def step1(**kwargs):
"""
setup and run all lammps jobs
"""
turn_knobs = OrderedDict(
[
('STRUCTURES', structures),
('PAIR_STYLE', pair_styles),
('PAIR_COEFF', pair_coeff_files)
])
# job directory and run settings
job_dir = 'lammps_job'
nprocs = 4
nnodes = 1
walltime = '00:15:00'
mem = 200
job_bin = '/home/km468/Software/lammps/src/lmp_ufhpc < inp'
qadapter, job_cmd = get_run_cmmnd(nnodes=nnodes, nprocs=nprocs,
walltime=walltime,
job_bin=job_bin, mem=mem)
checkpoint_files = []
chkpt_file = 'step1.json'
# setup calibration jobs and run
cal = CalibrateLammps(parameters, turn_knobs=turn_knobs,
qadapter=qadapter, job_cmd=job_cmd,
job_dir=job_dir, is_matrix=True,
checkpoint_file=chkpt_file,
cal_logger=logger)
cal.setup()
cal.run()
checkpoint_files.append(chkpt_file)
return checkpoint_files
def step1(**kwargs):
"""
setup and run all lammps jobs
"""
turn_knobs = OrderedDict([('STRUCTURES', structures),
('PAIR_STYLE', pair_styles),
('PAIR_COEFF', pair_coeff_files)])
# job directory and run settings
job_dir = 'lammps_job'
nprocs = 4
nnodes = 1
walltime = '00:15:00'
mem = 200
job_bin = '/home/km468/Software/lammps/src/lmp_ufhpc < inp'
qadapter, job_cmd = get_run_cmmnd(nnodes=nnodes,
nprocs=nprocs,
walltime=walltime,
job_bin=job_bin,
mem=mem)
checkpoint_files = []
chkpt_file = 'step1.json'
# setup calibration jobs and run
cal = CalibrateLammps(parameters,
turn_knobs=turn_knobs,
qadapter=qadapter,
job_cmd=job_cmd,
job_dir=job_dir,
is_matrix=True,
checkpoint_file=chkpt_file,
cal_logger=logger)
cal.setup()
cal.run()
checkpoint_files.append(chkpt_file)
return checkpoint_files
'fix': ['fix_nve all nve',
'1 all box/relax aniso 0.0 vmax 0.001',
'1a all qeq/comb 1 0.0001 file fq.out']}
# list of pair styles
pair_styles = ['comb3 polar_off']
# list of pair coefficient files
pair_coeff_files = [os.path.join(os.getcwd(), "ffield.comb3")]
# parameters tuned: structures, pair styles and pair coefficients
turn_knobs = OrderedDict(
[
('STRUCTURES', structures),
('PAIR_STYLES', pair_styles),
('PAIR_COEFFS', pair_coeff_files)
])
# job directory and run settings
job_dir = 'lammps_job'
nprocs = 4
nnodes = 1
walltime = '00:15:00'
mem = 500
job_bin = '/home/km468/Software/lammps/src/lmp_ufhpc < inp'
qadapter, job_cmd = get_run_cmmnd(nnodes=nnodes, nprocs=nprocs,
walltime=walltime,
job_bin=job_bin, mem=mem)
# setup calibration jobs and run
cal = CalibrateLammps(parameters, turn_knobs=turn_knobs,
qadapter=qadapter, job_cmd=job_cmd,
job_dir=job_dir)
cal.setup()
cal.run()
]
}
# list of pair styles
pair_styles = ['comb3 polar_off']
# list of pair coefficient files
pair_coeff_files = [os.path.join(os.getcwd(), "ffield.comb3")]
# parameters tuned: structures, pair styles and pair coefficients
turn_knobs = OrderedDict([('STRUCTURES', structures),
('PAIR_STYLES', pair_styles),
('PAIR_COEFFS', pair_coeff_files)])
# job directory and run settings
job_dir = 'lammps_job'
nprocs = 4
nnodes = 1
walltime = '00:15:00'
mem = 500
job_bin = '/home/km468/Software/lammps/src/lmp_ufhpc < inp'
qadapter, job_cmd = get_run_cmmnd(nnodes=nnodes,
nprocs=nprocs,
walltime=walltime,
job_bin=job_bin,
mem=mem)
# setup calibration jobs and run
cal = CalibrateLammps(parameters,
turn_knobs=turn_knobs,
qadapter=qadapter,
job_cmd=job_cmd,
job_dir=job_dir)
cal.setup()
cal.run()