main.py

import numpy as np
import pamd
from glob import glob

def replicate_initial_configurations(conf_regexpr, pamd):
    '''The variable "conf_regexpr" is used to find all
    available starting configuration which are replicated
    equally often.'''
    available = sorted(glob(conf_regexpr))
    count = len(available)
    assert count > 0,'No starting configurations found'
    
    config_degeneracy = np.empty(count,dtype=int)
    config_degeneracy[:] = pamd.replica // count
    config_degeneracy[:pamd.replica % count] += 1
    cum_config_degeneracy = np.cumsum(config_degeneracy)

    limits = (pamd.get_global_process_from_local_process(0),pamd.get_global_process_from_local_process(pamd.replicas_per_process))
    relevant_range = [np.argwhere(cum_config_degeneracy>limits[0])[0][0],np.argwhere(cum_config_degeneracy >= limits[1])[0][0] + 1]
    degeneracy = config_degeneracy[relevant_range[0]:relevant_range[1]]

    degeneracy[0] = cum_config_degeneracy[relevant_range[0]]-limits[0]
    degeneracy[-1] = -cum_config_degeneracy[relevant_range[1]-2]+limits[1]

    return degeneracy, available[slice(*relevant_range)]

def load_initial_configs(sim_object, conf_regexpr, pamd):
    degeneracy, available = replicate_initial_configurations(conf_regexpr, pamd)
    SIMULATIONS = np.array([sim_object(SIM.get_global_process_from_local_process(i), {'timestep':2, 'initial_temperature_seed':42, 'thermostat_seed':101010, 'damping_time':10}) for i in range(REPLICAS_PER_PROCESS)])
    index=0
    for i,deg in enumerate(degeneracy):
        for j in range(index, index+deg):
            SIMULATIONS[j].load_config(i)
        index += deg


if __name__ == '__main__':
    import argparse
    parser = argparse.ArgumentParser()
    parser.add_argument("-m","--mode", help="Set run-mode", type=str, default="demo")
    parser.add_argument("-N","--number_of_nodes", help="Set number of nodes on which the simulation runs.", type=int, default=1)
    parser.add_argument("-n","--threads_per_node", help="The number of threads on each node. Has to be the same for all nodes.", type=int, default=1)
    parser.add_argument("-r","--replicas_per_process", help="The number replicas per process. Is the same on each thread.", type=int, default=1)
    parser.add_argument("-s","--seed_offset", help="The seed offset which is used to initialize all the random number seeds needed for the simulation.", type=int, default=0)
    args = parser.parse_args()

    REPLICAS_PER_PROCESS = args.replicas_per_process
    SIM = pamd.Simulation(REPLICAS_PER_PROCESS,args.seed_offset)
    SIM.set_threads_per_compute_unit(args.threads_per_node)
    
    if args.mode == "demo":
        import demo
        #load_initial_configs(demo.Demo, 'test_configs/conf*', SIM)
    
        SIMULATIONS = np.array([demo.Demo(SIM.get_global_process_from_local_process(i)) for i in range(REPLICAS_PER_PROCESS)])
        
        SIM.run(SIMULATIONS)
    elif args.mode == "ising":
        import ising_pa
        SIM.overlap = 0.8
        SIM.equilibration_steps = 0
        SIM.simulation_steps_per_temp = 50
        SIM.start_temp = 2000 # actually starting at inf but for adaptive temp step to work choose large (finite) temp instead
        SIM.end_temp = 1 # well within the ordered phase
        SIMULATIONS = np.array([ising_pa.Ising(SIM.get_global_process_from_local_process(i)) for i in range(REPLICAS_PER_PROCESS)])
        SIM.run(SIMULATIONS)
    elif args.mode == "lammps":
        import lammps_pamd
        #load_initial_configs(lammps_pamd.Lammps, 'test_configs/conf*', SIM)

        SIMULATIONS = np.array([lammps_pamd.Lammps(SIM.get_global_process_from_local_process(i), {'timestep':2, 'initial_temperature_seed':42, 'thermostat_seed':101010, 'damping_time':10}) for i in range(REPLICAS_PER_PROCESS)])
        SIM.run(SIMULATIONS)
    elif args.mode == "openmm":
        import openmm_pamd

        SIMULATIONS = np.array([openmm_pamd.OpenMM(SIM.get_global_process_from_local_process(i)) for i in range(REPLICAS_PER_PROCESS)])
        SIM.simulation_steps_per_temp=1
        SIM.run(SIMULATIONS)

    # load_initial_configs(lammps_pamd.Lammps, 'test_configs/conf*', SIM)