ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

update MS-MEAM examples

Browse Source
This commit is contained in:
Axel Kohlmeyer
2024-03-01 18:53:32 -05:00
parent 54035fba79
commit 2a8d16ee4b
11 changed files with 274 additions and 223 deletions
Download Patch File Download Diff File Expand all files Collapse all files

30
examples/meam/msmeam/HGa.meam
View File

@ -1,30 +0,0 @@
bkgd_dyn = 1
emb_lin_neg = 1
augt1=0
ialloy=1
rc = 5.9
#H
attrac(1,1)=0.460
repuls(1,1)=0.460
Cmin(1,1,1)=1.3 # PuMS
Cmax(1,1,1)= 2.80
nn2(1,1)=1
#Ga
rho0(2) = 0.6
attrac(2,2)=0.097
repuls(2,2)=0.097
nn2(2,2)=1
#HGa
attrac(1,2)=0.300
repuls(1,2)=0.300
lattce(1,2)=l12
re(1,2)=3.19
delta(1,2)=-0.48
alpha(1,2)=6.6
Cmin(1,1,2)=2.0
Cmin(2,1,2)= 2.0
Cmin(1,2,1)=2.0
Cmin(2,2,1) = 1.4
Cmin(1,2,2) = 1.4
Cmin(1,1,2) = 1.4
nn2(1,2)=1

1
examples/meam/msmeam/HGa.msmeam Symbolic link
View File

@ -0,0 +1 @@
../../../potentials/HGa.msmeam

25
examples/meam/msmeam/data.msmeam.bu
View File

@ -1,25 +0,0 @@
LAMMPS data file via write_data, version 16 Feb 2016, timestep = 1
3 atoms
2 atom types
-4.0000000000000000e+00 4.0000000000000000e+00 xlo xhi
-4.0000000000000000e+00 4.0000000000000000e+00 ylo yhi
-4.0000000000000000e+00 4.0000000000000000e+00 zlo zhi
Masses
1 1.0079
2 69.723
Atoms # atomic
1 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
2 2 2.2000000000000002e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
3 2 2.9999999999999999e-01 2.2999999999999998e+00 0.0000000000000000e+00 0 0 0
Velocities
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00

8
examples/meam/msmeam/in.msmeam
View File

@ -1,5 +1,3 @@
echo both
log log.msmeam
# Test of MEAM potential for HGa
# ------------------------ INITIALIZATION ----------------------------
@ -21,11 +19,11 @@ create_atoms 1 single 0 0 0 units box
create_atoms 2 single 2.2 0 0 units box
create_atoms 2 single 0.3 2.3 0 units box
# ---------- Define Settings ---------------------
variable teng equal "c_eatoms"
variable teng equal "c_eatoms"
compute pot_energy all pe/atom
compute stress all stress/atom NULL
dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
run 1
write_data data.msmeam
run 1
#write_data data.msmeam
print "All done!"

14
examples/meam/msmeam/library.msmeam
View File

@ -1,14 +0,0 @@
# DATE: 2018-09-22 UNITS: metal CONTRIBUTOR: Steve Valone, smv@lanl.gov CITATION: Baskes, PRB 1992; smv, sr, mib, JNM 2010
# ms-meam data format May 2010
# elt lat z ielement atwt
# alpha b0 b1 b2 b3 b1m b2m b3m alat esub asub
# - t0 t1 t2 t3 t1m t2m t3m rozero ibar
# NOTE: leading character cannot be a space
'H' 'dim' 1.0 1 1.0079
2.960 2.960 3.0 1.0 1.0 1.0 3.0 1.0 0.741 2.235 2.50
1.0 0.44721 0.0 0.00 0.0 0.31623 0 6.70 0
'Ga4' 'fcc' 12.0 31 69.723
4.42 4.80 3.10 6.00 0.00 0.0 0.0 0.5 4.247 2.897 0.97
1.0 1.649 1.435 0.00 0.0 0.0 2.0 0.70 0

