""" Python APBS Driver File This module allows a user to run APBS through Python. Use this module if you wish to include APBS in a Python-based application. The module mimics the main.c driver that is used in the C version of APBS. The functions which are called are located in apbslib.py, which is automatically generated by SWIG to wrap each APBS function. See the APBS documentation for more information about each function. Todd Dolinsky (todd@ccb.wustl.edu) Nathan Baker (nathan.baker@pnl.gov) APBS -- Adaptive Poisson-Boltzmann Solver Nathan A. Baker (nathan.baker@pnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of Washington University in St. Louis nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. """ from apbslib import ( MGparm, NOsh_ctor, NOsh_elec2calc, NOsh_elecname, NOsh_getCalc, NOsh_parseInputFile, NOsh_printWhat, NOsh_setupElecCalc, NPT_APOLENERGY, NPT_APOLFORCE, NPT_ELECENERGY, NPT_ELECFORCE, NPT_ENERGY, NPT_FORCE, PBEparm, Vcom_ctor, Vcom_rank, Vcom_size, Vmem_ctor, atomForce, delete_Com, delete_Mem, delete_Nosh, delete_atomforcelist, delete_double_array, delete_gridlist, delete_int_array, delete_pbelist, delete_pmglist, delete_pmgplist, delete_valist, double_array, energyMG, get_AtomForce, get_Vpmg, initMG, int_array, killChargeMaps, killDielMaps, killEnergy, killForce, killKappaMaps, killMG, killMolecules, loadChargeMaps, loadDielMaps, loadKappaMaps, loadMolecules, new_atomforcelist, new_gridlist, new_pbelist, new_pmglist, new_pmgplist, new_valist, printApolEnergy, printApolForce, printElecEnergy, printElecForce, printEnergy, printForce, printMGPARM, printPBEPARM, setPartMG, solveMG, startVio, wrap_forceMG, writedataMG, writematMG, xrange, ) import sys import time from sys import stdout, stderr __author__ = "Todd Dolinsky, Nathan Baker, Yong Huang" __date__ = "September 2009" __version__ = "1.3" Python_kb = 1.3806581e-23 Python_Na = 6.0221367e23 NOSH_MAXMOL = 20 NOSH_MAXCALC = 20 class APBSError(Exception): """ APBSError class The APBSError class inherits off the Exception module and returns a string defining the nature of the error. """ def __init__(self, value): """ Initialize with error message Parameters value: Error Message (string) """ self.value = value def __str__(self): """ Return the error message """ return repr(self.value) def getHeader(): """ Get header information about APBS Returns (header) header: Information about APBS """ header = '\n\n\ ----------------------------------------------------------------------\n\ Adaptive Poisson-Boltzmann Solver (APBS)\n\ Version 1.6\n\ \n\ APBS -- Adaptive Poisson-Boltzmann Solver\n\ \n\ Nathan A. Baker (nathan.baker@pnl.gov)\n\ Pacific Northwest National Laboratory\n\ \n\ Additional contributing authors listed in the code documentation.\n\ \n\ Copyright (c) 2010-2020 Battelle Memorial Institute. \n\ Developed at the Pacific Northwest National Laboratory, \n\ operated by Battelle Memorial Institute, Pacific Northwest Division for \ the U.S. Department Energy.\n\ Portions Copyright (c) 2002-2010, Washington University in St. Louis.\n\ Portions Copyright (c) 2002-2020, Nathan A. Baker.\n\ Portions Copyright (c) 1999-2002, The Regents of the University of \ California.\n\ Portions Copyright (c) 1995, Michael Holst\n\ \n\ All rights reserved.\n\ \n\ Redistribution and use in source and binary forms, with or without\n\ modification, are permitted provided that the following conditions are \ met:\n\ \n\ * Redistributions of source code must retain the above copyright notice, \ this\n list of conditions and the following disclaimer.\n\ \n\ * Redistributions in binary form must reproduce the above copyright \ notice,\n\ this list of conditions and the following disclaimer in the \ documentation\n\ and/or other materials provided with the distribution.