Exemple #1
0
def system(config, alphaL=5.6, kmax_squared=38, rcut=False):
    if rcut:
        config.set_model_param("cutoff", 0, rcut)
        config.set_model_param("cutoff", 1, rcut)
    system = feasst.System()
    system.add(config)
    system.add(
        feasst.Potential(
            feasst.MakeEwald(
                feasst.args({
                    "kmax_squared":
                    str(kmax_squared),
                    "alpha":
                    str(alphaL /
                        system.configuration().domain().min_side_length())
                }))))
    # Unfortunatley, swig isn't accepting the below method of constructing a two body factory
    #    system.add(feasst.Potential(feasst.MakeModelTwoBodyFactory(
    #        feasst.ModelTwoBodyVector([feasst.MakeLennardJones(), feasst.MakeChargeScreened()]))))
    two = feasst.MakeModelTwoBodyFactory()
    two.add(feasst.MakeLennardJones())
    two.add(feasst.MakeChargeScreened())
    system.add(feasst.Potential(two))
    system.add(
        feasst.Potential(feasst.MakeChargeScreenedIntra(),
                         feasst.MakeVisitModelBond()))
    system.add(feasst.Potential(feasst.MakeChargeSelf()))
    system.add(feasst.Potential(feasst.MakeLongRangeCorrections()))
    # system.precompute()
    return system
def nvtw(num_particles, num_procs, num_equil, num_prod, num_hours, dccb_begin, temperature, mu, steps_per, model):
    mc = fst.MakeMonteCarlo()
    #mc.set(fst.MakeRandomMT19937(fst.args({"seed": "1633373856"})))
    beta = 1./temperature
    if model == "lj":
        mc.add(fst.MakeConfiguration(fst.args({"cubic_box_length": "8",
            "particle_type0": fst.install_dir() + "/forcefield/lj.fstprt"})))
        mc.add(fst.MakePotential(fst.MakeLennardJones()))
        mc.add(fst.MakePotential(fst.MakeLongRangeCorrections()))
    elif model == "sqw":
        config = fst.MakeConfiguration(fst.args({"cubic_box_length": "8", "particle_type0": fst.install_dir() + "/forcefield/atom.fstprt"}))
        config.set_model_param("cutoff", 0, 1.5)
        mc.add(config)
        mc.add(fst.MakePotential(fst.MakeSquareWell()))
    elif model == "spce":
        mc.add(fst.MakeConfiguration(fst.args({"cubic_box_length": "20",
            "particle_type0": fst.install_dir() + "/forcefield/spce.fstprt"})))
        mc.add(fst.MakePotential(fst.MakeEwald(fst.args({"alpha": str(5.6/20),
            "kmax_squared": "38"}))))
        mc.add(fst.MakePotential(fst.MakeModelTwoBodyFactory(fst.MakeLennardJones(), fst.MakeChargeScreened()),
                                          fst.args({"table_size": "1e6"})))
        mc.add(fst.MakePotential(fst.MakeChargeScreenedIntra(), fst.MakeVisitModelBond()))
        mc.add(fst.MakePotential(fst.MakeChargeSelf()))
        mc.add(fst.MakePotential(fst.MakeLongRangeCorrections()))
        beta = 1./fst.kelvin2kJpermol(temperature, mc.configuration())
    else:
        assert(False) # model not recognized

    # fill box with larger temperature and mu
    mc.set(fst.MakeThermoParams(fst.args({"beta": "0.01", "chemical_potential": "10"})))
    mc.set(fst.MakeMetropolis());
    #trial_args = {"particle_type": "0", "site": "0", "reference_index": ref, "num_steps": num_steps}
    mc.add(fst.MakeTrialTranslate(fst.args({"tunable_param": "0.1"})))
    #mc.add(fst.MakeTrialGrow(fst.ArgsVector([dict({"translate": "true", "tunable_param": "0.1"}, **trial_args)])))
    mc.add(fst.MakeTrialAdd(fst.args({"particle_type": "0", "weight": "4"})))
    mc.add(fst.MakeTune(fst.args({"steps_per": steps_per})))
    mc.add(fst.MakeCheckEnergy(fst.args({"steps_per": steps_per, "tolerance": "0.0001"})))
    mc.add(fst.MakeLogAndMovie(fst.args({"steps_per": steps_per,
                                         "file_name": model + str(num_particles)})))
    mc.set(fst.MakeCheckpoint(fst.args({"file_name": "checkpoint" + str(num_particles) + ".fst",
                                        "num_hours": str(0.1*num_procs*num_hours),
                                        "num_hours_terminate": str(0.9*num_procs*num_hours)})))
    mc.run(fst.MakeRun(fst.args({"until_num_particles": str(num_particles)})))
    mc.run(fst.MakeRemoveTrial(fst.args({"name": "TrialAdd"})))
    # nvt equilibration at desired temperature
    mc.set(fst.MakeThermoParams(fst.args({"beta": str(beta),
                                          "chemical_potential": str(mu)})))
    mc.attempt(int((num_particles+1)*num_equil))
    mc.run(fst.MakeRemoveModify(fst.args({"name": "Tune"})))
    mc.add(fst.MakeTrialTransfer(fst.args({"particle_type": "0", "weight": "4"})))
