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Update notation in APIP examples.

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This commit is contained in:
David Immel
2025-06-05 17:22:19 +02:00
parent bc93311309
commit 20f123ddd1
4 changed files with 45 additions and 39 deletions
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16
examples/PACKAGES/apip/in.surface.balance
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@ -45,19 +45,21 @@ group group_ignore_csp region bottom
# use adaptive-precision eam-ace potential with lambda_thermostat
pair_style hybrid/overlay eam/fs/apip pace/apip lambda_input/csp ${csp_lattice} cutoff ${csp_cutoff} lambda/zone ${r_sw_hi}
pair_style hybrid/overlay eam/fs/apip pace/apip lambda/input/csp/apip ${csp_lattice} cutoff ${csp_cutoff} lambda/zone/apip ${r_sw_hi}
pair_coeff * * eam/fs/apip ${eamfs_file} Cu
pair_coeff * * pace/apip ${ace_file2} Cu
pair_coeff * * lambda_input/csp
pair_coeff * * lambda/zone
fix lambda all lambda ${lambda_input_thr_lo} ${lambda_input_thr_hi} time_averaged_zone ${r_sw_lo} ${r_sw_hi} ${lambda_input_histlen} ${lambda_histlen} min_delta_lambda ${min_delta_lambda} group_ignore_lambda_input group_ignore_csp
fix lambda_thermostat all lambda_thermostat N_rescaling ${N_rescaling}
fix weight_atom all apip_atom_weight 10 eam ace lambda_input lambda/zone all
pair_coeff * * lambda/input/csp/apip
pair_coeff * * lambda/zone/apip
fix lambda all lambda/apip ${lambda_input_thr_lo} ${lambda_input_thr_hi} time_averaged_zone ${r_sw_lo} ${r_sw_hi} ${lambda_input_histlen} ${lambda_histlen} min_delta_lambda ${min_delta_lambda} group_ignore_lambda_input group_ignore_csp
fix lambda_thermostat all lambda_thermostat/apip N_rescaling ${N_rescaling}
fix weight_atom all atom_weight/apip 10 eam ace lambda/input lambda/zone all
# store weight in variable
fix property_atom all property/atom d_usedweight
variable myweight atom f_weight_atom
#dump 1 all custom 10 dump/surface_ap_balance.dump.* id type x y z lambda lambda_input f_weight_atom proc d_usedweight
#compute lambda all property/atom apip_lambda
#compute lambda_input all property/atom apip_lambda_input
#dump 1 all custom 10 dump/surface_ap_balance.dump.* id type x y z c_lambda c_lambda_input f_weight_atom proc d_usedweight
## apply load balancing

18
examples/PACKAGES/apip/in.vacancy.const.lambda
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@ -20,9 +20,9 @@ read_data data.vacancy
group vacancy id 145 147 148 149 150 994 997 995 1024 1026 1028 1922
group transition id 77 79 81 84 88 151 152 153 154 155 158 1089 188 189 192 1033 1039 1964 1022 1021 999 998 996 948 950 952 992 993 139 1025 1027 1029 1034 1035 1038 1088 1920 1921 1923 1924 1925 1930
group bulk subtract all vacancy transition
set group vacancy lambda precise
set group transition lambda 0.5
set group bulk lambda fast
set group vacancy apip_lambda precise
set group transition apip_lambda 0.5
set group bulk apip_lambda fast
fix nve all nve
@ -33,13 +33,15 @@ fix nve all nve
pair_style hybrid/overlay eam/fs/apip pace/apip
pair_coeff * * eam/fs/apip ${eamfs_file} Cu
pair_coeff * * pace/apip ${ace_file2} Cu
fix weight_atom all apip_atom_weight 50 eam ace 0.5 0 all
fix weight_atom all atom_weight/apip 50 eam ace 0.5 0 all
# get statistics about lambda
variable flag_simple atom lambda==1
variable flag_switch atom lambda<1&&lambda>0
variable flag_complex atom lambda==0
compute lambda all property/atom apip_lambda
compute lambda_input all property/atom apip_lambda_input
variable flag_simple atom c_lambda==1
variable flag_switch atom c_lambda<1&&c_lambda>0
variable flag_complex atom c_lambda==0
compute lambda_types all reduce sum v_flag_simple v_flag_switch v_flag_complex
@ -49,4 +51,4 @@ thermo 1
run 100
# dump atoms
# write_dump all custom dump.vacancy.* id type x y z fx fy fz lambda lambda_input f_weight_atom
#write_dump all custom dump.vacancy.* id type x y z fx fy fz c_lambda c_lambda_input f_weight_atom

