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Added Axel's suggestions for char* to string, updated potential files

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This commit is contained in:
James Chapman
2021-01-19 12:55:03 -08:00
parent 61c177ee63
commit 9da847e4c0
11 changed files with 6018 additions and 6376 deletions
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6015
examples/USER/misc/agni/Al_jpc.agni
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examples/USER/misc/agni/log.21Feb17.adatom.g++.1
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LAMMPS (21 Feb 2017)
using 1 OpenMP thread(s) per MPI task
processors * * 1
units metal
boundary p p f
read_data adatom.data
orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
1 by 1 by 1 MPI processor grid
reading atoms ...
181 atoms
pair_style agni
pair_coeff * * Al_jpc.agni Al
Reading potential file Al_jpc.agni with DATE: 2017-02-24
neighbor 0.3 bin
neigh_modify delay 2 check yes
timestep 0.0005
velocity all create 500 12345
fix 1 all nvt temp 250 250 0.2
fix 5 all momentum 1 linear 1 1 1
thermo 100
thermo_style custom step ke temp
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
run 1000
Neighbor list info ...
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.3
ghost atom cutoff = 8.3
binsize = 4.15, bins = 5 4 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair agni, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Memory usage per processor = 2.69795 Mbytes
Step KinEng Temp
0 11.633413 500
100 4.6059939 197.964
200 7.3700149 316.76065
300 6.0443913 259.78581
400 6.1631189 264.88868
500 6.2647272 269.25577
600 5.2732539 226.6426
700 5.6514471 242.89721
800 6.5572407 281.8279
900 6.0576738 260.35669
1000 6.5622233 282.04205
Loop time of 51.9308 on 1 procs for 1000 steps with 181 atoms
Performance: 0.832 ns/day, 28.850 hours/ns, 19.256 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 51.89 | 51.89 | 51.89 | 0.0 | 99.92
Neigh | 0.023158 | 0.023158 | 0.023158 | 0.0 | 0.04
Comm | 0.0049036 | 0.0049036 | 0.0049036 | 0.0 | 0.01
Output | 0.0002594 | 0.0002594 | 0.0002594 | 0.0 | 0.00
Modify | 0.010244 | 0.010244 | 0.010244 | 0.0 | 0.02
Other | | 0.002483 | | | 0.00
Nlocal: 181 ave 181 max 181 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 563 ave 563 max 563 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 19484 ave 19484 max 19484 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19484
Ave neighs/atom = 107.646
Neighbor list builds = 33
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:52

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examples/USER/misc/agni/log.21Feb17.adatom.g++.4
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LAMMPS (21 Feb 2017)
using 1 OpenMP thread(s) per MPI task
processors * * 1
units metal
boundary p p f
read_data adatom.data
orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
2 by 2 by 1 MPI processor grid
reading atoms ...
181 atoms
pair_style agni
pair_coeff * * Al_jpc.agni Al
Reading potential file Al_jpc.agni with DATE: 2017-02-24
neighbor 0.3 bin
neigh_modify delay 2 check yes
timestep 0.0005
velocity all create 500 12345
fix 1 all nvt temp 250 250 0.2
fix 5 all momentum 1 linear 1 1 1
thermo 100
thermo_style custom step ke temp
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
run 1000
Neighbor list info ...
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.3
ghost atom cutoff = 8.3
binsize = 4.15, bins = 5 4 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair agni, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Memory usage per processor = 3.06041 Mbytes
Step KinEng Temp
0 11.633413 500
100 4.6059941 197.96401
200 7.3700154 316.76067
300 6.0443913 259.78581
400 6.1631193 264.8887
500 6.2647281 269.25581
600 5.2732537 226.64259
700 5.651448 242.89725
800 6.5572405 281.82789
900 6.0576741 260.3567
1000 6.562224 282.04208
Loop time of 14.5263 on 4 procs for 1000 steps with 181 atoms
Performance: 2.974 ns/day, 8.070 hours/ns, 68.841 timesteps/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.858 | 13.227 | 13.574 | 8.0 | 91.06
Neigh | 0.0056965 | 0.0058173 | 0.0060787 | 0.2 | 0.04
Comm | 0.92934 | 1.276 | 1.6455 | 25.7 | 8.78
Output | 0.00013971 | 0.00017625 | 0.00025463 | 0.0 | 0.00
Modify | 0.012693 | 0.012756 | 0.012911 | 0.1 | 0.09
Other | | 0.004066 | | | 0.03
Nlocal: 45.25 ave 52 max 40 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost: 376.5 ave 382 max 366 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 4871 ave 5578 max 4374 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 19484
Ave neighs/atom = 107.646
Neighbor list builds = 33
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:14

