Merge branch 'develop' into remove-message-package
This commit is contained in:
Axel Kohlmeyer
@ -1,10 +1,16 @@
|
||||
Examples for Extended Dissipative Particle Dynamics (DPD)
|
||||
---------------------------------------------------------
|
||||
This directory contains examples for extended DPD simulations
|
||||
Examples for Basic Dissipative Particle Dynamics (DPD)
|
||||
------------------------------------------------------
|
||||
This directory contains examples for DPD simulations using
|
||||
pair styles from the DPD-BASIC package.
|
||||
|
||||
1) 'dpdext' - test case (DPD fluid) for 'dpdext' pair style (in.dpdext) and an initial
|
||||
configuration (dpdext.data)
|
||||
1) 'dpd' - simple example (DPD fluid) for 'dpd' pair style (in.dpd)
|
||||
|
||||
2) 'dpdext_tstat' - test case (coarse-grained SPC/E water) for 'dpdext/tstat' pair style
|
||||
(in.cg_spce), an initial configuration (dpdext.data) and tabulated potential
|
||||
2) 'dpd_tstat' - coarse-grained SPC/E water example for 'dpd/tstat' pair style
|
||||
(in.dpd_tstat), an initial configuration (dpdext.data) and tabulated potential
|
||||
(cg_spce_table.pot) obtained by bottom-up coarse-graining of the atomistic SPC/E water.
|
||||
|
||||
3) 'dpdext' - simple example (DPD fluid) for 'dpd/ext' pair style (in.dpdext)
|
||||
|
||||
4) 'dpdext_tstat' - coarse-grained SPC/E water example for 'dpd/ext/tstat' pair style
|
||||
(in.dpdext_tstat), an initial configuration (dpdext.data) and tabulated potential
|
||||
(cg_spce_table.pot) obtained by bottom-up coarse-graining of the atomistic SPC/E water.
|
||||
|
||||
43
examples/PACKAGES/dpd-basic/dpd/in.dpd
Normal file
43
examples/PACKAGES/dpd-basic/dpd/in.dpd
Normal file
@ -0,0 +1,43 @@
|
||||
# DPD Fluid
|
||||
|
||||
variable T equal 1.0
|
||||
variable rc equal 1.0
|
||||
variable rcD equal 1.2
|
||||
|
||||
units lj
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
### create box and configuration
|
||||
variable L equal 5.0
|
||||
lattice fcc 3.0
|
||||
region simBox block 0 ${L} 0 ${L} 0 ${L}
|
||||
create_box 2 simBox
|
||||
#create_atoms 1 region simBox
|
||||
create_atoms 1 random 100 12456 simBox
|
||||
create_atoms 2 random 100 13245 simBox
|
||||
mass 1 1.0
|
||||
mass 2 2.0
|
||||
###
|
||||
|
||||
pair_style dpd ${T} ${rc} 3854262
|
||||
|
||||
pair_coeff 1 1 25.0 4.5 1.2
|
||||
pair_coeff 1 2 25.1 4.51 1.21
|
||||
pair_coeff 2 2 25.2 4.52 1.22
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 5000
|
||||
|
||||
154
examples/PACKAGES/dpd-basic/dpd/log.5Apr22.dpd.g++.1
Normal file
154
examples/PACKAGES/dpd-basic/dpd/log.5Apr22.dpd.g++.1
Normal file
@ -0,0 +1,154 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DPD Fluid
|
||||
|
||||
variable T equal 1.0
|
||||
variable rc equal 1.0
|
||||
variable rcD equal 1.2
|
||||
|
||||
units lj
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
### create box and configuration
|
||||
variable L equal 5.0
|
||||
lattice fcc 3.0
|
||||
Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
|
||||
region simBox block 0 ${L} 0 ${L} 0 ${L}
|
||||
region simBox block 0 5 0 ${L} 0 ${L}
|
||||
region simBox block 0 5 0 5 0 ${L}
|
||||
region simBox block 0 5 0 5 0 5
|
||||
create_box 2 simBox
|
||||
Created orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
#create_atoms 1 region simBox
|
||||
create_atoms 1 random 100 12456 simBox
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 2 random 100 13245 simBox
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
mass 2 2.0
|
||||
###
|
||||
|
||||
pair_style dpd ${T} ${rc} 3854262
|
||||
pair_style dpd 1 ${rc} 3854262
|
||||
pair_style dpd 1 1 3854262
|
||||
|
||||
pair_coeff 1 1 25.0 4.5 1.2
|
||||
pair_coeff 1 2 25.1 4.51 1.21
|
||||
pair_coeff 2 2 25.2 4.52 1.22
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 1 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 5000
|
||||
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 = 1.52
|
||||
ghost atom cutoff = 1.52
|
||||
binsize = 0.76, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair dpd, 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) = 3.083 | 3.083 | 3.083 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 1 9.5226009
|
||||
100 1 1.9913643 9.2036029
|
||||
200 2 1.6321732 9.2787957
|
||||
300 3 1.3533438 8.3081433
|
||||
400 4 1.2125884 8.0809065
|
||||
500 5 1.0682216 8.0877925
|
||||
600 6 0.99100473 8.1100319
|
||||
700 7 0.99731243 7.8225195
|
||||
800 8 1.0597693 7.8368218
|
||||
900 9 0.99038588 7.9450569
|
||||
1000 10 1.077129 7.5857015
|
||||
1100 11 0.99070336 7.5138128
|
||||
1200 12 1.013894 7.2794857
|
||||
1300 13 1.0433203 7.7439871
|
||||
1400 14 1.0285528 7.5662235
|
||||
1500 15 0.99180601 7.8376313
|
||||
1600 16 0.98059071 8.0243735
|
||||
1700 17 1.0070947 8.3186893
|
||||
1800 18 0.99507569 7.0786393
|
||||
1900 19 1.0040168 7.8120389
|
||||
2000 20 0.98636164 7.472185
|
||||
2100 21 0.95811165 7.7085985
|
||||
2200 22 0.93568327 6.9424246
|
||||
2300 23 0.92804144 8.1239435
|
||||
2400 24 0.94940276 7.6108611
|
||||
2500 25 1.0535153 8.0772721
|
||||
2600 26 1.0902144 7.5609768
|
||||
2700 27 1.0737336 7.8706755
|
||||
2800 28 0.93074581 7.3699993
|
||||
2900 29 1.0440705 7.6454988
|
||||
3000 30 0.93868164 7.841168
|
||||
3100 31 1.0172025 7.6856163
|
||||
3200 32 1.0405368 7.5325735
|
||||
3300 33 0.96721201 7.8262809
|
||||
3400 34 0.90430758 7.1693921
|
||||
3500 35 0.89938433 7.865845
|
||||
3600 36 0.9907178 7.3462971
|
||||
3700 37 1.0311879 7.8876401
|
||||
3800 38 0.98339132 7.3413929
|
||||
3900 39 1.2111264 8.0968408
|
||||
4000 40 1.062489 7.7315959
|
||||
4100 41 0.94737492 7.3386028
|
||||
4200 42 1.0453816 8.2017304
|
||||
4300 43 0.97024897 7.7379624
|
||||
4400 44 0.9553861 7.8047635
|
||||
4500 45 1.043252 7.7486215
|
||||
4600 46 0.98611474 8.1237053
|
||||
4700 47 0.98624285 8.5801642
|
||||
4800 48 0.97176754 7.1540299
|
||||
4900 49 1.0165401 7.3853841
|
||||
5000 50 0.88359115 7.5541592
|
||||
Loop time of 0.359916 on 1 procs for 5000 steps with 200 atoms
|
||||
|
||||
Performance: 12002788.048 tau/day, 13892.116 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.24932 | 0.24932 | 0.24932 | 0.0 | 69.27
|
||||
Neigh | 0.068726 | 0.068726 | 0.068726 | 0.0 | 19.10
|
||||
Comm | 0.028691 | 0.028691 | 0.028691 | 0.0 | 7.97
|
||||
Output | 0.00066318 | 0.00066318 | 0.00066318 | 0.0 | 0.18
|
||||
Modify | 0.0078062 | 0.0078062 | 0.0078062 | 0.0 | 2.17
|
||||
Other | | 0.004713 | | | 1.31
|
||||
|
||||
Nlocal: 200 ave 200 max 200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 546 ave 546 max 546 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1649 ave 1649 max 1649 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1649
|
||||
Ave neighs/atom = 8.245
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 500
|
||||
|
||||
Total wall time: 0:00:00
|
||||
154
examples/PACKAGES/dpd-basic/dpd/log.5Apr22.dpd.g++.4
Normal file
154
examples/PACKAGES/dpd-basic/dpd/log.5Apr22.dpd.g++.4
Normal file
@ -0,0 +1,154 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DPD Fluid
|
||||
|
||||
variable T equal 1.0
|
||||
variable rc equal 1.0
|
||||
variable rcD equal 1.2
|
||||
|
||||
units lj
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
### create box and configuration
|
||||
variable L equal 5.0
|
||||
lattice fcc 3.0
|
||||
Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
|
||||
region simBox block 0 ${L} 0 ${L} 0 ${L}
|
||||
region simBox block 0 5 0 ${L} 0 ${L}
|
||||
region simBox block 0 5 0 5 0 ${L}
|
||||
region simBox block 0 5 0 5 0 5
|
||||
create_box 2 simBox
|
||||
Created orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
#create_atoms 1 region simBox
|
||||
create_atoms 1 random 100 12456 simBox
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 2 random 100 13245 simBox
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
mass 2 2.0
|
||||
###
|
||||
|
||||
pair_style dpd ${T} ${rc} 3854262
|
||||
pair_style dpd 1 ${rc} 3854262
|
||||
pair_style dpd 1 1 3854262
|
||||
|
||||
pair_coeff 1 1 25.0 4.5 1.2
|
||||
pair_coeff 1 2 25.1 4.51 1.21
|
||||
pair_coeff 2 2 25.2 4.52 1.22
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 1 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 5000
|
||||
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 = 1.52
|
||||
ghost atom cutoff = 1.52
|
||||
binsize = 0.76, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair dpd, 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) = 3.064 | 3.064 | 3.064 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 1 8.603339
|
||||
100 1 1.8691059 8.9058297
|
||||
200 2 1.4500635 8.7420141
|
||||
300 3 1.3089453 8.3985981
|
||||
400 4 1.1647803 8.2948808
|
||||
500 5 1.1399445 7.7421817
|
||||
600 6 1.0297918 7.2040397
|
||||
700 7 1.046713 7.6115758
|
||||
800 8 0.93523712 7.6885563
|
||||
900 9 0.94701493 7.9662712
|
||||
1000 10 0.99302416 7.7606189
|
||||
1100 11 0.98975674 7.5207427
|
||||
1200 12 0.98661662 7.3565222
|
||||
1300 13 1.0289377 7.6110453
|
||||
1400 14 0.9982501 7.8065701
|
||||
1500 15 1.0043888 7.3957185
|
||||
1600 16 1.0175816 7.7885955
|
||||
1700 17 1.0252117 7.5076258
|
||||
1800 18 1.0275139 8.1052823
|
||||
1900 19 1.0021054 7.0385989
|
||||
2000 20 1.0489009 7.7138149
|
||||
2100 21 0.91250488 7.3540839
|
||||
2200 22 0.92470996 7.9600233
|
||||
2300 23 0.96932725 7.3106045
|
||||
2400 24 0.93443088 7.4594635
|
||||
2500 25 0.95596038 7.2544715
|
||||
