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adjust drip potential example for new requirements for pair style rebo. recreate log files

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Axel Kohlmeyer 2019-05-09 12:29:38 -04:00
parent 47cf17e5c8
commit 2f580380a4
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9 changed files with 270 additions and 37656 deletions
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19
examples/USER/misc/drip/C.drip
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@ -1,19 +0,0 @@
# DATE: 2019-04-19 CONTRIBUTOR: Mingjian Wen, wenxx151@umn.edu
#
# Parameters of the Dihedral-angle-corrected registry-dependent interlayer (DRIP)
# potential for multilayer graphene structures.
#
# Cite as M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B, 98, 235404 (2018).
# C0 C2 C4 C delta lambda A z0 B eta rho_cut r_cut normal_cut
C C 1.1598e-02 1.2981e-02 3.2515e-02 7.8151e-03 8.3679e-01 2.7158 2.2216e-02 3.34 7.6799e-03 1.1432 1.562 12.0 3.7
# C0, C2, C4, C, A, and B in [eV]
# delta, z0, eta, rho_cut, r_cut, and normal_cut in [Angstrom]
# lambda in [1/Angstrom]
#
# "normal_cut" is a parameter not present in the Wen paper, but specific to the
# LAMMPS implementation, which is used to find the 3 nearest neighbors of an
# atom to construct the normal.

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examples/USER/misc/drip/C.drip Symbolic link
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../../../../potentials/C.drip

37595
examples/USER/misc/drip/CH.airebo
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File diff suppressed because it is too large Load Diff

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examples/USER/misc/drip/CH.rebo Symbolic link
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../../../../potentials/CH.rebo

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examples/USER/misc/drip/in.CH_drip
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@ -12,7 +12,7 @@ read_data data.CH
# potential
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C NULL # only applies to species 1, i.e. C
pair_coeff * * rebo CH.airebo C H # species 1 is C and species 2 is H
pair_coeff * * rebo CH.rebo C H # species 1 is C and species 2 is H
compute peratom all pe/atom

2
examples/USER/misc/drip/in.C_drip
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@ -12,7 +12,7 @@ read_data data.C
# potential
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C
pair_coeff * * rebo CH.airebo C
pair_coeff * * rebo CH.rebo C
compute peratom all pe/atom

52
examples/USER/misc/drip/log.4May2019.g++.in.CH_drip → examples/USER/misc/drip/log.30Apr19.CH_drip.g++.1
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@ -1,4 +1,6 @@
LAMMPS (29 Mar 2019)
LAMMPS (30 Apr 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Define unit set and class of atomic model
units metal
atom_style molecular
@ -16,16 +18,16 @@ read_data data.CH
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000221014 secs
read_data CPU = 0.00603986 secs
special bonds CPU = 0.000152826 secs
read_data CPU = 0.000973701 secs
# potential
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C NULL # only applies to species 1, i.e. C
Reading potential file C.drip with DATE: 2019-04-19
pair_coeff * * rebo CH.airebo C H # species 1 is C and species 2 is H
Reading potential file CH.airebo with DATE: 2011-10-25
pair_coeff * * rebo CH.rebo C H # species 1 is C and species 2 is H
Reading potential file CH.rebo with DATE: 2018-7-3
compute peratom all pe/atom
@ -40,7 +42,7 @@ dump_modify id sort id
# minimize energy
minimize 1.0e-15 1.0e-15 100 100
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -60,36 +62,36 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.92 | 12.92 | 12.92 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -2883.1071 0 -2883.1071 366130.38 2779.5956
10 0 -3229.1892 0 -3229.1892 -19780.166 2779.5956
20 0 -3268.3574 0 -3268.3574 -15169.468 2779.5956
30 0 -3270.013 0 -3270.013 -19827.419 2779.5956
40 0 -3270.1341 0 -3270.1341 -20652.569 2779.5956
50 0 -3270.2612 0 -3270.2612 -22644.747 2779.5956
57 0 -3270.2819 0 -3270.2819 -23254.995 2779.5956
Loop time of 3.06624 on 1 procs for 57 steps with 545 atoms
0 0 -2884.3731 0 -2884.3731 366196.9 2779.5956
10 0 -3240.4807 0 -3240.4807 -20237.368 2779.5956
20 0 -3281.0671 0 -3281.0671 -13303.696 2779.5956
30 0 -3282.2176 0 -3282.2176 -19187.215 2779.5956
40 0 -3282.4004 0 -3282.4004 -21740.059 2779.5956
50 0 -3282.4755 0 -3282.4755 -22659.554 2779.5956
57 0 -3282.5011 0 -3282.5011 -23313.198 2779.5956
Loop time of 3.04218 on 1 procs for 57 steps with 545 atoms
99.3% CPU use with 1 MPI tasks x no OpenMP threads
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-2883.10712045 -3270.28039929 -3270.28192718
Force two-norm initial, final = 114.766 0.235428
Force max component initial, final = 12.0195 0.0484347
Final line search alpha, max atom move = 1 0.0484347
Iterations, force evaluations = 57 101
-2884.37307546 -3282.49993222 -3282.5010627
Force two-norm initial, final = 115.342 0.193154
Force max component initial, final = 12.0934 0.03617
Final line search alpha, max atom move = 1 0.03617
Iterations, force evaluations = 57 100
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0539 | 3.0539 | 3.0539 | 0.0 | 99.60
Bond | 4.1485e-05 | 4.1485e-05 | 4.1485e-05 | 0.0 | 0.00
Pair | 3.0291 | 3.0291 | 3.0291 | 0.0 | 99.57
Bond | 1.8835e-05 | 1.8835e-05 | 1.8835e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0019863 | 0.0019863 | 0.0019863 | 0.0 | 0.06
Output | 0.0070152 | 0.0070152 | 0.0070152 | 0.0 | 0.23
Comm | 0.0016081 | 0.0016081 | 0.0016081 | 0.0 | 0.05
Output | 0.0079796 | 0.0079796 | 0.0079796 | 0.0 | 0.26
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.003321 | | | 0.11
Other | | 0.003517 | | | 0.12
Nlocal: 545 ave 545 max 545 min
Histogram: 1 0 0 0 0 0 0 0 0 0