46
examples/PACKAGES/apip/in.vacancy.dynamic.lambda
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@ -37,36 +37,38 @@ fix nve all nve
## Use adaptive-precision ace-ace potential without lambda_thermostat.
## Calculate atomic weight that could be used for load balancing.
#pair_style hybrid/overlay pace/apip/fast pace/apip/precise lambda_input/csp ${csp_lattice} cutoff ${csp_cutoff} lambda/zone ${r_sw_hi}
#pair_coeff * * pace/apip/fast ${ace_file1} Cu
#pair_coeff * * pace/apip/precise ${ace_file2} Cu
#pair_coeff * * lambda_input/csp
#pair_coeff * * lambda/zone
#fix lambda all lambda ${lambda_input_thr_lo} ${lambda_input_thr_hi} time_averaged_zone ${r_sw_lo} ${r_sw_hi} ${lambda_input_histlen} ${lambda_histlen} min_delta_lambda ${min_delta_lambda}
#fix weight_atom all apip_atom_weight 100 ace ace lambda_input lambda/zone all
#pair_style hybrid/overlay pace/fast/apip pace/precise/apip lambda/input/csp/apip ${csp_lattice} cutoff ${csp_cutoff} lambda/zone/apip ${r_sw_hi}
#pair_coeff * * pace/fast/apip ${ace_file1} Cu
#pair_coeff * * pace/precise/apip ${ace_file2} Cu
#pair_coeff * * lambda/input/csp/apip
#pair_coeff * * lambda/zone/apip
#fix lambda all lambda/apip ${lambda_input_thr_lo} ${lambda_input_thr_hi} time_averaged_zone ${r_sw_lo} ${r_sw_hi} ${lambda_input_histlen} ${lambda_histlen} min_delta_lambda ${min_delta_lambda}
#fix weight_atom all atom_weight/apip 100 ace ace lambda/input lambda/zone all
# Use adaptive-precision eam-ace potential without lambda_thermostat.
# Calculate atomic weight that could be used for load balancing.
pair_style hybrid/overlay eam/fs/apip pace/apip lambda_input/csp ${csp_lattice} cutoff ${csp_cutoff} lambda/zone ${r_sw_hi}
pair_style hybrid/overlay eam/fs/apip pace/apip lambda/input/csp/apip ${csp_lattice} cutoff ${csp_cutoff} lambda/zone/apip ${r_sw_hi}
pair_coeff * * eam/fs/apip ${eamfs_file} Cu
pair_coeff * * pace/apip ${ace_file2} Cu
pair_coeff * * lambda_input/csp
pair_coeff * * lambda/zone
fix lambda all lambda ${lambda_input_thr_lo} ${lambda_input_thr_hi} time_averaged_zone ${r_sw_lo} ${r_sw_hi} ${lambda_input_histlen} ${lambda_histlen} min_delta_lambda ${min_delta_lambda}
fix weight_atom all apip_atom_weight 100 eam ace lambda_input lambda/zone all
pair_coeff * * lambda/input/csp/apip
pair_coeff * * lambda/zone/apip
fix lambda all lambda/apip ${lambda_input_thr_lo} ${lambda_input_thr_hi} time_averaged_zone ${r_sw_lo} ${r_sw_hi} ${lambda_input_histlen} ${lambda_histlen} min_delta_lambda ${min_delta_lambda}
fix weight_atom all atom_weight/apip 100 eam ace lambda/input lambda/zone all
## One can comment out fix lambda_thermostat to see the energy change caused by the neglection of the
## gradient of the switching function. This neglection can be compensated by the local thermostat and the
## energy can be conserved within numerical precision.
fix lambda_thermostat all lambda_thermostat N_rescaling ${N_rescaling} store_atomic_forces 100
fix lambda_thermostat all lambda_thermostat/apip N_rescaling ${N_rescaling} store_atomic_forces 100
# get statistics about lambda
variable flag_simple atom lambda==1
variable flag_switch atom lambda<1&&lambda>0
variable flag_complex atom lambda==0
compute lambda all property/atom apip_lambda
compute lambda_input all property/atom apip_lambda_input
variable flag_simple atom c_lambda==1
variable flag_switch atom c_lambda<1&&c_lambda>0
variable flag_complex atom c_lambda==0
compute lambda_types all reduce sum v_flag_simple v_flag_switch v_flag_complex
@ -76,7 +78,7 @@ thermo 1
run 100
# dump atoms
#write_dump all custom dump/vacancy.dump.* id type x y z fx fy fz lambda lambda_input f_weight_atom f_lambda_thermostat[*]
#write_dump all custom dump/vacancy.dump.* id type x y z fx fy fz c_lambda c_lambda_input f_weight_atom f_lambda_thermostat[*]
@ -85,13 +87,13 @@ run 100
#write_restart vacancy_ap.restart
#clear
#read_restart vacancy_ap.restart
#pair_style hybrid/overlay eam/fs/apip pace/apip lambda_input/csp fcc cutoff 6.0 lambda/zone 12.0
#pair_style hybrid/overlay eam/fs/apip pace/apip lambda/input/csp/apip fcc cutoff 6.0 lambda/zone/apip 12.0
#pair_coeff * * eam/fs/apip "Cu_300K_Immel_2023.eam.fs" Cu
#pair_coeff * * pace/apip "../../../potentials/Cu-PBE-core-rep.ace" Cu
#pair_coeff * * lambda_input/csp
#pair_coeff * * lambda/zone
#fix lambda all lambda 2.5 3.0 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda $(1/110)
#fix lambda_thermostat all lambda_thermostat N_rescaling ${N_rescaling} store_atomic_forces 100
#pair_coeff * * lambda/input/csp/apip
#pair_coeff * * lambda/zone/apip
#fix lambda all lambda/apip 2.5 3.0 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda $(1/110)
#fix lambda_thermostat all lambda_thermostat/apip N_rescaling ${N_rescaling} store_atomic_forces 100
#fix nve all nve
#thermo_style custom step etotal
#thermo 1

4
examples/PACKAGES/apip/in.validate
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@ -38,11 +38,11 @@ pair_coeff * * eam/fs/apip ${eamfs_file} Cu
pair_coeff * * pace/apip ${ace_file} Cu
# use ACE of adaptive-precision potential
set group all lambda precise
set group all apip_lambda precise
run 0
# use EAM of adaptive-precision potential
set group all lambda fast
set group all apip_lambda fast
run 0
# Use EAM potential