2600 26 1.0368594 7.6229263
|
||||
2700 27 0.94639332 7.4869636
|
||||
2800 28 0.99917354 7.9806636
|
||||
2900 29 0.95048071 7.0086404
|
||||
3000 30 0.95226181 7.7807205
|
||||
3100 31 0.95864429 7.8059442
|
||||
3200 32 0.85678761 7.3416027
|
||||
3300 33 0.95951096 7.3467158
|
||||
3400 34 0.97665772 8.2900991
|
||||
3500 35 0.92885927 7.5385993
|
||||
3600 36 1.0455015 8.0627999
|
||||
3700 37 0.91911809 8.0371736
|
||||
3800 38 0.92022241 7.5803999
|
||||
3900 39 1.0465522 7.6920189
|
||||
4000 40 0.98568475 7.4529825
|
||||
4100 41 1.0389372 7.2273346
|
||||
4200 42 1.0257545 7.6081878
|
||||
4300 43 1.0937573 8.2158237
|
||||
4400 44 1.0908817 7.5021567
|
||||
4500 45 1.0482874 7.5924368
|
||||
4600 46 1.1468439 8.0285157
|
||||
4700 47 1.119683 8.3365123
|
||||
4800 48 1.0963877 7.51772
|
||||
4900 49 1.0766762 7.3137035
|
||||
5000 50 1.0359203 7.7354572
|
||||
Loop time of 0.148597 on 4 procs for 5000 steps with 200 atoms
|
||||
|
||||
Performance: 29071936.422 tau/day, 33648.075 timesteps/s
|
||||
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.059602 | 0.063397 | 0.068622 | 1.3 | 42.66
|
||||
Neigh | 0.017747 | 0.018193 | 0.018698 | 0.3 | 12.24
|
||||
Comm | 0.055145 | 0.061014 | 0.065369 | 1.5 | 41.06
|
||||
Output | 0.00042708 | 0.00050725 | 0.00071024 | 0.0 | 0.34
|
||||
Modify | 0.0023494 | 0.002532 | 0.0026434 | 0.2 | 1.70
|
||||
Other | | 0.002953 | | | 1.99
|
||||
|
||||
Nlocal: 50 ave 52 max 48 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 292.75 ave 299 max 287 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 413.5 ave 441 max 399 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1654
|
||||
Ave neighs/atom = 8.27
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 500
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -1,4 +1,4 @@
|
||||
DPD Fluid
|
||||
Coarse-Grained SPC/E Water
|
||||
|
||||
2180 atoms
|
||||
|
||||
354
examples/PACKAGES/dpd-basic/dpd_tstat/cg_spce_table.pot
Normal file
354
examples/PACKAGES/dpd-basic/dpd_tstat/cg_spce_table.pot
Normal file
@ -0,0 +1,354 @@
|
||||
VOTCA
|
||||
N 351 R 2.0 9.0
|
||||
|
||||
1 2.000000E+00 2.190202E+01 7.229762E+01
|
||||
2 2.020000E+00 2.048957E+01 6.887333E+01
|
||||
3 2.040000E+00 1.915004E+01 6.500604E+01
|
||||
4 2.060000E+00 1.789228E+01 6.069573E+01
|
||||
5 2.080000E+00 1.672516E+01 5.594242E+01
|
||||
6 2.100000E+00 1.565754E+01 5.074609E+01
|
||||
7 2.120000E+00 1.467088E+01 4.787307E+01
|
||||
8 2.140000E+00 1.374450E+01 4.471740E+01
|
||||
9 2.160000E+00 1.288407E+01 4.127908E+01
|
||||
10 2.180000E+00 1.209522E+01 3.755811E+01
|
||||
11 2.200000E+00 1.138363E+01 3.355449E+01
|
||||
12 2.220000E+00 1.072913E+01 3.188695E+01
|
||||
13 2.240000E+00 1.010845E+01 3.017359E+01
|
||||
14 2.260000E+00 9.522496E+00 2.841440E+01
|
||||
15 2.280000E+00 8.972182E+00 2.660938E+01
|
||||
16 2.300000E+00 8.458426E+00 2.475854E+01
|
||||
17 2.320000E+00 8.014166E+00 2.006698E+01
|
||||
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263 7.240000E+00 -3.087883E-03 -2.854317E-02
|
||||
264 7.260000E+00 -2.509635E-03 -2.879748E-02
|
||||
265 7.280000E+00 -1.955351E-03 -2.614680E-02
|
||||
266 7.300000E+00 -1.483130E-03 -2.059115E-02
|
||||
267 7.320000E+00 -1.113389E-03 -1.639767E-02
|
||||
268 7.340000E+00 -8.266321E-04 -1.229279E-02
|
||||
269 7.360000E+00 -6.210869E-04 -8.276492E-03
|
||||
270 7.380000E+00 -4.949818E-04 -4.348786E-03
|
||||
271 7.400000E+00 -4.465449E-04 -5.096684E-04
|
||||
272 7.420000E+00 -5.304321E-04 8.162452E-03
|
||||
273 7.440000E+00 -7.436056E-04 1.241897E-02
|
||||
274 7.460000E+00 -9.977534E-04 1.225988E-02
|
||||
275 7.480000E+00 -1.204563E-03 7.685191E-03
|
||||
276 7.500000E+00 -1.275724E-03 -1.305104E-03
|
||||
277 7.520000E+00 -1.199415E-03 -5.916706E-03
|
||||
278 7.540000E+00 -1.055417E-03 -8.074089E-03
|
||||
279 7.560000E+00 -8.928131E-04 -7.777253E-03
|
||||
280 7.580000E+00 -7.606883E-04 -5.026198E-03
|
||||
281 7.600000E+00 -7.081267E-04 1.790768E-04
|
||||
282 7.620000E+00 -7.213835E-04 1.157786E-03
|
||||
283 7.640000E+00 -7.548855E-04 2.203601E-03
|
||||
284 7.660000E+00 -8.099749E-04 3.316523E-03
|
||||
285 7.680000E+00 -8.879938E-04 4.496550E-03
|
||||
286 7.700000E+00 -9.902843E-04 5.743685E-03
|
||||
287 7.720000E+00 -1.122403E-03 7.421734E-03
|
||||
288 7.740000E+00 -1.285295E-03 8.820936E-03
|
||||
289 7.760000E+00 -1.473382E-03 9.941291E-03
|
||||
290 7.780000E+00 -1.681087E-03 1.078280E-02
|
||||
291 7.800000E+00 -1.902835E-03 1.134546E-02
|
||||
292 7.820000E+00 -2.225281E-03 2.008573E-02
|
||||
293 7.840000E+00 -2.673724E-03 2.394500E-02
|
||||
294 7.860000E+00 -3.150542E-03 2.292328E-02
|
||||
295 7.880000E+00 -3.558115E-03 1.702056E-02
|
||||
296 7.900000E+00 -3.798824E-03 6.236836E-03
|
||||
297 7.920000E+00 -3.844315E-03 -1.142168E-03
|
||||
298 7.940000E+00 -3.774961E-03 -5.247538E-03
|
||||
299 7.960000E+00 -3.656237E-03 -6.079274E-03
|
||||
300 7.980000E+00 -3.553615E-03 -3.637376E-03
|
||||
301 8.000000E+00 -3.532566E-03 2.078155E-03
|
||||
302 8.020000E+00 -3.611956E-03 5.494873E-03
|
||||
303 8.040000E+00 -3.737724E-03 6.716053E-03
|
||||
304 8.060000E+00 -3.865961E-03 5.741694E-03
|
||||
305 8.080000E+00 -3.952755E-03 2.571796E-03
|
||||
306 8.100000E+00 -3.954196E-03 -2.793640E-03
|
||||
307 8.120000E+00 -3.873685E-03 -5.086591E-03
|
||||
308 8.140000E+00 -3.757567E-03 -6.354313E-03
|
||||
309 8.160000E+00 -3.626347E-03 -6.596805E-03
|
||||
310 8.180000E+00 -3.500530E-03 -5.814068E-03
|
||||
311 8.200000E+00 -3.400620E-03 -4.006101E-03
|
||||
312 8.220000E+00 -3.334411E-03 -2.730570E-03
|
||||
313 8.240000E+00 -3.286762E-03 -2.150229E-03
|
||||
314 8.260000E+00 -3.243768E-03 -2.265076E-03
|
||||
315 8.280000E+00 -3.191524E-03 -3.075114E-03
|
||||
316 8.300000E+00 -3.116129E-03 -4.580340E-03
|
||||
317 8.320000E+00 -2.964210E-03 -1.014102E-02
|
||||
318 8.340000E+00 -2.729309E-03 -1.287854E-02
|
||||
319 8.360000E+00 -2.467889E-03 -1.279292E-02
|
||||
320 8.380000E+00 -2.236413E-03 -9.884157E-03
|
||||
321 8.400000E+00 -2.091344E-03 -4.152240E-03
|
||||
322 8.420000E+00 -2.034875E-03 -1.692189E-03
|
||||
323 8.440000E+00 -2.015752E-03 -4.177491E-04
|
||||
324 8.460000E+00 -2.010261E-03 -3.289192E-04
|
||||
325 8.480000E+00 -1.994691E-03 -1.425700E-03
|
||||
326 8.500000E+00 -1.945329E-03 -3.708091E-03
|
||||
327 8.520000E+00 -1.867098E-03 -4.115259E-03
|
||||
328 8.540000E+00 -1.780711E-03 -4.523663E-03
|
||||
329 8.560000E+00 -1.686143E-03 -4.933304E-03
|
||||
330 8.580000E+00 -1.583370E-03 -5.344181E-03
|
||||
331 8.600000E+00 -1.472368E-03 -5.756296E-03
|
||||
332 8.620000E+00 -1.328792E-03 -8.394009E-03
|
||||
333 8.640000E+00 -1.144899E-03 -9.787974E-03
|
||||
334 8.660000E+00 -9.455644E-04 -9.938189E-03
|
||||
335 8.680000E+00 -7.556630E-04 -8.844656E-03
|
||||
336 8.700000E+00 -6.000698E-04 -6.507373E-03
|
||||
337 8.720000E+00 -5.364035E-04 -3.286769E-04
|
||||
338 8.740000E+00 -5.681458E-04 3.033482E-03
|
||||
339 8.760000E+00 -6.389659E-04 3.579102E-03
|
||||
340 8.780000E+00 -6.925330E-04 1.308185E-03
|
||||
341 8.800000E+00 -6.725164E-04 -3.779270E-03
|
||||
342 8.820000E+00 -5.113768E-04 -1.169180E-02
|
||||
343 8.840000E+00 -2.305599E-04 -1.574700E-02
|
||||
344 8.860000E+00 9.278768E-05 -1.594487E-02
|
||||
345 8.880000E+00 3.815195E-04 -1.228542E-02
|
||||
346 8.900000E+00 5.584889E-04 -4.768636E-03
|
||||
347 8.920000E+00 6.079481E-04 -2.335309E-04
|
||||
348 8.940000E+00 5.700798E-04 3.964121E-03
|
||||
349 8.960000E+00 4.516330E-04 7.824320E-03
|
||||
350 8.980000E+00 2.593567E-04 1.134707E-02
|
||||
351 9.000000E+00 0.000000E+00 1.453236E-02
|
||||
31
examples/PACKAGES/dpd-basic/dpd_tstat/in.dpd_tstat
Normal file
31
examples/PACKAGES/dpd-basic/dpd_tstat/in.dpd_tstat
Normal file
@ -0,0 +1,31 @@
|
||||
# Coarse-Grained SPC/E Water
|
||||
|
||||
variable T equal 300.0
|
||||
variable rc equal 9.0
|
||||
variable rcD equal 10.0
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
read_data cg_spce.data
|
||||
|
||||
pair_style hybrid/overlay table spline 1000 dpd/tstat ${T} ${T} ${rc} 385262
|
||||
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
|
||||
pair_coeff 1 1 dpd/tstat 10.0 ${rcD}
|
||||
|
||||
timestep 1.0
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
106
examples/PACKAGES/dpd-basic/dpd_tstat/log.5Apr22.dpd_tstat.g++.1
Normal file
106
examples/PACKAGES/dpd-basic/dpd_tstat/log.5Apr22.dpd_tstat.g++.1
Normal file
@ -0,0 +1,106 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Coarse-Grained SPC/E Water
|
||||
|
||||
variable T equal 300.0
|
||||
variable rc equal 9.0
|
||||
variable rcD equal 10.0
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
read_data cg_spce.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (40.31 40.31 40.31)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2180 atoms
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
pair_style hybrid/overlay table spline 1000 dpd/tstat ${T} ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/tstat 300 ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/tstat 300 300 ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/tstat 300 300 9 385262
|
||||
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA 9
|
||||
WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
|
||||
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
|
||||
pair_coeff 1 1 dpd/tstat 10.0 ${rcD}
|
||||
pair_coeff 1 1 dpd/tstat 10.0 10
|
||||
|
||||
timestep 1.0