    #mc.add(fst.MakeTrialGrow(fst.ArgsVector([dict({"transfer": "true", "weight": "4"}, **trial_args)])))
    mc.set(fst.MakeFlatHistogram(fst.args({
        "Macrostate": "MacrostateNumParticles", "width": "1", "max": str(num_particles), "min": str(num_particles),
        "Bias": "TransitionMatrix", "min_sweeps": "1"})))
    mc.add(fst.MakeEnergy(fst.args({"steps_per_write": steps_per,
                                    "file_name": "en" + str(num_particles) + ".txt"})))
    mc.add(fst.MakeCriteriaWriter(fst.args({"steps_per": steps_per,
                                            "file_name": "crit" + str(num_particles) + ".txt"})))
    mc.attempt(int((num_particles+1)*num_prod))
Exemple #3
0
def system(config=None,
           box_length=8.109613,
           alphaL=6.870983963962610000,
           kmax_squared=38,
           rcut=4.891304347826090):
    if not config:
        config = feasst.Configuration(
            feasst.MakeDomain(
                feasst.args({"cubic_box_length": str(box_length)})),
            feasst.args({
                "particle_type0":
                feasst.install_dir() +
                "/plugin/ewald/forcefield/data.rpm_plus",
                "particle_type1":
                feasst.install_dir() +
                "/plugin/ewald/forcefield/data.rpm_minus"
            }))
    config.set_model_param("cutoff", 0, rcut)
    config.set_model_param("cutoff", 1, rcut)
    system = feasst.System()
    system.add(config)
    system.add(
        feasst.Potential(
            feasst.MakeEwald(
                feasst.args({
                    "kmax_squared":
                    str(kmax_squared),
                    "alpha":
                    str(alphaL /
                        system.configuration().domain().min_side_length())
                }))))
    # Unfortunatley, swig isn't accepting the below method of constructing a two body factory
    #    system.add(feasst.Potential(feasst.MakeModelTwoBodyFactory(
    #        feasst.ModelTwoBodyVector([feasst.MakeLennardJones(), feasst.MakeChargeScreened()]))))
    two = feasst.MakeModelTwoBodyFactory()
    two.add(feasst.MakeHardSphere())
    two.add(feasst.MakeChargeScreened())
    system.add(feasst.Potential(two))
    system.add(feasst.Potential(feasst.MakeChargeSelf()))
    # system.precompute()
    return system
def mc(thread, mn, mx):
    steps_per = int(1e5)
    avb, dccb = avb_or_dccb(mx)
    mc = fst.MakeMonteCarlo()
    mc.add(
        fst.MakeConfiguration(
            fst.args({
                "cubic_box_length":
                "20",
                "physical_constants":
                "CODATA2010",
                "particle_type0":
                fst.install_dir() + "/forcefield/spce.fstprt"
            })))
    mc.add(
        fst.MakePotential(
            fst.MakeEwald(
                fst.args({
                    "alpha": str(5.6 / 20),
                    "kmax_squared": "38"
                }))))
    mc.add(
        fst.MakePotential(
            fst.MakeModelTwoBodyFactory(fst.MakeLennardJones(),
                                        fst.MakeChargeScreened()),
            fst.args({"table_size": "1e6"})))
    mc.add(
        fst.MakePotential(fst.MakeChargeScreenedIntra(),
                          fst.MakeVisitModelBond()))
    mc.add(fst.MakePotential(fst.MakeChargeSelf()))
    mc.add(fst.MakePotential(fst.MakeLongRangeCorrections()))
    if dccb or avb:
        mc.run(
            fst.MakeAddReference(
                fst.args({
                    "potential_index": "1",
                    "cutoff": "3.16555789",
                    "use_cell": "true"
                })))
    if avb:
        initialize_neighbor_list(mc)
    beta = 1. / fst.kelvin2kJpermol(525, mc.configuration())
    mc.set(
        fst.MakeThermoParams(
            fst.args({
                "beta": str(beta),
                "chemical_potential": str(-8.14 / beta)
            })))
    mc.set(
        fst.MakeFlatHistogram(
            fst.MakeMacrostateNumParticles(
                fst.Histogram(
                    fst.args({
                        "width": "1",
                        "max": str(mx),
                        "min": str(mn)
                    }))),
            fst.MakeTransitionMatrix(fst.args({"min_sweeps": "10"}))))
    mc.add(
        fst.MakeTrialTranslate(
            fst.args({
                "weight": "1.",
                "tunable_param": "1.",
            })))
    mc.add(
        fst.MakeTrialRotate(fst.args({
            "weight": "1.",
            "tunable_param": "1."
