1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
|
LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# 3d soft repulsive particles
units real
atom_style atomic
lattice fcc 5.0 origin 0.1 0.1 0.1
Lattice spacing in x,y,z = 5 5 5
region box block -5 5 -5 5 -5 5
create_box 2 box
Created orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
using lattice units in orthogonal box = (-25 -25 -25) to (25 25 25)
create_atoms CPU = 0.000 seconds
set type 1 type/ratio 2 0.5 424662346
Setting atom values ...
2000 settings made for type/ratio
mass * 1.0
velocity all create 3.0 87287
pair_style python 9.0
pair_coeff * * py_pot.Harmonic A B
neighbor 1.0 bin
neigh_modify every 2 delay 4 check yes
fix 1 all nve
thermo 50
run 250 post no
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair python, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.225 | 3.225 | 3.225 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 423843.22 0 423878.98 249277.9
50 79.665061 422928.03 0 423877.66 248995.64
100 108.5878 422583.81 0 423878.21 250822.76
150 130.90607 422317.45 0 423877.89 251949.08
200 120.05458 422447.24 0 423878.33 252105.09
250 135.76605 422259.47 0 423877.84 252077.41
Loop time of 4.70112 on 4 procs for 250 steps with 4000 atoms
write_restart repulsive.restart
System init for write_restart ...
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart repulsive.restart
Reading restart file ...
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
restoring atom style atomic from restart
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
pair style python stores no restart info
4000 atoms
read_restart CPU = 0.001 seconds
pair_style python 10.0
pair_coeff * * py_pot.Harmonic A B
shell rm -f python.dat
pair_write 1 1 1000 rsq 0.1 10.0 python.dat PYTH_A_A
Creating table file python.dat with DATE: 2022-03-18
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair python, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
pair_write 2 2 1000 rsq 0.1 10.0 python.dat PYTH_B_B
Appending to table file python.dat with DATE: 2022-03-18
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
pair_write 1 2 1000 rsq 0.1 10.0 python.dat PYTH_A_B
Appending to table file python.dat with DATE: 2022-03-18
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
fix 1 all nve
thermo 50
run 250 post no
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.667 | 3.667 Mbytes
Step Temp E_pair E_mol TotEng Press
250 135.76605 422259.47 0 423877.84 252077.41
300 119.63404 422452.21 0 423878.28 251958.74
350 129.35013 422336.12 0 423878 252069.99
400 123.04377 422411.48 0 423878.19 252024.23
450 126.01375 422375.98 0 423878.1 252019.19
500 126.91094 422365.34 0 423878.15 252012.59
Loop time of 6.20423 on 4 procs for 250 steps with 4000 atoms
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart repulsive.restart
Reading restart file ...
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
restoring atom style atomic from restart
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
pair style python stores no restart info
4000 atoms
read_restart CPU = 0.001 seconds
pair_style harmonic/cut
pair_coeff 1 1 0.2 9.0
pair_coeff 2 2 0.4 9.0
shell rm -f harmonic.dat
pair_write 1 1 1000 rsq 0.1 10.0 harmonic.dat HARM_1_1
Creating table file harmonic.dat with DATE: 2022-03-18
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair harmonic/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
pair_write 2 2 1000 rsq 0.1 10.0 harmonic.dat HARM_2_2
Appending to table file harmonic.dat with DATE: 2022-03-18
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
pair_write 1 2 1000 rsq 0.1 10.0 harmonic.dat HARM_1_2
Appending to table file harmonic.dat with DATE: 2022-03-18
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
neighbor 1.0 bin
neigh_modify every 2 delay 4 check yes
fix 1 all nve
thermo 50
run 250 post no
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.227 | 3.227 | 3.229 Mbytes
Step Temp E_pair E_mol TotEng Press
250 135.76605 422259.47 0 423877.84 252077.41
300 119.63404 422452.21 0 423878.28 251958.74
350 129.35013 422336.12 0 423878 252069.99
400 123.04377 422411.48 0 423878.19 252024.23
450 126.01375 422375.98 0 423878.1 252019.19
500 126.91094 422365.34 0 423878.15 252012.59
Loop time of 0.257048 on 4 procs for 250 steps with 4000 atoms
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart repulsive.restart
Reading restart file ...
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
restoring atom style atomic from restart
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
pair style python stores no restart info
4000 atoms
read_restart CPU = 0.000 seconds
pair_style table spline 1000
pair_coeff 1 1 python.dat PYTH_A_A
Reading pair table potential file python.dat with DATE: 2022-03-18
pair_coeff 1 2 python.dat PYTH_A_B
Reading pair table potential file python.dat with DATE: 2022-03-18
pair_coeff 2 2 python.dat PYTH_B_B
Reading pair table potential file python.dat with DATE: 2022-03-18
neighbor 1.0 bin
neigh_modify every 2 delay 4 check yes
fix 1 all nve
thermo 50
run 250 post no
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.257 | 3.257 | 3.257 Mbytes
Step Temp E_pair E_mol TotEng Press
250 135.76605 422259.47 0 423877.84 252077.38
300 119.63401 422452.21 0 423878.28 251958.73
350 129.35009 422336.11 0 423878 252069.98
400 123.04383 422411.48 0 423878.19 252024.21
450 126.01378 422375.98 0 423878.1 252019.16
500 126.91078 422365.34 0 423878.15 252012.57
Loop time of 0.497624 on 4 procs for 250 steps with 4000 atoms
# remove temporary files
shell rm repulsive.restart harmonic.dat python.dat
Total wall time: 0:00:11
|