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 300 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
generated 0 of 0 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 = 7 7 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) pair dpd/tstat, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.38 | 5.38 | 5.38 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 300 7459.7935
|
||||
100 100 309.27219 6997.2438
|
||||
200 200 311.23318 9940.3922
|
||||
300 300 300.14145 7970.3486
|
||||
400 400 293.17924 8390.7272
|
||||
500 500 285.9647 7304.1147
|
||||
600 600 291.15512 6605.1675
|
||||
700 700 294.54557 7708.3815
|
||||
800 800 288.72442 8641.2675
|
||||
900 900 294.83288 7145.1684
|
||||
1000 1000 291.12446 8525.4556
|
||||
Loop time of 10.1894 on 1 procs for 1000 steps with 2180 atoms
|
||||
|
||||
Performance: 8.479 ns/day, 2.830 hours/ns, 98.141 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 10.02 | 10.02 | 10.02 | 0.0 | 98.34
|
||||
Neigh | 0.087623 | 0.087623 | 0.087623 | 0.0 | 0.86
|
||||
Comm | 0.055526 | 0.055526 | 0.055526 | 0.0 | 0.54
|
||||
Output | 0.00026505 | 0.00026505 | 0.00026505 | 0.0 | 0.00
|
||||
Modify | 0.013958 | 0.013958 | 0.013958 | 0.0 | 0.14
|
||||
Other | | 0.01163 | | | 0.11
|
||||
|
||||
Nlocal: 2180 ave 2180 max 2180 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6741 ave 6741 max 6741 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 261567 ave 261567 max 261567 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 261567
|
||||
Ave neighs/atom = 119.98486
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:10
|
||||
106
examples/PACKAGES/dpd-basic/dpd_tstat/log.5Apr22.dpd_tstat.g++.4
Normal file
106
examples/PACKAGES/dpd-basic/dpd_tstat/log.5Apr22.dpd_tstat.g++.4
Normal file
@ -0,0 +1,106 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Coarse-Grained SPC/E Water
|
||||
|
||||
variable T equal 300.0
|
||||
variable rc equal 9.0
|
||||
variable rcD equal 10.0
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
read_data cg_spce.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (40.31 40.31 40.31)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2180 atoms
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
pair_style hybrid/overlay table spline 1000 dpd/tstat ${T} ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/tstat 300 ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/tstat 300 300 ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/tstat 300 300 9 385262
|
||||
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA 9
|
||||
WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
|
||||
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
|
||||
pair_coeff 1 1 dpd/tstat 10.0 ${rcD}
|
||||
pair_coeff 1 1 dpd/tstat 10.0 10
|
||||
|
||||
timestep 1.0
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 300 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
generated 0 of 0 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 = 7 7 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) pair dpd/tstat, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.695 | 3.696 | 3.697 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 300 7929.9249
|
||||
100 100 305.51763 8531.8105
|
||||
200 200 304.43334 8697.989
|
||||
300 300 292.42805 6865.4712
|
||||
400 400 300.66447 7606.6995
|
||||
500 500 298.43456 8713.2403
|
||||
600 600 298.10981 6913.5475
|
||||
700 700 297.39737 9121.8642
|
||||
800 800 298.23888 7833.1307
|
||||
900 900 293.91793 8423.8417
|
||||
1000 1000 299.65933 7974.9976
|
||||
Loop time of 2.82436 on 4 procs for 1000 steps with 2180 atoms
|
||||
|
||||
Performance: 30.591 ns/day, 0.785 hours/ns, 354.062 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.6238 | 2.644 | 2.6909 | 1.7 | 93.61
|
||||
Neigh | 0.021524 | 0.021958 | 0.022778 | 0.3 | 0.78
|
||||
Comm | 0.10035 | 0.1479 | 0.16842 | 7.2 | 5.24
|
||||
Output | 0.00019058 | 0.00021173 | 0.00026852 | 0.0 | 0.01
|
||||
Modify | 0.0041395 | 0.0041846 | 0.0042798 | 0.1 | 0.15
|
||||
Other | | 0.006091 | | | 0.22
|
||||
|
||||
Nlocal: 545 ave 559 max 536 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Nghost: 3613.5 ave 3634 max 3604 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Neighs: 65402 ave 68101 max 63621 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 261608
|
||||
Ave neighs/atom = 120.00367
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
@ -4,9 +4,9 @@ variable T equal 1.0
|
||||
variable rc equal 1.0
|
||||
variable rcD equal 1.2
|
||||
|
||||
units lj
|
||||
units lj
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
@ -16,29 +16,27 @@ variable L equal 5.0
|
||||
lattice fcc 3.0
|
||||
region simBox block 0 ${L} 0 ${L} 0 ${L}
|
||||
create_box 2 simBox
|
||||
#create_atoms 1 region simBox
|
||||
create_atoms 1 random 100 132456 simBox
|
||||
create_atoms 2 random 100 132456 simBox
|
||||
create_atoms 1 random 100 12456 simBox
|
||||
create_atoms 2 random 100 13245 simBox
|
||||
mass 1 1.0
|
||||
mass 2 2.0
|
||||
###
|
||||
|
||||
pair_style dpd/ext ${T} ${rc} 3854262
|
||||
pair_style dpd/ext ${T} ${rc} 3854262
|
||||
|
||||
pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD}
|
||||
pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD}
|
||||
pair_coeff 2 2 25.2 4.52 4.55 0.52 0.55 1.22 #${rcD}
|
||||
|
||||
timestep 0.01
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 500
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 50000
|
||||
run 5000
|
||||
|
||||
write_data final.data pair ij
|
||||
153
examples/PACKAGES/dpd-basic/dpdext/log.5Apr22.dpdext.g++.1
Normal file
153
examples/PACKAGES/dpd-basic/dpdext/log.5Apr22.dpdext.g++.1
Normal file
@ -0,0 +1,153 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DPD Fluid
|
||||
|
||||
variable T equal 1.0
|
||||
variable rc equal 1.0
|
||||
variable rcD equal 1.2
|
||||
|
||||
units lj
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
### create box and configuration
|
||||
variable L equal 5.0
|
||||
lattice fcc 3.0
|
||||
Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
|
||||
region simBox block 0 ${L} 0 ${L} 0 ${L}
|
||||
region simBox block 0 5 0 ${L} 0 ${L}
|
||||
region simBox block 0 5 0 5 0 ${L}
|
||||
region simBox block 0 5 0 5 0 5
|
||||
create_box 2 simBox
|
||||
Created orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 random 100 12456 simBox
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 2 random 100 13245 simBox
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
mass 2 2.0
|
||||
###
|
||||
|
||||
pair_style dpd/ext ${T} ${rc} 3854262
|
||||
pair_style dpd/ext 1 ${rc} 3854262
|
||||
pair_style dpd/ext 1 1 3854262
|
||||
|
||||
pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD}
|
||||
pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD}
|
||||
pair_coeff 2 2 25.2 4.52 4.55 0.52 0.55 1.22 #${rcD}
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 1 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 5000
|
||||
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 = 1.52
|
||||
ghost atom cutoff = 1.52
|
||||
binsize = 0.76, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair dpd/ext, 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) = 3.083 | 3.083 | 3.083 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 1 10.864186
|
||||
100 1 1.1314376 7.1955963
|
||||
200 2 1.0058948 8.4574538
|
||||
300 3 0.93292241 7.7033353
|
||||
400 4 0.93599378 7.9649888
|
||||
500 5 1.0390423 7.9498546
|
||||
600 6 1.0750333 7.3594973
|
||||
700 7 1.119325 7.1843859
|
||||
800 8 0.96727219 6.8327896
|
||||
900 9 0.98826001 8.1974994
|
||||
1000 10 1.105819 7.8830702
|
||||
1100 11 0.99559202 7.8295372
|
||||
1200 12 0.9210428 8.2045593
|
||||
1300 13 0.96628584 8.6531905
|
||||
1400 14 1.1808689 7.7659964
|
||||
1500 15 0.96208743 7.9977415
|
||||
1600 16 1.0080123 7.6254557
|
||||
1700 17 0.96910957 8.3643075
|
||||
1800 18 1.0562621 7.5966268
|
||||
1900 19 0.93109173 7.7944606
|
||||
2000 20 1.1126085 9.3753501
|
||||
2100 21 1.1328553 7.6293793
|
||||
2200 22 0.8964042 7.5985061
|
||||
2300 23 1.0043044 8.0016943
|
||||
2400 24 1.0319521 8.1249684
|
||||
2500 25 0.95913468 7.2383318
|
||||
2600 26 0.99480311 7.6491295
|
||||
2700 27 0.9735191 7.5004628
|
||||
2800 28 0.96145308 8.222045
|
||||
2900 29 1.0131071 6.6390842
|
||||
3000 30 0.99463836 7.0147693
|
||||
3100 31 0.96803993 8.2738796
|
||||
3200 32 0.94066026 9.476403
|
||||
3300 33 0.97401823 6.409563
|
||||
3400 34 1.0548493 7.7301555
|
||||
3500 35 0.98567796 8.2949868
|
||||
3600 36 0.86621746 7.4759028
|
||||
3700 37 0.94934175 8.1189998
|
||||
3800 38 0.9626774 7.7986715
|
||||
3900 39 0.95728518 6.8669836
|
||||
4000 40 1.0866412 7.41281
|
||||
4100 41 0.98873564 6.4612262
|
||||
4200 42 0.9109925 7.1806331
|
||||
4300 43 1.0344723 8.4617679
|
||||
4400 44 0.98920584 7.3622901
|
||||
4500 45 0.99386139 6.8002442
|
||||
4600 46 1.0947487 6.8868352
|
||||
4700 47 0.98789482 7.8428621
|
||||
4800 48 1.0035907 8.3878628
|
||||
4900 49 1.0336467 8.1592349
|
||||
5000 50 1.0870964 8.217988
|
||||
Loop time of 0.907286 on 1 procs for 5000 steps with 200 atoms
|
||||
|
||||
Performance: 4761453.941 tau/day, 5510.942 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.79672 | 0.79672 | 0.79672 | 0.0 | 87.81
|
||||
Neigh | 0.066416 | 0.066416 | 0.066416 | 0.0 | 7.32
|
||||
Comm | 0.029801 | 0.029801 | 0.029801 | 0.0 | 3.28
|
||||
Output | 0.0010415 | 0.0010415 | 0.0010415 | 0.0 | 0.11
|
||||
Modify | 0.0078915 | 0.0078915 | 0.0078915 | 0.0 | 0.87