\n\ \n\ * Neither the name of Washington University in St. Louis nor the names of \ its\n\ contributors may be used to endorse or promote products derived from \ this\n\ software without specific prior written permission.\n\ \n\ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS\n\ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT\n\ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR\n\ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT \ OWNER OR\n\ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,\n\ EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,\n\ PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR\n\ PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF\n\ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING\n\ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS\n\ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n\ ----------------------------------------------------------------------\n\ \n\n' return header def getUsage(): """ Get usage information about running APBS via Python Returns (usage) usage: Text about running APBS via Python """ usage = "\n\n\ ----------------------------------------------------------------------\n\ This driver program calculates electrostatic potentials, energies,\n\ and forces using both multigrid methods.\n\ It is invoked as:\n\n\ python main.py apbs.in\n\ ----------------------------------------------------------------------\n\n" return usage def main(): """ Main driver for testing. Runs APBS on given input file """ # Initialize the MALOC library startVio() # Initialize variables, arrays com = Vcom_ctor(1) rank = Vcom_rank(com) size = Vcom_size(com) mgparm = MGparm() pbeparm = PBEparm() mem = Vmem_ctor("Main") pbe = new_pbelist(NOSH_MAXMOL) pmg = new_pmglist(NOSH_MAXMOL) pmgp = new_pmgplist(NOSH_MAXMOL) realCenter = double_array(3) totEnergy = [] nforce = int_array(NOSH_MAXCALC) atomforce = new_atomforcelist(NOSH_MAXCALC) # Start the main timer main_timer_start = time.clock() # Check invocation stdout.write(getHeader()) if len(sys.argv) != 2: stderr.write("main: Called with %d arguments!\n" % len(sys.argv)) stderr.write(getUsage()) raise APBSError("Incorrect Usage!") # Parse the input file nosh = NOsh_ctor(rank, size) input_file = sys.argv[1] stdout.write("Parsing input file %s...\n" % input_file) if NOsh_parseInputFile(nosh, input_file) != 1: stderr.write("main: Error while parsing input file.\n") raise APBSError("Error while parsing input file!") # Load the molecules using loadMolecules routine # loadMolecule passing NULL as second arg instead of Vparam alist = new_valist(NOSH_MAXMOL) if loadMolecules(nosh, None, alist) != 1: stderr.write("main: Error while loading molecules. \n") raise APBSError("Error while loading molecules!") # Setup the calculations if NOsh_setupElecCalc(nosh, alist) != 1: stderr.write("main: Error while setting up calculations. \n") raise APBSError("Error while setting up calculations!") # Load the necessary maps dielXMap = new_gridlist(NOSH_MAXMOL) dielYMap = new_gridlist(NOSH_MAXMOL) dielZMap = new_gridlist(NOSH_MAXMOL) if loadDielMaps(nosh, dielXMap, dielYMap, dielZMap) != 1: stderr.write("Error reading dielectric maps!\n") raise APBSError("Error reading dielectric maps!") kappaMap = new_gridlist(NOSH_MAXMOL) if loadKappaMaps(nosh, kappaMap) != 1: stderr.write("Error reading kappa maps!\n") raise APBSError("Error reading kappa maps!") chargeMap = new_gridlist(NOSH_MAXMOL) if loadChargeMaps(nosh, chargeMap) != 1: stderr.write("Error reading charge maps!\n") raise APBSError("Error reading charge maps!") # Do the calculations stdout.write("Preparing to run %d PBE calculations. \n" % nosh.ncalc) for icalc in xrange(nosh.ncalc): totEnergy.append(0.0) for icalc in xrange(nosh.ncalc): stdout.write("---------------------------------------------\n") calc = NOsh_getCalc(nosh, icalc) mgparm = calc.mgparm pbeparm = calc.pbeparm if calc.calctype != 0: stderr.write("main: Only multigrid calculations supported!