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How to use keyword_line method in SeleniumLibrary
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io.py
Source:io.py 
1# -*- coding: utf-8 -*-2from __future__ import print_function, absolute_import3import os.path, sys4import numpy as np5# PHYSICAL CONSTANTS UNITS6KCAL_TO_AU = 627.509541 # UNIT CONVERSION7# Radii used to determine connectivity in symmetry corrections8# Covalent radii taken from Cambridge Structural Database9RADII = {'H': 0.32, 'He': 0.93, 'Li': 1.23, 'Be': 0.90, 'B': 0.82, 'C': 0.77, 'N': 0.75, 'O': 0.73, 'F': 0.72,10 'Ne': 0.71, 'Na': 1.54, 'Mg': 1.36, 'Al': 1.18, 'Si': 1.11, 'P': 1.06, 'S': 1.02, 'Cl': 0.99, 'Ar': 0.98,11 'K': 2.03, 'Ca': 1.74, 'Sc': 1.44, 'Ti': 1.32, 'V': 1.22, 'Cr': 1.18, 'Mn': 1.17, 'Fe': 1.17, 'Co': 1.16,12 'Ni': 1.15, 'Cu': 1.17, 'Zn': 1.25, 'Ga': 1.26, 'Ge': 1.22, 'As': 1.20, 'Se': 1.16, 'Br': 1.14, 'Kr': 1.12,13 'Rb': 2.16, 'Sr': 1.91, 'Y': 1.62, 'Zr': 1.45, 'Nb': 1.34, 'Mo': 1.30, 'Tc': 1.27, 'Ru': 1.25, 'Rh': 1.25,14 'Pd': 1.28, 'Ag': 1.34, 'Cd': 1.48, 'In': 1.44, 'Sn': 1.41, 'Sb': 1.40, 'Te': 1.36, 'I': 1.33, 'Xe': 1.31,15 'Cs': 2.35, 'Ba': 1.98, 'La': 1.69, 'Lu': 1.60, 'Hf': 1.44, 'Ta': 1.34, 'W': 1.30, 'Re': 1.28, 'Os': 1.26,16 'Ir': 1.27, 'Pt': 1.30, 'Au': 1.34, 'Hg': 1.49, 'Tl': 1.48, 'Pb': 1.47, 'Bi': 1.46, 'X': 0}17# Bondi van der Waals radii for all atoms from: Bondi, A. J. Phys. Chem. 1964, 68, 441-452,18# except hydrogen, which is taken from Rowland, R. S.; Taylor, R. J. Phys. Chem. 1996, 100, 7384-7391.19# Radii unavailable in either of these publications are set to 2 Angstrom20# (Unfinished)21BONDI = {'H': 1.09, 'He': 1.40, 'Li': 1.82, 'Be': 2.00, 'B': 2.00, 'C': 1.70, 'N': 1.55, 'O': 1.52, 'F': 1.47,22 'Ne': 1.54}23# Some useful arrays24periodictable = ["", "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na", "Mg", "Al", "Si",25 "P", "S", "Cl", "Ar", "K", "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn",26 "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd",27 "Ag", "Cd", "In", "Sn", "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm",28 "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt",29 "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", "Pa", "U", "Np", "Pu",30 "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt", "Ds",31 "Rg", "Uub", "Uut", "Uuq", "Uup", "Uuh", "Uus", "Uuo"]32def element_id(massno, num=False):33 """34 Get element symbol from mass number.35 Used in parsing output files to determine elements present in file.36 Parameter:37 massno (int): mass of element.38 Returns:39 str: element symbol, or 'XX' if not found in periodic table.40 """41 try:42 if num:43 return periodictable.index(massno)44 return periodictable[massno]45 except IndexError:46 return "XX"47class xyz_out:48 """49 Enables output of optimized coordinates to a single xyz-formatted file.50 Writes Cartesian coordinates of parsed chemical input.51 Attributes:52 xyz (file object): path in current working directory to write Cartesian coordinates.53 """54 def __init__(self, filein, suffix, append):55 self.xyz = open('{}_{}.{}'.format(filein, append, suffix), 'w')56 def write_text(self, message):57 self.xyz.write(message + "\n")58 def write_coords(self, atoms, coords):59 for n, carts in enumerate(coords):60 self.xyz.write('{:>1}'.format(atoms[n]))61 for cart in carts:62 self.xyz.write('{:13.6f}'.format(cart))63 self.xyz.write('\n')64 def finalize(self):65 self.xyz.close()66class getoutData:67 """68 Read molecule data from a computational chemistry output file.69 Currently supports Gaussian and ORCA output types.70 Attributes:71 FREQS (list): list of frequencies parsed from Gaussian file.72 REDMASS (list): list of reduced masses parsed from Gaussian file.73 FORCECONST (list): list of force constants parsed from Gaussian file.74 NORMALMODE (list): list of normal modes parsed from Gaussian file.75 atom_nums (list): list of atom number IDs.76 atom_types (list): list of atom element symbols.77 cartesians (list): list of cartesian coordinates for each atom.78 atomictypes (list): list of atomic types output in Gaussian files.79 connectivity (list): list of atomic connectivity in a molecule, based on covalent radii80 """81 def __init__(self, file):82 with open(file) as f:83 data = f.readlines()84 program = 'none'85 for line in data:86 if "Gaussian" in line:87 program = "Gaussian"88 break89 if "* O R C A *" in line:90 program = "Orca"91 break92 if "NWChem" in line:93 program = "NWChem"94 break95 def get_freqs(self, outlines, natoms, format):96 self.FREQS = []97 self.REDMASS = []98 self.FORCECONST = []99 self.NORMALMODE = []100 freqs_so_far = 0101 if format == "Gaussian":102 for i in range(0, len(outlines)):103 if outlines[i].find(" Frequencies -- ") > -1:104 nfreqs = len(outlines[i].split())105 for j in range(2, nfreqs):106 self.FREQS.append(float(outlines[i].split()[j]))107 self.NORMALMODE.append([])108 for j in range(3, nfreqs + 1): self.REDMASS.append(float(outlines[i + 1].split()[j]))109 for j in range(3, nfreqs + 1): self.FORCECONST.append(float(outlines[i + 2].split()[j]))110 for j in range(0, natoms):111 for k in range(0, nfreqs - 2):112 self.NORMALMODE[(freqs_so_far + k)].append(113 [float(outlines[i + 5 + j].split()[3 * k + 2]),114 float(outlines[i + 5 + j].split()[3 * k + 3]),115 float(outlines[i + 5 + j].split()[3 * k + 4])])116 freqs_so_far = freqs_so_far + nfreqs - 2117 def getatom_types(self, outlines, program):118 if program == "Gaussian":119 for i, oline in enumerate(outlines):120 if "Input orientation" in oline or "Standard orientation" in oline:121 self.atom_nums, self.atom_types, self.cartesians, self.atomictypes, carts = [], [], [], [], \122 outlines[i + 5:]123 for j, line in enumerate(carts):124 if "-------" in line:125 break126 self.atom_nums.append(int(line.split()[1]))127 self.atom_types.append(element_id(int(line.split()[1])))128 self.atomictypes.append(int(line.split()[2]))129 if len(line.split()) > 5:130 self.cartesians.append(131 [float(line.split()[3]), float(line.split()[4]), float(line.split()[5])])132 else:133 self.cartesians.append(134 [float(line.split()[2]), float(line.split()[3]), float(line.split()[4])])135 if program == "Orca":136 for i, oline in enumerate(outlines):137 if "*" in oline and ">" in oline and "xyz" in oline:138 self.atom_nums, self.atom_types, self.cartesians, carts = [], [], [], outlines[i + 1:]139 for j, line in enumerate(carts):140 if ">" in line and "*" in line:141 break142 if len(line.split()) > 5:143 self.cartesians.append(144 [float(line.split()[3]), float(line.split()[4]), float(line.split()[5])])145 self.atom_types.append(line.split()[2])146 self.atom_nums.append(element_id(line.split()[2], num=True))147 else:148 self.cartesians.append(149 [float(line.split()[2]), float(line.split()[3]), float(line.split()[4])])150 self.atom_types.append(line.split()[1])151 self.atom_nums.append(element_id(line.split()[1], num=True))152 if program == "NWChem":153 for i, oline in enumerate(outlines):154 if "Output coordinates" in oline:155 self.atom_nums, self.atom_types, self.cartesians, self.atomictypes, carts = [], [], [], [], outlines[i+4:]156 for j, line in enumerate(carts):157 if line.strip()=='' :158 break159 self.atom_nums.append(int(float(line.split()[2])))160 self.atom_types.append(element_id(int(float(line.split()[2]))))161 self.atomictypes.append(int(float(line.split()[2])))162 self.cartesians.append([float(line.split()[3]),float(line.split()[4]),float(line.split()[5])])163 getatom_types(self, data, program)164 natoms = len(self.atom_types)165 try:166 get_freqs(self, data, natoms, program)167 except:168 pass169 # Convert coordinates to string that can be used by the symmetry.c program170 def coords_string(self):171 xyzstring = str(len(self.atom_nums)) + '\n'172 for atom, xyz in zip(self.atom_nums, self.cartesians):173 xyzstring += "{0} {1:.6f} {2:.6f} {3:.6f}\n".format(atom, *xyz)174 return xyzstring175 # Obtain molecule connectivity to be used for internal symmetry determination176 def get_connectivity(self):177 connectivity = []178 tolerance = 0.2179 for i, ai in enumerate(self.atom_types):180 row = []181 for j, aj in enumerate(self.atom_types):182 if i == j:183 continue184 cutoff = RADII[ai] + RADII[aj] + tolerance185 distance = np.linalg.norm(np.array(self.cartesians[i]) - np.array(self.cartesians[j]))186 if distance < cutoff:187 row.append(j)188 connectivity.append(row)189 self.connectivity = connectivity190def cosmo_rs_out(datfile, names, interval=False):191 """192 Read solvation free energies from a COSMO-RS data file193 Parameters:194 datfile (str): name of COSMO-RS output file.195 names (list): list of species in COSMO-RS file that correspond to names of other computational output files.196 interval (bool): flag for parser to read COSMO-RS temperature interval calculation.197 """198 gsolv = {}199 if os.path.exists(datfile):200 with open(datfile) as f:201 data = f.readlines()202 else:203 raise ValueError("File {} does not exist".format(datfile))204 temp = 0205 t_interval = []206 gsolv_dicts = []207 found = False208 oldtemp = 0209 gsolv_temp = {}210 if interval:211 for i, line in enumerate(data):212 for name in names:213 if line.find('(' + name.split('.')[0] + ')') > -1 and line.find('Compound') > -1:214 if data[i - 5].find('Temperature') > -1:215 temp = data[i - 5].split()[2]216 if float(temp) > float(interval[0]) and float(temp) < float(interval[1]):217 if float(temp) not in t_interval:218 t_interval.append(float(temp))219 if data[i + 10].find('Gibbs') > -1:220 gsolv = float(data[i + 10].split()[6].strip()) / KCAL_TO_AU221 gsolv_temp[name] = gsolv222 found = True223 if found:224 if oldtemp is 0:225 oldtemp = temp226 if temp is not oldtemp:227 gsolv_dicts.append(gsolv) # Store dict at one temp228 gsolv = {} # Clear gsolv229 gsolv.update(gsolv_temp) # Grab the first one for the new temp230 oldtemp = temp231 gsolv.update(gsolv_temp)232 gsolv_temp = {}233 found = False234 gsolv_dicts.append(gsolv) # Grab last dict235 else:236 for i, line in enumerate(data):237 for name in names:238 if line.find('(' + name.split('.')