126
examples/meam/msmeam/log.1Mar2024.msmeam.g++.1 Normal file
View File

@ -0,0 +1,126 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-182-g93942f2013-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Test of MEAM potential for HGa
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style atomic
variable latparam equal 4.646
variable ncell equal 3
# ----------------------- ATOM DEFINITION ----------------------------
region box block -4 4 -4 4 -4 4
create_box 2 box
Created orthogonal box = (-4 -4 -4) to (4 4 4)
1 by 1 by 1 MPI processor grid
#
include potential.mod
# NOTE: This script can be modified for different pair styles
# See in.elastic for more info.
variable Pu string H
print "potential chosen ${Pu}"
potential chosen H
# Choose potential
pair_style meam/ms
print "we just executed"
we just executed
pair_coeff * * library.msmeam ${Pu} Ga4 HGa.msmeam ${Pu} Ga4
pair_coeff * * library.msmeam H Ga4 HGa.msmeam ${Pu} Ga4
pair_coeff * * library.msmeam H Ga4 HGa.msmeam H Ga4
Reading MEAM library file library.msmeam with DATE: 2018-09-22
# Setup neighbor style
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Setup minimization style
variable dmax equal 1.0e-2
min_style cg
min_modify dmax ${dmax} line quadratic
min_modify dmax 0.01 line quadratic
compute eng all pe/atom
compute eatoms all reduce sum c_eng
# Setup output
thermo 100
thermo_style custom step temp etotal press pxx pyy pzz pxy pxz pyz lx ly lz vol c_eatoms
thermo_modify norm yes
create_atoms 1 single 0 0 0 units box
Created 1 atoms
using box units in orthogonal box = (-4 -4 -4) to (4 4 4)
create_atoms CPU = 0.000 seconds
create_atoms 2 single 2.2 0 0 units box
Created 1 atoms
using box units in orthogonal box = (-4 -4 -4) to (4 4 4)
create_atoms CPU = 0.000 seconds
create_atoms 2 single 0.3 2.3 0 units box
Created 1 atoms
using box units in orthogonal box = (-4 -4 -4) to (4 4 4)
create_atoms CPU = 0.000 seconds
# ---------- Define Settings ---------------------
variable teng equal "c_eatoms"
compute pot_energy all pe/atom
compute stress all stress/atom NULL
# dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
run 1
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.9
ghost atom cutoff = 6.9
binsize = 3.45, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam/ms, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam/ms, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 8.587 | 8.587 | 8.587 Mbytes
Step Temp TotEng Press Pxx Pyy Pzz Pxy Pxz Pyz Lx Ly Lz Volume c_eatoms
0 0 15.433079 491354.7 838670.96 635393.15 0 80195.797 0 0 8 8 8 512 15.433079
1 0 15.433079 491354.7 838670.96 635393.15 0 80195.797 0 0 8 8 8 512 15.433079
Loop time of 4.4446e-05 on 1 procs for 1 steps with 3 atoms
Performance: 1943.932 ns/day, 0.012 hours/ns, 22499.213 timesteps/s, 67.498 katom-step/s
31.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.9908e-05 | 2.9908e-05 | 2.9908e-05 | 0.0 | 67.29
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.033e-06 | 1.033e-06 | 1.033e-06 | 0.0 | 2.32
Output | 9.347e-06 | 9.347e-06 | 9.347e-06 | 0.0 | 21.03
Modify | 2.02e-07 | 2.02e-07 | 2.02e-07 | 0.0 | 0.45
Other | | 3.956e-06 | | | 8.90
Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 78 ave 78 max 78 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7 ave 7 max 7 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 14 ave 14 max 14 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14
Ave neighs/atom = 4.6666667
Neighbor list builds = 0
Dangerous builds = 0
#write_data data.msmeam
print "All done!"
All done!
Total wall time: 0:00:00

