSpherA2.ORCA_USE_CRYSTAL_QMMM') if embedding == True: self.write_orca_crystal_input(xyz) else: self.write_orca_input(xyz, basis, method, relativistic, charge, mult, strategy, conv, part) elif self.software == "Gaussian03" or self.software == "Gaussian09" or self.software == "Gaussian16": self.write_gX_input(xyz, basis, method, relativistic, charge, mult, part) elif self.software == "pySCF": self.write_pyscf_script(xyz, basis, method, relativistic, charge, mult, damp, part) elif self.software == "ELMOdb": self.write_elmodb_input(xyz) elif self.software == "Psi4": self.write_psi4_input(xyz) elif self.software == "Thakkar IAM" or self.software == "SALTED": self.write_xyz_file() elif self.software == "xTB": if xyz == True: self.write_xyz_file() elif self.software == "pTB": if xyz == True: self.write_xyz_file() def write_elmodb_input(self,xyz): if xyz: self.write_xyz_file() self.input_fn = os.path.join(self.full_dir, self.name) + ".inp" inp = open(self.input_fn,"w") basis_name = OV.GetParam('snum.NoSpherA2.basis_name') elmodb_libs = None if sys.platform[:3] == "win": temp = self.parent.elmodb_lib drive = temp[0].lower() folder = temp[2:] elmodb_libs = "/mnt/"+drive+folder.replace('\\' , r'/') else: elmodb_libs = self.parent.elmodb_lib inp.write(" $INPUT_METHOD" + '\n' + " job_title='" + self.name + "'" + '\n' + " iprint_level=0" + '\n') inp.write(" basis_set='" + basis_name + "'" + '\n' + " xyz=.true." + '\n' + " wfx=.true." + '\n') inp.write(" lib_path='" + elmodb_libs + "'" + '\n') inp.write(" bset_path='" + elmodb_libs + "'" + '\n') inp.write(" $END" + '\n') inp.write(" " + '\n') inp.write(" $INPUT_STRUCTURE" + '\n' + " pdb_file='" + self.name + ".pdb'" '\n' + " xyz_file='" + self.name + ".xyz'" + '\n') charge = OV.GetParam('snum.NoSpherA2.charge') if charge != '0': inp.write(" icharge=" + charge + '\n') ssbond = OV.GetParam('snum.NoSpherA2.ELMOdb.ssbond') if ssbond == True: nssbond = OV.GetParam('snum.NoSpherA2.ELMOdb.nssbond') inp.write(" nssbond=" + nssbond + '\n') cycl = OV.GetParam('snum.NoSpherA2.ELMOdb.cycl') if cycl == True: ncycl = OV.GetParam('snum.NoSpherA2.ELMOdb.ncycl') inp.write(" ncycl=" + ncycl + '\n') tail = OV.GetParam('snum.NoSpherA2.ELMOdb.tail') if tail == True: maxtail = OV.GetParam('snum.NoSpherA2.ELMOdb.maxtail') inp.write(" ntail=" + str(maxtail) + '\n') resnames = OV.GetParam('snum.NoSpherA2.ELMOdb.str_resname') resnames = resnames.split(';') nat = OV.GetParam('snum.NoSpherA2.ELMOdb.str_nat') nat = nat.split(';') nfrag = OV.GetParam('snum.NoSpherA2.ELMOdb.str_nfrag') nfrag = nfrag.split(';') ncltd = OV.GetParam('snum.NoSpherA2.ELMOdb.str_ncltd') ncltd = ncltd.split(';') specac = OV.GetParam('snum.NoSpherA2.ELMOdb.str_specac') specac = specac.split(';') exbsinp = OV.GetParam('snum.NoSpherA2.ELMOdb.str_exbsinp') exbsinp = exbsinp.split(';') fraginp = OV.GetParam('snum.NoSpherA2.ELMOdb.str_fraginp') fraginp = fraginp.split(';') if int(max(nfrag)) > 50: inp.write(" max_frtail=" + str(max(nfrag)) + '\n') if int(max(nat)) > 50: inp.write(" max_atail=" + str(max(nat)) + '\n') spect = OV.GetParam('snum.NoSpherA2.ELMOdb.spect') nspect = OV.GetParam('snum.NoSpherA2.ELMOdb.nspect') if spect == True: inp.write(" nspec=" + str(nspect) + '\n') inp.write(" $END" + '\n') inp.write(" " + '\n') if tail == True: # use default values if lists are too short if len(resnames) < maxtail: diff = maxtail - len(resnames) for i in range(diff): resnames.append('???') if len(nat) < maxtail: diff = maxtail - len(nat) for i in range(diff): nat.append('0') if len(nfrag) < maxtail: diff = maxtail - len(nfrag) for i in range(diff): nfrag.append('1') if len(ncltd) < maxtail: diff = maxtail - len(ncltd) for i in range(diff): ncltd.append(False) if len(specac) < maxtail: diff = maxtail - len(specac) for i in range(diff): specac.append(False) if len(exbsinp) < maxtail: diff = maxtail - len(exbsinp) for i in range(diff): exbsinp.append('') if len(fraginp) < maxtail: diff = maxtail - len(fraginp) for i in range(diff): fraginp.append('0') for i in range(0,maxtail): control = "" control = control + str(resnames[i]) + ' ' + str(nat[i]) + ' ' + str(nfrag[i]) + ' ' if specac[i] == "True": control += ".t. " else: control += ".f. " if ncltd[i] == "True": control += ".t. " else: control += ".f. " inp.write(' ' + control + '\n' + ' ' + '\n' ) if nat[i] != "0": inp.write( str(exbsinp[i]) + ' ' + '\n') inp.write(" " + '\n' + str(fraginp[i])+ '\n' + ' ' + '\n') if spect == True: inp.write(" " + '\n' + OV.GetParam('snum.NoSpherA2.ELMOdb.specinp') + '\n' + ' ' + '\n') if basis_name == "extrabasis": if os.path.exists(os.path.join(self.origin_folder,"extrabasis")): shutil.copy(os.path.join(self.origin_folder,"extrabasis"),os.path.join(self.full_dir,"extrabasis")) else: OV.SetVar('NoSpherA2-Error',"ELMOdb") raise NameError('No extrabasis file available!') if ssbond == True: inp.write(" " + '\n' + OV.GetParam('snum.NoSpherA2.ELMOdb.ssbondinp') + '\n' + ' ' + '\n') if cycl == True: inp.write(" " + '\n' + OV.GetParam('snum.NoSpherA2.ELMOdb.cyclinp') + '\n' + ' ' + '\n') inp.close() def write_gX_input(self,xyz,basis_name=None,method=None,relativistic=None,charge=None,mult=None,part=None): coordinates_fn = os.path.join(self.full_dir, self.name) + ".xyz" if xyz: self.write_xyz_file() xyz = open(coordinates_fn,"r") self.input_fn = os.path.join(self.full_dir, self.name) + ".com" com = open(self.input_fn,"w") if basis_name == None: basis_name = OV.GetParam("snum.NoSpherA2.basis_name") basis_set_fn = os.path.join(self.parent.basis_dir,OV.GetParam("snum.NoSpherA2.basis_name")) basis = open(basis_set_fn,"r") chk_destination = "%chk=./" + self.name + ".chk" if OV.GetParam('snum.NoSpherA2.ncpus') != '1': cpu = "%nproc=" + OV.GetParam('snum.NoSpherA2.ncpus') else: cpu = "%nproc=1" mem = "%mem=" + OV.GetParam('snum.NoSpherA2.mem') + "GB" control = "# " if method == None: method = OV.GetParam('snum.NoSpherA2.method') if method == "HF": control += "rhf" method = "RHF" else: if method == "PBE": control += "PBEPBE" else: control += method control += "/gen NoSymm 6D 10F IOp(3/32=2) formcheck output=wfx" if method == "BP86" or method == "PBE": control += " DensityFit " if relativistic == None: relativistic = OV.GetParam('snum.NoSpherA2.Relativistic') if relativistic == True: control = control + " Integral=DKH2" Full_HAR = OV.GetParam('snum.NoSpherA2.full_HAR') run = None if Full_HAR == True: run = OV.GetVar('Run_number') if run > 1: control += " Guess=Read" com.write(chk_destination + '\n') com.write(cpu + '\n') com.write(mem + '\n') com.write(control + '\n') com.write(" \n") title = "Wavefunction calculation for " + self.name + " on a level of theory of " + method + "/" + basis_name com.write(title + '\n') com.write(" " + '\n') if charge == None: charge = OV.GetParam('snum.NoSpherA2.charge') if mult == None: mult = OV.GetParam('snum.NoSpherA2.multiplicity') com.write(charge + " " + mult + '\n') atom_list = [] i = 0 for line in xyz: i = i+1 if i > 2: atom = line.split() if atom[0] == "D": atom[0] = "H" line = line.replace("D", "H") if atom[0] == "T": atom[0] = "H" line = line.replace("T", "H") com.write(line) if not atom[0] in atom_list: atom_list.append(atom[0]) xyz.close() com.write(" \n") for i in range(0, len(atom_list)): atom_type = atom_list[i] + " 0\n" com.write(atom_type) temp_atom = atom_list[i] + ":" + basis_name basis.seek(0,0) while True: line = basis.readline() if not line: raise RecursionError("Atom not found in the basis set!") if line[0] == "!": continue if "keys=" in line: key_line = line.split(" ") type = key_line[key_line.index("keys=")+2] if