[0] + ')') > -1 and line.find('Compound') > -1:239 if data[i + 11].find('Gibbs') > -1:240 gsolv = float(data[i + 11].split()[6].strip()) / KCAL_TO_AU241 gsolv[name] = gsolv242 if interval:243 return t_interval, gsolv_dicts244 else:245 return gsolv246def parse_data(file):247 """248 Read computational chemistry output file.249 Attempt to obtain single point energy, program type, program version, solvation_model,250 charge, empirical_dispersion, and multiplicity from file.251 Parameter:252 file (str): name of file to be parsed.253 Returns:254 float: single point energy.255 str: program used to run calculation.256 str: version of program used to run calculation.257 str: solvation model used in chemical calculation (if any).258 str: original filename parsed.259 int: overall charge of molecule or chemical system.260 str: empirical dispersion used in chemical calculation (if any).261 int: multiplicity of molecule or chemical system.262 """263 spe, program, data, version_program, solvation_model, keyword_line, a, charge, multiplicity = 'none', 'none', [], '', '', '', 0, None, None264 if os.path.exists(os.path.splitext(file)[0] + '.log'):265 with open(os.path.splitext(file)[0] + '.log') as f:266 data = f.readlines()267 elif os.path.exists(os.path.splitext(file)[0] + '.out'):268 with open(os.path.splitext(file)[0] + '.out') as f:269 data = f.readlines()270 else:271 raise ValueError("File {} does not exist".format(file))272 for line in data:273 if "Gaussian" in line:274 program = "Gaussian"275 break276 if "* O R C A *" in line:277 program = "Orca"278 break279 if "NWChem" in line:280 program = "NWChem"281 break282 repeated_link1 = 0283 for line in data:284 if program == "Gaussian":285 if line.strip().startswith('SCF Done:'):286 spe = float(line.strip().split()[4])287 elif line.strip().startswith('Counterpoise corrected energy'):288 spe = float(line.strip().split()[4])289 # For MP2 calculations replace with EUMP2290 elif 'EUMP2 =' in line.strip():291 spe = float((line.strip().split()[5]).replace('D', 'E'))292 # For ONIOM calculations use the extrapolated value rather than SCF value293 elif "ONIOM: extrapolated energy" in line.strip():294 spe = (float(line.strip().split()[4]))295 # For G4 calculations look for G4 energies (Gaussian16a bug prints G4(0 K) as DE(HF)) --Brian modified to work for G16c-where bug is fixed.296 elif line.strip().startswith('G4(0 K)'):297 spe = float(line.strip().split()[2])298 spe -= zero_point_corr_G4 #Remove G4 ZPE299 elif line.strip().startswith('E(ZPE)='): #Get G4 ZPE300 zero_point_corr_G4 = float(line.strip().split()[1])301 # For TD calculations look for SCF energies of the first excited state302 elif 'E(TD-HF/TD-DFT)' in line.strip():303 spe = float(line.strip().split()[4])304 # For Semi-empirical or Molecular Mechanics calculations305 elif "Energy= " in line.strip() and "Predicted" not in line.strip() and "Thermal" not in line.strip() and "G4" not in line.strip():306 spe = (float(line.strip().split()[1]))307 elif "Gaussian" in line and "Revision" in line and repeated_link1 == 0:308 for i in range(len(line.strip(",").split(",")) - 1):309 line.strip(",").split(",")[i]310 version_program += line.strip(",").split(",")[i]311 repeated_link1 = 1312 version_program = version_program[1:]313 elif "Charge" in line.strip() and "Multiplicity" in line.strip():314 charge = int(line.split('Multiplicity')[0].split('=')[-1].strip())315 multiplicity = line.split('=')[-1].strip()316 if program == "Orca":317 if line.strip().startswith('FINAL SINGLE POINT ENERGY'):318 spe = float(line.strip().split()[4])319 if 'Program Version' in line.strip():320 version_program = "ORCA version " + line.split()[2]321 if "Total Charge" in line.strip() and "...." in line.strip():322 charge = int(line.strip("=").split()[-1])323 if "Multiplicity" in line.strip() and "...." in line.strip():324 multiplicity = int(line.strip("=").split()[-1])325 if program == "NWChem":326 if line.strip().startswith('Total DFT energy'):327 spe = float(line.strip().split()[4])328 if 'nwchem branch' in line.strip():329 version_program = "NWChem version " + line.split()[3]330 if "charge" in line.strip():331 charge = int(line.strip().split()[-1])332 if "mult " in line.strip():333 multiplicity = int(line.strip().split()[-1])334 # Solvation model and empirical dispersion detection335 if 'Gaussian' in version_program.strip():336 for i, line in enumerate(data):337 if '#' in line.strip() and a == 0:338 for j, line in enumerate(data[i:i + 10]):339 if '--' in line.strip():340 a = a + 1341 break342 if a != 0:343 break344 else:345 for k in range(len(line.strip().split("\n"))):346 line.strip().split("\n")[k]347 keyword_line += line.strip().split("\n")[k]348 keyword_line = keyword_line.lower()349 if 'scrf' not in keyword_line.strip():350 solvation_model = "gas phase"351 else:352 start_scrf = keyword_line.strip().find('scrf') + 4353 if '(' in keyword_line[start_scrf:start_scrf + 4]:354 start_scrf += keyword_line[start_scrf:start_scrf + 4].find('(') + 1355 end_scrf = keyword_line.find(")", start_scrf)356 display_solvation_model = "scrf=(" + ','.join(357 keyword_line[start_scrf:end_scrf].lower().split(',')) + ')'358 sorted_solvation_model = "scrf=(" + ','.join(359 sorted(keyword_line[start_scrf:end_scrf].lower().split(','))) + ')'360 else:361 if ' = ' in keyword_line[start_scrf:start_scrf + 4]:362 start_scrf += keyword_line[start_scrf:start_scrf + 4].find(' = ') + 3363 elif ' =' in keyword_line[start_scrf:start_scrf + 4]:364 start_scrf += keyword_line[start_scrf:start_scrf + 4].find(' =') + 2365 elif '=' in keyword_line[start_scrf:start_scrf + 4]:366 start_scrf += keyword_line[start_scrf:start_scrf + 4].find('=') + 1367 end_scrf = keyword_line.find(" ", start_scrf)368 if end_scrf == -1:369 display_solvation_model = "scrf=(" + ','.join(keyword_line[start_scrf:].lower().split(',')) + ')'370 sorted_solvation_model = "scrf=(" + ','.join(371 sorted(keyword_line[start_scrf:].lower().split(','))) + ')'372 else:373 display_solvation_model = "scrf=(" + ','.join(374 keyword_line[start_scrf:end_scrf].lower().split(',')) + ')'375 sorted_solvation_model = "scrf=(" + ','.join(376 sorted(keyword_line[start_scrf:end_scrf].lower().split(','))) + ')'377 if solvation_model != "gas phase":378 solvation_model = [sorted_solvation_model, display_solvation_model]379 empirical_dispersion = ''380 if keyword_line.strip().find('empiricaldispersion') == -1 and keyword_line.strip().find(381 'emp=') == -1 and keyword_line.strip().find('emp =') == -1 and keyword_line.strip().find('emp(') == -1:382 empirical_dispersion = "No empirical dispersion detected"383 elif keyword_line.strip().find('empiricaldispersion') > -1:384 start_emp_disp = keyword_line.strip().find('empiricaldispersion') + 19385 if '(' in keyword_line[start_emp_disp:start_emp_disp + 4]:386 start_emp_disp += keyword_line[start_emp_disp:start_emp_disp + 4].find('(') + 1387 end_emp_disp = keyword_line.find(")", start_emp_disp)388 empirical_dispersion = 'empiricaldispersion=(' + ','.join(389 sorted(keyword_line[start_emp_disp:end_emp_disp].lower().split(','))) + ')'390 else:391 if ' = ' in keyword_line[start_emp_disp:start_emp_disp + 4]:392 start_emp_disp += keyword_line[start_emp_disp:start_emp_disp + 4].find(' = ') + 3393 elif ' =' in keyword_line[start_emp_disp:start_emp_disp + 4]:394 start_emp_disp += keyword_line[start_emp_disp:start_emp_disp + 4].find(' =') + 2395 elif '=' in keyword_line[start_emp_disp:start_emp_disp + 4]:396 start_emp_disp += keyword_line[start_emp_disp:start_emp_disp + 4].find('=') + 1397 end_emp_disp = keyword_line.find(" ", start_emp_disp)398 if end_emp_disp == -1:399 empirical_dispersion = "empiricaldispersion=(" + ','.join(400 sorted(keyword_line[start_emp_disp:].lower().split(','))) + ')'401 else:402 empirical_dispersion = "empiricaldispersion=(" + ','.join(403 sorted(keyword_line[start_emp_disp:end_emp_disp].lower().split(','))) + ')'404 elif keyword_line.strip().find('emp=') > -1 or keyword_line.strip().find(405 'emp =') > -1 or keyword_line.strip().find('emp(') > -1:406 # Check for temp keyword407 temp, emp_e, emp_p = False, False, False408 check_temp = keyword_line.strip().find('emp=')409 start_emp_disp = keyword_line.strip().find('emp=')410 if check_temp == -1:411 check_temp = keyword_line.strip().find('emp =')412 start_emp_disp = keyword_line.strip().find('emp =')413 if check_temp == -1:414 check_temp = keyword_line.strip().find('emp=(')415 start_emp_disp = keyword_line.strip().find('emp(')416 check_temp += -1417 if keyword_line[check_temp].lower() == 't':418 temp = True # Look for a new one419 if keyword_line.strip().find('emp=', check_temp + 5) > -1:420 emp_e = True421 start_emp_disp = keyword_line.strip().find('emp=', check_temp + 5) + 3422 elif keyword_line.strip().find('emp =', check_temp + 5) > -1:423 emp_e = True424 start_emp_disp = keyword_line.strip().find('emp =', check_temp + 5) + 3425 elif keyword_line.strip().find('emp(', check_temp + 5) > -1:426 emp_p = True427 start_emp_disp = keyword_line.strip().find('emp(', check_temp + 5) + 3428 else:429 empirical_dispersion = "No empirical dispersion detected"430 else:431 start_emp_disp += 3432 if (temp and emp_e) or (not temp and keyword_line.strip().find('emp=') > -1) or (433 not temp and keyword_line.strip().find('emp =')):434 if '(' in keyword_line[start_emp_disp:start_emp_disp + 4]:435 start_emp_disp += keyword_line[start_emp_disp:start_emp_disp + 4].find('(') + 1436 end_emp_disp = keyword_line.find(")", start_emp_disp)437 empirical_dispersion = 'empiricaldispersion=(' + ','.join(438 sorted(keyword_line[start_emp_disp:end_emp_disp].lower().split(','))) + ')'439 else:440 if ' = ' in keyword_line[start_emp_disp:start_emp_disp + 4]:441 start_emp_disp += keyword_line[start_emp_disp:start_emp_disp + 4].find(' = ') + 3442 elif ' =' in keyword_line[start_emp_disp:start_emp_disp + 4]:443 start_emp_disp += keyword_line[start_emp_disp:start_emp_disp + 4].find(' =') + 2444 elif '=' in keyword_line[start_emp_disp:start_emp_disp + 4]:445 start_emp_disp += keyword_line[start_emp_disp:start_emp_disp + 4].find('=') + 1446 end_emp_disp = keyword_line.find(" ", start_emp_disp)447 if end_emp_disp == -1:448 empirical_dispersion = "empiricaldispersion=(" + ','.join(449 sorted(keyword_line[start_emp_disp:].lower().split(','))) + ')'450 else:451 empirical_dispersion = "empiricaldispersion=(" + ','.join(452 sorted(keyword_line[start_emp_disp:end_emp_disp].lower().split(','))) + ')'453 elif (temp and emp_p) or (not temp and keyword_line.strip().find('emp(') > -1):454 start_emp_disp += keyword_line[start_emp_disp:start_emp_disp + 4].find('(') + 1455 end_emp_disp = keyword_line.find(")", start_emp_disp)456 empirical_dispersion = 'empiricaldispersion=(' + ','.join(457 sorted(keyword_line[start_emp_disp:end_emp_disp].lower().split(','))) + ')'458 if 'ORCA' in version_program.strip():459 keyword_line_1 = "gas phase"460 keyword_line_2 = ''461 keyword_line_3 = ''462 for i, line in enumerate(data):463 if 'CPCM SOLVATION MODEL' in line.strip():464 keyword_line_1 = "CPCM,"465 if 'SMD CDS free energy correction energy' in line.strip():466 