126
examples/meam/msmeam/log.1Mar2024.msmeam.g++.4 Normal file
View File

@ -0,0 +1,126 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-182-g93942f2013-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Test of MEAM potential for HGa
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style atomic
variable latparam equal 4.646
variable ncell equal 3
# ----------------------- ATOM DEFINITION ----------------------------
region box block -4 4 -4 4 -4 4
create_box 2 box
Created orthogonal box = (-4 -4 -4) to (4 4 4)
1 by 2 by 2 MPI processor grid
#
include potential.mod
# NOTE: This script can be modified for different pair styles
# See in.elastic for more info.
variable Pu string H
print "potential chosen ${Pu}"
potential chosen H
# Choose potential
pair_style meam/ms
print "we just executed"
we just executed
pair_coeff * * library.msmeam ${Pu} Ga4 HGa.msmeam ${Pu} Ga4
pair_coeff * * library.msmeam H Ga4 HGa.msmeam ${Pu} Ga4
pair_coeff * * library.msmeam H Ga4 HGa.msmeam H Ga4
Reading MEAM library file library.msmeam with DATE: 2018-09-22
# Setup neighbor style
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Setup minimization style
variable dmax equal 1.0e-2
min_style cg
min_modify dmax ${dmax} line quadratic
min_modify dmax 0.01 line quadratic
compute eng all pe/atom
compute eatoms all reduce sum c_eng
# Setup output
thermo 100
thermo_style custom step temp etotal press pxx pyy pzz pxy pxz pyz lx ly lz vol c_eatoms
thermo_modify norm yes
create_atoms 1 single 0 0 0 units box
Created 1 atoms
using box units in orthogonal box = (-4 -4 -4) to (4 4 4)
create_atoms CPU = 0.000 seconds
create_atoms 2 single 2.2 0 0 units box
Created 1 atoms
using box units in orthogonal box = (-4 -4 -4) to (4 4 4)
create_atoms CPU = 0.000 seconds
create_atoms 2 single 0.3 2.3 0 units box
Created 1 atoms
using box units in orthogonal box = (-4 -4 -4) to (4 4 4)
create_atoms CPU = 0.000 seconds
# ---------- Define Settings ---------------------
variable teng equal "c_eatoms"
compute pot_energy all pe/atom
compute stress all stress/atom NULL
# dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
run 1
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.9
ghost atom cutoff = 6.9
binsize = 3.45, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam/ms, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam/ms, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.965 | 8.123 | 8.594 Mbytes
Step Temp TotEng Press Pxx Pyy Pzz Pxy Pxz Pyz Lx Ly Lz Volume c_eatoms
0 0 15.433079 491354.7 838670.96 635393.15 0 80195.797 0 0 8 8 8 512 15.433079
1 0 15.433079 491354.7 838670.96 635393.15 0 80195.797 0 0 8 8 8 512 15.433079
Loop time of 8.70645e-05 on 4 procs for 1 steps with 3 atoms
Performance: 992.368 ns/day, 0.024 hours/ns, 11485.738 timesteps/s, 34.457 katom-step/s
29.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.3957e-05 | 4.67e-05 | 5.1056e-05 | 0.0 | 53.64
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.105e-05 | 1.3822e-05 | 1.7033e-05 | 0.0 | 15.88
Output | 1.5765e-05 | 1.9045e-05 | 2.5216e-05 | 0.0 | 21.87
Modify | 2.58e-07 | 3.465e-07 | 3.81e-07 | 0.0 | 0.40
Other | | 7.151e-06 | | | 8.21
Nlocal: 0.75 ave 3 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 38.25 ave 42 max 36 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 1.75 ave 7 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
FullNghs: 3.5 ave 14 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 14
Ave neighs/atom = 4.6666667
Neighbor list builds = 0
Dangerous builds = 0
#write_data data.msmeam
print "All done!"
All done!
Total wall time: 0:00:00

107
examples/meam/msmeam/log.msmeam.bu
View File

@ -1,107 +0,0 @@
# Test of MEAM potential for HGa
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style atomic
variable latparam equal 4.646
variable ncell equal 3
# ----------------------- ATOM DEFINITION ----------------------------
region box block -4 4 -4 4 -4 4
create_box 2 box
Created orthogonal box = (-4 -4 -4) to (4 4 4)
1 by 1 by 1 MPI processor grid
#
include potential.mod
# NOTE: This script can be modified for different pair styles
# See in.elastic for more info.
variable Pu string H
print "potential chosen ${Pu}"
potential chosen H
# Choose potential
pair_style MSmeam
print "we just executed"
we just executed
pair_coeff * * library.MSmeam ${Pu} Ga4 HGaMS.meam ${Pu} Ga4
pair_coeff * * library.MSmeam H Ga4 HGaMS.meam ${Pu} Ga4
pair_coeff * * library.MSmeam H Ga4 HGaMS.meam H Ga4
Reading potential file library.MSmeam with DATE: 2018-09-22
# Setup neighbor style
neighbor 1.0 nsq
neigh_modify once no every 1 delay 0 check yes
# Setup minimization style
variable dmax equal 1.0e-2
min_style cg
min_modify dmax ${dmax} line quadratic
min_modify dmax 0.01 line quadratic
compute eng all pe/atom
compute eatoms all reduce sum c_eng
# Setup output
thermo 100
thermo_style custom step temp etotal press pxx pyy pzz pxy pxz pyz lx ly lz vol c_eatoms
thermo_modify norm yes
create_atoms 1 single 0 0 0 units box
Created 1 atoms
create_atoms 2 single 2.2 0 0 units box
Created 1 atoms
create_atoms 2 single 0.3 2.3 0 units box
Created 1 atoms
# ---------- Define Settings ---------------------
variable teng equal "c_eatoms"
compute pot_energy all pe/atom
compute stress all stress/atom NULL
dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
run 1
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.9
ghost atom cutoff = 6.9
Memory usage per processor = 12.9295 Mbytes
Step Temp TotEng Press Pxx Pyy Pzz Pxy Pxz Pyz Lx Ly Lz Volume eatoms
0 0 15.433079 491354.68 838670.91 635393.13 0 80195.793 0 0 8 8 8 512 15.433079
1 0 15.433079 491354.68 838670.91 635393.13 0 80195.793 0 0 8 8 8 512 15.433079
Loop time of 0.000172138 on 1 procs for 1 steps with 3 atoms
Performance: 501.922 ns/day, 0.048 hours/ns, 5809.285 timesteps/s
81.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.6996e-05 | 6.6996e-05 | 6.6996e-05 | 0.0 | 38.92
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.9073e-06 | 1.9073e-06 | 1.9073e-06 | 0.0 | 1.11
Output | 9.7036e-05 | 9.7036e-05 | 9.7036e-05 | 0.0 | 56.37
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 6.199e-06 | | | 3.60
Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 78 ave 78 max 78 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7 ave 7 max 7 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 14 ave 14 max 14 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14
Ave neighs/atom = 4.66667
Neighbor list builds = 0
Dangerous builds = 0
write_data data.msmeam
print "All done!"
All done!
Total wall time: 0:00:00