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examples/USER/misc/drip/log.30Apr19.CH_drip.g++.4 Normal file
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LAMMPS (30 Apr 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Define unit set and class of atomic model
units metal
atom_style molecular
# BC
boundary p p s
# read config
read_data data.CH
triclinic box = (0 0 0) to (24.65 21.3475 30) with tilt (12.325 0 0)
1 by 2 by 2 MPI processor grid
reading atoms ...
545 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000135422 secs
read_data CPU = 0.00368595 secs
# potential
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C NULL # only applies to species 1, i.e. C
Reading potential file C.drip with DATE: 2019-04-19
pair_coeff * * rebo CH.rebo C H # species 1 is C and species 2 is H
Reading potential file CH.rebo with DATE: 2018-7-3
compute peratom all pe/atom
# set what thermodynamic information to print to log
thermo 10 # print every 1 timestep
# set what information to write to dump file
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
dump_modify id sort id
# minimize energy
minimize 1.0e-15 1.0e-15 100 100
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17.7
ghost atom cutoff = 17.7
binsize = 8.85, bins = 5 3 1
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair drip, perpetual, skip from (2)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.03 | 11.1 | 11.16 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -2884.3731 0 -2884.3731 366196.9 2779.5956
10 0 -3240.4807 0 -3240.4807 -20237.368 2779.5956
20 0 -3281.0671 0 -3281.0671 -13303.696 2779.5956
30 0 -3282.2176 0 -3282.2176 -19187.216 2779.5956
40 0 -3282.4004 0 -3282.4004 -21740.027 2779.5956
50 0 -3282.4753 0 -3282.4753 -22682.604 2779.5956
57 0 -3282.5023 0 -3282.5023 -23355.081 2779.5956
Loop time of 1.66218 on 4 procs for 57 steps with 545 atoms
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-2884.37307546 -3282.50070864 -3282.50227121
Force two-norm initial, final = 115.342 0.228488
Force max component initial, final = 12.0934 0.03365
Final line search alpha, max atom move = 1 0.03365
Iterations, force evaluations = 57 100
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5571 | 1.5945 | 1.6314 | 2.3 | 95.93
Bond | 2.265e-05 | 2.9087e-05 | 3.4571e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.020248 | 0.05608 | 0.092328 | 11.8 | 3.37
Output | 0.0053282 | 0.0054213 | 0.0056982 | 0.2 | 0.33
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.006172 | | | 0.37
Nlocal: 136.25 ave 177 max 100 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 2874.75 ave 2912 max 2835 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 73530.5 ave 73544 max 73517 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 294122
Ave neighs/atom = 539.673
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