keyword_line_2 = "SMD,"467 if "Solvent: " in line.strip():468 keyword_line_3 = line.strip().split()[-1]469 solvation_model = keyword_line_1 + keyword_line_2 + keyword_line_3470 empirical_dispersion1 = 'No empirical dispersion detected'471 empirical_dispersion2 = ''472 empirical_dispersion3 = ''473 for i, line in enumerate(data):474 if keyword_line.strip().find('DFT DISPERSION CORRECTION') > -1:475 empirical_dispersion1 = ''476 if keyword_line.strip().find('DFTD3') > -1:477 empirical_dispersion2 = "D3"478 if keyword_line.strip().find('USING zero damping') > -1:479 empirical_dispersion3 = ' with zero damping'480 empirical_dispersion = empirical_dispersion1 + empirical_dispersion2 + empirical_dispersion3481 if 'NWChem' in version_program.strip():482 # keyword_line_1 = "gas phase"483 # keyword_line_2 = ''484 # keyword_line_3 = ''485 # for i, line in enumerate(data):486 # if 'CPCM SOLVATION MODEL' in line.strip():487 # keyword_line_1 = "CPCM,"488 # if 'SMD CDS free energy correction energy' in line.strip():489 # keyword_line_2 = "SMD,"490 # if "Solvent: " in line.strip():491 # keyword_line_3 = line.strip().split()[-1]492 # solvation_model = keyword_line_1 + keyword_line_2 + keyword_line_3493 empirical_dispersion1 = 'No empirical dispersion detected'494 empirical_dispersion2 = ''495 empirical_dispersion3 = ''496 for i, line in enumerate(data):497 if keyword_line.strip().find('Dispersion correction') > -1:498 empirical_dispersion1 = ''499 if keyword_line.strip().find('disp vdw 3') > -1:500 empirical_dispersion2 = "D3"501 if keyword_line.strip().find('disp vdw 4') > -1:502 empirical_dispersion2 = "D3BJ"503 empirical_dispersion = empirical_dispersion1 + empirical_dispersion2 + empirical_dispersion3504 return spe, program, version_program, solvation_model, file, charge, empirical_dispersion, multiplicity505def sp_cpu(file):506 """Read single-point output for cpu time."""507 spe, program, data, cpu = None, None, [], None508 if os.path.exists(os.path.splitext(file)[0] + '.log'):509 with open(os.path.splitext(file)[0] + '.log') as f:510 data = f.readlines()511 elif os.path.exists(os.path.splitext(file)[0] + '.out'):512 with open(os.path.splitext(file)[0] + '.out') as f:513 data = f.readlines()514 else:515 raise ValueError("File {} does not exist".format(file))516 for line in data:517 if line.find("Gaussian") > -1:518 program = "Gaussian"519 break520 if line.find("* O R C A *") > -1:521 program = "Orca"522 break523 if line.find("NWChem") > -1:524 program = "NWChem"525 break526 for line in data:527 if program == "Gaussian":528 if line.strip().startswith('SCF Done:'):529 spe = float(line.strip().split()[4])530 if line.strip().find("Job cpu time") > -1:531 days = int(line.split()[3])532 hours = int(line.split()[5])533 mins = int(line.split()[7])534 secs = 0535 msecs = int(float(line.split()[9]) * 1000.0)536 cpu = [days, hours, mins, secs, msecs]537 if program == "Orca":538 if line.strip().startswith('FINAL SINGLE POINT ENERGY'):539 spe = float(line.strip().split()[4])540 if line.strip().find("TOTAL RUN TIME") > -1:541 days = int(line.split()[3])542 hours = int(line.split()[5])543 mins = int(line.split()[7])544 secs = int(line.split()[9])545 msecs = float(line.split()[11])546 cpu = [days, hours, mins, secs, msecs]547 if program == "NWChem":548 if line.strip().startswith('Total DFT energy ='):549 spe = float(line.strip().split()[4])550 if line.strip().find("Total times") > -1:551 days = 0552 hours = 0553 mins = 0554 secs = float(line.split()[3][0:-1])555 msecs = 0556 cpu = [days,hours,mins,secs,msecs]557 return cpu558def level_of_theory(file):559 """Read output for the level of theory and basis set used."""560 repeated_theory = 0561 with open(file) as f:562 data = f.readlines()563 level, bs = 'none', 'none'564 for line in data:565 if line.strip().find('External calculation') > -1:566 level, bs = 'ext', 'ext'567 break568 if '\\Freq\\' in line.strip() and repeated_theory == 0:569 try:570 level, bs = (line.strip().split("\\")[4:6])571 repeated_theory = 1572 except IndexError:573 pass574 elif '|Freq|' in line.strip() and repeated_theory == 0:575 try:576 level, bs = (line.strip().split("|")[4:6])577 repeated_theory = 1578 except IndexError:579 pass580 if '\\SP\\' in line.strip() and repeated_theory == 0:581 try:582 level, bs = (line.strip().split("\\")[4:6])583 repeated_theory = 1584 except IndexError:585 pass586 elif '|SP|' in line.strip() and repeated_theory == 0:587 try:588 level, bs = (line.strip().split("|")[4:6])589 repeated_theory = 1590 except IndexError:591 pass592 if 'DLPNO BASED TRIPLES CORRECTION' in line.strip():593 level = 'DLPNO-CCSD(T)'594 if 'Estimated CBS total energy' in line.strip():595 try:596 bs = ("Extrapol." + line.strip().split()[4])597 except IndexError:598 pass599 # Remove the restricted R or unrestricted U label600 if level[0] in ('R', 'U'):601 level = level[1:]602 level_of_theory = '/'.join([level, bs])603 return level_of_theory604def read_initial(file):605 """At beginning of procedure, read level of theory, solvation model, and check for normal termination"""606 with open(file) as f:607 data = f.readlines()608 level, bs, program, keyword_line = 'none', 'none', 'none', 'none'609 progress, orientation = 'Incomplete', 'Input'610 a, repeated_theory = 0, 0611 no_grid = True612 DFT, dft_used, level, bs, scf_iradan, cphf_iradan = False, 'F', 'none', 'none', False, False613 grid_lookup = {1: 'sg1', 2: 'coarse', 4: 'fine', 5: 'ultrafine', 7: 'superfine'}614 for line in data:615 # Determine program616 if "Gaussian" in line:617 program = "Gaussian"618 break619 if "* O R C A *" in line:620 program = "Orca"621 break622 if "NWChem" in line:623 program = "NWChem"624 break625 for line in data:626 # Grab pertinent information from file627 if line.strip().find('External calculation') > -1:628 level, bs = 'ext', 'ext'629 if line.strip().find('Standard orientation:') > -1:630 orientation = 'Standard'631 if line.strip().find('IExCor=') > -1 and no_grid:632 try:633 dft_used = line.split('=')[2].split()[0]634 grid = grid_lookup[int(dft_used)]635 no_grid = False636 except:637 pass638 if '\\Freq\\' in line.strip() and repeated_theory == 0:639 try:640 level, bs = (line.strip().split("\\")[4:6])641 repeated_theory = 1642 except IndexError:643 pass644 elif '|Freq|' in line.strip() and repeated_theory == 0:645 try:646 level, bs = (line.strip().split("|")[4:6])647 repeated_theory = 1648 except IndexError:649 pass650 if '\\SP\\' in line.strip() and repeated_theory == 0:651 try:652 level, bs = (line.strip().split("\\")[4:6])653 repeated_theory = 1654 except IndexError:655 pass656 elif '|SP|' in line.strip() and repeated_theory == 0:657 try:658 level, bs = (line.strip().split("|")[4:6])659 repeated_theory = 1660 except IndexError:661 pass662 if 'DLPNO BASED TRIPLES CORRECTION' in line.strip():663 level = 'DLPNO-CCSD(T)'664 if 'Estimated CBS total energy' in line.strip():665 try:666 bs = ("Extrapol." + line.strip().split()[4])667 except IndexError:668 pass669 # Remove the restricted R or unrestricted U label670 if level[0] in ('R', 'U'):671 level = level[1:]672 #NWChem specific parsing673 if program is 'NWChem':674 keyword_line_1 = "gas phase"675 keyword_line_2 = ''676 keyword_line_3 = ''677 for i, line in enumerate(data):678 if line.strip().startswith("xc "):679 level=line.strip().split()[1]680 if line.strip().startswith("* library "):681 bs = line.strip().replace("* library ",'')682 #need to update these tags for NWChem solvation later683 if 'CPCM SOLVATION MODEL' in line.strip():684 keyword_line_1 = "CPCM,"685 if 'SMD CDS free energy correction energy' in line.strip():686 keyword_line_2 = "SMD,"687 if "Solvent: " in line.strip():688 keyword_line_3 = line.strip().split()[-1]689 #need to update NWChem keyword for error calculation690 if 'Total times' in line:691 progress = 'Normal'692 elif 'error termination' in line:693 progress = 'Error'694 solvation_model = keyword_line_1 + keyword_line_2 + keyword_line_3695 # Grab solvation models - Gaussian files696 if program is 'Gaussian':697 for i, line in enumerate(data):698 if '#' in line.strip() and a == 0:699 for j, line in enumerate(data[i:i + 10]):700 if '--' in line.strip():701 a = a + 1702 break703 if a != 0:704 break705 else:706 for k in range(len(line.strip().split("\n"))):707 line.strip().split("\n")[k]708 keyword_line += line.strip().split("\n")[k]709 if 'Normal termination' in line:710 progress = 'Normal'711 elif 'Error termination' in line:712 progress = 'Error'713 keyword_line = keyword_line.lower()714 if 'scrf' not in keyword_line.strip():715 solvation_model = "gas phase"716 else:717 start_scrf = keyword_line.strip().find('scrf') + 5718 if keyword_line[start_scrf] == "(":719 end_scrf = keyword_line.find(")", start_scrf)720 solvation_model = "scrf=" + keyword_line[start_scrf:end_scrf]721 if solvation_model[-1] != ")":722 solvation_model = solvation_model + ")"723 else:724 start_scrf2 = keyword_line.strip().find('scrf') + 4725 if keyword_line.find(" ", start_scrf) > -1:726 end_scrf = keyword_line.find(" ", start_scrf)727 else:728 end_scrf = len(keyword_line)729 if keyword_line[start_scrf2] == "(":730 solvation_model = "scrf=(" + keyword_line[start_scrf:end_scrf]731 if solvation_model[-1] != ")":732 solvation_model = solvation_model + ")"733 else:734 if keyword_line.find(" ", start_scrf) > -1:735 end_scrf = keyword_line.find(" ", start_scrf)736 else:737 end_scrf = len(keyword_line)738 solvation_model = "scrf=" + keyword_line[start_scrf:end_scrf]739 # ORCA parsing for solvation model740 elif program is 'Orca':741 keyword_line_1 = "gas phase"742 keyword_line_2 = ''743 keyword_line_3 = ''744 for i, line in enumerate(data):745 if 'CPCM SOLVATION MODEL' in line.strip():746 keyword_line_1 = "CPCM,"747 if 'SMD CDS free energy correction energy' in line.strip():748 keyword_line_2 = "SMD,"749 if "Solvent: " in line.strip():750 keyword_line_3 = line.strip().split()[-1]751 if 'ORCA TERMINATED NORMALLY' in line:752 progress = 'Normal'753 elif 'error termination' in line:754 progress = 'Error'755 solvation_model = keyword_line_1 + keyword_line_2 + keyword_line_3756 level_of_theory = '/'.join([level, bs])757 return level_of_theory, solvation_model, progress, orientation, dft_used758def jobtype(file):759 """Read output for the level of theory and basis set used."""760 with open(file) as f:761 data = f.readlines()762 job = ''763 for line in data:764 if line.strip().find('\\SP\\') > -1:765 job += 'SP'766 if line.strip().find('\\FOpt\\') > -1:767 job += 'GS'768 if line.strip().find('\\FTS\\') > -1:769 job += 'TS'770 if line.strip().find('\\Freq\\') > -1:771 job += 'Freq'...