|
||||
Other | | 0.005414 | | | 0.60
|
||||
|
||||
Nlocal: 200 ave 200 max 200 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: 1624 ave 1624 max 1624 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1624
|
||||
Ave neighs/atom = 8.12
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 500
|
||||
|
||||
Total wall time: 0:00:00
|
||||
153
examples/PACKAGES/dpd-basic/dpdext/log.5Apr22.dpdext.g++.4
Normal file
153
examples/PACKAGES/dpd-basic/dpdext/log.5Apr22.dpdext.g++.4
Normal file
@ -0,0 +1,153 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DPD Fluid
|
||||
|
||||
variable T equal 1.0
|
||||
variable rc equal 1.0
|
||||
variable rcD equal 1.2
|
||||
|
||||
units lj
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
### create box and configuration
|
||||
variable L equal 5.0
|
||||
lattice fcc 3.0
|
||||
Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
|
||||
region simBox block 0 ${L} 0 ${L} 0 ${L}
|
||||
region simBox block 0 5 0 ${L} 0 ${L}
|
||||
region simBox block 0 5 0 5 0 ${L}
|
||||
region simBox block 0 5 0 5 0 5
|
||||
create_box 2 simBox
|
||||
Created orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 random 100 12456 simBox
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 2 random 100 13245 simBox
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
mass 2 2.0
|
||||
###
|
||||
|
||||
pair_style dpd/ext ${T} ${rc} 3854262
|
||||
pair_style dpd/ext 1 ${rc} 3854262
|
||||
pair_style dpd/ext 1 1 3854262
|
||||
|
||||
pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD}
|
||||
pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD}
|
||||
pair_coeff 2 2 25.2 4.52 4.55 0.52 0.55 1.22 #${rcD}
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 1 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 5000
|
||||
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 = 1.52
|
||||
ghost atom cutoff = 1.52
|
||||
binsize = 0.76, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair dpd/ext, 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) = 3.064 | 3.064 | 3.064 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 1 9.2729849
|
||||
100 1 1.1416138 7.7058466
|
||||
200 2 0.91696292 8.1601454
|
||||
300 3 0.96358166 6.7987934
|
||||
400 4 0.94726377 7.6196059
|
||||
500 5 1.0941462 7.5974711
|
||||
600 6 0.91469027 8.3921536
|
||||
700 7 1.0912559 7.362721
|
||||
800 8 0.96537861 9.2089379
|
||||
900 9 0.9986577 8.0072887
|
||||
1000 10 0.9580071 7.2399027
|
||||
1100 11 0.94763774 7.8075521
|
||||
1200 12 0.9942368 7.5215461
|
||||
1300 13 1.0312465 8.2684258
|
||||
1400 14 0.95133276 7.2734722
|
||||
1500 15 0.97273431 7.1831939
|
||||
1600 16 1.0052028 7.929104
|
||||
1700 17 0.93909435 8.2831308
|
||||
1800 18 1.0647294 8.850861
|
||||
1900 19 1.0268112 7.2828461
|
||||
2000 20 0.91293528 8.208191
|
||||
2100 21 0.94719411 8.3353929
|
||||
2200 22 0.90507637 9.1708397
|
||||
2300 23 1.0663386 7.1415871
|
||||
2400 24 1.0132089 9.2210634
|
||||
2500 25 1.0633849 8.3368039
|
||||
2600 26 0.95803955 8.8247976
|
||||
2700 27 0.95264552 7.3204561
|
||||
2800 28 0.93548595 7.290555
|
||||
2900 29 0.96876322 7.4969147
|
||||
3000 30 0.99554648 8.2055023
|
||||
3100 31 1.0190751 7.907751
|
||||
3200 32 1.0887502 7.7247246
|
||||
3300 33 1.0059692 7.4039814
|
||||
3400 34 1.0055991 7.3469353
|
||||
3500 35 1.0067689 7.2161248
|
||||
3600 36 1.1103667 8.4373236
|
||||
3700 37 1.0668979 7.1922528
|
||||
3800 38 0.97902043 5.5426601
|
||||
3900 39 1.0268733 6.7786635
|
||||
4000 40 1.0036613 7.8078466
|
||||
4100 41 1.0714377 7.4129166
|
||||
4200 42 0.99168608 6.0096099
|
||||
4300 43 1.084818 7.4932992
|
||||
4400 44 0.98348896 8.9950057
|
||||
4500 45 1.045253 6.1309568
|
||||
4600 46 1.0266723 6.3227645
|
||||
4700 47 1.0183525 8.1505786
|
||||
4800 48 1.0527309 8.2824928
|
||||
4900 49 0.96877903 7.6341751
|
||||
5000 50 1.0178917 7.5037327
|
||||
Loop time of 0.320182 on 4 procs for 5000 steps with 200 atoms
|
||||
|
||||
Performance: 13492326.176 tau/day, 15616.118 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.20185 | 0.21019 | 0.2166 | 1.4 | 65.65
|
||||
Neigh | 0.017652 | 0.018339 | 0.019085 | 0.5 | 5.73
|
||||
Comm | 0.076802 | 0.084707 | 0.094197 | 2.6 | 26.46
|
||||
Output | 0.00057039 | 0.00066408 | 0.00093301 | 0.0 | 0.21
|
||||
Modify | 0.0025036 | 0.0027709 | 0.0030403 | 0.5 | 0.87
|
||||
Other | | 0.003508 | | | 1.10
|
||||
|
||||
Nlocal: 50 ave 53 max 45 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 288.5 ave 300 max 279 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Neighs: 418.25 ave 438 max 384 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
|
||||
Total # of neighbors = 1673
|
||||
Ave neighs/atom = 8.365
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 500
|
||||
|
||||
Total wall time: 0:00:00
|
||||
File diff suppressed because it is too large
Load Diff
1
examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce.data
Symbolic link
1
examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce.data
Symbolic link
@ -0,0 +1 @@
|
||||
../dpd_tstat/cg_spce.data
|
||||
@ -1,354 +0,0 @@
|
||||
VOTCA
|
||||
N 351 R 2.0 9.0
|
||||
|
||||
1 2.000000E+00 2.190202E+01 7.229762E+01
|
||||
2 2.020000E+00 2.048957E+01 6.887333E+01
|
||||
3 2.040000E+00 1.915004E+01 6.500604E+01
|
||||
4 2.060000E+00 1.789228E+01 6.069573E+01
|
||||
5 2.080000E+00 1.672516E+01 5.594242E+01
|
||||
6 2.100000E+00 1.565754E+01 5.074609E+01
|
||||
7 2.120000E+00 1.467088E+01 4.787307E+01
|
||||
8 2.140000E+00 1.374450E+01 4.471740E+01
|
||||
9 2.160000E+00 1.288407E+01 4.127908E+01
|
||||
10 2.180000E+00 1.209522E+01 3.755811E+01
|
||||
11 2.200000E+00 1.138363E+01 3.355449E+01
|
||||
12 2.220000E+00 1.072913E+01 3.188695E+01
|
||||
13 2.240000E+00 1.010845E+01 3.017359E+01
|
||||
14 2.260000E+00 9.522496E+00 2.841440E+01
|
||||
15 2.280000E+00 8.972182E+00 2.660938E+01
|
||||
16 2.300000E+00 8.458426E+00 2.475854E+01
|
||||
17 2.320000E+00 8.014166E+00 2.006698E+01
|
||||
18 2.340000E+00 7.639767E+00 1.777244E+01
|
||||
19 2.360000E+00 7.287288E+00 1.787493E+01
|
||||
20 2.380000E+00 6.908790E+00 2.037445E+01
|
||||
21 2.400000E+00 6.456330E+00 2.527099E+01
|
||||
22 2.420000E+00 5.858025E+00 3.384695E+01
|
||||
23 2.440000E+00 5.130955E+00 3.814748E+01
|
||||
24 2.460000E+00 4.360629E+00 3.817257E+01
|
||||
25 2.480000E+00 3.632555E+00 3.392224E+01
|
||||
26 2.500000E+00 3.032242E+00 2.539647E+01
|
||||
27 2.520000E+00 2.547993E+00 2.297813E+01
|
||||
28 2.540000E+00 2.115131E+00 2.025763E+01
|
||||
29 2.560000E+00 1.739702E+00 1.723497E+01
|
||||
30 2.580000E+00 1.427747E+00 1.391013E+01
|
||||
31 2.600000E+00 1.185311E+00 1.028314E+01
|
||||
32 2.620000E+00 9.860176E-01 9.578245E+00
|
||||
33 2.640000E+00 8.048986E-01 8.465708E+00
|
||||
34 2.660000E+00 6.501069E-01 6.945526E+00
|
||||
35 2.680000E+00 5.297952E-01 5.017699E+00
|
||||
36 2.700000E+00 4.521166E-01 2.682227E+00
|
||||
37 2.720000E+00 3.986447E-01 2.615311E+00
|
||||
38 2.740000E+00 3.494900E-01 2.250522E+00
|
||||
39 2.760000E+00 3.106097E-01 1.587859E+00
|
||||
40 2.780000E+00 2.879614E-01 6.273237E-01
|
||||
41 2.800000E+00 2.875026E-01 -6.310851E-01
|
||||
42 2.820000E+00 3.002733E-01 -6.543549E-01
|
||||
43 2.840000E+00 3.140112E-01 -7.277911E-01
|
||||
44 2.860000E+00 3.297194E-01 -8.513935E-01
|
||||
45 2.880000E+00 3.484014E-01 -1.025162E+00
|
||||
46 2.900000E+00 3.710604E-01 -1.249097E+00
|
||||
47 2.920000E+00 3.974884E-01 -1.380483E+00
|
||||
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|
||||
292 7.820000E+00 -2.225281E-03 2.008573E-02
|
||||
293 7.840000E+00 -2.673724E-03 2.394500E-02
|
||||
294 7.860000E+00 -3.150542E-03 2.292328E-02
|
||||
295 7.880000E+00 -3.558115E-03 1.702056E-02
|
||||
296 7.900000E+00 -3.798824E-03 6.236836E-03
|
||||
297 7.920000E+00 -3.844315E-03 -1.142168E-03
|
||||
298 7.940000E+00 -3.774961E-03 -5.247538E-03
|
||||
299 7.960000E+00 -3.656237E-03 -6.079274E-03
|
||||
300 7.980000E+00 -3.553615E-03 -3.637376E-03
|
||||
301 8.000000E+00 -3.532566E-03 2.078155E-03
|
||||
302 8.020000E+00 -3.611956E-03 5.494873E-03
|
||||
303 8.040000E+00 -3.737724E-03 6.716053E-03
|
||||
304 8.060000E+00 -3.865961E-03 5.741694E-03
|
||||
305 8.080000E+00 -3.952755E-03 2.571796E-03
|
||||
306 8.100000E+00 -3.954196E-03 -2.793640E-03
|
||||
307 8.120000E+00 -3.873685E-03 -5.086591E-03
|
||||
308 8.140000E+00 -3.757567E-03 -6.354313E-03
|
||||
309 8.160000E+00 -3.626347E-03 -6.596805E-03
|
||||
310 8.180000E+00 -3.500530E-03 -5.814068E-03
|
||||
311 8.200000E+00 -3.400620E-03 -4.006101E-03
|
||||
312 8.220000E+00 -3.334411E-03 -2.730570E-03
|
||||
313 8.240000E+00 -3.286762E-03 -2.150229E-03
|
||||
314 8.260000E+00 -3.243768E-03 -2.265076E-03
|
||||
315 8.280000E+00 -3.191524E-03 -3.075114E-03
|
||||
316 8.300000E+00 -3.116129E-03 -4.580340E-03
|
||||
317 8.320000E+00 -2.964210E-03 -1.014102E-02
|
||||
318 8.340000E+00 -2.729309E-03 -1.287854E-02
|
||||
319 8.360000E+00 -2.467889E-03 -1.279292E-02
|
||||
320 8.380000E+00 -2.236413E-03 -9.884157E-03
|
||||
321 8.400000E+00 -2.091344E-03 -4.152240E-03
|
||||
322 8.420000E+00 -2.034875E-03 -1.692189E-03
|
||||
323 8.440000E+00 -2.015752E-03 -4.177491E-04
|
||||
324 8.460000E+00 -2.010261E-03 -3.289192E-04
|
||||
325 8.480000E+00 -1.994691E-03 -1.425700E-03
|
||||
326 8.500000E+00 -1.945329E-03 -3.708091E-03
|
||||
327 8.520000E+00 -1.867098E-03 -4.115259E-03
|
||||
328 8.540000E+00 -1.780711E-03 -4.523663E-03
|
||||
329 8.560000E+00 -1.686143E-03 -4.933304E-03