temp_atom in line: break line_run = basis.readline() if "{" in line_run: line_run = basis.readline() while (not "}" in line_run): shell_line = line_run.split() if type == "turbomole=": n_primitives = shell_line[0] shell_type = shell_line[1] elif type == "gamess-us=": n_primitives = shell_line[1] shell_type = shell_line[0] shell_gaussian = " " + shell_type.upper() + " " + n_primitives + " 1.0\n" com.write(shell_gaussian) for n in range(0,int(n_primitives)): if type == "turbomole=": com.write(basis.readline()) else: temp_line = basis.readline() temp = temp_line.split() com.write(temp[1] + " " + temp[2] + '\n') line_run = basis.readline() com.write("****\n") basis.close() com.write(" \n./%s.wfx\n\n" %self.name) com.close() def write_grids_4(self, method, grid): res = "" if method == "M062X": if grid == "Normal": res += "Grid6 " elif grid == "Low": res += "Grid5 " elif grid == "High": res += "Grid7 " elif grid == "Max": res += "Grid7 " else: if grid == "Low": res += "Grid1 " elif grid == "High": res += "Grid4 " elif grid == "Max": res += "Grid7 " if method == "BP86" or method == "PBE" or method == "PWLDA": return res else: if grid == "Normal": res += " NoFinalGridX " elif grid == "Low": res += " GridX2 NoFinalGridX " elif grid == "High": res += " GridX5 NoFinalGridX " elif grid == "Max": res += " GridX9 NoFinalGridX " return res def write_grids_5(self, method, grid): res = "" if method == "M062X": if grid == "Normal": res += "DefGrid3 " elif grid == "Low": res += "DefGrid2 " elif grid == "High": res += "DefGrid3 " elif grid == "Max": res += "DefGrid3 " else: if grid == "Low": res += "DefGrid1 " elif grid == "High": res += "DefGrid2 " elif grid == "Max": res += "DefGrid3 " if method == "BP86" or method == "PBE" or method == "PWLDA": return res else: res += " NoFinalGridX " return res def write_orca_crystal_input(self,xyz): known_charges = { "Ca": 2.0, "F": -1.0, "Na": 1.0, "Cl": -1.0, "Mg": 2.0, "Br": -1.0, "K": 1.0, "Li": 1.0, "Be": 2.0, "O": -2.0 } coordinates_fn1 = os.path.join(self.full_dir, "asu") + ".xyz" charge = OV.GetParam('snum.NoSpherA2.charge') mult = OV.GetParam('snum.NoSpherA2.multiplicity') olx.Kill("$Q") if xyz: olx.File(coordinates_fn1, p=10) xyz1 = open(coordinates_fn1, "r") coordinates_fn2 = os.path.join(self.full_dir, self.name) + ".xyz" radius = OV.GetParam("snum.NoSpherA2.ORCA_CRYSTAL_QMMM_RADIUS") olex.m("XYZCluster_4NoSpherA2 %s"%radius) shutil.move(self.name + ".xyz", os.path.join(self.full_dir, self.name) + ".xyz") xyz2 = open(coordinates_fn2,"r") self.input_fn = os.path.join(self.full_dir, self.name) + ".inp" inp = open(self.input_fn,"w") basis_name = OV.GetParam('snum.NoSpherA2.basis_name') ncpus = OV.GetParam('snum.NoSpherA2.ncpus') if OV.GetParam('snum.NoSpherA2.ncpus') != '1': cpu = "nprocs " + ncpus else: cpu = "nprocs 1" mem = OV.GetParam('snum.NoSpherA2.mem') mem_value = float(mem) * 1024 / int(ncpus) mem = "%maxcore " + str(mem_value) qmmmtype = OV.GetParam("snum.NoSpherA2.ORCA_CRYSTAL_QMMM_TYPE") control = "! NoPop MiniPrint 3-21G " ECP = False if "ECP" in basis_name: ECP = True if ECP == False: control += " 3-21G " else: control += basis_name.replace("ECP-", "") + ' ' if qmmmtype == "Mol": control += "MOL-CRYSTAL-QMMM " else: control += "IONIC-CRYSTAL-QMMM " method = OV.GetParam('snum.NoSpherA2.method') grid = OV.GetParam('snum.NoSpherA2.becke_accuracy') mp2_block = "" if method == "HF": control += "rhf " grids = "" else: if mult != 1 and OV.GetParam("snum.NoSpherA2.ORCA_FORCE_ROKS") == True: control += " ROKS " SCNL = OV.GetParam('snum.NoSpherA2.ORCA_SCNL') if SCNL == True: if method != "wB97X": control += method + ' SCNL ' else: control += method + '-V SCNL ' else: if method == "DSD-BLYP": control += method + ' D3BJ def2-TZVPP/C ' mp2_block += "%mp2 Density relaxed RI true end" else: control += method + ' ' software = OV.GetParam("snum.NoSpherA2.source") if software == "ORCA 5.0" or software == "ORCA 6.0": grids = self.write_grids_5(method, grid) else: print("MOL-CRYSTAL-QMMM only works from ORCA 5.0 upwards") convergence = OV.GetParam('snum.NoSpherA2.ORCA_SCF_Conv') if convergence == "NoSpherA2SCF": conv = " LooseSCF" else: conv = convergence control += grids + ' ' + conv + ' ' + OV.GetParam('snum.NoSpherA2.ORCA_SCF_Strategy') relativistic = OV.GetParam('snum.NoSpherA2.Relativistic') if relativistic == True: control += " DKH2 SARC/J RIJCOSX" else: control += " def2/J RIJCOSX" Solvation = OV.GetParam('snum.NoSpherA2.ORCA_Solvation') if Solvation != "Vacuum" and Solvation != None: control += " CPCM("+Solvation+") " inp.write(control + '\n' + "%pal\n" + cpu + '\n' + "end\n" + mem + '\n' + "%coords\n CTyp xyz\n charge " + charge + "\n mult " + mult + "\n units angs\n coords\n") atom_list = [] i = 0 for line in xyz2: i = i+1 if i > 2: atom = line.split() if atom[0] == "D": atom[0] = "H" line = line.replace("D", "H") if atom[0] == "T": atom[0] = "H" line = line.replace("T", "H") inp.write(line) if not atom[0] in atom_list: atom_list.append(atom[0]) inp.write(" end\nend\n") if mp2_block != "": inp.write(mp2_block+"\n") el_list = atom_list if ECP == False: basis_set_fn = os.path.join(self.parent.basis_dir,basis_name) basis = open(basis_set_fn,"r") inp.write("%basis\n") for i in range(0,len(atom_list)): atom_type = "newgto " +atom_list[i] + '\n' inp.write(atom_type) temp_atom = atom_list[i] + ":" + basis_name basis.seek(0,0) while True: line = basis.readline() if not line: raise RecursionError("Atom not found in the basis set!") if line == '': continue if line[0] == "!": continue if "keys=" in line: key_line = line.split(" ") type = key_line[key_line.index("keys=")+2] if temp_atom in line: break line_run = basis.readline() if "{" in line_run: line_run = basis.readline() while (not "}" in line_run): shell_line = line_run.split() if type == "turbomole=": n_primitives = shell_line[0] shell_type = shell_line[1] elif type == "gamess-us=": n_primitives = shell_line[1] shell_type = shell_line[0] shell_gaussian = " " + shell_type.upper() + " " + n_primitives + "\n" inp.write(shell_gaussian) for n in range(0,int(n_primitives)): if type == "turbomole=": inp.write(" " + str(n+1) + " " + basis.readline().replace("D","E")) else: inp.write(basis.readline().replace("D","E")) line_run = basis.readline() inp.write("end\n") basis.close() inp.write("end\n") conv = OV.GetParam('snum.NoSpherA2.ORCA_CRYSTAL_QMMM_CONV') hflayer = OV.GetParam('snum.NoSpherA2.ORCA_CRYSTAL_QMMM_HF_LAYERS') ecplayer = OV.GetParam('snum.NoSpherA2.ORCA_CRYSTAL_QMMM_ECP_LAYERS') inp.write("%qmmm\n") asu_lines = xyz1.readlines() natoms = int(asu_lines[0]) xyz2.seek(0) all_lines = xyz2.readlines() atom_list = [] i = 0 for line in asu_lines: i += 1 if i < 3: continue j = 0 for line2 in all_lines: j += 1 if j < 3: continue if line == line2: atom_list.append(j-3) break if len(atom_list) != natoms: print("Did not find all atoms in the big XYZ-file! Make sure the ASU is in included when running 'pack %f -c'"%radius) return inp.write(" NUnitCellAtoms %d\n"%natoms) qm_atoms = "" for atom in atom_list: qm_atoms += " %d"%atom inp.write(" QMAtoms {%s } end"%qm_atoms) params_filename = self.name + ".ORCAFF.prms" if qmmmtype == "Ion": inp.write(""" Conv_Charges true Conv_Charges_MaxNCycles 30 Conv_Charges_ConvThresh %f ECPLayers %d HFLayers %d HFLayerGTO "3-21G" Charge_Total 0 EnforceTotalCharge true OuterPCLayers 1 ORCAFFFilename "%s" end"""%(float(conv),ecplayer,hflayer,params_filename)) else: inp.write(" Conv_Charges_MaxNCycles 30\n Conv_Charge_UseQMCoreOnly true\n Conv_Charges_ConvThresh %f\n HFLayers %d\nend" % (float(conv), hflayer)) inp.close() if