__main__.py
Source:__main__.py
1#!/usr/bin/python32import argparse3import collections4import datetime5import re6import sys7import tempfile8import numpy as np9class Model:10 def __init__(self):11 self.assembly = None12 @staticmethod13 def parse(cls, file_or_name):14 NotImplemented()15 def write(cls, file_or_name):16 NotImplemented()17class Assembly:18 def __init__(self):19 self.name = None20 self.instances = []21 self.sets = {}22class Instance:23 def __init__(self):24 self.name = None25 self.part = None26 self.translation = None27 self.rotation = None28class Part:29 def __init__(self):30 self.name = None31 self.nodes = None32 self.elements = None33 self.sets = None34class AbaqusInput:35 def __init__(self):36 self.assembly = None37 self.header = None38 @staticmethod39 def parse(cls, file_or_name):40 ret = cls()41 return ret42class Orientation():43 system = None44 a = None45 b = None46 c = None47 rot_axis = None48 rot = None49 def __init__(self):50 self.a = np.empty(3)51 self.a.fill(np.nan)52 self.b = np.empty(3)53 self.b.fill(np.nan)54 self.c = np.empty(3)55 self.c.fill(0)56class Element():57 id = 058 type = None59 def __init__(self):60 self.node = []61class Node():62 id = 063 pos = None64 def __init__(self):65 self.pos = np.zeros(3)66class Section():67 elset = None68 orientation = None69class Part():70 id = 071class Set(list):72 name = None73 instance = None74 part = None75class AbaqusPart(Part):76 orientation = None77 set = None78 section = None79 def __init__(self, name):80 self.name = name81 self.element = {}82 self.node = {}83 self.set = {}84 self.set['node'] = {}85 self.set['element'] = {}86 self.section = []87 self.orientation = {}88def GetRotationMatrix(a,b,th):89 ux = b[0] - a[0]90 uy = b[1] - a[1]91 uz = b[2] - a[2]92 rm = np.ndarray([3,3])93 th = th * np.pi/180.94 cos = np.cos(th)95 sin = np.sin(th)96 one_cos = 1-cos97 rm[0,0] = cos + ux**2*one_cos98 rm[0,1] = ux*uy*one_cos - uz*sin99 rm[0,2] = ux*uz*one_cos + uy*sin100 rm[1,0] = uy*ux*one_cos + uz*sin101 rm[1,1] = cos + uy**2*one_cos102 rm[1,2] = uy*uz*one_cos - ux*sin103 rm[2,0] = uz*ux*one_cos - uy*sin104 rm[2,1] = uz*uy*one_cos + ux*sin105 rm[2,2] = cos + uz**2*one_cos106 return rm107class AbaqusInstance():108 name = None109 part = None110 translation = None111 rotation = None112 @property113 def rotation_matrix(self):114 th = self.rotation['deg']115 a = self.rotation['a']116 b = self.rotation['b']117 rm = GetRotationMatrix(a,b,th)118 return rm119 def __init__(self):120 self.translation = np.zeros(3)121 self.rotation = {}122 self.rotation['a'] = np.zeros(3)123 self.rotation['b'] = np.zeros(3)124 self.rotation['deg'] = 0125class AbaqusInput():126 def __init__(self):127 self.part = {}128 self.instance = {}129 self.count = collections.Counter()130 self.set = {}131 self.set['node'] = {}132 self.set['element'] = {}133# parse Abaqus input file134def ParseAbaqus(file):135 ret = AbaqusInput()136 count = collections.Counter()137 regex = {}138 regex['comment'] = re.compile(r'^\*\*')139 regex['keyword'] = re.compile(r'^\*[a-zA-Z0-9 ]+[,\n]')140 regex['data'] = re.compile(r'^(?!\*)')141 line_counter = collections.Counter()142 line_counter['total'] = len(file.readlines())143 file.seek(0)144 def ends_at(kw,loc):145 if loc == '*':146 if section[len(section)-1] != kw:147 section.pop(section.index(kw))148 if type(loc) is int:149 if count['keyword_line'] == loc:150 section.pop(section.index(kw))151 if type(loc) is str:152 if loc in section:153 section.pop(section.index(kw))154 def update_term(complete=False):155 total = line_counter['total']156 count = line_counter['current']157 perc = int(100 * count * 1.0 / total)158 old_perc = int(100 * (count-1)*1.0/total)159 if perc != old_perc or count == 1 or perc == 1:160 perc = count * 1.0 / total161 #import pdb; pdb.set_trace()162 fmt = 'Parsing ({:3.0f}% complete)'.format(100*perc)163 if complete:164 to_write = fmt + '...done!\n'165 sys.stdout.write(to_write)166 else:167 to_write = fmt + '\r'168 sys.stdout.write(to_write)169 sys.stdout.flush()170 for line in file:171 line_counter['current'] += 1172 update_term()173 current_instance = None174 ret.count['line'] += 1175 if regex['comment'].search(line):176 # This is a comment line177 ret.count['comment'] += 1178 continue179 if regex['keyword'].search(line):180 match = regex['keyword'].search(line)181 # This is a keyword line182 ret.count['keyword'] += 1183 kw = match.group(0).upper().strip(' ,\n*')184 ret.count['*' + kw] += 1185 count['keyword_line'] = 0186 # parse keyword arguments187 kwargs = {}188 splitline = line.split(',')189 splitline.pop(0)190 for i in splitline:191 i = i.strip(' \n')192 if '=' in i:193 i = i.split('=')194 kwargs[i[0]] = i[1].strip('\'\"')195 else:196 kwargs[i] = True197 #print('{:5d}:{:15s}'.format(ret.count['line'],kw))198 #if len(kwargs) > 0:199 #print(kwargs)200 if regex['data'].search(line):201 count['keyword_line'] += 1202 # from here on, process the current keyword203 if kw == 'PART':204 if count['keyword_line'] == 0:205 name = kwargs['name']206 ret.part[name] = AbaqusPart(name)207 current_part = name208 if kw == 'END PART':209 current_part = None210 if kw == 'ASSEMBLY':211 in_assembly = True212 if kw == 'END ASSEMBLY':213 in_assembly = False214 if kw == 'INSTANCE':215 if count['keyword_line'] == 0:216 instance = AbaqusInstance()217 instance.name = kwargs['name']218 instance.part = kwargs['part']219 current_instance = instance.name220 ret.instance[instance.name] = instance221 if count['keyword_line'] == 1:222 parts = line.split(',')223 instance.translation[:] = parts224 if count['keyword_line'] == 2:225 parts = line.split(',')226 instance.rotation['a'][:] = parts[0:3]227 instance.rotation['b'][:] = parts[3:6]228 instance.rotation['deg'] = float(parts[6])229 if kw == 'END INSTANCE':230 current_instance = None231 if kw == 'ORIENTATION':232 if count['keyword_line'] == 0:233 orient = Orientation()234 orient.name = kwargs['name']235 if 'system' in kwargs:236 orient.system = kwargs['system']237 else:238 orient.system = 'RECTANGULAR'239 ret.part[current_part].orientation[orient.name] = orient240 elif count['keyword_line'] == 1:241 parts = line.split(',')242 orient.a[:] = parts[0:3]243 orient.b[:] = parts[3:6]244 if len(parts) == 9:245 orient.c[:] = parts[6:9]246 elif count['keyword_line'] == 2:247 parts = line.split(',')248 orient.rot_axis = int(parts[0])249 orient.rot = float(parts[1])250 if 'SECTION' in kw:251 if count['keyword_line'] == 0 and 'orientation' in kwargs:252 section = Section()253 section.elset = kwargs['elset']254 section.orientation = kwargs['orientation']255 ret.part[current_part].section.append(section)256 if kw == 'NODE':257 #import pdb; pdb.set_trace()258 if count['keyword_line'] > 0:259 parts = line.split(',')260 node = Node()261 node.id = int(parts[0])262 node.pos[0] = float(parts[1])263 node.pos[1] = float(parts[2])264 try:265 node.pos[2] = float(parts[3])266 except:267 pass268 ret.part[current_part].node[node.id] = node269 if kw == 'ELEMENT':270 if count['keyword_line'] > 0:271 parts = line.split(',')272 element = Element()273 element.id = int(parts[0])274 for i in range(1,len(parts)):275 element.node.append(int(parts[i]))276 element.type = kwargs['type']277 ret.part[current_part].element[element.id] = element278 if kw == 'ELSET':279 if count['keyword_line'] == 0:280 elset = Set()281 elset.name = kwargs['elset']282 if 'instance' in kwargs:283 elset.instance = kwargs['instance']284 ret.set['element'][elset.name] = elset285 else:286 elset.part = current_part287 ret.part[current_part].set['element'][elset.name] = elset288 if count['keyword_line'] > 0:289 parts = line.split(',')290 try:291 if kwargs['generate']:292 start = int(parts[0])293 stop = int(parts[1]) + 1294 inc = int(parts[2])295 for i in range(start, stop, inc):296 elset.append(i)297 except:298 for i in parts:299 elset.append(int(i))300 if kw == 'NSET':301 if count['keyword_line'] == 0:302 nset = Set()303 nset.name = kwargs['nset']304 if 'instance' in kwargs:305 nset.instance = kwargs['instance']306 ret.set['node'][nset.name] = nset307 else:308 nset.part = current_part309 ret.part[current_part].set['node'][nset.name] = nset310 if count['keyword_line'] > 0:311 parts = line.split(',')312 try:313 if kwargs['generate']:314 start = int(parts[0])315 stop = int(parts[1]) + 1316 inc = int(parts[2])317 for i in range(start, stop, inc):318 nset.append(i)319 except:320 for i in parts:321 nset.append(int(i))322 update_term(True)323 #import pdb; pdb.set_trace()324 return ret325def WriteDynaFromAbaqus(total_nodel, inp_name, abaqus_keyword, ostream):326 #global total_nodel327 written_nodel = 0328 def update_term(complete=False):329 #global total_nodel330 #global ostream331 total = total_nodel332 counted = count['node'] + count['element']333 perc = int(1000 * counted * 1.0 / total)334 old_perc = int(1000 * (counted-1)*1.0/total)335 if perc != old_perc or counted == 1:336 status = 'Compiling data ({:5.1f}% complete)'.format(perc/10)337 if complete:338 to_write = status + '...done\n'339 else:340 to_write = status + '\r'341 sys.stdout.write(to_write)342 sys.stdout.flush()343 