Skip to content

Devel 1.3.0 #102

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
kevinwenminion merged 5 commits into from
Jun 3, 2026
Merged

Devel 1.3.0 #102

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
badd321
Add Anearling properties calculation example, update annealing functi…
Zikkying Jun 3, 2026
1d85849
optimize error retrieve
Zikkying Jun 3, 2026
5dda58b
Improve Annealing function to production level
Zikkying Jun 3, 2026
488367f
remove model
Zikkying Jun 3, 2026
4842a1e
Merge pull request #20 from Zikkying/devel-1.3.0
kevinwenminion Jun 3, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
24 changes: 18 additions & 6 deletions apex/core/calculator/Lammps.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -446,6 +446,15 @@ def make_input_file(self, output_dir, task_type, task_param):
fp.write(fc)

def compute(self, output_dir):
task_json = os.path.join(output_dir, "task.json")
try:
task_param = loadfn(task_json) if os.path.isfile(task_json) else {}
except Exception:
task_param = {}
task_type = task_param.get("type", task_param.get("cal_type"))
if task_type in ["annealing", "Annealing"]:
return None

log_lammps = os.path.join(output_dir, "log.lammps")
dump_lammps = os.path.join(output_dir, "dump.relax")
if not os.path.isfile(log_lammps) or not os.path.isfile(dump_lammps):
Expand Down Expand Up @@ -724,12 +733,15 @@ def backward_files(self, property_type="relaxation"):
"log.lammps",
"outlog",
*debug_files,
"dump.anneal_ramp",
"dump.anneal_cool",
"heating_interval.dat",
"cooling_interval.dat",
"rdf_ramp.dat",
"rdf_cool.dat",
"dump.init.*",
"dump.eq_*",
"dump.T_ramp_*",
"dump.T_decline_*",
"dump.final_eq_*",
"heating_interval_*.dat",
"cooling_interval_*.dat",
"rdf.*.txt",
"msd.*.txt",
"restart.*",
]
elif property_type == "finite_t_elastic":
Expand Down
227 changes: 156 additions & 71 deletions apex/core/calculator/lib/lammps_utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -690,20 +690,85 @@ def make_lammps_press_relax(
return ret

def make_lammps_annealing(conf, type_map, interaction, param, cal_setting):
"""LAMMPS input for annealing: equilibrate -> heat (ramp) -> optional hold -> cool.
"""LAMMPS input for annealing using the same stage controls as annealing/.

Uses variables provided by `variable_Annealing.in` in the task directory.
- thermostat: nose_hoover | langevin
- ensemble: for nose_hoover: npt|nvt; for langevin: nph|nve (barostat on/off)
"""

type_map_list = element_list(type_map)
dump_step = int(cal_setting.get("dump_step", 1000))
tdamp = cal_setting.get("tdamp", 100)
pdamp = cal_setting.get("pdamp", 1000)
dump_interval = int(cal_setting.get("dump_interval", cal_setting.get("dump_step", 2000)))
thermo_interval = int(cal_setting.get("thermo_interval", 2000))
restart_interval = int(cal_setting.get("restart_interval", 20000))
tdamp = cal_setting.get("tdamp", "${tdamp}")
pdamp = cal_setting.get("pdamp", "${pdamp}")
thermostat = cal_setting.get("thermostat", "nose_hoover")
ensemble = cal_setting.get("ensemble", "npt")
vseed = int(cal_setting.get("velocity_seed", 12345))
vseed = int(cal_setting.get("velocity_seed", cal_setting.get("init_v_seed", 123457)))
lgv_seed = int(cal_setting.get("lgv_seed", vseed))
req_lgv_damping = cal_setting.get("req_lgv_damping", False)
req_compute_rdf = cal_setting.get("req_compute_rdf", True)
req_compute_msd = cal_setting.get("req_compute_msd", True)
req_write_restart = cal_setting.get("req_write_restart", True)
req_dump_init_atom = cal_setting.get("req_dump_init_atom", True)
req_dump_ave_atom = cal_setting.get("req_dump_ave_atom", False)
rdf_nevery = int(cal_setting.get("rdf_nevery", cal_setting.get("rdf_interval", 100)))
rdf_nrepeat = int(cal_setting.get("rdf_nrepeat", 1))
rdf_nfreq = int(cal_setting.get("rdf_nfreq", cal_setting.get("rdf_interval", 200)))
msd_nevery = int(cal_setting.get("msd_nevery", 100))
msd_nrepeat = int(cal_setting.get("msd_nrepeat", 1))
msd_nfreq = int(cal_setting.get("msd_nfreq", 200))