        })))
    mc.add(
        fst.MakeTrialTransfer(fst.args({
            "particle_type": "0",
            "weight": "4"
        })))
    regrow1 = [{
        "angle": "true",
        "mobile_site": "1",
        "anchor_site": "0",
        "anchor_site2": "2"
    }]
    regrow2 = [{
        "angle": "true",
        "mobile_site": "2",
        "anchor_site": "0",
        "anchor_site2": "1"
    }]
    regrow12 = [{
        "bond": "true",
        "mobile_site": "1",
        "anchor_site": "0"
    }] + copy.deepcopy(regrow2)
    regrow21 = [{
        "bond": "true",
        "mobile_site": "2",
        "anchor_site": "0"
    }] + copy.deepcopy(regrow1)
    if dccb:
        grow012 = [{
            "transfer": "true",
            "site": "0",
            "weight": "4"
        }] + copy.deepcopy(regrow12)
        grow021 = [{
            "transfer": "true",
            "site": "0",
            "weight": "4"
        }] + copy.deepcopy(regrow21)
        for grow in [regrow1, regrow2]:
            grow[0]["weight"] = "0.3"
        for grow in [regrow12, regrow21]:
            grow[0]["weight"] = "0.2"
        for grow in [grow012, grow021, regrow12, regrow21, regrow1, regrow2]:
            grow[0]["particle_type"] = "0"
            mc.add(
                fst.MakeTrialGrow(
                    fst.ArgsVector(grow),
                    fst.args({
                        "reference_index": "0",
                        "num_steps": "4"
                    })))
    if avb:
        for avbtype in ["transfer_avb", "regrow_avb2", "regrow_avb4"]:
            avb = [{
                avbtype: "true",
                "site": "0",
                "neighbor_index": "0",
                "target_particle_type": "0",
                "target_site": "0"
            }]
            avb_012 = copy.deepcopy(avb) + copy.deepcopy(regrow12)
            avb_021 = copy.deepcopy(avb) + copy.deepcopy(regrow21)
            for grow in [avb_012, avb_021]:
                grow[0]["weight"] = "0.5"
                grow[0]["particle_type"] = "0"
                mc.add(
                    fst.MakeTrialGrow(
                        fst.ArgsVector(grow),
                        fst.args({
                            "num_steps": "4",
                            "reference_index": "0"
                        })))
    mc.add(
        fst.MakeCheckEnergyAndTune(
            fst.args({
                "steps_per": str(steps_per),
                "tolerance": "0.0001"
            })))
    mc.add(
        fst.MakeLogAndMovie(
            fst.args({
                "steps_per": str(steps_per),
                "file_name": "clones" + str(thread)
            })))
    mc.add(fst.MakeCriteriaUpdater(fst.args({"steps_per": str(steps_per)})))
    mc.add(
        fst.MakeCriteriaWriter(
            fst.args({
                "steps_per": str(steps_per),
                "file_name": "clones" + str(thread) + "_crit.txt"
            })))
    mc.add(
        fst.MakeEnergy(
            fst.args({
                "steps_per_write": str(steps_per),
                "file_name": "en" + str(thread),
                "multistate": "true"
            })))
    mc.set(
        fst.MakeCheckpoint(
            fst.args({
                "file_name":
                "checkpoint" + str(thread) + ".fst",
                "num_hours_terminate":
                str(0.9 * args.num_procs * args.num_hours)
            })))
    return mc
Exemple #5
0
def mc(thread, mn, mx):
    mc = fst.MakeMonteCarlo()
    #mc.set(fst.MakeRandomMT19937(fst.args({"seed": "123"})))