inp = abaqus_keyword344 output = {}345 output['header'] = (346 '$ LS-DYNA keyword input file\n' +347 '$ Auto-translated from ' + inp_name +348 ' by abaqus2dyna.py\n')349 output['timestamp'] = ('$ translated at: ' +350 datetime.datetime.utcnow().strftime("%y-%m-%d %H:%M:%S UTC") + '\n')351 output['data'] = tempfile.TemporaryFile(mode='w+')352 output['stats'] = {}353 output['stats']['pid'] = []354 output['stats']['esid'] = []355 output['stats']['nsid'] = []356 def comment_line(string, fill='', newline=True):357 ret = ('${:' + fill + '^78s}$').format(string)358 if newline:359 ret += '\n'360 return ret361 set_comment_sep = comment_line('',fill='-')362 set_comment_fmt = '${:>12s}{:12d}' + ' '*12 + '{:42s}$\n'363 set_comment_head = ('${:_>12s}{:_>12s}'+'_'*12 + '{:_<42s}$\n'364 ).format('type','id','name')365 output['sep'] = comment_line('',fill='*')366 count = collections.Counter()367 offset = collections.Counter()368 # need to write nodes, then elements, then sets369 for i in inp.instance:370 #print('Writing instance ' + i)371 count['part'] += 1372 output['data'].write(comment_line('',fill='*'))373 output['data'].write(comment_line('Data for part ' + i + ', pid=' + str(count['part'])))374 output['data'].write(comment_line('',fill='*'))375 instance = inp.instance[i]376 rotation_matrix = instance.rotation_matrix377 output['stats']['pid'].append([count['part'],instance.name])378 # write nodes379 offset['node'] = count['node']380 offset['element'] = count['element']381 #import pdb; pdb.set_trace()382 if inp.part[instance.part].node:383 output['data'].write('*NODE\n')384 node_fmt = '{0:8d}{1[0]:16.8e}{1[1]:16.8e}{1[2]:16.8e}\n'385 for j in inp.part[instance.part].node:386 node = inp.part[instance.part].node[j]387 id = node.id + offset['node']388 orig_pos = node.pos389 final_pos = rotation_matrix.dot(orig_pos) #rotation390 final_pos += instance.translation #translation391 output['data'].write(node_fmt.format(id,final_pos))392 count['node'] += 1393 update_term()394 element_conversion = {'C3D8R':'SOLID',395 'S4R':'SHELL'}396 if inp.part[instance.part].element:397 current_type = None398 current_has_orient = None399 element_fmt = '{:8d}{:8d}{:8d}{:8d}{:8d}{:8d}{:8d}{:8d}{:8d}{:8d}\n'400 for j in inp.part[instance.part].element:401 element = inp.part[instance.part].element[j]402 id = element.id + offset['element']403 this_has_orient = False404 this_orient = None405 if element_conversion[element.type] == 'SOLID':406 for k in inp.part[instance.part].section:407 if element.id in inp.part[instance.part].set['element'][k.elset]:408 this_has_orient = True409 this_orient = inp.part[instance.part].orientation[k.orientation]410 continue411 if element.type != current_type or this_has_orient != current_has_orient:412 output['data'].write('*ELEMENT_' + element_conversion[element.type])413 if this_has_orient:414 output['data'].write('_ORTHO')415 output['data'].write('\n')416 current_type = element.type417 current_has_orient = this_has_orient418 nodes = (np.array(element.node) + offset['node']).tolist()419 for k in range(8 - len(nodes)):420 nodes.append(0)421 #import pdb; pdb.set_trace()422 output['data'].write(element_fmt.format(id,count['part'],*nodes))423 if current_has_orient:424 a = np.empty(3)425 d = np.empty(3)426 # get element centroid427 centroid = np.zeros(3)428 for k in element.node:429 centroid += inp.part[instance.part].node[k].pos430 centroid /= len(nodes)431 system = this_orient.system432 if system == 'CYLINDRICAL':433 #import pdb; pdb.set_trace()434 c = this_orient.b - this_orient.a435 c /= np.linalg.norm(c)436 g = centroid - this_orient.a # to centroid from a437 h = c.dot(g) # distance along _ab_ to centroid438 h = this_orient.a + h*c # vector along _ab_ to centroid439 a = centroid - h440 a /= np.linalg.norm(a)441 d = np.cross(c,a)442 # maybe an additional rotation?443 if this_orient.rot_axis == 1:444 axis_point = a445 elif this_orient.rot_axis == 2:446 axis_point = d447 else:448 axis_point = c449 rotation_matrix = GetRotationMatrix([0,0,0],axis_point,this_orient.rot)450 a = rotation_matrix.dot(a)451 d = rotation_matrix.dot(d)452 # rotate local CS with instance453 rotation_matrix = instance.rotation_matrix454 a = rotation_matrix.dot(a) #rotation455 #a += instance.translation #translation456 d = rotation_matrix.dot(d) #rotation457 #d += instance.translation #translation458 d /= np.linalg.norm(d)459 a /= np.linalg.norm(a)460 #import pdb; pdb.set_trace()461 if system in ['RECTANGULAR',None]:462 a = this_orient.a463 a /= np.linalg.norm(a)464 b = this_orient.b465 b /= np.linalg.norm(b)466 c = np.cross(a,b)467 d = np.cross(c,a)468 # maybe an additional rotation?469 if this_orient.rot_axis == 1:470 axis_point = a471 elif this_orient.rot_axis == 2:472 axis_point = d473 else:474 axis_point = c475 rotation_matrix = GetRotationMatrix([0,0,0],axis_point,this_orient.rot)476 a = rotation_matrix.dot(a)477 d = rotation_matrix.dot(d)478 # rotate local CS with instance479 rotation_matrix = instance.rotation_matrix480 a = rotation_matrix.dot(a) #rotation481 #a += instance.translation #translation482 d = rotation_matrix.dot(d) #rotation483 #d += instance.translation #translation484 d /= np.linalg.norm(d)485 a /= np.linalg.norm(a)486 #import pdb; pdb.set_trace()487 else:488 raise Exception('yep, ' + system + ' not yet implemented')489 output['data'].write('{0[0]:16.7e}{0[1]:16.7e}{0[2]:16.7e}\n'.format(a))490 output['data'].write('{0[0]:16.7e}{0[1]:16.7e}{0[2]:16.7e}\n'.format(d))491 count['element'] += 1492 update_term()493 # sets494 for k in inp.set['element']:495 if inp.set['element'][k].instance == instance.name:496 #TODO, need to check that all elements are same type (for DYNA sake)497 start = True498 set_naming_parts = k.split(':')499 set_name = set_naming_parts[1]500 set_id = int(set_naming_parts[0][1:])501 tmp_element_count = 0502 for m in inp.set['element'][k]:503 if start:504 element = inp.part[instance.part].element[m]505 output['data'].write('*SET_' + element_conversion[element.type] + '\n')506 output['data'].write('{:10d}\n'.format(set_id))507 start = False508 if tmp_element_count > 7:509 output['data'].write('\n')510 tmp_element_count = 0511 output['data'].write('{:10d}'.format(m + offset['element']))512 tmp_element_count += 1513 if tmp_element_count <= 8:514 output['data'].write('\n')515 count['elset'] += 1516 output['stats']['esid'].append([set_id,set_name])517 for k in inp.set['node']:518 if inp.set['node'][k].instance == instance.name:519 #TODO, need to check that all elements are same type (for DYNA sake)520 start = True521 set_naming_parts = k.split(':')522 set_name = set_naming_parts[1]523 set_id = int(set_naming_parts[0][1:])524 tmp_node_count = 0525 for m in inp.set['node'][k]:526 if start:527 output['data'].write('*SET_NODE\n')528 output['data'].write('{:10d}\n'.format(set_id))529 start = False530 if tmp_node_count > 7:531 output['data'].write('\n')532 tmp_node_count = 0533 output['data'].write('{:10d}'.format(m + offset['node']))534 tmp_node_count += 1535 if tmp_node_count <= 8:536 output['data'].write('\n')537 count['nodeset'] += 1538 output['stats']['nsid'].append([set_id,set_name])539 update_term(True)540 k = ostream541 k.write(output['header'])542 k.write(output['timestamp'])543 k.write(output['sep'])544 # statistics545 k.write(comment_line('Model Stats'))546 k.write(set_comment_head)547 for i in output['stats']:548 for j in output['stats'][i]:549 k.write(set_comment_fmt.format(i,j[0],j[1]))550 k.write(set_comment_sep)551 output['data'].seek(0)552 k.write(output['sep'] + output['data'].read())553 output['data'].close()554 k.write(output['sep'])555 k.write('*END\n')556 k.write(comment_line('End of translated output.', fill='-', newline=False))557 return558def cmdline(argv = None):559 """ command line processor560 returns namespace via argparse, or throws SystemExit561 if argv is none, get from sys.argv (via argparse)562 """563 from . import _version564 version = _version.get_versions()['version']565 # argument parsing definitions566 parser = argparse.ArgumentParser(prog='abaqus2dyna',567 description='Translate Abaqus to LS-DYNA')568 parser.add_argument('--version',569 action='version',570 version='%(prog)s ' + version)571 parser.add_argument('input',572 metavar='INPUT',573 help='Abaqus keyword file')574 parser.add_argument('-o', '--output',575 dest='output',576 metavar='OUTPUT',577 help='LS-DYNA keyword file output location')578 args = parser.parse_args(argv)579 return args580def convert(fin, fout):581 inp = ParseAbaqus(fin)582 #print(inp.count)583 # get nodes + elements (these will take the longest)584 total_nodel = 0585 for i in inp.instance:586 part = inp.part[inp.instance[i].part]587 total_nodel += len(part.node)588 total_nodel += len(part.element)589 # finally, output dyna keyword590 WriteDynaFromAbaqus(total_nodel, fin.name, inp, fout)591def main():592 args = cmdline()593 with open(args.input) as fin:594 if args.output:595 fout = open(args.output, 'w')596 else:597 fout = sys.stdout598 try:599 return convert(fin, fout)600 finally:601 if args.output:602 fout.close()603if __name__ == '__main__':...