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examples/USER/misc/agni/log.21Feb17.vacancy.g++.1
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LAMMPS (21 Feb 2017)
using 1 OpenMP thread(s) per MPI task
units metal
boundary p p p
read_data vacancy.data
orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
1 by 1 by 1 MPI processor grid
reading atoms ...
31 atoms
pair_style agni
pair_coeff * * Al_jpc.agni Al
Reading potential file Al_jpc.agni with DATE: 2017-02-24
neighbor 0.3 bin
neigh_modify delay 2 check yes
timestep 0.0005
velocity all create 1000 12345
fix 1 all nvt temp 900 900 200
fix 5 all momentum 1 linear 1 1 1
thermo 100
thermo_style custom step ke etotal temp
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
run 1000
Neighbor list info ...
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.3
ghost atom cutoff = 8.3
binsize = 4.15, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair agni, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Memory usage per processor = 2.73416 Mbytes
Step KinEng TotEng Temp
0 3.8778043 3.8778043 1000
100 2.9986261 2.9986261 773.27937
200 3.6860314 3.6860314 950.54599
300 3.813315 3.813315 983.36961
400 3.7330285 3.7330285 962.6655
500 3.5875467 3.5875467 925.14896
600 3.5331529 3.5331529 911.12202
700 2.6509449 2.6509449 683.62008
800 3.3763492 3.3763492 870.68582
900 3.903673 3.903673 1006.6709
1000 3.0884824 3.0884824 796.45133
Loop time of 9.02712 on 1 procs for 1000 steps with 31 atoms
Performance: 4.786 ns/day, 5.015 hours/ns, 110.777 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.0039 | 9.0039 | 9.0039 | 0.0 | 99.74
Neigh | 0.011892 | 0.011892 | 0.011892 | 0.0 | 0.13
Comm | 0.0061693 | 0.0061693 | 0.0061693 | 0.0 | 0.07
Output | 0.00014615 | 0.00014615 | 0.00014615 | 0.0 | 0.00
Modify | 0.0035009 | 0.0035009 | 0.0035009 | 0.0 | 0.04
Other | | 0.001521 | | | 0.02
Nlocal: 31 ave 31 max 31 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 869 ave 869 max 869 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 4360 ave 4360 max 4360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4360
Ave neighs/atom = 140.645
Neighbor list builds = 53
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:09

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examples/USER/misc/agni/log.21Feb17.vacancy.g++.4
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@ -1,87 +0,0 @@
LAMMPS (21 Feb 2017)
using 1 OpenMP thread(s) per MPI task
units metal
boundary p p p
read_data vacancy.data
orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
1 by 2 by 2 MPI processor grid
reading atoms ...
31 atoms
pair_style agni
pair_coeff * * Al_jpc.agni Al
Reading potential file Al_jpc.agni with DATE: 2017-02-24
neighbor 0.3 bin
neigh_modify delay 2 check yes
timestep 0.0005
velocity all create 1000 12345
fix 1 all nvt temp 900 900 200
fix 5 all momentum 1 linear 1 1 1
thermo 100
thermo_style custom step ke etotal temp
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
run 1000
Neighbor list info ...
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.3
ghost atom cutoff = 8.3
binsize = 4.15, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair agni, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Memory usage per processor = 2.72175 Mbytes
Step KinEng TotEng Temp
0 3.8778044 3.8778044 1000
100 2.9986263 2.9986263 773.27942
200 3.6860315 3.6860315 950.54602
300 3.8133145 3.8133145 983.3695
400 3.7330282 3.7330282 962.66543
500 3.5875466 3.5875466 925.14895
600 3.5331523 3.5331523 911.12186
700 2.6509448 2.6509448 683.62005
800 3.3763493 3.3763493 870.68584
900 3.9036733 3.9036733 1006.671
1000 3.0884818 3.0884818 796.45116
Loop time of 2.46785 on 4 procs for 1000 steps with 31 atoms
Performance: 17.505 ns/day, 1.371 hours/ns, 405.212 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.0737 | 2.299 | 2.3902 | 8.7 | 93.16
Neigh | 0.0025222 | 0.0027327 | 0.0028174 | 0.2 | 0.11
Comm | 0.059817 | 0.15141 | 0.37684 | 33.8 | 6.14
Output | 0.0001502 | 0.00016767 | 0.00021219 | 0.0 | 0.01
Modify | 0.0098755 | 0.010248 | 0.010664 | 0.3 | 0.42
Other | | 0.004321 | | | 0.18
Nlocal: 7.75 ave 8 max 7 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 617.25 ave 621 max 612 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1090 ave 1131 max 993 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Total # of neighbors = 4360
Ave neighs/atom = 140.645
Neighbor list builds = 53
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02

2
potentials/Al_Batra_2019.agni
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@ -1,10 +1,10 @@
# DATE: 2020-11-12 CONTRIBUTOR: James Chapman, email chapman37@llnl.gov
# Huan Tran, Rohit Batra, James Chapman, Chiho Kim, Anand Chandrasekaran, and Rampi Ramprasad, Iterative-Learning Strategy for the Development of Application-Specific Atomistic Force Fields, J. Phys. Chem. C., 123, 34, 20715-20722 (2019)
n_elements 1
element Al
interaction Al
generation 2
neta 32
eta +1.00000000E+00 +1.22580645E+00 +1.45161290E+00 +1.67741935E+00 +1.90322581E+00 +2.12903226E+00 +2.35483871E+00 +2.58064516E+00 +2.80645161E+00 +3.03225806E+00 +3.25806452E+00 +3.48387097E+00 +3.70967742E+00 +3.93548387E+00 +4.16129032E+00 +4.38709677E+00 +4.61290323E+00 +4.83870968E+00 +5.06451613E+00 +5.29032258E+00 +5.51612903E+00 +5.74193548E+00 +5.96774194E+00 +6.19354839E+00 +6.41935484E+00 +6.64516129E+00 +6.87096774E+00 +7.09677419E+00 +7.32258065E+00 +7.54838710E+00 +7.77419355E+00 +8.00000000E+00
gwidth 0.3
Rc 8.0