24
examples/meam/msmeam/msmeam.dump.bu
View File

@ -1,24 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
3
ITEM: BOX BOUNDS pp pp pp
-4 4
-4 4
-4 4
ITEM: ATOMS id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
1 0 0 0 -131.925 -88.3005 0 22.9153 -2.147e+08 -1.62661e+08 -0 -2.05301e+07 -0 -0
2 2.2 0 0 120.809 -0.482171 0 14.7692 -2.12028e+08 -0 -0 403352 -0 -0
3 0.3 2.3 0 11.1159 88.7827 0 8.61478 -2.67145e+06 -1.62661e+08 -0 -2.09335e+07 -0 -0
ITEM: TIMESTEP
1
ITEM: NUMBER OF ATOMS
3
ITEM: BOX BOUNDS pp pp pp
-4 4
-4 4
-4 4
ITEM: ATOMS id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
1 0 0 0 -131.925 -88.3005 0 22.9153 -2.147e+08 -1.62661e+08 -0 -2.05301e+07 -0 -0
2 2.2 0 0 120.809 -0.482171 0 14.7692 -2.12028e+08 -0 -0 403352 -0 -0
3 0.3 2.3 0 11.1159 88.7827 0 8.61478 -2.67145e+06 -1.62661e+08 -0 -2.09335e+07 -0 -0

2
examples/meam/msmeam/potential.mod
View File

@ -7,7 +7,7 @@ print "potential chosen ${Pu}"
pair_style meam/ms
print "we just executed"
pair_coeff * * library.msmeam ${Pu} Ga4 HGa.meam ${Pu} Ga4
pair_coeff * * library.msmeam ${Pu} Ga4 HGa.msmeam ${Pu} Ga4
# Setup neighbor style
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes

34
potentials/HGa.msmeam
View File

@ -1,29 +1,29 @@
bkgd_dyn = 1
emb_lin_neg = 1
augt1=0
ialloy=1
rc = 5.9
augt1=0
ialloy=1
rc = 5.9
#H
attrac(1,1)=0.460
repuls(1,1)=0.460
attrac(1,1)=0.460
repuls(1,1)=0.460
Cmin(1,1,1)=1.3 # PuMS
Cmax(1,1,1)= 2.80
Cmax(1,1,1)= 2.80
nn2(1,1)=1
#Ga
rho0(2) = 0.6
attrac(2,2)=0.097
repuls(2,2)=0.097
attrac(2,2)=0.097
repuls(2,2)=0.097
nn2(2,2)=1
#HGa
attrac(1,2)=0.300
repuls(1,2)=0.300
lattce(1,2)=l12
re(1,2)=3.19
delta(1,2)=-0.48
alpha(1,2)=6.6
Cmin(1,1,2)=2.0
Cmin(2,1,2)= 2.0
Cmin(1,2,1)=2.0
attrac(1,2)=0.300
repuls(1,2)=0.300
lattce(1,2)=l12
re(1,2)=3.19
delta(1,2)=-0.48
alpha(1,2)=6.6
Cmin(1,1,2)=2.0
Cmin(2,1,2)= 2.0
Cmin(1,2,1)=2.0
Cmin(2,2,1) = 1.4
Cmin(1,2,2) = 1.4
Cmin(1,1,2) = 1.4