def _truthy(value):
if isinstance(value, bool):
return value
if isinstance(value, str):
return value.strip().lower() in {"1", "true", "yes", "on"}
return bool(value)

def _thermo_fix(name, t_start, t_stop):
if thermostat == "langevin":
if ensemble == "nve":
fix = f"fix {name}_int all nve\n"
else:
fix = f"fix {name}_int all nph aniso 0.0 0.0 {pdamp} drag 1.0\n"
fix += f"fix {name}_lgv all langevin {t_start} {t_stop} {tdamp} {lgv_seed}\n"
return fix
if ensemble == "nvt":
return f"fix {name}_nh all nvt temp {t_start} {t_stop} {tdamp}\n"
return (
f"fix {name}_nh all npt temp {t_start} {t_stop} {tdamp} "
f"x 0.0 0.0 {pdamp} y 0.0 0.0 {pdamp} z 0.0 0.0 {pdamp}\n"
)

def _unfix_thermo(name):
if thermostat == "langevin":
return f"unfix {name}_lgv\nunfix {name}_int\n"
return f"unfix {name}_nh\n"

def _stage_analysis(stage, rdf_file, msd_file):
ret = ""
if _truthy(req_compute_rdf):
ret += (
f"fix rdf_{stage} all ave/time {rdf_nevery} {rdf_nrepeat} {rdf_nfreq} "
f"c_myRDF[*] file {rdf_file} mode vector\n"
)
if _truthy(req_compute_msd):
ret += f"compute myMSD_{stage} all msd com yes\n"
ret += (
f"fix msd_{stage} all ave/time {msd_nevery} {msd_nrepeat} {msd_nfreq} "
f"c_myMSD_{stage} file {msd_file} mode vector\n"
)
return ret

def _unfix_stage_analysis(stage):
ret = ""
if _truthy(req_compute_rdf):
ret += f"unfix rdf_{stage}\n"
if _truthy(req_compute_msd):
ret += f"unfix msd_{stage}\nuncompute myMSD_{stage}\n"
return ret

ret = ""
ret += "include variable_Annealing.in\n"
Expand All @@ -720,8 +785,9 @@ def make_lammps_annealing(conf, type_map, interaction, param, cal_setting):
ret += "neigh_modify every 1 delay 0 check no\n"
ret += interaction(param)
ret += "compute mype all pe\n"
ret += "thermo 100\n"
ret += ("thermo_style custom step temp pe pxx pyy pzz pxy pxz pyz lx ly lz vol c_mype\n")
ret += f"thermo {thermo_interval}\n"
ret += ("thermo_style custom step temp atoms epair pe ke etotal press vol pxx pyy pzz pxy pxz pyz lx ly lz xlo xhi ylo yhi zlo zhi fnorm fmax\n")
ret += "thermo_modify lost error flush yes format 4 %.8f\n"
ret += "timestep ${timestep}\n"
ret += "variable N equal count(all)\n"
ret += "variable V equal vol\n"
Expand All @@ -731,80 +797,99 @@ def make_lammps_annealing(conf, type_map, interaction, param, cal_setting):
ret += "variable Etotal equal etotal\n"
ret += "variable Press equal press\n"
ret += "variable stepVal equal step\n"
ret += "compute myRDF all rdf ${rdf_bins} cutoff ${rdf_cutoff}\n"
if _truthy(req_compute_rdf):
ret += "variable rdf_comm_cutoff equal ${rdf_cutoff}+2.0\n"
ret += "comm_modify cutoff ${rdf_comm_cutoff}\n"
ret += "compute myRDF all rdf ${rdf_bins} cutoff ${rdf_cutoff}\n"

if _truthy(req_dump_init_atom):
ret += "dump init_dump all atom 1 dump.init.*\n"
ret += "run 0\n"
ret += "undump init_dump\n"