qmmmtype == "Ion": import subprocess mm_prep_args = [] mm_prep_args.append(os.path.join(os.path.dirname(self.parent.orca_exe), "orca_mm")) if sys.platform[:3] == 'win': mm_prep_args[0] += ".exe" mm_prep_args.append("-makeff") mm_prep_args.append(self.name+".xyz") for t in el_list: mm_prep_args.append("-CEL") mm_prep_args.append(t) if t in known_charges: mm_prep_args.append(str(known_charges[t])) else: mm_prep_args.append("0.0") if sys.platform[:3] == 'win': startinfo = subprocess.STARTUPINFO() startinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW startinfo.wShowWindow = 7 m = subprocess.Popen(mm_prep_args, cwd=self.full_dir, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, stdin=subprocess.PIPE, startupinfo=startinfo) else: m = subprocess.Popen(mm_prep_args, cwd=self.full_dir, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, stdin=subprocess.PIPE) while m.poll() is None: time.sleep(1) n = os.path.join(self.full_dir, self.name) if not os.path.exists(os.path.join(self.full_dir,params_filename)): OV.SetVar('NoSpherA2-Error', "NoORCAMMFile") raise NameError("No MM File for ORCA file generated!") def write_orca_input(self,xyz,basis_name=None,method=None,relativistic=None,charge=None,mult=None,strategy=None,convergence=None,part=None, efield=None): coordinates_fn = os.path.join(self.full_dir, self.name) + ".xyz" software = OV.GetParam("snum.NoSpherA2.source") ECP = False if basis_name == None: basis_name = OV.GetParam('snum.NoSpherA2.basis_name') if "ECP" in basis_name: ECP = True if xyz: self.write_xyz_file() xyz = open(coordinates_fn,"r") self.input_fn = os.path.join(self.full_dir, self.name) + ".inp" inp = open(self.input_fn,"w") if method == None: method = OV.GetParam('snum.NoSpherA2.method') ncpus = OV.GetParam('snum.NoSpherA2.ncpus') if OV.GetParam('snum.NoSpherA2.ncpus') != '1': cpu = "nprocs " + ncpus else: cpu = "nprocs 1" mem = OV.GetParam('snum.NoSpherA2.mem') mem_value = float(mem) * 1024 / int(ncpus) mem = "%maxcore " + str(mem_value) control = "! NoPop MiniPrint " if ECP == False: control += "3-21G " else: control += basis_name.replace("ECP-", "") + ' ' grid = OV.GetParam('snum.NoSpherA2.becke_accuracy') mp2_block = "" if method == "HF": if mult != 1 and OV.GetParam("snum.NoSpherA2.ORCA_FORCE_ROKS") == True: control += " ROHF " else: control += " rhf " grids = "" else: if mult != 1 and OV.GetParam("snum.NoSpherA2.ORCA_FORCE_ROKS") == True: control += " ROKS " if software == "Hybrid": software = OV.GetParam("snum.NoSpherA2.Hybrid.software_Part%d"%part) elif software == "fragHAR": software = "ORCA 5.0" if software == "ORCA 5.0" or software == "ORCA 6.0": SCNL = OV.GetParam('snum.NoSpherA2.ORCA_SCNL') if SCNL == True: if method != "wB97X": control += method + ' SCNL ' else: control += method + '-V SCNL ' else: if method == "DSD-BLYP": control += method + ' D3BJ def2-TZVPP/C ' mp2_block += "%mp2 Density relaxed RI true end" else: control += method + ' ' grids = self.write_grids_5(method, grid) else: control += method + ' ' grids = self.write_grids_4(method, grid) if convergence == None: convergence = OV.GetParam('snum.NoSpherA2.ORCA_SCF_Conv') if convergence == "NoSpherA2SCF": conv = "LooseSCF" else: conv = convergence if strategy == None: strategy = OV.GetParam('snum.NoSpherA2.ORCA_SCF_Strategy') control += grids + conv + ' ' + strategy if relativistic == None: relativistic = OV.GetParam('snum.NoSpherA2.Relativistic') if method == "BP86" or method == "PBE" or method == "PWLDA": if relativistic == True: t = OV.GetParam('snum.NoSpherA2.ORCA_Relativistic') if t == "DKH2": control += " DKH2 SARC/J RI" elif t == "ZORA": control += " ZORA SARC/J RI" elif t == "ZORA/RI": control += " ZORA/RI SARC/J RI" elif t == "IORA": control += " IORA SARC/J RI" else: control += " IORA/RI SARC/J RI" else: control += " def2/J RI" else: if relativistic == True: t = OV.GetParam('snum.NoSpherA2.ORCA_Relativistic') if t == "DKH2": control += " DKH2 SARC/J RIJCOSX" elif t == "ZORA": control += " ZORA SARC/J RIJCOSX" elif t == "IORA": control += " IORA SARC/J RIJCOSX" elif t == "ZORA/RI": control += " ZORA/RI SARC/J RIJCOSX" elif t == "IORA/RI": control += " IORA/RI SARC/J RIJCOSX" else: print("============= Relativity kind not known! Will use ZORA! =================") control += " ZORA SARC/J RIJCOSX" else: control += " def2/J RIJCOSX" Solvation = OV.GetParam('snum.NoSpherA2.ORCA_Solvation') if Solvation != "Vacuum" and Solvation != None: control += " CPCM(" + Solvation + ") " GBW_file = OV.GetParam("snum.NoSpherA2.ORCA_USE_GBW") if "5.0" not in OV.GetParam("snum.NoSpherA2.source") and "6.0" not in OV.GetParam("snum.NoSpherA2.source"): GBW_file = False if GBW_file == False: control += " AIM " if charge == None: charge = OV.GetParam('snum.NoSpherA2.charge') if mult == None: mult = OV.GetParam('snum.NoSpherA2.multiplicity') if mult == 0: mult = 1 if "5.0" in software or "6.0" in software: inp.write(control + ' NOTRAH\n%pal\n' + cpu + '\nend\n' + mem + '\n%coords\n CTyp xyz\n charge ' + charge + "\n mult " + mult + "\n units angs\n coords\n") else: inp.write(control + '\n%pal\n' + cpu + '\nend\n' + mem + '\n%coords\n CTyp xyz\n charge ' + charge + "\n mult " + mult + "\n units angs\n coords\n") atom_list = [] i = 0 for line in xyz: i = i+1 if i > 2: atom = line.split() if atom[0] == "D": atom[0] = "H" line = line.replace("D", "H") if atom[0] == "T": atom[0] = "H" line = line.replace("T", "H") inp.write(line) if not atom[0] in atom_list: atom_list.append(atom[0]) xyz.close() inp.write(" end\nend\n") if mp2_block != "": inp.write(mp2_block+'\n') if ECP == False: basis_set_fn = os.path.join(self.parent.basis_dir, basis_name) basis = open(basis_set_fn,"r") inp.write("%basis\n") for i in range(0, len(atom_list)): atom_type = "newgto " + atom_list[i] + '\n' inp.write(atom_type) temp_atom = atom_list[i] + ":" + basis_name basis.seek(0, 0) while True: line = basis.readline() if not line: raise RecursionError("Atom not found in the basis set!") if line == '': continue if line[0] == "!": continue if "keys=" in line: key_line = line.split(" ") type = key_line[key_line.index("keys=") + 2] if temp_atom in line: break line_run = basis.readline() if "{" in line_run: line_run = basis.readline() while (not "}" in line_run): shell_line = line_run.split() if type == "turbomole=": n_primitives = shell_line[0] shell_type = shell_line[1] elif type == "gamess-us=": n_primitives = shell_line[1] shell_type = shell_line[0] shell_gaussian = " " + shell_type.upper() + " " + n_primitives + "\n" inp.write(shell_gaussian) for n in range(0, int(n_primitives)): if type == "turbomole=": inp.write(" " + str(n + 1) + " " + basis.readline().replace("D", "E")) else: inp.write(basis.readline().replace("D", "E")) line_run = basis.readline() inp.write("end\n") basis.close() inp.write("end\n") Full_HAR = OV.GetParam('snum.NoSpherA2.full_HAR') run = None damping = OV.GetParam('snum.NoSpherA2.ORCA_DAMP') scf_block = "" if damping: scf_block += " CNVZerner true\n" if strategy == "SlowConv": scf_block += " DampMax 0.9\n" elif strategy == "VerySlowConv": scf_block += " DampMax 0.975\n" elif strategy == "NormalConv": scf_block += " DampMax 0.8\n" elif strategy == "EasyConv": scf_block += " DampMax 0.72\n" if not efield == None: amp = float(efield[1:]) direction = efield[0] if direction == "x": scf_block += f" EField {amp}, 0.0, 0.0" elif direction == "y": scf_block += f" EField 0.0, {amp}, 0.0" elif direction == "z": scf_block += f" EField 0.0, 0.0, {amp}" if direction != "0": scf_block += f" Guess MORead\n MOInp \"zero.gbw\"\n" if Full_HAR == True: run = OV.GetVar('Run_number') source = OV.GetParam('snum.NoSpherA2.source') if source == "Hybrid": run = 0 if run > 1: if os.path.exists(os.path.join(self.full_dir, self.name + "2.gbw")): scf_block += f" Guess MORead\n MOInp \"{self.name}2.gbw\"" if convergence == "NoSpherA2SCF": scf_block += "\n TolE 3E-5\n TolErr 1E-4\n Thresh 1E-9\n TolG 3E-4\n TolX 3E-4" elif convergence == "NoSpherA2SCF": scf_block += " TolE 3E-5\n TolErr 1E-4\n Thresh 1E-9\n TolG 3E-4\n TolX 3E-4" else: if convergence == "NoSpherA2SCF": scf_block += " TolE 3E-5\n TolErr 1E-4\n Thresh 1E-9\n TolG 3E-4\n TolX 3E-4" else: if convergence == "NoSpherA2SCF": scf_block += " TolE 3E-5\n TolErr 1E-4\n Thresh 1E-9\n TolG 3E-4\n TolX 3E-4" if scf_block != "": inp.write(f"%scf\n{scf_block}\nend\n") inp.close() def write_psi4_input(self,xyz): if xyz: self.write_xyz_file() coordinates_fn = os.path.join(self.full_dir, self.name) + ".xyz" pbc = OV.GetParam('snum.NoSpherA2.pySCF_PBC') if pbc == True: olex.m("pack cell") if xyz: self.write_xyz_file() xyz = open(coordinates_fn,"r") self.input_fn = os.path.join(self.full_dir, self.name) + ".py" inp = open(self.input_fn,"w") if basis_name == None: basis_name = OV.GetParam('snum.NoSpherA2.basis_name') basis_set_fn = os.path.join(self.parent.basis_dir,basis_name) basis = open(basis_set_fn,"r") ncpus = OV.GetParam('snum.NoSpherA2.ncpus') if charge == None: charge = int(OV.GetParam('snum.NoSpherA2.charge')) mem = OV.GetParam('snum.NoSpherA2.mem') mem_value = float(mem) * 1024 if pbc == False: inp.write("#!/usr/bin/env python\n%s\n\nfrom pyscf import gto, scf, dft, lib\n"%fixed_wfn_function) inp.write("lib.num_threads(%s)\nmol = gto.M(\n atom = '''"%ncpus) atom_list = [] i = 0 for line in xyz: i = i+1 if i > 2: atom = line.split() inp.write(line) if not atom[0] in atom_list: atom_list.append(atom[0]) xyz.close() inp.write("''',\n verbose = 4,\n charge = %d,\n spin = %d\n)\nmol.output = '%s_pyscf.log'\n"%(int(charge),int(mult-1),self.name)) inp.write("mol.max_memory = %s\n"%str(mem_value)) inp.write("mol.basis = {") for i in range(0,len(atom_list)): atom_type = "'" +atom_list[i] + "': [" inp.write(atom_type) temp_atom = atom_list[i] + ":" + basis_name basis.seek(0,0) while True: line = basis.readline() if not line: raise RecursionError("Atom not found in the basis set!") if line[0] == "!": continue if "keys=" in line: key_line = line.split(" ") type = key_line[key_line.index("keys=")+2] if temp_atom in line: break line_run = basis.readline() if "{" in line_run: line_run = basis.readline() while (not "}" in line_run): shell_line = line_run.split() if type == "turbomole=": n_primitives = shell_line[0] shell_type = shell_line[1] elif type == "gamess-us=": n_primitives = shell_line[1] shell_type = shell_line[0] if shell_type.upper() == "S": momentum = '0' elif shell_type.upper() == "P": momentum = '1' elif shell_type.upper() == "D": momentum = '2' elif shell_type.upper() == "F": momentum = '3' inp.write("[%s,"%momentum) for n in range(0,int(n_primitives)): if type == "turbomole=": number1, number2 = basis.readline().replace("D","E").split() inp.write("\n (" + number1 + ', ' + number2 + "),") else: number1, number2, number3 = basis.readline().replace("D","E").split() inp.write("\n (" + number2 + ', ' + number3 + "),") inp.write("],\n") line_run = basis.readline() inp.write("],\n") basis.close() inp.write("\n}\nmol.build()\n") model_line = None if method == None: method = OV.GetParam('snum.NoSpherA2.method') if method == "HF": if mult == 1: model_line = "scf.RHF(mol)" else: model_line = "scf.UHF(mol)" else: if mult == 1: model_line = "dft.RKS(mol)" else: model_line = "dft.UKS(mol)" if relativistic == None: relativistic = OV.GetParam('snum.NoSpherA2.Relativistic') if relativistic == True: model_line += ".x2c()" #inp.write("mf = sgx.sgx_fit(%s)\n"%model_line) inp.write("mf = %s\n"%model_line) if method == "B3LYP": #inp.write("mf.xc = 'b3lyp'\nmf.with_df.dfj = True\n") inp.write("mf.xc = 'b3lyp'\n") elif method == "PBE": inp.write("mf.xc = 'pbe,pbe'\n") elif method == "BLYP": inp.write("mf.xc = 'b88,lyp'\n") elif method == "M062X": inp.write("mf.xc = 'M062X'\n") elif method == "PBE0": inp.write("mf.xc = 'PBE0'\n") elif method == "R2SCAN": inp.write("mf.xc = 'R2SCAN'\n") grid_accuracy = OV.GetParam('snum.NoSpherA2.becke_accuracy') grid = None if grid_accuracy == "Low": grid = 0 elif grid_accuracy == "Normal": grid = 0 elif grid_accuracy == "High": grid = 3 else: grid = 9 rest = "mf = mf.density_fit()\n" if method != "HF": rest += "mf.grids.radi_method = dft.gauss_chebyshev\n" rest += "mf.grids.level = "+str(grid)+"\n" rest += """mf.with_df.auxbasis = 'def2-tzvp-jkfit' mf.diis_space = 19 mf.conv_tol = 0.0033 mf.conv_tol_grad = 1e-2 mf.level_shift = 0.25""" if damp == None: damp = float(OV.GetParam('snum.NoSpherA2.pySCF_Damping')) rest += "\nmf.damp = %f\n"%damp rest += "mf.chkfile = '%s.chk'\n"%self.name Full_HAR = OV.GetParam('snum.NoSpherA2.full_HAR') run = None if Full_HAR == True: run = OV.GetVar('Run_number') if run > 1: rest += "mf.init_guess = 'chk'\n" solv = OV.GetParam('snum.NoSpherA2.ORCA_Solvation') if solv != "Vacuum": rest += "from pyscf import solvent\nmf = mf.ddCOSMO()\nmf.with_solvent.lebedev_order = 11\nmf.with_solvent.lmax = 5\nmf.with_solvent.grids.radi_method = dft.gauss_chebyshev\nmf.with_solvent.grids.level = %d\nmf.with_solvent.eps = %f\n"%(int(grid),float(solv_epsilon[solv])) rest +="""mf.kernel() print("Switching to SOSCF and shutting down damping & levelshift") mf.conv_tol = 1e-9 mf.conv_tol_grad = 1e-5 mf.level_shift = 0.0 mf.damp = 0.0 mf = scf.newton(mf) mf.kernel()""" rest += "\nwith open('%s.wfn', 'w') as f1:\n write_wfn(f1,mol,mf.mo_coeff,mf.mo_energy,mf.mo_occ,mf.e_tot)"%self.name inp.write(rest) inp.close() def write_pyscf_script(self,xyz,basis_name=None,method=None,relativistic=None,charge=None,mult=None,damp=None,part=None): solv_epsilon = { "Water" :78.3553, "Acetonitrile" :35.688 , "Methanol" :32.613 , "Ethanol" :24.852 , "IsoQuinoline" :11.00 , "Quinoline" :9.16 , "Chloroform" :4.7113 , "DiethylEther" :4.2400 , "Dichloromethane" :8.93 , "DiChloroEthane" :10.125 , "CarbonTetraChloride" :2.2280 , "Benzene" :2.2706 , "Toluene" :2.3741 , "ChloroBenzene" :5.6968 , "NitroMethane" :36.562 , "Heptane" :1.9113 , "CycloHexane" :2.0165 , "Aniline" :6.8882 , "Acetone" :20.493 , "TetraHydroFuran" :7.4257 , "DiMethylSulfoxide" :46.826 , "Argon" :1.430 , "Krypton" :1.519 , "Xenon" :1.706 , "n-Octanol" :9.8629 , "1,1,1-TriChloroEthane" :7.0826 , "1,1,2-TriChloroEthane" :7.1937 , "1,2,4-TriMethylBenzene" :2.3653 , "1,2-DiBromoEthane" :4.9313 , "1,2-EthaneDiol" :40.245 , "1,4-Dioxane" :2.2099 , "1-Bromo-2-MethylPropane" :7.7792 , "1-BromoOctane" :5.0244 , "1-BromoPentane" :6.269 , "1-BromoPropane" :8.0496 , "1-Butanol" :17.332 , "1-ChloroHexane" :5.9491 , "1-ChloroPentane" :6.5022 , "1-ChloroPropane" :8.3548 , "1-Decanol" :7.5305 , "1-FluoroOctane" :3.89 , "1-Heptanol" :11.321 , "1-Hexanol" :12.51 , "1-Hexene" :2.0717 , "1-Hexyne" :2.615 , "1-IodoButane" :6.173 , "1-IodoHexaDecane" :3.5338 , "1-IodoPentane" :5.6973 , "1-IodoPropane" :6.9626 , "1-NitroPropane" :23.73 , "1-Nonanol" :8.5991 , "1-Pentanol" :15.13 , "1-Pentene" :1.9905 , "1-Propanol" :20.524 , "2,2,2-TriFluoroEthanol" :26.726 , "2,2,4-TriMethylPentane" :1.9358 , "2,4-DiMethylPentane" :1.8939 , "2,4-DiMethylPyridine" :9.4176 , "2,6-DiMethylPyridine" :7.1735 , "2-BromoPropane" :9.3610 , "2-Butanol" :15.944 , "2-ChloroButane" :8.3930 , "2-Heptanone" :11.658 , "2-Hexanone" :14.136 , "2-MethoxyEthanol" :17.2 , "2-Methyl-1-Propanol" :16.777 , "2-Methyl-2-Propanol" :12.47 , "2-MethylPentane" :1.89 , "2-MethylPyridine" :9.9533 , "2-NitroPropane" :25.654 , "2-Octanone" :9.4678 , "2-Pentanone" :15.200 , "2-Propanol" :19.264 , "2-Propen-1-ol" :19.011 , "3-MethylPyridine" :11.645 , "3-Pentanone" :16.78 , "4-Heptanone" :12.257 , "4-Methyl-2-Pentanone" :12.887 , "4-MethylPyridine" :11.957 , "5-Nonanone" :10.6 , "AceticAcid" :6.2528 , "AcetoPhenone" :17.44 , "a-ChloroToluene" :6.7175 , "Anisole" :4.2247 , "Benzaldehyde" :18.220 , "BenzoNitrile" :25.592 , "BenzylAlcohol" :12.457 , "BromoBenzene" :5.3954 , "BromoEthane" :9.01 , "Bromoform" :4.2488 , "Butanal" :13.45 , "ButanoicAcid" :2.9931 , "Butanone" :18.246 , "ButanoNitrile" :24.291 , "ButylAmine" :4.6178 , "ButylEthanoate" :4.9941 , "CarbonDiSulfide" :2.6105 , "Cis-1,2-DiMethylCycloHexane" :2.06 , "Cis-Decalin" :2.2139 , "CycloHexanone" :15.619 , "CycloPentane" :1.9608 , "CycloPentanol" :16.989 , "CycloPentanone" :13.58 , "Decalin-mixture" :2.196 , "DiBromomEthane" :7.2273 , "DiButylEther" :3.0473 , "DiEthylAmine" :3.5766 , "DiEthylSulfide" :5.723 , "DiIodoMethane" :5.32 , "DiIsoPropylEther" :3.38 , "DiMethylDiSulfide" :9.6 , "DiPhenylEther" :3.73 , "DiPropylAmine" :2.9112 , "e-1,2-DiChloroEthene" :2.14 , "e-2-Pentene" :2.051 , "EthaneThiol" :6.667 , "EthylBenzene" :2.4339 , "EthylEthanoate" :5.9867 , "EthylMethanoate" :8.3310 , "EthylPhenylEther" :4.1797 , "FluoroBenzene" :5.42 , "Formamide" :108.94 , "FormicAcid" :51.1 , "HexanoicAcid" :2.6 , "IodoBenzene" :4.5470 , "IodoEthane" :7.6177 , "IodoMethane" :6.8650 , "IsoPropylBenzene" :2.3712 , "m-Cresol" :12.44 , "Mesitylene" :2.2650 , "MethylBenzoate" :6.7367 , "MethylButanoate" :5.5607 , "MethylCycloHexane" :2.024 , "MethylEthanoate" :6.8615 , "MethylMethanoate" :8.8377 , "MethylPropanoate" :6.0777 , "m-Xylene" :2.3478 , "n-ButylBenzene" :2.36 , "n-Decane" :1.9846 , "n-Dodecane" :2.0060 , "n-Hexadecane" :2.0402 , "n-Hexane" :1.8819 , "NitroBenzene" :34.809 , "NitroEthane" :28.29 , "n-MethylAniline" :5.9600 , "n-MethylFormamide-mixture" :181.56 , "n,n-DiMethylAcetamide" :37.781 , "n,n-DiMethylFormamide" :37.219 , "n-Nonane" :1.9605 , "n-Octane" :1.9406 , "n-Pentadecane" :2.0333 , "n-Pentane" :1.8371 , "n-Undecane" :1.9910 , "o-ChloroToluene" :4.6331 , "o-Cresol" :6.76 , "o-DiChloroBenzene" :9.9949 , "o-NitroToluene" :25.669 , "o-Xylene" :2.5454 , "Pentanal" :10.0 , "PentanoicAcid" :2.6924 , "PentylAmine" :4.2010 , "PentylEthanoate" :4.7297 , "PerFluoroBenzene" :2.029 , "p-IsoPropylToluene" :2.2322 , "Propanal" :18.5 , "PropanoicAcid" :3.44 , "PropanoNitrile" :29.324 , "PropylAmine" :4.9912 , "PropylEthanoate" :5.5205 , "p-Xylene" :2.2705 , "Pyridine" :12.978 , "sec-ButylBenzene" :2.3446 , "tert-ButylBenzene" :2.3447 , "TetraChloroEthene" :2.268 , "TetraHydroThiophene-s,s-dioxide" :43.962 , "Tetralin" :2.771 , "Thiophene" :2.7270 , "Thiophenol" :4.2728 , "trans-Decalin" :2.1781 , "TriButylPhosphate" :8.1781 , "TriChloroEthene" :3.422 , "TriEthylAmine" :2.3832 , "Xylene-mixture" :2.3879 , "z-1,2-DiChloroEthene" :9.2 } if mult == None: mult = int(OV.GetParam('snum.NoSpherA2.multiplicity')) fixed_wfn_function = """ import numpy TYPE_MAP = [ [1], # S [2, 3, 4], # P [5, 8, 9, 6, 10, 7], # D [11,14,15,17,20,18,12,16,19,13], # F [21,24,25,30,33,31,26,34,35,28,22,27,32,29,23], # G [56,55,54,53,52,51,50,49,48,47,46,45,44,43,42,41,40,39,38,37,36], # H ] def write_wfn(fout, mol, mo_coeff, mo_energy, mo_occ, tot_ener): from pyscf.x2c import x2c from pyscf import gto, lib """ if mult != 1: fixed_wfn_function +=""" total_nmo = 0 MO_offset = 0 for s in range(2): for i in range(len(mo_occ[s])): if mo_occ[s][i] != 0: total_nmo += 1 for s in range(2): temp_mol, ctr = x2c._uncontract_mol(mol, True, 0.) temp_mo_coeff = numpy.dot(ctr, mo_coeff[s]) nmo = temp_mo_coeff.shape[1] mo_cart = [] centers = [] types = [] exps = [] p0 = 0 for ib in range(temp_mol.nbas): ia = temp_mol.bas_atom(ib) l = temp_mol.bas_angular(ib) es = temp_mol.bas_exp(ib) c = temp_mol._libcint_ctr_coeff(ib) np, nc = c.shape nd = nc*(2*l+1) mosub = temp_mo_coeff[p0:p0+nd].reshape(-1,nc,nmo) c2s = gto.cart2sph(l) new_mosub = numpy.einsum('yki,cy,pk->pci', mosub, c2s, c) mo_cart.append(new_mosub.transpose(1,0,2).reshape(-1,nmo)) for t in TYPE_MAP[l]: types.append([t]*np) ncart = temp_mol.bas_len_cart(ib) exps.extend([es]*ncart) centers.extend([ia+1]*(np*ncart)) p0 += nd mo_cart = numpy.vstack(mo_cart) centers = numpy.hstack(centers) types = numpy.hstack(types) exps = numpy.hstack(exps) nprim, nmo = mo_cart.shape if s == 0: fout.write('From PySCF\\n') fout.write('GAUSSIAN %14d MOL ORBITALS %6d PRIMITIVES %8d NUCLEI\\n'%(total_nmo, mo_cart.shape[0], mol.natm)) for ia in range(mol.natm): x, y, z = temp_mol.atom_coord(ia) fout.write('%3s%8d (CENTRE%3d) %12.8f%12.8f%12.8f CHARGE = %4.1f\\n'%(mol.atom_pure_symbol(ia), ia+1, ia+1, x, y, z, mol.atom_charge(ia))) for i0, i1 in lib.prange(0, nprim, 20): fout.write('CENTRE ASSIGNMENTS %s\\n'% ''.join('%3d'%x for x in centers[i0:i1])) for i0, i1 in lib.prange(0, nprim, 20): fout.write('TYPE ASSIGNMENTS %s\\n'% ''.join('%3d'%x for x in types[i0:i1])) for i0, i1 in lib.prange(0, nprim, 5): fout.write('EXPONENTS %s\\n'% ' '.join('%13.7E'%x for x in exps[i0:i1])) for k in range(nmo): if mo_occ[s][k] != 0.0: mo = mo_cart[:,k] fout.write('MO %-12d OCC NO = %12.8f ORB. ENERGY = %12.8f\\n'%(k+1+MO_offset, mo_occ[s][k], mo_energy[s][k])) if s == 0: MO_offset += 1 for i0, i1 in lib.prange(0, nprim, 5): fout.write(' %s\\n' % ' '.join('%15.8E'%x for x in mo[i0:i1])) if s == 1: fout.write('END DATA\\n') fout.write(' THE SCF ENERGY =%20.12f THE VIRIAL(-V/T)= 0.00000000\\n'%tot_ener)""" else: fixed_wfn_function +=""" mol, ctr = x2c._uncontract_mol(mol, True, 0.) mo_coeff = numpy.dot(ctr, mo_coeff) nmo = mo_coeff.shape[1] mo_cart = [] centers = [] types = [] exps = [] p0 = 0 for ib in range(mol.nbas): ia = mol.bas_atom(ib) l = mol.bas_angular(ib) es = mol.bas_exp(ib) c = mol._libcint_ctr_coeff(ib) np, nc = c.shape nd = nc*(2*l+1) mosub = mo_coeff[p0:p0+nd].reshape(-1,nc,nmo) c2s = gto.cart2sph(l) mosub = numpy.einsum('yki,cy,pk->pci', mosub, c2s, c) mo_cart.append(mosub.transpose(1,0,2).reshape(-1,nmo)) for t in TYPE_MAP[l]: types.append([t]*np) ncart = mol.bas_len_cart(ib) exps.extend([es]*ncart) centers.extend([ia+1]*(np*ncart)) p0 += nd mo_cart = numpy.vstack(mo_cart) centers = numpy.hstack(centers) types = numpy.hstack(types) exps = numpy.hstack(exps) nprim, nmo = mo_cart.shape fout.write('From PySCF\\n') fout.write('GAUSSIAN %14d MOL ORBITALS %6d PRIMITIVES %8d NUCLEI\\n'%(mo_cart.shape[1], mo_cart.shape[0], mol.natm)) for ia in range(mol.natm): x, y, z = mol.atom_coord(ia) fout.write('%3s%8d (CENTRE%3d) %12.8f%12.8f%12.8f CHARGE = %4.1f\\n'%(mol.atom_pure_symbol(ia), ia+1, ia+1, x, y, z, mol.atom_charge(ia))) for i0, i1 in lib.prange(0, nprim, 20): fout.write('CENTRE ASSIGNMENTS %s\\n'% ''.join('%3d'%x for x in centers[i0:i1])) for i0, i1 in lib.prange(0, nprim, 20): fout.write('TYPE ASSIGNMENTS %s\\n'% ''.join('%3d'%x for x in types[i0:i1])) for i0, i1 in lib.prange(0, nprim, 5): fout.write('EXPONENTS %s\\n'% ' '.join('%13.7E'%x for x in exps[i0:i1])) for k in range(nmo): mo = mo_cart[:,k] fout.write('MO %-12d OCC NO = %12.8f ORB. ENERGY = %12.8f\\n'%(k+1, mo_occ[k], mo_energy[k])) for i0, i1 in lib.prange(0, nprim, 5): fout.write(' %s\\n' % ' '.join('%15.8E'%x for x in mo[i0:i1])) fout.write('END DATA\\n') fout.write(' THE SCF ENERGY =%20.12f THE VIRIAL(-V/T)= 0.00000000\\n'%tot_ener)""" coordinates_fn = os.path.join(self.full_dir, self.name) + ".xyz" pbc = OV.GetParam('snum.NoSpherA2.pySCF_PBC') if pbc == True: olex.m("pack cell") if xyz: self.write_xyz_file() xyz = open(coordinates_fn,"r") self.input_fn = os.path.join(self.full_dir, self.name) + ".py" inp = open(self.input_fn,"w") if basis_name == None: basis_name = OV.GetParam('snum.NoSpherA2.basis_name') basis_set_fn = os.path.join(self.parent.basis_dir,basis_name) basis = open(basis_set_fn,"r") ncpus = OV.GetParam('snum.NoSpherA2.ncpus') if charge == None: charge = int(OV.GetParam('snum.NoSpherA2.charge')) mem = OV.GetParam('snum.NoSpherA2.mem') mem_value = float(mem) * 1024 if pbc == False: inp.write("#!