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potentials/Al_jpc.agni
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potentials/Cu_Huan_2019_fp1.agni
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@ -1,10 +1,10 @@
# DATE: 2020-11-12 CONTRIBUTOR: James Chapman, email chapman37@llnl.gov
# Huan Tran, Rohit Batra, James Chapman, Chiho Kim, Anand Chandrasekaran, and Rampi Ramprasad, Iterative-Learning Strategy for the Development of Application-Specific Atomistic Force Fields, J. Phys. Chem. C., 123, 34, 20715-20722 (2019)
n_elements 1
element Cu
interaction Cu
generation 1
neta 32
eta +1.56250000E-02 +1.78683272E-02 +2.04337354E-02 +2.33674669E-02 +2.67224028E-02 +3.05590168E-02 +3.49464646E-02 +3.99638313E-02 +4.57015560E-02 +5.22630628E-02 +5.97666243E-02 +6.83474943E-02 +7.81603450E-02 +8.93820555E-02 +1.02214900E-01 +1.16890194E-01 +1.33672462E-01 +1.52864211E-01 +1.74811375E-01 +1.99909558E-01 +2.28611161E-01 +2.61433537E-01 +2.98968319E-01 +3.41892079E-01 +3.90978530E-01 +4.47112467E-01 +5.11305718E-01 +5.84715383E-01 +6.68664689E-01 +7.64666844E-01 +8.74452311E-01 +1.00000000E+00
Rc 8.0
n_train 1650

2
potentials/Cu_Huan_2019_fp2.agni
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@ -1,10 +1,10 @@
# DATE: 2020-11-12 CONTRIBUTOR: James Chapman, email chapman37@llnl.gov
# Huan Tran, Rohit Batra, James Chapman, Chiho Kim, Anand Chandrasekaran, and Rampi Ramprasad, Iterative-Learning Strategy for the Development of Application-Specific Atomistic Force Fields, J. Phys. Chem. C., 123, 34, 20715-20722 (2019)
n_elements 1
element Cu
interaction Cu
generation 2
neta 32
eta +1.00000000E+00 +1.22580645E+00 +1.45161290E+00 +1.67741935E+00 +1.90322581E+00 +2.12903226E+00 +2.35483871E+00 +2.58064516E+00 +2.80645161E+00 +3.03225806E+00 +3.25806452E+00 +3.48387097E+00 +3.70967742E+00 +3.93548387E+00 +4.16129032E+00 +4.38709677E+00 +4.61290323E+00 +4.83870968E+00 +5.06451613E+00 +5.29032258E+00 +5.51612903E+00 +5.74193548E+00 +5.96774194E+00 +6.19354839E+00 +6.41935484E+00 +6.64516129E+00 +6.87096774E+00 +7.09677419E+00 +7.32258065E+00 +7.54838710E+00 +7.77419355E+00 +8.00000000E+00
gwidth 0.3
Rc 8.0

2
potentials/Pt_Chapman_2020.agni
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@ -1,10 +1,10 @@
# DATE: 2020-11-12 CONTRIBUTOR: James Chapman, email chapman37@llnl.gov
# James Chapman and Rampi Ramprasad, Multiscale Modeling of Defect Phenomena in Platinum Using Machine Learning of Force Fields, JOM, (2020)
n_elements 1
element Pt
interaction Pt
generation 1
neta 8
eta +1.00000000E+00 +5.33741212E-01 +2.84879681E-01 +1.52052026E-01 +8.11564326E-02 +4.33165327E-02 +2.31198186E-02 +1.23400000E-02
Rc 8.0
n_train 4500

8
src/USER-MISC/pair_agni.cpp
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@ -389,9 +389,9 @@ void PairAGNI::read_file(char *filename)
values = reader.next_values(2);
values.next_string(); // ignore
for (i = 0; i < nparams; ++i) {
const char* element = values.next_string().c_str();
std::string element = values.next_string();
for (j = 0; j < nelements; ++j)
if (strcmp(element,elements[j]) == 0) break;
if (strcmp(element.c_str(),elements[j]) == 0) break;
if (j == nelements)
error->all(FLERR,"No suitable parameters for requested element found");
else params[i].ielement = j;
@ -400,8 +400,8 @@ void PairAGNI::read_file(char *filename)
values = reader.next_values(2);
values.next_string(); // ignore
for (i = 0; i < nparams; ++i){
const char* element = values.next_string().c_str();
if (strcmp(element,elements[params[i].ielement]) == 0) curparam = i;
std::string element = values.next_string();
if (strcmp(element.c_str(),elements[params[i].ielement]) == 0) curparam = i;
}
values = reader.next_values(2);