    mc.add(
        fst.MakeConfiguration(
            fst.args({
                "cubic_box_length": str(args.cubic_box_length),
                "physical_constants": "CODATA2010",
                "particle_type0": args.molecule
            })))
    mc.add(
        fst.MakePotential(
            fst.MakeEwald(
                fst.args({
                    "alpha": str(5.6 / args.cubic_box_length),
                    "kmax_squared": "38"
                }))))
    mc.add(
        fst.MakePotential(
            fst.MakeModelTwoBodyFactory(fst.MakeLennardJones(),
                                        fst.MakeChargeScreened()),
            fst.args({"table_size": "1e6"})))
    mc.add(
        fst.MakePotential(fst.MakeChargeScreenedIntra(),
                          fst.MakeVisitModelBond()))
    mc.add(fst.MakePotential(fst.MakeChargeSelf()))
    mc.add(fst.MakePotential(fst.MakeLongRangeCorrections()))
    if mx > args.dccb_begin:
        mc.run(
            fst.MakeAddReference(
                fst.args({
                    "potential_index": "1",
                    "cutoff": "3.16555789",
                    "use_cell": "true"
                })))
    beta = 1. / fst.kelvin2kJpermol(args.temperature, mc.configuration())
    mc.set(
        fst.MakeThermoParams(
            fst.args({
                "beta": str(beta),
                "chemical_potential": str(args.beta_mu / beta)
            })))
    mc.set(
        fst.MakeFlatHistogram(
            fst.MakeMacrostateNumParticles(
                fst.Histogram(
                    fst.args({
                        "width": "1",
                        "max": str(mx),
                        "min": str(mn)
                    }))),
            fst.MakeTransitionMatrix(fst.args({"min_sweeps": "10"}))))
    mc.add(
        fst.MakeTrialTranslate(
            fst.args({
                "weight": "1.",
                "tunable_param": "1.",
            })))
    if mx > args.dccb_begin:
        regrow1 = [{
            "angle": "true",
            "mobile_site": "1",
            "anchor_site": "0",
            "anchor_site2": "2"
        }]
        regrow2 = [{
            "angle": "true",
            "mobile_site": "2",
            "anchor_site": "0",
            "anchor_site2": "1"
        }]
        regrow12 = [{
            "bond": "true",
            "mobile_site": "1",
            "anchor_site": "0"
        }] + copy.deepcopy(regrow2)
        regrow21 = [{
            "bond": "true",
            "mobile_site": "2",
            "anchor_site": "0"
        }] + copy.deepcopy(regrow1)
        grow012 = [{
            "transfer": "true",
            "site": "0",
            "weight": "4"
        }] + copy.deepcopy(regrow12)
        grow021 = [{
            "transfer": "true",
            "site": "0",
            "weight": "4"
        }] + copy.deepcopy(regrow21)
        for grow in [regrow1, regrow2]:
            grow[0]["weight"] = "0.3"
        for grow in [regrow12, regrow21]:
            grow[0]["weight"] = "0.2"
        for grow in [grow012, grow021, regrow12, regrow21, regrow1, regrow2]:
            grow[0]["particle_type"] = "0"
            mc.add(
                fst.MakeTrialGrow(
                    fst.ArgsVector(grow),
                    fst.args({
                        "reference_index": "0",
                        "num_steps": "4"
                    })))
    else:
        mc.add(
            fst.MakeTrialRotate(
                fst.args({
                    "weight": "1.",
                    "tunable_param": "1."