/usr/bin/env python\n%s\n\nfrom pyscf import gto, scf, dft, lib\n"%fixed_wfn_function) inp.write("lib.num_threads(%s)\nmol = gto.M(\n atom = '''"%ncpus) atom_list = [] i = 0 for line in xyz: i = i+1 if i > 2: atom = line.split() inp.write(line) if not atom[0] in atom_list: atom_list.append(atom[0]) xyz.close() inp.write("''',\n verbose = 4,\n charge = %d,\n spin = %d\n)\nmol.output = '%s_pyscf.log'\n"%(int(charge),int(mult-1),self.name)) inp.write("mol.max_memory = %s\n"%str(mem_value)) inp.write("mol.basis = {") for i in range(0,len(atom_list)): atom_type = "'" +atom_list[i] + "': [" inp.write(atom_type) temp_atom = atom_list[i] + ":" + basis_name basis.seek(0,0) while True: line = basis.readline() if not line: raise RecursionError("Atom not found in the basis set!") if line[0] == "!": continue if "keys=" in line: key_line = line.split(" ") type = key_line[key_line.index("keys=")+2] if temp_atom in line: break line_run = basis.readline() if "{" in line_run: line_run = basis.readline() while (not "}" in line_run): shell_line = line_run.split() if type == "turbomole=": n_primitives = shell_line[0] shell_type = shell_line[1] elif type == "gamess-us=": n_primitives = shell_line[1] shell_type = shell_line[0] if shell_type.upper() == "S": momentum = '0' elif shell_type.upper() == "P": momentum = '1' elif shell_type.upper() == "D": momentum = '2' elif shell_type.upper() == "F": momentum = '3' inp.write("[%s,"%momentum) for n in range(0,int(n_primitives)): if type == "turbomole=": number1, number2 = basis.readline().replace("D","E").split() inp.write("\n (" + number1 + ', ' + number2 + "),") else: number1, number2, number3 = basis.readline().replace("D","E").split() inp.write("\n (" + number2 + ', ' + number3 + "),") inp.write("],\n") line_run = basis.readline() inp.write("],\n") basis.close() inp.write("\n}\nmol.build()\n") model_line = None if method == None: method = OV.GetParam('snum.NoSpherA2.method') if method == "HF": if mult == 1: model_line = "scf.RHF(mol)" else: model_line = "scf.UHF(mol)" else: if mult == 1: model_line = "dft.RKS(mol)" else: model_line = "dft.UKS(mol)" if relativistic == None: relativistic = OV.GetParam('snum.NoSpherA2.Relativistic') if relativistic == True: model_line += ".x2c()" #inp.write("mf = sgx.sgx_fit(%s)\n"%model_line) inp.write("mf = %s\n"%model_line) if method == "B3LYP": #inp.write("mf.xc = 'b3lyp'\nmf.with_df.dfj = True\n") inp.write("mf.xc = 'b3lyp'\n") elif method == "PBE": inp.write("mf.xc = 'pbe,pbe'\n") elif method == "BLYP": inp.write("mf.xc = 'b88,lyp'\n") elif method == "M062X": inp.write("mf.xc = 'M062X'\n") elif method == "PBE0": inp.write("mf.xc = 'PBE0'\n") elif method == "R2SCAN": inp.write("mf.xc = 'R2SCAN'\n") grid_accuracy = OV.GetParam('snum.NoSpherA2.becke_accuracy') grid = None if grid_accuracy == "Low": grid = 0 elif grid_accuracy == "Normal": grid = 0 elif grid_accuracy == "High": grid = 3 else: grid = 9 rest = "mf = mf.density_fit()\n" if method != "HF": rest += "mf.grids.radi_method = dft.gauss_chebyshev\n" rest += "mf.grids.level = "+str(grid)+"\n" rest += """mf.with_df.auxbasis = 'def2-tzvp-jkfit' mf.diis_space = 19 mf.conv_tol = 0.0033 mf.conv_tol_grad = 1e-2 mf.level_shift = 0.25""" if damp == None: damp = float(OV.GetParam('snum.NoSpherA2.pySCF_Damping')) rest += "\nmf.damp = %f\n"%damp rest += "mf.chkfile = '%s.chk'\n"%self.name Full_HAR = OV.GetParam('snum.NoSpherA2.full_HAR') run = None if Full_HAR == True: run = OV.GetVar('Run_number') if run > 1: rest += "mf.init_guess = 'chk'\n" solv = OV.GetParam('snum.NoSpherA2.ORCA_Solvation') if solv != "Vacuum": rest += "from pyscf import solvent\nmf = mf.ddCOSMO()\nmf.with_solvent.lebedev_order = 11\nmf.with_solvent.lmax = 5\nmf.with_solvent.grids.radi_method = dft.gauss_chebyshev\nmf.with_solvent.grids.level = %d\nmf.with_solvent.eps = %f\n"%(int(grid),float(solv_epsilon[solv])) rest +="""mf.kernel() print("Switching to SOSCF and shutting down damping & levelshift") mf.conv_tol = 1e-9 mf.conv_tol_grad = 1e-5 mf.level_shift = 0.0 mf.damp = 0.0 mf = scf.newton(mf) mf.kernel()""" rest += "\nwith open('%s.wfn', 'w') as f1:\n write_wfn(f1,mol,mf.mo_coeff,mf.mo_energy,mf.mo_occ,mf.e_tot)"%self.name inp.write(rest) inp.close() else: from cctbx_olex_adapter import OlexCctbxAdapter cctbx_adaptor = OlexCctbxAdapter() uc = cctbx_adaptor.reflections.f_obs.unit_cell() cm = uc.metrical_matrix() from math import sqrt import numpy as np inp.write("#!/usr/bin/env python\n\nfrom pyscf.pbc import gto, scf, dft, df\nfrom pyscf import lib\n") inp.write("lib.num_threads(%s)\ncell = gto.M(\n atom = '''"%ncpus) atom_list = [] i = 0 for line in xyz: i = i+1 if i > 2: atom = line.split() inp.write(line) if not atom[0] in atom_list: atom_list.append(atom[0]) xyz.close() print(cm) inp.write("''',\n verbose = 5,\n)\ncell.output = '%s_pyscf.log'\n"%self.name) inp.write("cell.a = '''%.5f %.5f %.5f\n"%(np.sign(cm[0])*sqrt(abs(cm[0])),np.sign(cm[3])*sqrt(abs(cm[3])),np.sign(cm[4])*sqrt(abs(cm[4])))) inp.write("%.5f %.5f %.5f\n"%(np.sign(cm[3])*sqrt(abs(cm[3])),np.sign(cm[1])*sqrt(abs(cm[1])),np.sign(cm[5])*sqrt(abs(cm[5])))) inp.write("%.5f %.5f %.5f'''\n"%(np.sign(cm[4])*sqrt(abs(cm[4])),np.sign(cm[5])*sqrt(abs(cm[5])),np.sign(cm[2])*sqrt(abs(cm[2])))) inp.write("cell.charge = %s\n"%charge) inp.write("cell.spin = %s\n"%str(int(mult)-1)) inp.write("cell.max_memory = %s\n"%str(mem_value)) inp.write("cell.precision = 1.0e-06\ncell.exp_to_discard = 0.1\n") inp.write("cell.basis = {") for i in range(0,len(atom_list)): atom_type = "'" +atom_list[i] + "': [" inp.write(atom_type) temp_atom = atom_list[i] + ":" + basis_name basis.seek(0,0) while True: line = basis.readline() if line[0] == "!": continue if "keys=" in line: key_line = line.split(" ") type = key_line[key_line.index("keys=")+2] if temp_atom in line: break line_run = basis.readline() if "{" in line_run: line_run = basis.readline() while (not "}" in line_run): shell_line = line_run.split() if type == "turbomole=": n_primitives = shell_line[0] shell_type = shell_line[1] elif type == "gamess-us=": n_primitives = shell_line[1] shell_type = shell_line[0] if shell_type.upper() == "S": momentum = '0' elif shell_type.upper() == "P": momentum = '1' elif shell_type.upper() == "D": momentum = '2' elif shell_type.upper() == "F": momentum = '3' inp.write("[%s,"%momentum) for n in range(0,int(n_primitives)): if type == "turbomole=": number1, number2 = basis.readline().replace("D","E").split() inp.write("\n (" + number1 + ', ' + number2 + "),") else: number1, number2, number3 = basis.readline().replace("D","E").split() inp.write("\n (" + number2 + ', ' + number3 + "),") inp.write("],\n") line_run = basis.readline() inp.write("],\n") basis.close() inp.write("\n}\ncell.build()\nnk=[1,1,1]\nkpts = cell.make_kpts(nk)\n") model_line = None if method == None: method = OV.GetParam('snum.NoSpherA2.method') if method == "HF": if mult == 1: model_line = "scf.KRHF(cell,kpts)" else: model_line = "scf.KUHF(cell,kpts)" else: if mult == 1: model_line = "dft.KRKS(cell,kpts)" else: model_line = "dft.KUKS(cell,kpts)" #inp.write("mf = sgx.sgx_fit(%s)\n"%model_line) inp.write("cf = %s\n"%model_line) if method == "B3LYP": #inp.write("mf.xc = 'b3lyp'\nmf.with_df.dfj = True\n") inp.write("cf.xc = 'b3lyp'\n") elif method == "PBE": inp.write("cf.xc = 'pbe,pbe'\n") elif method == "BLYP": inp.write("cf.xc = 'b88,lyp'\n") elif method == "M062X": inp.write("cf.xc = 'M06X2X,M06X2C'\n") elif method == "PBE0": inp.write("cf.xc = 'PBE0'\n") grid_accuracy = OV.GetParam('snum.NoSpherA2.becke_accuracy') grid = None if grid_accuracy == "Low": grid = 0 elif grid_accuracy == "Normal": grid = 0 elif grid_accuracy == "High": grid = 3 else: grid = 9 #rest = "cf = cf.mix_density_fit()\ncf.grids.radi_method = dft.gauss_chebyshev\ncf.grids.level = "+str(grid)+"\n" rest = "cf = cf.mix_density_fit()\ncf.grids.level = "+str(grid)+"\n" rest += """ cf.with_df.auxbasis = 'def2-universal-jkfit' cf.diis_space = 10 cf.with_df.linear_dep_threshold = 1e-6 cf.with_df.mesh = [21,21,21] cf.conv_tol = 0.0033 cf.conv_tol_grad = 1e-2 cf.level_shift = 0.25 cf.damp = 0.7 cf.kernel() print("Switching to SOSCF and shutting down damping & levelshift") cf.conv_tol = 1e-9 cf.conv_tol_grad = 1e-5 cf.level_shift = 0.0 cf.damp = 0.0 cf = scf.newton(cf) ener = cf.kernel()""" rest += "\nwith open('%s.wfn', 'w') as f1:\n write_wfn(f1,cell,cf.mo_coeff[0],cf.mo_energy[0],cf.mo_occ[0],ener)"%self.name inp.write(rest) #inp.write("cf = cf.mix_density_fit()\ncf.with_df.auxbasis = 'weigend'\ncf.kernel()\nwith open('%s.wfn', 'w') as f1:\n from pyscf.tools import wfn_format\n wfn_format.write_mo(f1,cell,cf.mo_coeff, mo_energy=cf.mo_energy, mo_occ=cf.mo_occ)\n"%self.name) inp.close() @run_with_bitmap('Calculating WFN') def run(self,part=0,software=None,basis_name=None, copy = True): args = [] if basis_name == None: basis_name = OV.GetParam('snum.NoSpherA2.basis_name') if software == None: software = OV.GetParam('snum.NoSpherA2.source') gui.get_default_notification( txt="Calculating Wavefunction for %s using %s..."%(self.name,software), txt_col='black_text') if OV.HasGUI(): olx.html.Update() olx.xf.EndUpdate() olex.m('refresh') python_script = "fchk-launch.py" if software == "ORCA": args.append(self.parent.orca_exe) input_fn = self.name + ".inp" args.append(input_fn) if software == "ORCA 5.0" or software == "fragHAR" or software == "ORCA 6.0": args.append(self.parent.orca_exe) input_fn = self.name + ".inp" args.append(input_fn) elif software == "Gaussian03": args.append(self.parent.g03_exe) input_fn = self.name + ".com" args.append(input_fn) elif software == "Gaussian09": args.append(self.parent.g09_exe) input_fn = self.name + ".com" args.append(input_fn) elif software == "Gaussian16": args.append(self.parent.g16_exe) input_fn = self.name + ".com" args.append(input_fn) elif software == "Psi4": basis_set_fn = os.path.join(OV.BaseDir(),"basis_sets",basis_name) ncpus = OV.GetParam('snum.NoSpherA2.ncpus') mult = OV.GetParam('snum.NoSpherA2.multiplicity') charge = OV.GetParam('snum.NoSpherA2.charge') mem = OV.GetParam('snum.NoSpherA2.mem') method = OV.GetParam('snum.NoSpherA2.method') args.append(basis_name) args.append(basis_set_fn) args.append(ncpus) args.append(mult) args.append(charge) args.append(mem) args.append(method) python_script = "psi4-launch.py" elif software == "pySCF": input_fn = self.name + ".py" if self.parent.ubuntu_exe != None and os.path.exists(self.parent.ubuntu_exe): args.append(self.parent.ubuntu_exe) args.append('run') args.append("python %s"%input_fn) elif self.parent.ubuntu_exe == None: args.append('python') args.append(input_fn) elif software == "ELMOdb": if self.parent.ubuntu_exe != None and os.path.exists(self.parent.ubuntu_exe): args.append(self.parent.ubuntu_exe) args.append('run') temp = self.parent.elmodb_exe drive = temp[0].lower() folder = temp[2:] elmodb_exe = "/mnt/"+drive+folder.replace('\\' , r'/') args.append(elmodb_exe) elif self.parent.ubuntu_exe == None: args.append(self.parent.elmodb_exe) args.append("<") args.append(self.name + ".inp") args.append(">") args.append(self.name + ".out") elif software == "xTB": method = OV.GetParam('snum.NoSpherA2.method') args.append(self.parent.xtb_exe) if method == "GFN0": args.append("--gfn") args.append("0") elif method == "GFN1": args.append("--gfn") args.append("1") elif method == "GFN2": args.append("--gfn") args.append("2") elif method == "GFNFF": args.append("--gfnff") acc = OV.GetParam("snum.NoSpherA2.becke_accuracy") if acc == "Low": args.append("--acc") args.append("30") elif acc == "Normal": args.append("--acc") args.append("1") elif acc == "High": args.append("--acc") args.append("0.2") elif acc == "Max": args.append("--acc") args.append("0.1") temperature = OV.GetParam("snum.NoSpherA2.temperature") args.append("--etemp") args.append(str(temperature)) args.append("--molden") args.append(self.name+".xyz") charge = OV.GetParam("snum.NoSpherA2.charge") args.append("--chrg") args.append(str(charge)) mult = OV.GetParam("snum.NoSpherA2.multiplicity") if mult != 1: args.append("--uhf") args.append(str(int(mult)-1)) elif software == "pTB": method = OV.GetParam('snum.NoSpherA2.method') charge = OV.GetParam("snum.NoSpherA2.charge") mult = OV.GetParam("snum.NoSpherA2.multiplicity") base = os.path.dirname(self.parent.ptb_exe) args.append(self.parent.ptb_exe) args.append(self.name+".xyz") args.append("-stda") args.append("-par") args.append(os.path.join(base, ".atompara")) args.append("-bas") args.append(os.path.join(base, ".basis_vDZP")) args.append("-chrg") args.append(str(charge)) if mult != 1: args.append("-uhf") args.append(str(int(mult)-1)) out_fn = None path = self.full_dir nr = 0 if sys.platform[:3] == 'win': nr = 2 # if part != 0: # path = os.path.join(path,"Part_"+str(part)) if software == "Psi4": out_fn = os.path.join(path, self.name + "_psi4.log") else: if "orca" in args[0]: out_fn = os.path.join(path, self.name + "_orca.log") elif software == "ELMOdb" and "elmo" in args[nr]: out_fn = os.path.join(path, self.name + ".out") elif software == "pySCF" and"python" in args[nr]: out_fn = os.path.join(path, self.name + "_pyscf.log") if "ubuntu" in args[0]: print("Starting Ubuntu for wavefunction calculation, please be patient for start") if out_fn == None: if "ubuntu" in args[0]: out_fn = os.path.join(path, self.name + "_pyscf.log") else: out_fn = os.path.join(path, self.name + ".log") os.environ['fchk_cmd'] = '+&-'.join(args) os.environ['fchk_file'] = self.name os.environ['fchk_dir'] = os.path.join(OV.FilePath(), self.full_dir) os.environ['fchk_out_fn'] = out_fn pidfile = os.path.join(path, "NoSpherA2.pidfile") if os.path.exists(out_fn): print("Moving file to old!") shutil.move(out_fn, out_fn + '_old') if os.path.exists(pidfile): os.remove(pidfile) import subprocess p = None if sys.platform[:3] == 'win': startinfo = subprocess.STARTUPINFO() startinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW startinfo.wShowWindow = 7 pyl = OV.getPYLPath() if not pyl: print("A problem with pyl is encountered, aborting.") return p = subprocess.Popen([pyl, os.path.join(p_path, python_script)], startupinfo=startinfo ) else: pyl = OV.getPYLPath() if not pyl: print("A problem with pyl is encountered, aborting.") return p = subprocess.Popen([pyl, os.path.join(p_path, python_script)]) tries = 0 time.sleep(0.5) while not os.path.exists(out_fn): time.sleep(1) tries += 1 if tries >= 5: if "python" in args[nr] and tries <=10: continue print("Failed to locate the output file at "+str(out_fn)) OV.SetVar('NoSpherA2-Error',"Wfn-Output