|
||||
330 8.580000E+00 -1.583370E-03 -5.344181E-03
|
||||
331 8.600000E+00 -1.472368E-03 -5.756296E-03
|
||||
332 8.620000E+00 -1.328792E-03 -8.394009E-03
|
||||
333 8.640000E+00 -1.144899E-03 -9.787974E-03
|
||||
334 8.660000E+00 -9.455644E-04 -9.938189E-03
|
||||
335 8.680000E+00 -7.556630E-04 -8.844656E-03
|
||||
336 8.700000E+00 -6.000698E-04 -6.507373E-03
|
||||
337 8.720000E+00 -5.364035E-04 -3.286769E-04
|
||||
338 8.740000E+00 -5.681458E-04 3.033482E-03
|
||||
339 8.760000E+00 -6.389659E-04 3.579102E-03
|
||||
340 8.780000E+00 -6.925330E-04 1.308185E-03
|
||||
341 8.800000E+00 -6.725164E-04 -3.779270E-03
|
||||
342 8.820000E+00 -5.113768E-04 -1.169180E-02
|
||||
343 8.840000E+00 -2.305599E-04 -1.574700E-02
|
||||
344 8.860000E+00 9.278768E-05 -1.594487E-02
|
||||
345 8.880000E+00 3.815195E-04 -1.228542E-02
|
||||
346 8.900000E+00 5.584889E-04 -4.768636E-03
|
||||
347 8.920000E+00 6.079481E-04 -2.335309E-04
|
||||
348 8.940000E+00 5.700798E-04 3.964121E-03
|
||||
349 8.960000E+00 4.516330E-04 7.824320E-03
|
||||
350 8.980000E+00 2.593567E-04 1.134707E-02
|
||||
351 9.000000E+00 0.000000E+00 1.453236E-02
|
||||
1
examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce_table.pot
Symbolic link
1
examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce_table.pot
Symbolic link
@ -0,0 +1 @@
|
||||
../dpd_tstat/cg_spce_table.pot
|
||||
@ -4,7 +4,7 @@ variable T equal 300.0
|
||||
variable rc equal 9.0
|
||||
variable rcD equal 10.0
|
||||
|
||||
units real
|
||||
units real
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
@ -13,7 +13,7 @@ comm_modify vel yes
|
||||
|
||||
read_data cg_spce.data
|
||||
|
||||
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
|
||||
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
|
||||
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
|
||||
@ -24,8 +24,8 @@ run_style verlet
|
||||
velocity all create ${T} 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 10
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 2000
|
||||
run 1000
|
||||
@ -1,293 +0,0 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
# Coarse-Grained SPC/E Water
|
||||
|
||||
variable T equal 300.0
|
||||
variable rc equal 9.0
|
||||
variable rcD equal 10.0
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
read_data cg_spce.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.310000 40.310000 40.310000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2180 atoms
|
||||
read_data CPU = 0.020 seconds
|
||||
|
||||
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 ${rc} 385262
|
||||
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 9 385262
|
||||
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA 9
|
||||
WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:461)
|
||||
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
|
||||
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10
|
||||
|
||||
timestep 1.0
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 300 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 10
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 2000
|
||||
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 = 7 7 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair dpd/ext/tstat, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.380 | 5.380 | 5.380 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 300 7368.7186
|
||||
10 10 298.34842 6443.6033
|
||||
20 20 303.36187 9303.0158
|
||||
30 30 301.59356 7533.7912
|
||||
40 40 300.97217 5623.9089
|
||||
50 50 300.31652 9105.8093
|
||||
60 60 296.92173 9213.304
|
||||
70 70 294.36593 12701.327
|
||||
80 80 295.30077 6098.4732
|
||||
90 90 296.35396 8051.719
|
||||
100 100 293.72532 5555.983
|
||||
110 110 290.95711 9001.8346
|
||||
120 120 290.91972 10264.241
|
||||
130 130 294.14911 11450.959
|
||||
140 140 299.11994 7244.1639
|
||||
150 150 301.20082 7675.7516
|
||||
160 160 300.71883 9718.1901
|
||||
170 170 295.47176 8931.1414
|
||||
180 180 290.45284 7381.7674
|
||||
190 190 291.66922 11028.436
|
||||
200 200 294.0543 11897.269
|
||||
210 210 299.17955 8939.2171
|
||||
220 220 298.45193 8047.038
|
||||
230 230 300.48548 10033.64
|
||||
240 240 299.24752 6310.7247
|
||||
250 250 304.51487 8710.5626
|
||||
260 260 303.6513 5230.8162
|
||||
270 270 300.76074 12164.773
|
||||
280 280 302.60275 11145.98
|
||||
290 290 297.22957 9521.4384
|
||||
300 300 297.1365 7446.9006
|
||||
310 310 292.18323 8021.8344
|
||||
320 320 295.03958 9130.8594
|
||||
330 330 293.9622 4647.512
|
||||
340 340 290.77751 8001.486
|
||||
350 350 292.34687 11887.668
|
||||
360 360 295.95968 9262.148
|
||||
370 370 293.50476 4181.549
|
||||
380 380 288.69498 7632.071
|
||||
390 390 289.63957 5130.0205
|
||||
400 400 295.02212 5643.5024
|
||||
410 410 296.3944 7267.235
|
||||
420 420 299.22019 7149.9305
|
||||
430 430 298.36689 8384.595
|
||||
440 440 295.33149 10515.75
|
||||
450 450 294.76959 11569.389
|
||||
460 460 300.141 7272.4453
|
||||
470 470 299.14431 7792.5419
|
||||
480 480 302.3697 5837.8675
|
||||
490 490 301.94692 6999.1059
|
||||
500 500 300.25929 4885.3948
|
||||
510 510 302.50013 8231.0438
|
||||
520 520 300.76412 8445.0349
|
||||
530 530 298.5016 9110.432
|
||||
540 540 301.14513 9348.6421
|
||||
550 550 297.36425 10753.314
|
||||
560 560 296.50046 10476.823
|
||||
570 570 300.57267 9889.7968
|
||||
580 580 300.4868 8377.423
|
||||
590 590 296.65103 6859.32
|
||||
600 600 298.50013 7080.5995
|
||||
610 610 300.28274 9502.5438
|
||||
620 620 298.45508 8819.7846
|
||||
630 630 300.24859 6291.4944
|
||||
640 640 299.38719 7430.2366
|
||||
650 650 297.91915 9435.3218
|
||||
660 660 300.61208 6287.9931
|
||||
670 670 303.59291 8357.7639
|
||||
680 680 301.85511 1697.3038
|
||||
690 690 298.96873 5210.2286
|
||||
700 700 298.09035 7510.4359
|
||||
710 710 303.11692 10129.526
|
||||
720 720 302.65473 10488.388
|
||||
730 730 300.15444 7118.5953
|
||||
740 740 300.19245 10582.032
|
||||
750 750 296.73618 6538.0363
|
||||
760 760 299.72857 7588.9487
|
||||
770 770 299.00347 6633.9983
|
||||
780 780 301.38129 8053.5347
|
||||
790 790 298.54819 8711.4965
|
||||
800 800 305.54197 9717.9727
|
||||
810 810 302.96497 7582.0444
|
||||
820 820 306.81537 9433.6446
|
||||
830 830 309.16373 10088.582
|
||||
840 840 313.53881 9509.8624
|
||||
850 850 310.82992 5366.015
|
||||
860 860 306.49798 8499.9157
|
||||
870 870 308.93421 5690.3242
|
||||
880 880 302.56668 5526.3636
|
||||
890 890 306.72501 7380.8469
|
||||
900 900 308.87199 10388.13
|
||||
910 910 312.7367 6613.0734
|
||||
920 920 308.34508 5903.4291
|
||||
930 930 306.39924 8615.6622
|
||||
940 940 310.37544 6849.4694
|
||||
950 950 310.13051 6188.7605
|
||||
960 960 308.68049 7637.532
|
||||
970 970 302.85465 6448.7926
|
||||
980 980 307.40719 8763.0959
|
||||
990 990 304.02815 8373.6518
|
||||
1000 1000 300.69539 5682.6678
|
||||
1010 1010 299.16385 6012.246
|
||||
1020 1020 305.118 7913.4144
|
||||
1030 1030 304.20382 10580.788
|
||||
1040 1040 302.91134 7698.4548
|
||||
1050 1050 298.08593 8952.6724
|
||||
1060 1060 302.56196 10602.997
|
||||
1070 1070 305.98211 12174.358
|
||||
1080 1080 305.70253 12288.219
|
||||
1090 1090 303.22805 7922.7166
|
||||
1100 1100 301.54879 5031.3836
|
||||
1110 1110 302.57611 8547.4189
|
||||
1120 1120 302.00845 12966.595
|
||||
1130 1130 296.10912 4514.1707
|
||||
1140 1140 295.11601 6543.7239
|
||||
1150 1150 287.29188 6453.3386
|
||||
1160 1160 284.83881 7168.9427
|
||||
1170 1170 289.77871 7895.7434
|
||||
1180 1180 293.48011 7680.6885
|
||||
1190 1190 295.69035 8609.6593
|
||||
1200 1200 296.0653 7343.68
|
||||
1210 1210 302.72922 6973.6048
|
||||
1220 1220 304.11805 7322.7664
|
||||
1230 1230 300.24647 6418.2612
|
||||
1240 1240 293.24074 9039.1214
|
||||
1250 1250 300.56214 7877.4055
|
||||
1260 1260 308.03086 5644.2135
|
||||
1270 1270 311.12289 6875.5126
|
||||
1280 1280 307.83182 7204.9894
|
||||
1290 1290 309.58491 9993.2255
|
||||
1300 1300 305.36536 8626.859
|
||||
1310 1310 304.35084 3471.1205
|
||||
1320 1320 304.40125 2149.2701
|
||||
1330 1330 295.74547 6252.9592
|
||||
1340 1340 293.16034 3407.4408
|
||||
1350 1350 298.6302 10139.977
|
||||
1360 1360 300.46627 7312.9011
|
||||
1370 1370 298.00367 2780.8886
|
||||
1380 1380 300.97807 9403.3451
|
||||
1390 1390 294.32612 12005.453
|
||||
1400 1400 296.13403 5569.4907
|
||||
1410 1410 297.86152 9558.6064
|
||||
1420 1420 303.01992 8678.345
|
||||
1430 1430 298.53849 5544.6316
|
||||
1440 1440 293.60633 12879.765
|
||||
1450 1450 296.28813 9312.4229
|
||||
1460 1460 292.64466 8344.5877
|
||||
1470 1470 295.28975 7689.9396
|
||||
1480 1480 300.10761 7436.7346
|
||||
1490 1490 291.6152 8909.6757
|
||||
1500 1500 286.644 9756.5014
|
||||
1510 1510 294.52064 10383.164
|
||||
1520 1520 297.49618 4972.89
|
||||
1530 1530 295.63379 6192.5729
|
||||
1540 1540 295.04528 4987.7191
|
||||
1550 1550 290.41403 7013.6076
|
||||
1560 1560 295.62326 7222.5009
|
||||
1570 1570 299.90584 4282.5688
|
||||
1580 1580 299.04532 7885.433
|
||||
1590 1590 300.03907 5508.0652
|
||||
1600 1600 298.05683 9262.3744
|
||||
1610 1610 297.50015 9544.6913
|
||||
1620 1620 303.21217 6393.6756
|
||||
1630 1630 304.44383 9674.6583
|
||||
1640 1640 302.68977 9065.4408
|
||||
1650 1650 303.62415 6851.1575
|
||||
1660 1660 306.11103 8592.0481
|
||||
1670 1670 300.84566 8483.551
|
||||
1680 1680 303.92882 10113.096
|
||||
1690 1690 305.02534 7389.9402
|
||||
1700 1700 303.52902 5541.9256
|
||||
1710 1710 299.27905 9547.7344