SQLlib.py
Source:SQLlib.py
1import copy2import pymysql3class mainSQL(object):4 def __init__(self, host, port, user, password, database, charset):5 '''MySQLæ ¸å¿æå¡'''6 self.host = host7 self.port = port8 self.user = user9 self.password = password10 self.database = database11 self.charset = charset12 self.db = pymysql.connect(host=self.host,13 port=self.port,14 user=self.user,15 passwd=self.password,16 db=self.database,17 charset=self.charset)18 def find(self, mode, line, table, keyword_line, keyword):19 '''æç´¢æ°æ®20 模å¼ï¼FULLTEXT(精确å¹é
) DIM(模ç³æç´¢)21 æªæ¾å°å¹é
çå¼æ¶è¿åFalse22 lineï¼å¹é
åæåçå23 tableï¼æ¥è¯¢ç表24 keyword_lineï¼éè¦å¹é
çå25 keywordï¼éè¦å¹é
çå
³é®å26 è¾åºæ ¼å¼:[ç»æå表[æ¯åç»æ]]'''27 fill_data = dict(line=line, table=table,28 keyword_line=keyword_line, keyword=keyword)29 sql = "SELECT {line} FROM {table} WHERE {keyword_line}"30 if mode == "FULLTEXT":31 sql += "'{keyword}'"32 if mode == "DIM":33 sql += "LIKE '%%%%{keyword}%%%%'"34 sql = sql.format(**fill_data)35 self._link_checkout()36 cursor = self.db.cursor()37 try:38 cursor.execute(sql)39 results = cursor.fetchall()40 self.db.commit()41 cursor.close()42 return results43 except:44 return False45 def multires_finds(self, line, table, keyword_line, keyword, compare_mode="="):46 '''æç´¢æ°æ®ï¼å¤ç»æçï¼47 ãç±ä¸ä¸ªå¹é
ç»æè¾åºå¤ä¸ªåæ°æ®ã48 模å¼ï¼FULLTEXT(精确å¹é
)49 æªæ¾å°å¹é
çå¼æ¶è¿åFalse50 lineï¼å¹é
åæåçåãå表å
ç´ ã51 tableï¼æ¥è¯¢ç表52 keyword_lineï¼éè¦å¹é
çå53 keywordï¼éè¦å¹é
çå
³é®å54 compare_mode:æ¯è¾æ¨¡å¼ï¼æ¯æ<,>,=ï¼é»è®¤= 55 è¾åºæ ¼å¼:[{åå:ç»æ, åå:ç»æ...}]'''56 fill_data = dict(table=table, keyword_line=keyword_line,57 compare_mode=compare_mode, keyword=keyword)58 sql = "SELECT "59 index = 160 # 1234 >> ["1","2","3","4"] >> ["1",",","2",",","3",",","4"] >> 1,2,3,461 while index < len(line):62 line.insert(index, ',')63 index += 264 for x in line:65 sql += x66 sql += " FROM {table} WHERE {keyword_line} {compare_mode} "67 if isinstance(keyword, (int, float)):68 sql += "{keyword}"69 else:70 sql += "'{keyword}'"71 sql = sql.format(**fill_data)72 self._link_checkout()73 cursor = self.db.cursor(pymysql.cursors.DictCursor)74 try:75 cursor.execute(sql)76 results = cursor.fetchall()77 self.db.commit()78 cursor.close()79 # return tuple(results[0])80 return list(results)81 except:82 results = []83 [results.append(False) for x in range(len(line))]84 return tuple(results)85 def multi_finds(self, fulltext_mode, line, table, keyword_line, keyword, compare_mode=[]):86 '''æç´¢æ°æ®ï¼å¤å
³é®åå¤ç»æçï¼87 ãæ¯æå¤å
³é®åã88 ãæ¯æå¤å
³é®è¡ã89 ãæ¯æè¾åºååç»æ//å·²éå²ã90 ãæ¯æè¾åºå¤ä¸ªç»æã91 ï½å®ç¨çï½92 fulltext模å¼ï¼True(精确å¹é
) False(模ç³æç´¢)93 compare模å¼ï¼>,<,=(ä»
æ=æ¶æ¨¡ç³æç´¢çæï¼æªæå®æ¶ä¸ºé»è®¤å¼=)94 æªæ¾å°å¹é
çå¼æ¶è¿åFalse95 lineï¼å¹é
åæåçå96 tableï¼æ¥è¯¢ç表97 keyword_lineï¼éè¦å¹é
çåãå表å
ç´ ã98 keywordï¼éè¦å¹é
çå
³é®åãå表å
ç´ ã99 è¾åºæ ¼å¼:[ç»æ, ç»æ...]100 注ï¼keyword_lineä¸keywordæ°ç®å¿
é¡»ä¸è´ï¼å¹é
模å¼æ°ç®ä¸è¶³é»è®¤æFULLTEXT模å¼å¡«å
'''101 sql = ""102 sql = self._sel_part(sql, [line], table)103 # Processing keyword&line104 sql = self._where_part(105 sql, fulltext_mode, keyword_line, keyword, compare_mode)106 self._link_checkout()107 cursor = self.db.cursor()108 try:109 cursor.execute(sql)110 results_raw = cursor.fetchall()111 self.db.commit()112 cursor.close()113 results = []114 [results.extend(list(x)) for x in results_raw]115 return results116 except:117 return False118 # 以ä¸ä¸ºæ§çåè½å®ç°å½æ°119 def _sel_part(self, sql_sent, line, table):120 '''å离æé ï¼SELECT FROM é¨åï¼å¤ç»æ121 å
ç½®WHEREï¼å æ¤å¿
é¡»æ¼æ¥æ¡ä»¶'''122 sql_sent += "SELECT "123 index = 1124 dot = 0125 line_queue = copy.deepcopy(line)126 # 1234 >> ["1","2","3","4"] >> ["1",",","2",",","3",",","4"] >> 1,2,3,4127 while index < len(line) + dot:128 line_queue.insert(index, ',')129 index += 2130 dot += 1131 for x in line_queue:132 sql_sent += x133 sql_sent += " FROM {} WHERE ".format(table)134 return sql_sent135 def _del_part(self, sql_sent, table):136 '''å离æé ï¼DELETE FROM é¨å137 å
ç½®WHERE'''138 sql_sent += "DELETE FROM {} WHERE ".format(table)139 return sql_sent140 def _ins_part(self, sql_sent, line, value, table):141 '''å离æé ï¼INSERT INTO é¨åï¼å¤åæ°æ®'''142 index = 0143 queue_line = "("144 for i in line:145 queue_line += i146 index += 1147 if index < len(line):148 queue_line += ","149 queue_line += ")"150 # éè¦é¢å¤è¿è¡æ¼æ¥é²æ¢lineåå为åå符串è导è´å¼å·é®é¢151 if len(value) == 1:152 val = "('{}')".format(tuple(value)[0]) # æ¤å¤ä¸ºäºä¿®å¤ä»
æå个å
ç´ è½¬æ¢æ¶æ®çä¸ä¸ªéå·é®é¢153 else:154 val = tuple(value)155 sql_sent += "INSERT INTO {table_name} {field} VALUES {value}".format(156 table_name=table, field=queue_line, value=str(val))157 return sql_sent158 def _up_part(self, sql_sent, line, value, table):159 '''å离æé ï¼UPDATE SET é¨åï¼å¤åæ°æ®160 å
ç½®WHEREï¼å æ¤å¿
é¡»æ¼æ¥æ¡ä»¶'''161 sql_sent += "UPDATE {table_name} SET ".format(table_name=table)162 index = 0163 for k, v in zip(line, value):164 if isinstance(v, (int, float)):165 sql_sent += "{field}={value}".format(field=k, value=v)166 else:167 sql_sent += "{field}='{value}'".format(field=k, value=v)168 index += 1169 if index < len(line):170 sql_sent += ", "171 sql_sent += " WHERE "172 return sql_sent173 def _where_part(self, sql_sent, fulltext_mode, keyword_line, keyword, compare_mode=[]):174 '''å离æé ï¼WHERE é¨å(ä¸ä¼èªå¨å WHERE),å¤æ¡ä»¶175 é»è¾å¤æä»
æANDæ¹å¼176 å离WHEREçç®çæ¯ä¸ºäºä¸»è°å½æ°å¨ä¹å追å é¢å¤æ¡ä»¶ï¼å¦è¡¨æ¼æ¥ï¼'''177 if len(fulltext_mode) < len(keyword):178 [179 fulltext_mode.append(True)180 for i in range(len(keyword) - len(fulltext_mode))181 ] # Auto fill 'false' when mode_list not enough182 if len(compare_mode) < len(keyword):183 [184 compare_mode.append("=")185 for i in range(len(keyword) - len(compare_mode))186 ] # Auto fill '=' when compare_mode not enough by defult187 index = 0188 for m, n, l, w in zip(fulltext_mode, compare_mode, keyword_line, keyword):189 fill_data = dict(compare_mode=n, keyword_line=l, keyword=w)190 sql_sent += "{keyword_line} "191 if n == "=" and not m:192 sql_sent += "LIKE '%%%%{keyword}%%%%'"193 else:194 sql_sent += " {compare_mode} "195 if isinstance(w, (int, float)):196 sql_sent += "{keyword}"197 else:198 sql_sent += "'{keyword}'"199 index += 1200 if index < len(keyword):201 sql_sent += " AND "202 sql_sent = sql_sent.format(**fill_data)203 return sql_sent204 def _link_checkout(self):205 '''å离æé ï¼èªå¨è¿æ¥æ£æ¥æºå¶'''206 try:207 self.db.ping()208 except self.db.OperationalError:209 self.__init__(self.host, self.port, self.user, self.password,210 self.database, self.charset)211 def multi_table_find(self, fulltext_mode, line, table, keyword_line,212 keyword, bind_key, compare_mode=[]):213 '''æç´¢æ°æ®ï¼å¤å