# Initialize velocities and equilibrate at start_temp
ret += f"velocity all create ${{start_temp}} {vseed} mom yes rot yes dist gaussian\n"

if thermostat == "langevin":
# Langevin + barostat (nph) or without (nve)
if ensemble == "nve":
ret += "fix 1 all nve\n"
else:
ret += f"fix 1 all nph aniso 0.0 0.0 {pdamp} drag 1.0\n"
ret += f"fix tg all langevin ${{start_temp}} ${{start_temp}} {tdamp} {vseed}\n"
else:
# Nose-Hoover NPT or NVT
if ensemble == "nvt":
ret += f"fix 1 all nvt temp ${{start_temp}} ${{start_temp}} {tdamp}\n"
else:
ret += f"fix 1 all npt temp ${{start_temp}} ${{start_temp}} {tdamp} x 0.0 0.0 {pdamp} y 0.0 0.0 {pdamp} z 0.0 0.0 {pdamp}\n"

ret += "run ${equi_step}\n"
ret += "unfix 1\n"
if thermostat == "langevin":
ret += "unfix tg\n"
if _truthy(req_lgv_damping):
ret += "fix eq_lgv_int all nve\n"
ret += f"fix eq_lgv all langevin ${{start_temp}} ${{start_temp}} {tdamp} {lgv_seed}\n"
ret += f"dump eq_lgv_dump all atom {dump_interval} dump.eq_lgv_${{start_temp}}K.*\n"
if _truthy(req_write_restart):
ret += f"restart {restart_interval} restart.eq_lgv.*\n"
ret += "run ${init_lgv_thermo_equil_step}\n"
ret += "restart 0\n"
ret += "undump eq_lgv_dump\n"
ret += "unfix eq_lgv\n"
ret += "unfix eq_lgv_int\n"
ret += "write_restart restart.eq_lgv_final\n"

ret += _stage_analysis("eq", "rdf.eq_${start_temp}K.txt", "msd.eq_${start_temp}K.txt")
ret += _thermo_fix("eq", "${start_temp}", "${start_temp}")
ret += f"dump eq_nh_dump all atom {dump_interval} dump.eq_nh_${{start_temp}}K.*\n"
if _truthy(req_dump_ave_atom):
ret += "compute atom_u_pos all property/atom xu yu zu\n"
ret += "fix ave_atom_u_pos all ave/atom ${ave_atom_sample_feq} ${ave_atom_sample_length} ${dump_interval} c_atom_u_pos[*]\n"
ret += f"dump eq_nh_ave_dump all custom {dump_interval} dump.eq_nh_${{start_temp}}K_ave.* id type f_ave_atom_u_pos[1] f_ave_atom_u_pos[2] f_ave_atom_u_pos[3]\n"
if _truthy(req_write_restart):
ret += f"restart {restart_interval} restart.eq_nh.*\n"
ret += "run ${init_thermo_equil_step}\n"
ret += "restart 0\n"
ret += "undump eq_nh_dump\n"
if _truthy(req_dump_ave_atom):
ret += "undump eq_nh_ave_dump\nunfix ave_atom_u_pos\nuncompute atom_u_pos\n"
ret += _unfix_thermo("eq")
ret += _unfix_stage_analysis("eq")
ret += "reset_timestep 0\n"
ret += "write_restart restart.eq_final\n"

# Temperature ramp to target_temp
if thermostat == "langevin":
if ensemble == "nve":
ret += "fix 1 all nve\n"
else:
ret += f"fix 1 all nph aniso 0.0 0.0 {pdamp} drag 1.0\n"
ret += f"fix tg all langevin ${{start_temp}} ${{target_temp}} {tdamp} {vseed}\n"
else:
if ensemble == "nvt":
ret += f"fix 1 all nvt temp ${{start_temp}} ${{target_temp}} {tdamp}\n"
else:
ret += f"fix 1 all npt temp ${{start_temp}} ${{target_temp}} {tdamp} x 0.0 0.0 {pdamp} y 0.0 0.0 {pdamp} z 0.0 0.0 {pdamp}\n"
ret += f"dump 1 all custom {dump_step} dump.anneal_ramp id type xs ys zs fx fy fz\n"
ret += "fix rdf_ramp all ave/time ${rdf_interval} 1 ${rdf_interval} c_myRDF[*] file rdf_ramp.dat mode vector\n"
ret += "fix heat_log all ave/time ${rdf_interval} 1 ${rdf_interval} v_stepVal v_N v_Temp v_Vatom v_pote v_Etotal v_Press file heating_interval.dat\n"
ret += "run ${ramp_step}\n"
ret += _stage_analysis("ramp", "rdf.T_ramp_${start_temp}K_${temp}K.txt", "msd.T_ramp_${start_temp}K_${temp}K.txt")
ret += _thermo_fix("ramp", "${start_temp}", "${temp}")
ret += f"dump T_ramp_nh_dump all atom {dump_interval} dump.T_ramp_nh_${{start_temp}}K_${{temp}}K.*\n"
ret += "fix heat_log all ave/time 1 100 ${thermo_interval} v_N v_Temp v_Vatom v_pote v_Etotal v_Press file heating_interval_${thermo_interval}.dat\n"
if _truthy(req_write_restart):
ret += f"restart {restart_interval} restart.T_ramp_nh.*\n"
ret += "run ${temp_ramp_remain_step}\n"
ret += "restart 0\n"
ret += "unfix heat_log\n"
ret += "unfix rdf_ramp\n"
ret += "undump 1\n"
ret += "unfix 1\n"
if thermostat == "langevin":
ret += "unfix tg\n"