not found!") raise NameError('Wfn-Output not found!') with open(out_fn, "r") as stdout: while p.poll() is None: x = None try: x = stdout.read() except: pass if x: print(x, end='') if OV.GetVar("stop_current_process"): try: #import signal #pid = None # with open(pidfile, "r") as pf: # line = pf.read() # pid = int(line) #os.kill(pid, signal.SIGABRT) #os.kill(pid, signal.SIGTERM) print("Calculation aborted by INTERRUPT!") except Exception as e: print(e) pass OV.SetVar("stop_current_process", False) else: time.sleep(0.5) print("\nWavefunction calculation ended!") wfnlog = os.path.join(OV.FilePath(), self.name + ".wfnlog") shutil.copy(out_fn, wfnlog, follow_symlinks=False) if software == "ORCA 6.0" or software == "ORCA 5.0": if '****ORCA TERMINATED NORMALLY****' in open(wfnlog).read(): pass else: OV.SetVar('NoSpherA2-Error',"ORCA") with open(wfnlog) as file: lines = file.readlines() for line in lines: if "Error" in line: print(line) raise NameError('Orca did not terminate normally!') elif "Gaussian" in software: if 'Normal termination of Gaussian' in open(wfnlog).read(): pass else: OV.SetVar('NoSpherA2-Error',"Gaussian") raise NameError('Gaussian did not terminate normally!') elif software == "ELMOdb": if 'CONGRATULATIONS: THE ELMO-TRANSFERs ENDED GRACEFULLY!!!' in open(wfnlog).read(): pass else: OV.SetVar('NoSpherA2-Error',"ELMOdb") lines = open(wfnlog).readlines() for line in lines: if "Error" in line: print(line) raise NameError('ELMOdb did not terminate normally!') elif software == "pTB": if 'cpu time for all' in open(wfnlog).read(): pass else: OV.SetVar('NoSpherA2-Error',"pTB") lines = open(wfnlog).readlines() for line in lines: if "Error" in line: print(line) raise NameError('pTB did not terminate normally!') embedding = OV.GetParam('snum.NoSpherA2.ORCA_USE_CRYSTAL_QMMM') if ("ECP" in basis_name and "orca" in args[0]) or ("orca" in args[0] and embedding == True): molden_args = [] molden_args.append(os.path.join(os.path.dirname(self.parent.orca_exe), "orca_2mkl")) if sys.platform[:3] == 'win': molden_args[0] += ".exe" molden_args.append(self.name) molden_args.append("-emolden") if sys.platform[:3] == 'win': startinfo = subprocess.STARTUPINFO() startinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW startinfo.wShowWindow = 7 m = subprocess.Popen(molden_args, cwd=self.full_dir, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, stdin=subprocess.PIPE, startupinfo=startinfo) else: m = subprocess.Popen(molden_args, cwd=self.full_dir, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, stdin=subprocess.PIPE) while m.poll() is None: time.sleep(1) n = os.path.join(self.full_dir, self.name) if os.path.exists(n + ".molden.input"): shutil.move(n + ".molden.input", n + ".molden") else: OV.SetVar('NoSpherA2-Error', "NoMoldenFile") raise NameError("No molden file generated!") if copy == True: if("g03" in args[0]): shutil.move(os.path.join(self.full_dir,"Test.FChk"),os.path.join(self.full_dir,self.name+".fchk")) shutil.move(os.path.join(self.full_dir,self.name + ".log"),os.path.join(self.full_dir,self.name+"_g03.log")) if (os.path.isfile(os.path.join(self.full_dir,self.name + ".wfn"))): shutil.copy(os.path.join(self.full_dir,self.name + ".wfn"), self.name+".wfn") if (os.path.isfile(os.path.join(self.full_dir,self.name + ".wfx"))): shutil.copy(os.path.join(self.full_dir, self.name + ".wfx"), self.name + ".wfx") elif("g09" in args[0]): shutil.move(os.path.join(self.full_dir, "Test.FChk"), os.path.join(self.full_dir, self.name + ".fchk")) shutil.move(os.path.join(self.full_dir, self.name + ".log"), os.path.join(self.full_dir, self.name + "_g09.log")) if (os.path.isfile(os.path.join(self.full_dir, self.name + ".wfn"))): shutil.copy(os.path.join(self.full_dir, self.name + ".wfn"), self.name + ".wfn") if (os.path.isfile(os.path.join(self.full_dir, self.name + ".wfx"))): shutil.copy(os.path.join(self.full_dir, self.name + ".wfx"), self.name + ".wfx") elif("g16" in args[0]): shutil.move(os.path.join(self.full_dir, "Test.FChk"), os.path.join(self.full_dir, self.name + ".fchk")) shutil.move(os.path.join(self.full_dir, self.name + ".log"), os.path.join(self.full_dir, self.name + "_g16.log")) if (os.path.isfile(os.path.join(self.full_dir, self.name + ".wfn"))): shutil.copy(os.path.join(self.full_dir, self.name + ".wfn"), self.name + ".wfn") if (os.path.isfile(os.path.join(self.full_dir, self.name + ".wfx"))): shutil.copy(os.path.join(self.full_dir, self.name + ".wfx"), self.name + ".wfx") elif("orca" in args[0]): if software == "ORCA 5.0" or software == "ORCA 6.0": if (os.path.isfile(os.path.join(self.full_dir, self.name + ".gbw"))): shutil.copy(os.path.join(self.full_dir, self.name + ".gbw"), self.name + ".gbw") if (os.path.isfile(os.path.join(self.full_dir, self.name + ".wfn"))): shutil.copy(os.path.join(self.full_dir, self.name + ".wfn"), self.name + ".wfn") if (os.path.isfile(os.path.join(self.full_dir, self.name + ".wfx"))): shutil.copy(os.path.join(self.full_dir, self.name + ".wfx"), self.name + ".wfx") if (os.path.isfile(os.path.join(self.full_dir, self.name + ".molden"))): shutil.copy(os.path.join(self.full_dir, self.name + ".molden"), self.name + ".molden") elif("xtb" in args[0]): if (os.path.isfile(os.path.join(self.full_dir, "molden.input"))): shutil.copy(os.path.join(self.full_dir, "molden.input"), self.name + ".molden") shutil.move(os.path.join(self.full_dir, "molden.input"), os.path.join(self.full_dir, self.name + ".molden")) elif("ptb" in args[0]): if (os.path.isfile(os.path.join(self.full_dir, "wfn.xtb"))): shutil.copy(os.path.join(self.full_dir, "wfn.xtb"), self.name + ".xtb") shutil.move(os.path.join(self.full_dir, "wfn.xtb"), os.path.join(self.full_dir, self.name + ".xtb")) elif("elmodb" in args[0]): if (os.path.isfile(os.path.join(self.full_dir, self.name + ".wfx"))): shutil.copy(os.path.join(self.full_dir, self.name + ".wfx"), self.name + ".wfx") elif(software == "Psi4"): if (os.path.isfile(os.path.join(self.full_dir, self.name + ".fchk"))): shutil.copy(os.path.join(self.full_dir, self.name + ".fchk"), self.name + ".fchk") elif software == "pySCF": if (os.path.isfile(os.path.join(self.full_dir, self.name + ".wfn"))): shutil.copy(os.path.join(self.full_dir, self.name + ".wfn"), self.name + ".wfn") experimental_SF = OV.GetParam('snum.NoSpherA2.NoSpherA2_SF') if (experimental_SF == False) and ("g" not in args[0]): self.convert_to_fchk() @run_with_bitmap("Converting to .fchk") def convert_to_fchk(self): move_args = [] basis_dir = self.parent.basis_dir move_args.append(self.parent.NoSpherA2) move_args.append("-wfn") move_args.append(self.name + ".wfn") move_args.append("-mult") move_args.append(OV.GetParam('snum.NoSpherA2.multiplicity')) move_args.append("-b") move_args.append(OV.GetParam('snum.NoSpherA2.basis_name')) move_args.append("-d") if sys.platform[:3] == 'win': move_args.append(basis_dir.replace("/", "\\")) else: move_args.append(basis_dir + '/') move_args.append("-method") method = OV.GetParam('snum.NoSpherA2.method') if method == "HF": move_args.append("rhf") else: move_args.append("rks") m = subprocess.Popen(move_args, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, stdin=subprocess.PIPE) while m.poll() is None: time.sleep(1) with open("NoSpherA2.log", "r") as log: x = log.read() if x: print(x) if os.path.exists(self.name + ".fchk"): shutil.copy(self.name + ".fchk", os.path.join(self.full_dir, self.name + ".fchk")) else: OV.SetVar('NoSpherA2-Error', "NoFchk") raise NameError("No fchk generated!") shutil.move("NoSpherA2.log", os.path.join(self.full_dir, self.name + "_fchk.log"))