|
||||
1720 1720 294.14366 7269.2402
|
||||
1730 1730 299.49977 8086.0601
|
||||
1740 1740 298.66942 7026.6067
|
||||
1750 1750 296.94428 9595.2435
|
||||
1760 1760 297.36921 6268.7436
|
||||
1770 1770 299.88423 10598.189
|
||||
1780 1780 293.76868 7405.7641
|
||||
1790 1790 297.19444 10837.102
|
||||
1800 1800 296.46054 8345.699
|
||||
1810 1810 299.06801 5256.5992
|
||||
1820 1820 294.17725 5510.7529
|
||||
1830 1830 286.78527 6310.8881
|
||||
1840 1840 284.89686 8249.1144
|
||||
1850 1850 293.79389 4578.9263
|
||||
1860 1860 298.31279 8752.305
|
||||
1870 1870 295.31087 8401.2736
|
||||
1880 1880 298.13297 4354.8694
|
||||
1890 1890 298.90786 11454.088
|
||||
1900 1900 299.1416 9121.4138
|
||||
1910 1910 296.43134 12157.884
|
||||
1920 1920 292.05445 8613.1522
|
||||
1930 1930 300.3421 7898.3626
|
||||
1940 1940 304.55746 6311.259
|
||||
1950 1950 304.03899 8789.3537
|
||||
1960 1960 305.08259 7243.5622
|
||||
1970 1970 304.0858 8712.4796
|
||||
1980 1980 299.14574 5166.3501
|
||||
1990 1990 300.07254 10019.769
|
||||
2000 2000 301.78176 8789.7968
|
||||
Loop time of 91.2059 on 1 procs for 2000 steps with 2180 atoms
|
||||
|
||||
Performance: 1.895 ns/day, 12.667 hours/ns, 21.928 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 90.668 | 90.668 | 90.668 | 0.0 | 99.41
|
||||
Neigh | 0.23231 | 0.23231 | 0.23231 | 0.0 | 0.25
|
||||
Comm | 0.20819 | 0.20819 | 0.20819 | 0.0 | 0.23
|
||||
Output | 0.0049558 | 0.0049558 | 0.0049558 | 0.0 | 0.01
|
||||
Modify | 0.052906 | 0.052906 | 0.052906 | 0.0 | 0.06
|
||||
Other | | 0.03904 | | | 0.04
|
||||
|
||||
Nlocal: 2180.00 ave 2180 max 2180 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6693.00 ave 6693 max 6693 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 261496.0 ave 261496 max 261496 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 261496
|
||||
Ave neighs/atom = 119.95229
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:31
|
||||
@ -1,293 +0,0 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
# Coarse-Grained SPC/E Water
|
||||
|
||||
variable T equal 300.0
|
||||
variable rc equal 9.0
|
||||
variable rcD equal 10.0
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
read_data cg_spce.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.310000 40.310000 40.310000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2180 atoms
|
||||
read_data CPU = 0.005 seconds
|
||||
|
||||
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 ${rc} 385262
|
||||
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 9 385262
|
||||
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA 9
|
||||
WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:461)
|
||||
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
|
||||
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10
|
||||
|
||||
timestep 1.0
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 300 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 10
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 2000
|
||||
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 = 7 7 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair dpd/ext/tstat, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.695 | 3.696 | 3.697 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 300 5965.5396
|
||||
10 10 303.16391 8779.1574
|
||||
20 20 306.9014 8268.573
|
||||
30 30 305.84291 9976.0547
|
||||
40 40 301.20527 8832.3902
|
||||
50 50 305.72012 8041.0146
|
||||
60 60 305.1676 7118.8042
|
||||
70 70 305.01132 9423.9307
|
||||
80 80 308.10236 10781.423
|
||||
90 90 309.18703 3637.9961
|
||||
100 100 305.11814 7726.7672
|
||||
110 110 298.37346 8575.1602
|
||||
120 120 304.79786 8910.8048
|
||||
130 130 309.05401 6351.4839
|
||||
140 140 304.28367 4805.137
|
||||
150 150 300.28903 7412.6411
|
||||
160 160 299.39358 10183.593
|
||||
170 170 296.80729 5437.1054
|
||||
180 180 295.2755 8317.0414
|
||||
190 190 303.25949 8338.3453
|
||||
200 200 303.24607 9636.5224
|
||||
210 210 298.56684 10288.264
|
||||
220 220 293.42999 9001.0482
|
||||
230 230 293.12497 9083.5194
|
||||
240 240 291.92847 9659.3388
|
||||
250 250 299.2202 6328.759
|
||||
260 260 297.45209 10405.677
|
||||
270 270 292.12257 7273.9369
|
||||
280 280 289.81113 8957.8747
|
||||
290 290 299.06683 6695.3776
|
||||
300 300 300.75468 6298.5705
|
||||
310 310 296.26524 7432.4815
|
||||
320 320 294.21403 9941.7038
|
||||
330 330 293.01776 4750.2993
|
||||
340 340 295.22553 4968.3595
|
||||
350 350 293.95589 9224.5496
|
||||
360 360 297.94278 8792.0395
|
||||
370 370 298.99075 5453.7814
|
||||
380 380 302.1188 6229.2283
|
||||
390 390 298.48943 8517.5273
|
||||
400 400 295.3701 11328.394
|
||||
410 410 287.74238 4058.0382
|
||||
420 420 288.83732 5706.6773
|
||||
430 430 298.8242 6178.7142
|
||||
440 440 304.42682 10138.321
|
||||
450 450 300.28695 9731.3417
|
||||
460 460 300.34539 9249.4691
|
||||
470 470 303.32231 11638.718
|
||||
480 480 301.46777 4186.402
|
||||
490 490 292.56069 9184.8386
|
||||
500 500 297.26162 11766.733
|
||||
510 510 295.34018 6436.33
|
||||
520 520 300.16314 9325.3669
|
||||
530 530 305.00513 5947.6408
|
||||
540 540 300.88805 5222.7384
|
||||
550 550 301.56707 6669.1808
|
||||
560 560 304.89854 10730.053
|
||||
570 570 299.50424 7956.1042
|
||||
580 580 301.23382 10192.246
|
||||
590 590 298.81222 6017.2125
|
||||
600 600 300.57891 4575.433
|
||||
610 610 301.95936 6309.7515
|
||||
620 620 301.09393 5993.6489
|
||||
630 630 300.47565 4388.7137
|
||||
640 640 299.31886 9535.6093
|
||||
650 650 295.06025 7954.5811
|
||||
660 660 298.72666 8630.7466
|
||||
670 670 302.53833 5636.1305
|
||||
680 680 306.32833 12539.149
|
||||
690 690 296.1951 11345.293
|
||||
700 700 297.00325 6352.1448
|
||||
710 710 298.51181 6922.4379
|
||||
720 720 293.80125 4849.4922
|
||||
730 730 296.52677 11141.583
|
||||
740 740 294.15306 3527.8677
|
||||
750 750 294.74737 8454.0815
|
||||
760 760 292.53913 8187.9032
|
||||
770 770 294.37078 7487.5703
|
||||
780 780 297.50085 9198.7697
|
||||
790 790 298.37773 8969.0024
|
||||
800 800 293.29879 6506.6479
|
||||
810 810 296.58266 8805.7872
|
||||
820 820 290.85616 5248.8123
|
||||
830 830 292.29488 5123.8203
|
||||
840 840 292.77623 8263.5675
|
||||
850 850 297.88225 6777.7444
|
||||
860 860 300.01913 10439.087
|
||||
870 870 295.79578 7318.1322
|
||||
880 880 301.5994 8242.4774
|
||||
890 890 306.63208 8090.6106
|
||||
900 900 303.53759 6831.2666
|
||||
910 910 300.70481 3811.0498
|
||||
920 920 299.96274 8351.1573
|
||||
930 930 299.67435 7046.0534
|
||||
940 940 310.81742 6887.6925
|
||||
950 950 305.09984 4811.088
|
||||
960 960 301.33039 4184.851
|
||||
970 970 301.19205 6417.6542
|
||||
980 980 299.6491 7738.2233
|
||||
990 990 297.33655 9264.0874
|
||||
1000 1000 302.33418 7166.2751
|
||||
1010 1010 300.08402 9121.0882
|
||||
1020 1020 302.82225 6405.7109
|
||||
1030 1030 304.01683 6944.0839
|
||||
1040 1040 305.82618 6160.3838
|
||||
1050 1050 308.12518 4356.0931
|
||||
1060 1060 307.64811 6954.7245
|
||||
1070 1070 313.70509 5558.9804
|
||||
1080 1080 316.09239 7250.6147
|
||||
1090 1090 310.2845 5441.3722
|
||||
1100 1100 300.18899 4417.8774
|
||||
1110 1110 304.02471 5609.1668
|
||||
1120 1120 303.46016 10355.031
|
||||
1130 1130 305.68165 6400.913
|
||||
1140 1140 308.78348 7235.1894
|
||||
1150 1150 299.30025 9246.4856
|
||||
1160 1160 302.70799 9866.9536
|
||||
1170 1170 302.0977 8643.5532
|
||||
1180 1180 307.15407 8866.4664
|
||||
1190 1190 305.78146 7562.4911
|
||||
1200 1200 302.54605 7974.9973
|
||||
1210 1210 306.14264 9554.2381
|
||||
1220 1220 308.89843 6219.5361
|
||||
1230 1230 305.71844 7633.9105
|
||||
1240 1240 306.51911 7705.4795
|
||||
1250 1250 304.78473 8590.5595
|
||||
1260 1260 300.82969 9281.5964
|
||||
1270 1270 305.9271 4951.1323
|
||||
1280 1280 310.32728 9446.3989
|
||||
1290 1290 318.27879 9102.5544
|
||||
1300 1300 310.45777 5931.5457
|
||||
1310 1310 304.81268 1214.4291
|
||||
1320 1320 307.08811 10315.961
|
||||
1330 1330 306.86917 8584.9658
|
||||
1340 1340 307.26912 7254.864
|
||||
1350 1350 310.02754 8508.6256
|
||||
1360 1360 306.12763 4912.6641
|
||||
1370 1370 301.67924 6715.8196
|
||||
1380 1380 298.37239 6149.8821
|
||||
1390 1390 299.62894 8181.4761
|
||||
1400 1400 301.60395 6714.4244
|
||||
1410 1410 297.65752 7035.6575
|
||||
1420 1420 297.02817 7510.2637
|
||||
1430 1430 303.59177 10361.937
|
||||
1440 1440 300.10771 8473.2311
|
||||
1450 1450 291.21837 6097.9954
|
||||
1460 1460 291.58663 7729.0841
|
||||
1470 1470 292.52447 6555.8661
|
||||
1480 1480 294.48264 6960.0201
|
||||
1490 1490 298.34869 8044.2321
|
||||
1500 1500 296.8193 11731.289
|
||||
1510 1510 296.52073 5452.8935
|
||||
1520 1520 294.54819 9591.7969
|
||||
1530 1530 297.36394 5148.5383
|
||||
1540 1540 289.08137 6057.0981
|
||||
1550 1550 288.27007 8965.1965
|
||||
1560 1560 294.84398 8316.9487
|
||||
1570 1570 299.79573 8760.7322
|
||||
1580 1580 295.66745 5045.5322
|
||||
1590 1590 298.14356 7161.1834
|
||||
1600 1600 297.10402 6529.9938
|
||||
1610 1610 299.69137 7741.6027
|
||||
1620 1620 304.93043 11222.109
|
||||
1630 1630 302.01322 10893.107
|
||||
1640 1640 295.47422 8400.3124
|
||||
1650 1650 301.93122 7190.2609
|
||||
1660 1660 305.02639 6140.5552
|
||||
1670 1670 302.86047 8651.5366
|
||||
1680 1680 304.82151 9909.407
|
||||
1690 1690 300.48426 8428.8845
|
||||
1700 1700 293.06643 5333.8144
|
||||
1710 1710 295.43687 9103.4353
|
||||
1720 1720 298.77208 8162.1053
|
||||
1730 1730 300.08189 9603.4371