                })))
        mc.add(
            fst.MakeTrialTransfer(
                fst.args({
                    "particle_type": "0",
                    "weight": "4"
                })))
    mc.add(
        fst.MakeCheckEnergyAndTune(
            fst.args({
                "steps_per": str(args.steps_per),
                "tolerance": "0.0001"
            })))
    mc.add(
        fst.MakeLogAndMovie(
            fst.args({
                "steps_per": str(args.steps_per),
                "file_name": "clones" + str(thread)
            })))
    mc.add(
        fst.MakeCriteriaUpdater(fst.args({"steps_per": str(args.steps_per)})))
    mc.add(
        fst.MakeCriteriaWriter(
            fst.args({
                "steps_per": str(args.steps_per),
                "file_name": "clones" + str(thread) + "_crit.txt"
            })))
    mc.add(
        fst.MakeEnergy(
            fst.args({
                "steps_per_write": str(args.steps_per),
                "file_name": "en" + str(thread),
                "multistate": "true"
            })))
    mc.set(
        fst.MakeCheckpoint(
            fst.args({
                "file_name":
                "checkpoint" + str(thread) + ".fst",
                "num_hours_terminate":
                str(0.9 * args.num_procs * args.num_hours)
            })))
    return mc
Exemple #6
0
def mc(thread, mn, mx):
    steps_per = int(1e4)
    mc = fst.MakeMonteCarlo()
    mc.add(
        fst.MakeConfiguration(
            fst.args({
                "cubic_box_length":
                "12",
                "particle_type0":
                fst.install_dir() +
                "/plugin/charge/forcefield/rpm_plus.fstprt",
                "particle_type1":
                fst.install_dir() +
                "/plugin/charge/forcefield/rpm_minus.fstprt",
                "cutoff":
                "4.891304347826090",
                "charge0":
                str(1. / math.sqrt(fst.CODATA2018().charge_conversion())),
                "charge1":
                str(-1. / math.sqrt(fst.CODATA2018().charge_conversion()))
            })))
    mc.add(
        fst.MakePotential(
            fst.MakeEwald(
                fst.args({
                    "alpha": str(6.87098396396261 / 12),
                    "kmax_squared": "38"
                }))))
    mc.add(
        fst.MakePotential(
            fst.MakeModelTwoBodyFactory(fst.MakeHardSphere(),
                                        fst.MakeChargeScreened()),
            fst.args({"table_size": "1e6"})))
    mc.add(fst.MakePotential(fst.MakeChargeSelf()))
    num_steps = "1"
    ref = "-1"
    if mx >= args.dccb_begin:
        mc.run(
            fst.MakeAddReference(
                fst.args({
                    "potential_index": "1",
                    "cutoff": "1",
                    "use_cell": "true"
                })))
        ref = "0"
        num_steps = "4"
    beta = 1. / args.temperature
    mc.set(
        fst.MakeThermoParams(
            fst.args({
                "beta": str(beta),
                "chemical_potential0": str(args.beta_mu / beta),
                "chemical_potential1": str(args.beta_mu / beta)
            })))
    mc.set(
        fst.MakeFlatHistogram(
            fst.MakeMacrostateNumParticles(
                fst.Histogram(
                    fst.args({
                        "width": "1",
                        "max": str(mx),
                        "min": str(mn)
                    }))),
            # fst.MakeTransitionMatrix(fst.args({"min_sweeps": str(args.min_sweeps)})),
            fst.MakeWLTM(
                fst.args({
                    "collect_flatness": "18",
                    "min_flatness": "22",
                    "min_sweeps": str(args.min_sweeps)
                })),
            fst.MakeAEqualB(fst.args({"extra_A": "1"}))))
    mc.add(
        fst.MakeTrialTranslate(
            fst.args({
                "weight": "1.",
                "tunable_param": "1."
            })))
    for particle_type in range(mc.configuration().num_particle_types()):
        mc.add(
            fst.MakeTrialTransfer(
                fst.args({
                    "weight": "4",
                    "particle_type": str(particle_type),
                    "reference_index": ref,
                    "num_steps": num_steps
                })))
    mc.add(
        fst.MakeCheckEnergy(
            fst.args({
                "steps_per": str(steps_per),
                "tolerance": "0.0001"
            })))
    mc.add(
        fst.MakeTune(
            fst.args({
                "steps_per": str(steps_per),
                "stop_after_phase": "0"
            })))
    mc.add(
        fst.MakeLogAndMovie(
            fst.args({
                "steps_per": str(steps_per),
                "file_name": "clones" + str(thread),
                "file_name_append_phase": "True"
            })))
    mc.add(
        fst.MakeEnergy(
            fst.args({
                "steps_per_write": str(steps_per),
                "file_name": "en" + str(thread) + ".txt.",
                "file_name_append_phase": "True",
                "start_after_phase": "0",
                "multistate": "True"
            })))
    mc.add(fst.MakeCriteriaUpdater(fst.args({"steps_per": str(steps_per)})))
    mc.add(
        fst.MakeCriteriaWriter(
            fst.args({
                "steps_per": str(steps_per),
                "file_name": "clones" + str(thread) + "_crit.txt",
                "file_name_append_phase": "True"
            })))
    mc.set(
        fst.MakeCheckpoint(
            fst.args({
                "file_name":
                "checkpoint" + str(thread) + ".fst",
                "num_hours":
                str(0.1 * args.num_procs * args.num_hours),
                "num_hours_terminate":
                str(0.9 * args.num_procs * args.num_hours)
            })))
    return mc