# Optional hold at target_temp
ret += f'if "${{hold_step}} > 0" then "fix 1 all nvt temp ${{target_temp}} ${{target_temp}} {tdamp}" "run ${{hold_step}}" "unfix 1"\n'
ret += "undump T_ramp_nh_dump\n"
ret += _unfix_thermo("ramp")
ret += _unfix_stage_analysis("ramp")
ret += "reset_timestep 0\n"
ret += "write_restart restart.T_ramp_nh_final\n"

# Cool to end_temp
if thermostat == "langevin":
if ensemble == "nve":
ret += "fix 1 all nve\n"
else:
ret += f"fix 1 all nph aniso 0.0 0.0 {pdamp} drag 1.0\n"
ret += f"fix tg all langevin ${{target_temp}} ${{end_temp}} {tdamp} {vseed}\n"
else:
if ensemble == "nvt":
ret += f"fix 1 all nvt temp ${{target_temp}} ${{end_temp}} {tdamp}\n"
else:
ret += f"fix 1 all npt temp ${{target_temp}} ${{end_temp}} {tdamp} x 0.0 0.0 {pdamp} y 0.0 0.0 {pdamp} z 0.0 0.0 {pdamp}\n"
ret += f"dump 2 all custom {dump_step} dump.anneal_cool id type xs ys zs fx fy fz\n"
ret += "fix rdf_cool all ave/time ${rdf_interval} 1 ${rdf_interval} c_myRDF[*] file rdf_cool.dat mode vector\n"
ret += "fix cool_log all ave/time ${rdf_interval} 1 ${rdf_interval} v_stepVal v_N v_Temp v_Vatom v_pote v_Etotal v_Press file cooling_interval.dat\n"
ret += "run ${cool_step}\n"
ret += _stage_analysis("decline", "rdf.T_decline_${temp}K_${end_temp}K.txt", "msd.T_decline_${temp}K_${end_temp}K.txt")
ret += _thermo_fix("decline", "${temp}", "${end_temp}")
ret += f"dump T_decline_nh_dump all atom {dump_interval} dump.T_decline_nh_${{temp}}K_${{end_temp}}K.*\n"
ret += "fix cool_log all ave/time 1 100 ${thermo_interval} v_N v_Temp v_Vatom v_pote v_Etotal v_Press file cooling_interval_${thermo_interval}.dat\n"
if _truthy(req_write_restart):
ret += f"restart {restart_interval} restart.T_decline_nh.*\n"
ret += "run ${temp_decline_remain_step}\n"
ret += "restart 0\n"
ret += "unfix cool_log\n"
ret += "unfix rdf_cool\n"
ret += "undump 2\n"
ret += "unfix 1\n"
if thermostat == "langevin":
ret += "unfix tg\n"

ret += 'print "All done"\n'
ret += "undump T_decline_nh_dump\n"
ret += _unfix_thermo("decline")
ret += _unfix_stage_analysis("decline")
ret += "reset_timestep 0\n"
ret += "write_restart restart.T_decline_final\n"

ret += 'if "${final_thermo_equil_step} <= 0" then "jump SELF end_of_run"\n'
ret += _stage_analysis("final_eq", "rdf.final_eq_${end_temp}K.txt", "msd.final_eq_${end_temp}K.txt")
ret += _thermo_fix("final_eq", "${end_temp}", "${end_temp}")
ret += f"dump final_eq_nh_dump all atom {dump_interval} dump.final_eq_nh_${{end_temp}}K.*\n"
if _truthy(req_write_restart):
ret += f"restart {restart_interval} restart.final_eq_nh.*\n"
ret += "run ${final_thermo_equil_remain_step}\n"
ret += "restart 0\n"
ret += "undump final_eq_nh_dump\n"
ret += _unfix_thermo("final_eq")
ret += _unfix_stage_analysis("final_eq")
ret += "reset_timestep 0\n"
ret += "write_restart restart.final_eq_final\n"

ret += 'print "__end_of_lmp_annealing_calculation__"\n'
ret += 'label end_of_run\n'
return ret

"""
Expand Down
Loading
Loading