\n") raise APBSError("Only multigrid calculations supported!") k = 0 for k in range(0, nosh.nelec): if NOsh_elec2calc(nosh, k) >= icalc: break name = NOsh_elecname(nosh, k) if name == "": stdout.write("CALCULATION #%d: MULTIGRID\n" % (icalc + 1)) else: stdout.write( "CALCULATION #%d (%s): MULTIGRID\n" % ((icalc + 1), name) ) stdout.write("Setting up problem...\n") # Routine initMG if ( initMG( icalc, nosh, mgparm, pbeparm, realCenter, pbe, alist, dielXMap, dielYMap, dielZMap, kappaMap, chargeMap, pmgp, pmg, ) != 1 ): stderr.write("Error setting up MG calculation!\n") raise APBSError("Error setting up MG calculation!") # Print problem parameters if desired (comment out if you want # to minimize output to stdout) printMGPARM(mgparm, realCenter) printPBEPARM(pbeparm) # Solve the problem : Routine solveMG thispmg = get_Vpmg(pmg, icalc) if solveMG(nosh, thispmg, mgparm.type) != 1: stderr.write("Error solving PDE! \n") raise APBSError("Error Solving PDE!") # Set partition information : Routine setPartMG if setPartMG(nosh, mgparm, thispmg) != 1: stderr.write("Error setting partition info!\n") raise APBSError("Error setting partition info!") # Get the energies - the energy for this calculation # (calculation number icalc) will be stored in the totEnergy array ret, totEnergy[icalc] = energyMG( nosh, icalc, thispmg, 0, totEnergy[icalc], 0.0, 0.0, 0.0 ) # Calculate forces aforce = get_AtomForce(atomforce, icalc) wrap_forceMG( mem, nosh, pbeparm, mgparm, thispmg, aforce, alist, nforce, icalc ) # Write out data from MG calculations : Routine writedataMG writedataMG(rank, nosh, pbeparm, thispmg) # Write out matrix from MG calculations writematMG(rank, nosh, pbeparm, thispmg) # Handle print statements - comment out if limiting output to stdout if nosh.nprint > 0: stdout.write("---------------------------------------------\n") stdout.write("PRINT STATEMENTS\n") for iprint in xrange(nosh.nprint): if NOsh_printWhat(nosh, iprint) == NPT_ENERGY: printEnergy(com, nosh, totEnergy, iprint) elif NOsh_printWhat(nosh, iprint) == NPT_FORCE: printForce(com, nosh, nforce, atomforce, iprint) elif NOsh_printWhat(nosh, iprint) == NPT_ELECENERGY: printElecEnergy(com, nosh, totEnergy, iprint) elif NOsh_printWhat(nosh, iprint) == NPT_ELECFORCE: printElecForce(com, nosh, nforce, atomForce, iprint) elif NOsh_printWhat(nosh, iprint) == NPT_APOLENERGY: printApolEnergy(nosh, iprint) elif NOsh_printWhat(nosh, iprint) == NPT_APOLFORCE: printApolForce(com, nosh, nforce, atomForce, iprint) else: stdout.write("Undefined PRINT keyword!\n") break stdout.write("----------------------------------------\n") stdout.write("CLEANING UP AND SHUTTING DOWN...\n") # Clean up APBS structures killForce(mem, nosh, nforce, atomforce) killEnergy() killMG(nosh, pbe, pmgp, pmg) killChargeMaps(nosh, chargeMap) killKappaMaps(nosh, kappaMap) killDielMaps(nosh, dielXMap, dielYMap, dielZMap) killMolecules(nosh, alist) delete_Nosh(nosh) # Clean up Python structures delete_double_array(realCenter) delete_int_array(nforce) delete_atomforcelist(atomforce) delete_valist(alist) delete_gridlist(dielXMap) delete_gridlist(dielYMap) delete_gridlist(dielZMap) delete_gridlist(kappaMap) delete_gridlist(chargeMap) delete_pmglist(pmg) delete_pmgplist(pmgp) delete_pbelist(pbe) # Clean up MALOC structures delete_Com(com) delete_Mem(mem) stdout.write("\n") stdout.write("Thanks for using APBS!\n\n") # Stop the main timer main_timer_stop = time.clock() stdout.write( "Total execution time: %1.6e sec\n" % (main_timer_stop - main_timer_start) ) if __name__ == "__main__": main()