|
||||
1740 1740 303.16004 10693.291
|
||||
1750 1750 303.54199 9151.023
|
||||
1760 1760 300.99281 4641.2985
|
||||
1770 1770 297.36657 3888.5753
|
||||
1780 1780 298.32969 7286.2299
|
||||
1790 1790 297.34183 8975.8956
|
||||
1800 1800 295.83042 6366.7607
|
||||
1810 1810 295.92044 9308.4953
|
||||
1820 1820 298.10087 7117.2369
|
||||
1830 1830 296.13936 4849.3739
|
||||
1840 1840 296.5869 8321.4011
|
||||
1850 1850 296.74513 9530.6806
|
||||
1860 1860 298.57398 8788.0603
|
||||
1870 1870 299.12825 6015.4777
|
||||
1880 1880 301.91639 11706.441
|
||||
1890 1890 309.85968 10909.493
|
||||
1900 1900 302.64998 8779.8967
|
||||
1910 1910 301.62919 9176.3902
|
||||
1920 1920 300.66238 5369.8681
|
||||
1930 1930 297.64499 8185.09
|
||||
1940 1940 296.47852 10188.803
|
||||
1950 1950 297.802 6679.4466
|
||||
1960 1960 299.78754 7316.8198
|
||||
1970 1970 300.09083 6008.9414
|
||||
1980 1980 297.94119 5615.6403
|
||||
1990 1990 298.37687 9727.308
|
||||
2000 2000 296.08394 6400.2746
|
||||
Loop time of 41.5171 on 4 procs for 2000 steps with 2180 atoms
|
||||
|
||||
Performance: 4.162 ns/day, 5.766 hours/ns, 48.173 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 38.667 | 38.954 | 39.453 | 4.8 | 93.83
|
||||
Neigh | 0.10947 | 0.11039 | 0.11153 | 0.3 | 0.27
|
||||
Comm | 1.8661 | 2.3644 | 2.652 | 19.6 | 5.70
|
||||
Output | 0.0082644 | 0.0094232 | 0.01281 | 2.0 | 0.02
|
||||
Modify | 0.024678 | 0.025206 | 0.025888 | 0.3 | 0.06
|
||||
Other | | 0.05335 | | | 0.13
|
||||
|
||||
Nlocal: 545.000 ave 559 max 531 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 3619.00 ave 3655 max 3594 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
Neighs: 65415.5 ave 66835 max 64310 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 261662
|
||||
Ave neighs/atom = 120.02844
|
||||
Neighbor list builds = 26
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:41
|
||||
@ -0,0 +1,106 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Coarse-Grained SPC/E Water
|
||||
|
||||
variable T equal 300.0
|
||||
variable rc equal 9.0
|
||||
variable rcD equal 10.0
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
read_data cg_spce.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (40.31 40.31 40.31)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2180 atoms
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat 300 ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat 300 300 ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat 300 300 9 385262
|
||||
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA 9
|
||||
WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
|
||||
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
|
||||
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
|
||||
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10
|
||||
|
||||
timestep 1.0
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 300 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
generated 0 of 0 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 = 7 7 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) pair dpd/ext/tstat, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.38 | 5.38 | 5.38 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 300 7353.4129
|
||||
100 100 303.74025 4964.013
|
||||
200 200 298.35396 8007.7802
|
||||
300 300 298.28547 6291.5807
|
||||
400 400 298.01797 6252.1041
|
||||
500 500 299.88984 3489.931
|
||||
600 600 302.5718 9092.203
|
||||
700 700 305.38722 5909.02
|
||||
800 800 294.81401 10282.286
|
||||
900 900 292.40724 8338.6878
|
||||
1000 1000 293.64788 6951.569
|
||||
Loop time of 28.1058 on 1 procs for 1000 steps with 2180 atoms
|
||||
|
||||
Performance: 3.074 ns/day, 7.807 hours/ns, 35.580 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 27.948 | 27.948 | 27.948 | 0.0 | 99.44
|
||||
Neigh | 0.071647 | 0.071647 | 0.071647 | 0.0 | 0.25
|
||||
Comm | 0.058215 | 0.058215 | 0.058215 | 0.0 | 0.21
|
||||
Output | 0.00026724 | 0.00026724 | 0.00026724 | 0.0 | 0.00
|
||||
Modify | 0.014429 | 0.014429 | 0.014429 | 0.0 | 0.05
|
||||
Other | | 0.01283 | | | 0.05
|
||||
|
||||
Nlocal: 2180 ave 2180 max 2180 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6643 ave 6643 max 6643 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 261826 ave 261826 max 261826 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 261826
|
||||
Ave neighs/atom = 120.10367
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:28
|
||||
@ -0,0 +1,106 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Coarse-Grained SPC/E Water
|
||||
|
||||
variable T equal 300.0
|
||||
variable rc equal 9.0
|
||||
variable rcD equal 10.0
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
read_data cg_spce.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (40.31 40.31 40.31)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2180 atoms
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat 300 ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat 300 300 ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat 300 300 9 385262
|
||||
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA 9
|
||||
WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
|
||||
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
|
||||
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
|
||||
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10
|
||||
|
||||
timestep 1.0
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 300 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
generated 0 of 0 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 = 7 7 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) pair dpd/ext/tstat, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.695 | 3.696 | 3.697 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 300 5950.2338
|
||||
100 100 301.15012 9090.2244
|
||||
200 200 301.28795 10589.557
|
||||
300 300 293.61974 5971.7781
|
||||
400 400 310.4217 8198.7972
|
||||
500 500 299.89888 9140.3132
|
||||
600 600 305.56607 7783.4481
|
||||
700 700 295.99415 6276.9444
|
||||
800 800 296.50051 5058.1115
|
||||
900 900 288.68499 8637.0269
|
||||
1000 1000 291.17292 6516.4192
|
||||
Loop time of 7.57429 on 4 procs for 1000 steps with 2180 atoms
|
||||
|
||||
Performance: 11.407 ns/day, 2.104 hours/ns, 132.026 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.2745 | 7.3674 | 7.4316 | 2.1 | 97.27
|
||||
Neigh | 0.01863 | 0.018866 | 0.019429 | 0.2 | 0.25
|
||||
Comm | 0.1123 | 0.17708 | 0.27025 | 13.8 | 2.34
|
||||
Output | 0.00019274 | 0.00021224 | 0.00026504 | 0.0 | 0.00
|
||||
Modify | 0.0041691 | 0.0042729 | 0.0043136 | 0.1 | 0.06
|
||||
Other | | 0.006464 | | | 0.09
|
||||
|
||||
Nlocal: 545 ave 552 max 531 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 2 1
|
||||
Nghost: 3620.5 ave 3656 max 3584 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 65419 ave 66338 max 64104 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 261676
|
||||
Ave neighs/atom = 120.03486
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:07
|
||||
@ -23,3 +23,5 @@ to the final states.
|
||||
|
||||
* `quicktests` -- very short runs with charged Lennard-Jones atoms to test
|
||||
*compute fep*, *fix adapt/fep* and *pair lj/cut/coul/long/soft*.
|
||||
|
||||
* `ta` -- surface tension of SPCE water without constraints. Test-area method.
|
||||
|
||||
6174
examples/PACKAGES/fep/ta/data.spce
Normal file
6174
examples/PACKAGES/fep/ta/data.spce
Normal file
File diff suppressed because it is too large
Load Diff
49
examples/PACKAGES/fep/ta/in.spce.lmp
Normal file
49
examples/PACKAGES/fep/ta/in.spce.lmp
Normal file
@ -0,0 +1,49 @@
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style lj/cut/coul/long 12.0 12.0
|
||||
pair_modify tail no
|
||||
kspace_style pppm 1.0e-5
|
||||
|
||||
read_data data.spce # 8x8x16 SPCE molecules in a 30x30x100 box
|
||||
|
||||
bond_coeff 1 517.630258 1.0
|
||||
angle_coeff 1 37.950526 109.47
|
||||
pair_coeff 1 1 0.1553 3.166 # O O
|
||||
pair_coeff 1 2 0.0 1.0 # O H
|
||||
pair_coeff 2 2 0.0 1.0 # H H
|
||||
|
||||
# don't use fix shake with compute fep/ta
|
||||
# fix SHAKE all shake 0.0001 20 0 b 1
|
||||
|
||||
neighbor 2.0 bin
|
||||
# neigh_modify delay 0 every 1 check yes
|
||||
|
||||
timestep 1.0
|
||||
|
||||
variable TK equal 300.0
|
||||
compute TA all fep/ta ${TK} xy 1.0005
|
||||
|
||||
velocity all create ${TK} 12345
|
||||
|
||||
thermo_style custom step temp press etotal pe c_TA[*]
|
||||
thermo 5000
|
||||
|
||||
fix NVT all nvt temp ${TK} ${TK} 100
|
||||
run 300000
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
variable gamma_v equal 100*(pzz-0.5*(pxx+pyy))/2/100 # surface tension via the mechanical route
|
||||
|
||||
fix FEP all ave/time 100 1000 100000 c_TA[*] v_gamma_v ave running file spce.fep.ta
|
||||
|
||||
run 2000000
|
||||
|
||||
689
examples/PACKAGES/fep/ta/log.spce
Normal file
689
examples/PACKAGES/fep/ta/log.spce
Normal file
@ -0,0 +1,689 @@
|
||||
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
|
||||
package gpu 0
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style lj/cut/coul/long 12.0 12.0
|
||||
pair_modify tail no
|
||||
kspace_style pppm 1.0e-5
|
||||
|
||||
read_data data.spce # 8x8x16 SPCE molecules in a 30x30x100 box
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (30 30 100)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3072 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
2048 bonds
|
||||
reading angles ...