³é®åå¤ç»æç以å表èç»ä¸çï¼214 ãæ¯æå¤å
³é®åã215 ãæ¯æå¤å
³é®è¡ã216 ãæ¯æè¾åºå¤åç»æ//å²è¯ç继æ¿è
ã217 ãæ¯æè¾åºå¤ä¸ªç»æã218 ãå¤è¡¨æ¼æ¥ä¸ç¨ï¼ç®åä»
æ¯æèç»ä¸¤ä¸ªè¡¨ã219 ï½ä¸ç¨çï½220 fulltext模å¼ï¼True(精确å¹é
) False(模ç³æç´¢)221 compare模å¼ï¼>,<,=(ä»
æ=æ¶æ¨¡ç³æç´¢çæï¼ä¸ºæå®æ¶ä¸ºé»è®¤å¼=)222 æªæ¾å°å¹é
çå¼æ¶è¿åFalse223 lineï¼å¹é
åæåçåãå表å
ç´ ã224 tableï¼æ¥è¯¢ç表ã两个å表å
ç´ ã225 keyword_lineï¼éè¦å¹é
çåãå表å
ç´ ã226 keywordï¼éè¦å¹é
çå
³é®åãå表å
ç´ ã227 bind_keyï¼èç»ä½¿ç¨çç»å®é®ã两个å表å
ç´ ã228 è¾åºæ ¼å¼:[{åå:ç»æ, åå:ç»æ...}]229 注ï¼keyword_lineä¸keywordæ°ç®å¿
é¡»ä¸è´ï¼å¹é
模å¼æ°ç®ä¸è¶³é»è®¤æFULLTEXT模å¼å¡«å
'''230 sql = ""231 index = 1232 index = 1233 str_table = ""234 while index < len(table): # table235 table.insert(index, ',')236 index += 2237 for x in table:238 str_table += x239 sql = self._sel_part(sql, line, str_table)240 sql += '{}.{} = {}.{} AND '.format(table[0], bind_key[0], table[-1:][0],241 bind_key[1])242 sql = self._where_part(243 sql, fulltext_mode, keyword_line, keyword, compare_mode)244 self._link_checkout()245 cursor = self.db.cursor(pymysql.cursors.DictCursor)246 try:247 cursor.execute(sql)248 results = cursor.fetchall()249 self.db.commit()250 cursor.close()251 return list(results)252 except:253 # print(e)254 return False255 def epic_finds(self, fulltext_mode, line, table, keyword_line, keyword):256 '''æç´¢æ°æ®ï¼å¤å
³é®åå¤ç»æçï¼257 ãæ¯æå¤å
³é®åã258 ãæ¯æå¤å
³é®è¡ã259 ãæ¯æè¾åºå¤åç»æã260 ãæ¯æè¾åºå¤ä¸ªç»æã261 ï½ç©¶æç»æçï¼ç°å¨ä¸æ¯äºï¼//å®å
¨æ éå²ï½262 模å¼ï¼True(精确å¹é
) False(模ç³æç´¢)263 æªæ¾å°å¹é
çå¼æ¶è¿åFalse264 lineï¼å¹é
åæåçåãå表å
ç´ ã265 tableï¼æ¥è¯¢ç表266 keyword_lineï¼éè¦å¹é
çåãå表å
ç´ ã267 keywordï¼éè¦å¹é
çå
³é®åãå表å
ç´ ã268 è¾åºæ ¼å¼:[{åå:ç»æ, åå:ç»æ...}]269 注ï¼keyword_lineä¸keywordæ°ç®å¿
é¡»ä¸è´ï¼å¹é
模å¼æ°ç®ä¸è¶³é»è®¤æFULLTEXT模å¼å¡«å
'''270 sql = "SELECT "271 index = 1272 # Processing lines273 # 1234 >> ["1","2","3","4"] >> ["1",",","2",",","3",",","4"] >> 1,2,3,4274 while index < len(line):275 line.insert(index, ',')276 index += 2277 for x in line:278 sql += x279 # Processing table280 sql += ' FROM %s WHERE ' % table281 # Processing keyword&line282 index = 1283 if len(fulltext_mode) < len(keyword):284 [285 fulltext_mode.append(False)286 for i in range(len(keyword) - len(fulltext_mode))287 ] # Auto fill 'false' when mode_list not enough288 for m, l, w in zip(fulltext_mode, keyword_line, keyword):289 if m:290 sql += "%s = '%s'" % (l, w)291 index += 1292 else:293 sql += "%s LIKE '%%%%%s%%%%'" % (l, w)294 index += 1295 if index < len(keyword):296 sql += " AND "297 self._link_checkout()298 cursor = self.db.cursor(pymysql.cursors.DictCursor)299 try:300 cursor.execute(sql)301 results = cursor.fetchall()302 self.db.commit()303 cursor.close()304 # return tuple(results[0])305 return results306 except:307 return False308 def finder_single(self, fulltext_mode, line, table, keyword_line, keyword, compare_mode=[],):309 '''æ°æ®åºæç´¢å¨ï¼å表æç»çï¼310 æ¯æå¤å
³é®åï¼å
³é®è¡ï¼å¤åç»æåå¤ä¸ªç»æ311 {é«åº¦å
¼å®¹ç}312 tableï¼æ¥è¯¢ç表313 ã以ä¸åéå使ç¨å表å
ç´ ã314 fulltext模å¼ï¼True(精确å¹é
) False(模ç³æç´¢)315 compare模å¼ï¼>,<,=(ä»
æ=æ¶æ¨¡ç³æç´¢çæï¼æªæå®æ¶ä¸ºé»è®¤å¼=)316 lineï¼å¹é
åæåçå317 keyword_lineï¼éè¦å¹é
çå318 keywordï¼éè¦å¹é
çå
³é®å319 è¾åºæ ¼å¼:[{åå:ç»æ, åå:ç»æ...}] #æ°ç»å¯¹è±¡320 å½hookåæ°å¯ç¨æ¶ï¼å为æ°æ®åºéæ©å¨ï¼è¿åæé è¯å¥321 ãæªæ¾å°å¹é
çå¼æ¶è¿åFalseã322 '''323 sql = ""324 sql = self._sel_part(sql, line, table)325 sql = self._where_part(326 sql, fulltext_mode, keyword_line, keyword, compare_mode)327 self._link_checkout()328 cursor = self.db.cursor(pymysql.cursors.DictCursor)329 try:330 cursor.execute(sql)331 results = cursor.fetchall()332 self.db.commit()333 cursor.close()334 return list(results)335 except:336 return False337 def adder_single(self, fulltext_mode, line, table, value, keyword_line, keyword, compare_mode=[]):338 '''æ°æ®åºæ·»å /æ´æ°å¨ï¼å表åï¼339 æ¯æå¤å
³é®åï¼å
³é®è¡ï¼å¤åç»æåå¤è¾å
¥æ°æ®340 ä¼æ ¹æ®è¯·æ±çæ°æ®åå¨æ
åµä½¿ç¨æå
¥æè
æ´æ°æä½341 tableï¼æä½ç表342 ã以ä¸åéå使ç¨å表å
ç´ ã343 fulltext模å¼ï¼True(精确å¹é
) False(模ç³æç´¢)344 compare模å¼ï¼>,<,=(ä»
æ=æ¶æ¨¡ç³æç´¢çæï¼æªæå®æ¶ä¸ºé»è®¤å¼=)345 lineï¼å¹é
åæä½çå346 value:æå
¥/æ´æ°å
容347 {ååå
容å¿
é¡»ä¸¥æ ¼å¹é
}348 keyword_lineï¼éè¦å¹é
çå349 keywordï¼éè¦å¹é
çå
³é®å350 è¾åºæ ¼å¼ï¼æä½æåæ¶ï¼æç
§å®é
æä½æ
åµä¸º INS(æå
¥)ï¼ UP(æ´æ°)ï¼å¤±è´¥æ¶è¿åFalse351 '''352 if not len(line) == len(value):353 return False354 sql = ""355 operation = ""356 if self.finder_single(fulltext_mode, line, table, keyword_line, keyword, compare_mode):357 sql = self._up_part(sql, line, value, table)358 sql = self._where_part(sql, fulltext_mode, keyword_line, keyword)359 operation = "UP"360 else:361 sql = self._ins_part(sql, line, value, table)362 operation = "INS"363 self._link_checkout()364 cursor = self.db.cursor(pymysql.cursors.DictCursor)365 try:366 cursor.execute(sql)367 cursor.fetchall()368 self.db.commit()369 cursor.close()370 return operation371 except:372 self.db.rollback()373 return False374 def delete_single(self, fulltext_mode, table, keyword_line, keyword, compare_mode=[]):375 '''376 å é¤å¨377 æ¯æå¤å
³é®åï¼å
³é®è¡378 tableï¼æ¥è¯¢ç表379 ã以ä¸åéå使ç¨å表å
ç´ ã380 fulltext模å¼ï¼True(精确å¹é
) False(模ç³æç´¢)381 compare模å¼ï¼>,<,=(ä»
æ=æ¶æ¨¡ç³æç´¢çæï¼æªæå®æ¶ä¸ºé»è®¤å¼=)382 keyword_lineï¼éè¦å¹é
çå383 keywordï¼éè¦å¹é
çå
³é®å384 æ è¾åºæ°æ®åºå
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åµè¾åºTrueåFalseã386 '''387 sql = ""388 sql = self._del_part(sql, table)389 sql = self._where_part(390 sql, fulltext_mode, keyword_line, keyword, compare_mode)391 self._link_checkout()392 cursor = self.db.cursor(pymysql.cursors.DictCursor)393 try:394 cursor.execute(sql)395 cursor.fetchall()396 self.db.commit()397 cursor.close()398 return True399 except:...