32
examples/USER/misc/drip/log.4May2019.g++.in.C_drip → examples/USER/misc/drip/log.30Apr19.C_drip.g++.1
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@ -1,4 +1,6 @@
LAMMPS (29 Mar 2019)
LAMMPS (30 Apr 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Define unit set and class of atomic model
units metal
atom_style molecular
@ -16,16 +18,16 @@ read_data data.C
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000164032 secs
read_data CPU = 0.00137401 secs
special bonds CPU = 0.000912905 secs
read_data CPU = 0.00252986 secs
# potential
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C
Reading potential file C.drip with DATE: 2019-04-19
pair_coeff * * rebo CH.airebo C
Reading potential file CH.airebo with DATE: 2011-10-25
pair_coeff * * rebo CH.rebo C
Reading potential file CH.rebo with DATE: 2018-7-3
compute peratom all pe/atom
@ -39,7 +41,7 @@ dump_modify id sort id
# minimize energy
minimize 1.0e-15 1.0e-15 100 100
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -66,14 +68,14 @@ Step Temp E_pair E_mol TotEng Press Volume
40 0 -2967.0888 0 -2967.0888 -29997.486 2052.0534
50 0 -2967.0896 0 -2967.0896 -30072.387 2052.0534
51 0 -2967.0896 0 -2967.0896 -30076.548 2052.0534
Loop time of 2.89944 on 1 procs for 51 steps with 400 atoms
Loop time of 2.93337 on 1 procs for 51 steps with 400 atoms
99.6% CPU use with 1 MPI tasks x no OpenMP threads
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-2941.05486168 -2967.08958346 -2967.08962043
-2941.05486197 -2967.08958376 -2967.08962073
Force two-norm initial, final = 35.5666 0.0471918
Force max component initial, final = 6.23617 0.0050012
Final line search alpha, max atom move = 1 0.0050012
@ -82,13 +84,13 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.8899 | 2.8899 | 2.8899 | 0.0 | 99.67
Bond | 3.171e-05 | 3.171e-05 | 3.171e-05 | 0.0 | 0.00
Pair | 2.9239 | 2.9239 | 2.9239 | 0.0 | 99.68
Bond | 1.2398e-05 | 1.2398e-05 | 1.2398e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.001483 | 0.001483 | 0.001483 | 0.0 | 0.05
Output | 0.0055339 | 0.0055339 | 0.0055339 | 0.0 | 0.19
Comm | 0.0010808 | 0.0010808 | 0.0010808 | 0.0 | 0.04
Output | 0.0059283 | 0.0059283 | 0.0059283 | 0.0 | 0.20
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.002449 | | | 0.08
Other | | 0.002466 | | | 0.08
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -105,4 +107,4 @@ Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02
Total wall time: 0:00:03

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examples/USER/misc/drip/log.30Apr19.C_drip.g++.4 Normal file
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LAMMPS (30 Apr 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Define unit set and class of atomic model
units metal
atom_style molecular
# BC
boundary p p s
# read config
read_data data.C
triclinic box = (0 0 0) to (24.65 21.3475 30) with tilt (12.325 0 0)
1 by 2 by 2 MPI processor grid
reading atoms ...
400 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.0003407 secs
read_data CPU = 0.00411105 secs
# potential
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C
Reading potential file C.drip with DATE: 2019-04-19
pair_coeff * * rebo CH.rebo C
Reading potential file CH.rebo with DATE: 2018-7-3
compute peratom all pe/atom
# set what thermodynamic information to print to log
thermo 10 # print every 1 timestep
# set what information to write to dump file
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
dump_modify id sort id
# minimize energy
minimize 1.0e-15 1.0e-15 100 100
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17.7
ghost atom cutoff = 17.7
binsize = 8.85, bins = 5 3 1
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair drip, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair rebo, perpetual, copy from (1)
attributes: full, newton on, ghost
pair build: copy
stencil: none
bin: none
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:934)
Per MPI rank memory allocation (min/avg/max) = 10.7 | 10.77 | 10.83 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -2941.0549 0 -2941.0549 -52204.715 2052.0534
10 0 -2966.9787 0 -2966.9787 -29717.01 2052.0534
20 0 -2967.0695 0 -2967.0695 -29614.636 2052.0534
30 0 -2967.0859 0 -2967.0859 -29867.385 2052.0534
40 0 -2967.0888 0 -2967.0888 -29997.486 2052.0534
50 0 -2967.0896 0 -2967.0896 -30072.387 2052.0534
51 0 -2967.0896 0 -2967.0896 -30076.548 2052.0534
Loop time of 1.47901 on 4 procs for 51 steps with 400 atoms
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-2941.05486197 -2967.08958376 -2967.08962073
Force two-norm initial, final = 35.5666 0.0471918
Force max component initial, final = 6.23617 0.0050012
Final line search alpha, max atom move = 1 0.0050012
Iterations, force evaluations = 51 101
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.4314 | 1.4405 | 1.4548 | 0.8 | 97.40
Bond | 1.955e-05 | 2.265e-05 | 2.4796e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.014506 | 0.029363 | 0.038964 | 5.5 | 1.99
Output | 0.00424 | 0.0043345 | 0.0046172 | 0.2 | 0.29
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.004772 | | | 0.32
Nlocal: 100 ave 100 max 100 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2132 ave 2132 max 2132 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 73530.5 ave 73544 max 73517 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 294122
Ave neighs/atom = 735.305
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01