extract_model_params_from_terachem.py
Source:extract_model_params_from_terachem.py
1#! /usr/bin/env python2import sys 3import os.path4import numpy as np5import math6import numba7from spec_pkg.constants import constants as const8def get_gs_energy(input_path_gs):9 search_phrase='FINAL ENERGY:'10 searchfile = open(input_path_gs,"r")11 line_count=012 keyword_line=99999999913 for line in searchfile:14 if search_phrase in line and keyword_line==999999999:15 keyword_line=line_count16 line_count=line_count+117 # if we haven't found reference geometry, break18 if keyword_line==999999999:19 sys.exit('Error: Could not find final ground state energy in Terachem file: '+input_path)20 linefile=open(input_path_gs,"r")21 lines=linefile.readlines()22 energy_line=lines[keyword_line].split()23 return float(energy_line[2])24# root determines which root is the root of interest. by default this is 125def get_ex_energy_dipole_mom(input_path_ex,root):26 search_phrase='Final Excited State Results:'27 searchfile = open(input_path_ex,"r")28 line_count=029 keyword_line=99999999930 for line in searchfile:31 if search_phrase in line and keyword_line==999999999:32 keyword_line=line_count33 line_count=line_count+134 if keyword_line==999999999:35 sys.exit('Error: Could not find excited state energy and dipole moment in Terachem file: '+input_path)36 searchfile.close()37 linefile=open(input_path_ex,"r")38 lines=linefile.readlines()39 energy_line=lines[keyword_line+3+root].split()40 energy=float(energy_line[1])41 ex_energy=float(energy_line[2])/const.Ha_to_eV # convert to Ha 42 searchfile = open(input_path_ex,"r")43 search_phrase='Transition dipole moments:'44 line_count=045 keyword_line=99999999946 for line in searchfile:47 if search_phrase in line and keyword_line==999999999:48 keyword_line=line_count49 line_count=line_count+150 if keyword_line==999999999:51 sys.exit('Error: Could not find excited state energy and dipole moment in Terachem file: '+input_path)52 searchfile.close()53 linefile=open(input_path_ex,"r")54 lines=linefile.readlines() 55 dipole_line=lines[keyword_line+3+root].split()56 dipole_mom=np.zeros(3)57 dipole_mom[0]=float(dipole_line[1])58 dipole_mom[1]=float(dipole_line[2])59 dipole_mom[2]=float(dipole_line[3])60 return energy,dipole_mom61def get_e_adiabatic_dipole(input_path_gs,input_path_ex,root):62 ex_energy,dipole_mom=get_ex_energy_dipole_mom(input_path_ex,root)63 gs_energy=get_gs_energy(input_path_gs)64 return dipole_mom,ex_energy-gs_energy65# Test this66def get_specific_dipole(input_path,displacement,root,ref_dipole):67 search_phrase1='*** Displacement '+str(displacement)+' ***'68 search_phrase2='Transition dipole moments:'69 dipole_vec=np.zeros(3)70 searchfile = open(input_path,"r")71 line_count=072 keyword_line=99999999973 for line in searchfile:74 if search_phrase1 in line and keyword_line==999999999:75 keyword_line=line_count76 line_count=line_count+177 total_line_number=line_count-178 linefile=open(input_path,"r")79 lines=linefile.readlines()80 # if we haven't found specific displacement, break81 if keyword_line==999999999:82 sys.exit('Error: Could not find transition dipole moment for Displacement '+str(displacement))83 line_count=keyword_line84 keyword_line2=99999999985 while line_count<total_line_number:86 if search_phrase2 in lines[line_count] and keyword_line2==999999999:87 keyword_line2=line_count88 line_count=line_count+189 # if we havent found the gradient following the displacement, break90 if keyword_line2==999999999:91 sys.exit('Error: Could not find transition dipole moment for Displacement '+str(displacement))92 line_start=keyword_line2+3+root93 current_line=lines[line_start].split()94 95 dipole_vec[0]=float(current_line[1])96 dipole_vec[1]=float(current_line[2])97 dipole_vec[2]=float(current_line[3])98 # Check sign relative to reference dipole moment99 if np.dot(dipole_vec,ref_dipole)/(np.dot(dipole_vec,dipole_vec)*np.dot(ref_dipole,ref_dipole))<-0.5:100 dipole_vec=-1.0*dipole_vec101 return dipole_vec102# Works103def get_specific_grad(input_path,displacement,num_atoms):104 search_phrase1='*** Displacement '+str(displacement)+' ***'105 search_phrase2='dE/dX dE/dY dE/dZ'106 grad_vec=np.zeros(num_atoms*3)107 searchfile = open(input_path,"r")108 line_count=0109 keyword_line=999999999110 for line in searchfile:111 if search_phrase1 in line and keyword_line==999999999:112 keyword_line=line_count113 line_count=line_count+1114 total_line_number=line_count-1115 linefile=open(input_path,"r")116 lines=linefile.readlines()117 # if we haven't found specific displacement, break118 if keyword_line==999999999:119 sys.exit('Error: Could not find gradient for Displacement '+str(displacement))120 line_count=keyword_line121 keyword_line2=999999999122 while line_count<total_line_number:123 if search_phrase2 in lines[line_count] and keyword_line2==999999999:124 keyword_line2=line_count125 line_count=line_count+1126 # if we havent found the gradient following the displacement, break127 if keyword_line2==999999999:128 sys.exit('Error: Could not find gradient for Displacement '+str(displacement))129 line_start=keyword_line2+1130 # loop over number of atoms to extract the gradient vec131 atom_count=0132 while atom_count<num_atoms:133 current_line=lines[line_start+atom_count].split()134 dx=float(current_line[0])135 dy=float(current_line[1])136 dz=float(current_line[2])137 grad_vec[atom_count*3]=dx138 grad_vec[atom_count*3+1]=dy139 grad_vec[atom_count*3+2]=dz140 atom_count=atom_count+1141 return grad_vec 142def get_dipole_deriv_from_terachem(input_path,frozen_atom_list,num_frozen_atoms,root):143 # ref dipole: 144 energy,ref_dipole=get_ex_energy_dipole_mom(input_path,root)145 num_atoms=frozen_atom_list.shape[0]146 dipole_deriv=np.zeros((3,num_atoms*3))147 displacement=0.0148 # find displacement:149 searchphrase='Using displacements of '150 searchfile = open(input_path,"r")151 line_count=0152 keyword_line=999999999153 for line in searchfile:154 if searchphrase in line and keyword_line==999999999:155 keyword_line=line_count156 line_count=line_count+1157 searchfile.close()158 if keyword_line < 9999999:159 linefile=open(input_path,"r")160 lines=linefile.readlines()161 keyword=lines[keyword_line].split()162 displacement=float(keyword[3])163 else:164 sys.exit('Error: Could not find displacement used in numerical Hessian calculation in Terachem file') 165 print('FD parameter: 2*displacement')166 print(displacement*2)167 # Now construct the dipole_derivative. First displacement is the (x+delta x) displacement, then the (x-delta x) displacement 168 unfrozen_atoms=num_atoms-num_frozen_atoms169 unfrozen_count=0170 total_atom_count=0171 while total_atom_count<num_atoms:172 # check whether this is a frozen or an unfrozen atom:173 if frozen_atom_list[total_atom_count]==0: # unfrozen174 # loop over xyz coordinates:175 xyz_count=0176 while xyz_count<3:177 print('Getting dipole ', unfrozen_count, ' of ',3*unfrozen_atoms)178 dipole1=get_specific_dipole(input_path,unfrozen_count*2+1,root,ref_dipole)179 dipole2=get_specific_dipole(input_path,unfrozen_count*2+2,root,ref_dipole)180 print(dipole1)181 print(dipole2)182 print(dipole1-dipole2)183 # build the effective row of the Hessian through the finite difference scheme. 184 fd_dipole=(dipole1-dipole2)/(2.0*displacement)185 # this seems to be the correct approach. This way, off diagonal Hessian elements are the average of the numerical and the 186 # analytical force constants187 dipole_deriv[:,total_atom_count*3+xyz_count]=fd_dipole[:]188 print(fd_dipole)189 unfrozen_count=unfrozen_count+1190 xyz_count=xyz_count+1191 total_atom_count=total_atom_count+1192 # no need to symmetrize like in the Hessian. Just return193 print('Full Dipole derivative. Units should be in a.u')194 print(dipole_deriv)195 return dipole_deriv196#Works197def get_hessian_from_terachem(input_path,frozen_atom_list,num_frozen_atoms):198 num_atoms=frozen_atom_list.shape[0] # frozen atom list is a list Natoms long, where frozen atoms199 # are labelled by 1 and unfrozen atoms labelled by 0200 hessian=np.zeros((num_atoms*3,num_atoms*3))201 displacement=0.0202 # find displacement:203 searchphrase='Using displacements of '204 searchfile = open(input_path,"r")205 line_count=0206 keyword_line=999999999207 for line in searchfile:208 if searchphrase in line and keyword_line==999999999:209 keyword_line=line_count210 line_count=line_count+1211 searchfile.close() 212 if keyword_line < 9999999:213 linefile=open(input_path,"r")214 lines=linefile.readlines()215 keyword=lines[keyword_line].split()216 displacement=float(keyword[3])217 else:218 sys.exit('Error: Could not find displacement used in numerical Hessian calculation in Terachem file')219 # Now construct the Hessian. First displacement is the (x+delta x) displacement, then the (x-delta x) displacement 220 unfrozen_atoms=num_atoms-num_frozen_atoms221 unfrozen_count=0222 total_atom_count=0223 while total_atom_count<num_atoms: 224 # check whether this is a frozen or an unfrozen atom:225 if frozen_atom_list[total_atom_count]==0: # unfrozen226 # loop over xyz coordinates:227 xyz_count=0228 while xyz_count<3:229 print('Getting gradient ', unfrozen_count, ' of ',3*unfrozen_atoms)230 grad1=get_specific_grad(input_path,unfrozen_count*2+1,num_atoms)231 grad2=get_specific_grad(input_path,unfrozen_count*2+2,num_atoms)232 # build the effective row of the Hessian through the finite difference scheme. 233 fd_grad=(grad1-grad2)/(2.0*displacement)234 235 # this seems to be the correct approach. This way, off diagonal Hessian elements are the average of the numerical and the 236 # analytical force constants237 hessian[total_atom_count*3+xyz_count,:]=fd_grad[:]238 239 unfrozen_count=unfrozen_count+1240 xyz_count=xyz_count+1241 else: # frozen atom242 # loop over xyz coordinates:243 xyz_count=0244 while xyz_count<3:245 # set block diagonal elements corresponding to purely frozen atoms to 1246 hessian[total_atom_count*3+xyz_count,total_atom_count*3+xyz_count]=1.0247 xyz_count=xyz_count+1248 total_atom_count=total_atom_count+1249 # currently the Hessian has only one off diagonal block if there are frozen atoms. Need to fix this250 i_count=0251 while i_count<num_atoms:252 j_count=i_count253 while j_count<num_atoms:254 if frozen_atom_list[i_count]==0 and frozen_atom_list[j_count]==1: # icount refers to unfrozen and jcount refers to frozen atom255 # make sure the hessian element with the frozen atom as its first index is set.256 for xyz1 in range(3):257 for xyz2 in range(3):258 hessian[j_count*3+xyz2,i_count*3+xyz1]=hessian[i_count*3+xyz1,j_count*3+xyz2]259 j_count=j_count+1260 i_count=i_count+1 261 # symmetrize hessian h_sym=0.5*(H+H.T)262 sym_hessian=0.5*(hessian+np.transpose(hessian))263 return sym_hessian264# extract both list of atomic masses and reference geometry from terachem265# Works266def get_masses_geom_from_terachem(input_path, num_atoms):267 geom=np.zeros((num_atoms,3))268 masses=np.zeros(num_atoms)269 search_phrase='*** Reference Geometry ***'270 searchfile = open(input_path,"r")271 line_count=0272 keyword_line=999999999273 for line in searchfile:274 if search_phrase in line and keyword_line==999999999:275 keyword_line=line_count276 line_count=line_count+1277 linefile=open(input_path,"r")278 lines=linefile.readlines()279 # if we haven't found reference geometry, break280 if keyword_line==999999999:281 sys.exit('Error: Could not find reference geometry in terachem file '+input_path)282 line_start=keyword_line+2283 atom_count=0284 while atom_count<num_atoms:285 current_line=lines[line_start+atom_count].split()286 geom[atom_count,0]=float(current_line[1])287 geom[atom_count,1]=float(current_line[2])288 geom[atom_count,2]=float(current_line[3])289 elem=current_line[0] # match element with mass number then store in masses array290 if elem=='H':291 masses[atom_count]=const.Mass_list[0]292 elif elem=='He':293 masses[atom_count]=const.Mass_list[1]294 elif elem=='Li':295 masses[atom_count]=const.Mass_list[2]296 elif elem=='Be':297 masses[atom_count]=const.Mass_list[3]298 elif elem=='B':299 masses[atom_count]=const.Mass_list[4]300 elif elem=='C':301 masses[atom_count]=const.Mass_list[5]302 elif elem=='N':303 masses[atom_count]=const.Mass_list[6]304 elif elem=='O':305 masses[atom_count]=const.Mass_list[7]306 elif elem=='F':307 masses[atom_count]=const.Mass_list[8]308 elif elem=='Ne':309 masses[atom_count]=const.Mass_list[9]310 elif elem=='Na':311 masses[atom_count]=const.Mass_list[10]312 elif elem=='Mg':313 masses[atom_count]=const.Mass_list[11] 314 elif elem=='Al':315 masses[atom_count]=const.Mass_list[12]316 elif elem=='Si':317 masses[atom_count]=const.Mass_list[13]318 elif elem=='P':319 masses[atom_count]=const.Mass_list[14]320 elif elem=='S':321 masses[atom_count]=const.Mass_list[15]322 elif elem=='Cl':323 masses[atom_count]=const.Mass_list[16]324 elif elem=='Ar':325 masses[atom_count]=const.Mass_list[17]326 else:327 sys.exit('Error: Could not find atomic mass for element '+elem)328 329 atom_count=atom_count+1...
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