|
||||
1024 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0.5
|
||||
special bond factors coul: 0 0 0.5
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.006 seconds
|
||||
|
||||
bond_coeff 1 517.630258 1.0
|
||||
angle_coeff 1 37.950526 109.47
|
||||
pair_coeff 1 1 0.1553 3.166 # O O
|
||||
pair_coeff 1 2 0.0 1.0 # O H
|
||||
pair_coeff 2 2 0.0 1.0 # H H
|
||||
|
||||
# don't use fix shake with compute fep/ta
|
||||
# fix SHAKE all shake 0.0001 20 0 b 1
|
||||
|
||||
neighbor 2.0 bin
|
||||
# neigh_modify delay 0 every 1 check yes
|
||||
|
||||
timestep 1.0
|
||||
|
||||
variable TK equal 300.0
|
||||
compute TA all fep/ta ${TK} xy 1.0005
|
||||
compute TA all fep/ta 300 xy 1.0005
|
||||
|
||||
velocity all create ${TK} 12345
|
||||
velocity all create 300 12345
|
||||
|
||||
thermo_style custom step temp press etotal pe c_TA[*]
|
||||
thermo 5000
|
||||
|
||||
fix NVT all nvt temp ${TK} ${TK} 100
|
||||
fix NVT all nvt temp 300 ${TK} 100
|
||||
fix NVT all nvt temp 300 300 100
|
||||
run 300000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- GPU package (short-range, long-range and three-body potentials):
|
||||
|
||||
@Article{Brown11,
|
||||
author = {W. M. Brown, P. Wang, S. J. Plimpton, A. N. Tharrington},
|
||||
title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Short Range Forces},
|
||||
journal = {Comp.~Phys.~Comm.},
|
||||
year = 2011,
|
||||
volume = 182,
|
||||
pages = {898--911}
|
||||
}
|
||||
|
||||
@Article{Brown12,
|
||||
author = {W. M. Brown, A. Kohlmeyer, S. J. Plimpton, A. N. Tharrington},
|
||||
title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh},
|
||||
journal = {Comp.~Phys.~Comm.},
|
||||
year = 2012,
|
||||
volume = 183,
|
||||
pages = {449--459}
|
||||
}
|
||||
|
||||
@Article{Brown13,
|
||||
author = {W. M. Brown, Y. Masako},
|
||||
title = {Implementing Molecular Dynamics on Hybrid High Performance Computers – Three-Body Potentials},
|
||||
journal = {Comp.~Phys.~Comm.},
|
||||
year = 2013,
|
||||
volume = 184,
|
||||
pages = {2785--2793}
|
||||
}
|
||||
|
||||
@Article{Trung15,
|
||||
author = {T. D. Nguyen, S. J. Plimpton},
|
||||
title = {Accelerating dissipative particle dynamics simulations for soft matter systems},
|
||||
journal = {Comput.~Mater.~Sci.},
|
||||
year = 2015,
|
||||
volume = 100,
|
||||
pages = {173--180}
|
||||
}
|
||||
|
||||
@Article{Trung17,
|
||||
author = {T. D. Nguyen},
|
||||
title = {GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations},
|
||||
journal = {Comp.~Phys.~Comm.},
|
||||
year = 2017,
|
||||
volume = 212,
|
||||
pages = {113--122}
|
||||
}
|
||||
|
||||
@Article{Nikolskiy19,
|
||||
author = {V. Nikolskiy, V. Stegailov},
|
||||
title = {GPU acceleration of four-site water models in LAMMPS},
|
||||
journal = {Proceeding of the International Conference on Parallel Computing (ParCo 2019), Prague, Czech Republic},
|
||||
year = 2019
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
|
||||
G vector (1/distance) = 0.24270009
|
||||
grid = 20 20 50
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0037271514
|
||||
estimated relative force accuracy = 1.1224206e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 40824 20000
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
FEP/TA settings ...
|
||||
temperature = 300.000000
|
||||
scale factor = 1.000500
|
||||
tail no
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.59 | 10.59 | 10.59 Mbytes
|
||||
Step Temp Press TotEng PotEng c_TA[1] c_TA[2] c_TA[3]
|
||||
0 300 5742.8831 8061.6965 5315.4762 -10.940045 93249708 0.45
|
||||
5000 301.43029 -118.64017 -7888.4723 -10647.786 -0.13617205 1.2566061 0.45
|
||||
10000 294.49018 -301.44062 -8063.3808 -10759.164 -0.14897537 1.2838851 0.45
|
||||
15000 294.36123 -407.07728 -8189.2912 -10883.894 0.34568257 0.55998421 0.45
|
||||
20000 300.95171 111.50248 -8104.1193 -10859.052 0.11293291 0.82742794 0.45
|
||||
25000 300.28473 388.00598 -8147.8655 -10896.692 0.11270184 0.82774872 0.45
|
||||
30000 306.62229 -113.93849 -8191.7529 -10998.594 0.26068823 0.6457922 0.45
|
||||
35000 303.66349 -426.81556 -8269.8364 -11049.593 0.78191631 0.26939311 0.45
|
||||
40000 291.70214 -50.50854 -8368.0775 -11038.339 0.20120788 0.71354814 0.45
|
||||
45000 299.74326 -289.18081 -8346.2716 -11090.142 0.4163404 0.49739645 0.45
|
||||
50000 300.53193 36.834691 -8367.5726 -11118.662 0.20517137 0.70881996 0.45
|
||||
55000 298.20207 -107.76906 -8274.386 -11004.148 0.7409946 0.2885342 0.45
|
||||
60000 298.32558 -65.20542 -8433.4884 -11164.381 0.16210976 0.76191344 0.45
|
||||
65000 297.3149 -102.87381 -8379.2515 -11100.892 0.21193701 0.70082127 0.45
|
||||
70000 300.78423 -463.75811 -8381.3317 -11134.731 0.32109349 0.58356406 0.45
|
||||
75000 299.53099 -53.264996 -8495.159 -11237.086 0.44828935 0.47144212 0.45
|
||||
80000 295.55879 -590.1244 -8432.3435 -11137.909 0.28788374 0.61699451 0.45
|
||||
85000 298.73289 -234.73297 -8473.8721 -11208.493 -0.11723275 1.2173128 0.45
|
||||
90000 307.02709 -264.9035 -8303.7625 -11114.309 -0.098959935 1.1805672 0.45
|
||||
95000 304.79112 199.8891 -8364.2553 -11154.334 0.036986735 0.93984396 0.45
|
||||
100000 295.49748 -743.18974 -8453.8066 -11158.811 0.249981 0.65749559 0.45
|
||||
105000 303.11352 -163.70166 -8324.4846 -11099.206 -0.012286442 1.0208231 0.45
|
||||
110000 294.30278 -33.731015 -8512.8168 -11206.884 -0.0129379 1.0219392 0.45
|
||||
115000 293.65421 393.24871 -8481.1933 -11169.324 0.75255277 0.28299408 0.45
|
||||
120000 300.56448 16.832298 -8507.3819 -11258.769 0.13389897 0.79883437 0.45
|
||||
125000 297.92506 -398.77893 -8576.4403 -11303.666 0.07292658 0.88485917 0.45
|
||||
130000 303.007 -589.11865 -8560.7259 -11334.472 0.42876446 0.48713794 0.45
|
||||
135000 310.82674 -203.4991 -8565.3181 -11410.647 0.075268046 0.88139064 0.45
|
||||
140000 303.68345 -710.20709 -8570.895 -11350.834 -0.1023741 1.1873476 0.45
|
||||
145000 293.86825 129.05781 -8457.0747 -11147.165 0.39475138 0.51573896 0.45
|
||||
150000 296.93136 -734.03863 -8577.2763 -11295.406 0.73600373 0.29095985 0.45
|
||||
155000 296.67522 -290.20206 -8631.0579 -11346.843 -0.30049664 1.6554154 0.45
|
||||
160000 301.5685 -656.03394 -8646.3196 -11406.898 0.08494101 0.86720512 0.45
|
||||
165000 295.8808 342.45206 -8602.0309 -11310.544 -0.30873864 1.6784606 0.45
|
||||
170000 303.33048 -64.144957 -8580.8446 -11357.552 0.13622456 0.79572423 0.45
|
||||
175000 300.75245 -908.44969 -8566.8005 -11319.909 0.15795135 0.76724659 0.45
|
||||
180000 301.34603 -350.00512 -8489.0111 -11247.553 0.21089487 0.70204744 0.45
|
||||
185000 305.96254 62.840515 -8458.0542 -11258.856 -0.050029338 1.0875408 0.45
|
||||
190000 300.14392 256.935 -8684.6591 -11432.197 0.40144188 0.50998337 0.45
|
||||
195000 299.32366 -218.70113 -8505.3328 -11245.362 -0.19428451 1.3852659 0.45
|
||||
200000 307.89424 -569.89954 -8615.1541 -11433.639 0.55121888 0.39668508 0.45
|
||||
205000 299.34873 334.69765 -8657.6353 -11397.894 0.17751997 0.74247109 0.45
|
||||
210000 298.54619 -261.12193 -8601.2439 -11334.156 0.74219016 0.28795615 0.45
|
||||
215000 304.02395 -306.81112 -8531.9913 -11315.047 0.86987192 0.23244073 0.45
|
||||
220000 299.95916 278.60921 -8682.394 -11428.24 -0.26474202 1.559051 0.45
|
||||
225000 302.839 -226.36906 -8515.0815 -11287.29 0.060381353 0.90367684 0.45
|
||||
230000 299.54085 240.08589 -8636.8991 -11378.916 -0.46699438 2.1887589 0.45
|
||||
235000 297.62792 -138.20813 -8627.0888 -11351.595 -0.035013312 1.0604901 0.45
|
||||
240000 299.15558 442.88999 -8749.2731 -11487.763 0.14696819 0.78151268 0.45
|
||||
245000 291.76323 174.70322 -8597.8808 -11268.701 -0.3979188 1.9492946 0.45
|
||||
250000 308.21961 37.282506 -8603.7127 -11425.176 0.021882894 0.96395922 0.45
|
||||
255000 307.18484 -493.77408 -8459.5942 -11271.585 0.16914044 0.75298079 0.45
|
||||
260000 294.17364 -238.05366 -8677.8379 -11370.723 -0.35710078 1.8202968 0.45
|
||||
265000 289.14461 -304.12454 -8727.2613 -11374.111 0.18045129 0.73882932 0.45
|
||||
270000 301.51228 -255.75558 -8640.9577 -11401.022 0.49252861 0.43772444 0.45
|
||||
275000 294.98349 -351.00974 -8678.3965 -11378.695 -0.31576914 1.6983718 0.45
|
||||
280000 294.37376 279.87325 -8668.9575 -11363.675 0.26328091 0.64298978 0.45
|
||||
285000 295.68351 249.3086 -8748.533 -11455.24 0.6820904 0.31849899 0.45
|
||||
290000 298.74266 -749.43024 -8583.8679 -11318.578 0.030414997 0.95026156 0.45
|
||||
295000 292.67215 -573.39647 -8713.3223 -11392.463 0.25656615 0.65027291 0.45
|
||||
300000 302.48853 186.71329 -8655.8918 -11424.892 0.20319721 0.71117107 0.45
|
||||
Loop time of 706.805 on 1 procs for 300000 steps with 3072 atoms
|
||||
|
||||
Performance: 36.672 ns/day, 0.654 hours/ns, 424.445 timesteps/s
|
||||
95.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 149.88 | 149.88 | 149.88 | 0.0 | 21.21
|
||||
Bond | 17.824 | 17.824 | 17.824 | 0.0 | 2.52
|
||||
Kspace | 517.46 | 517.46 | 517.46 | 0.0 | 73.21
|
||||
Neigh | 1.3789 | 1.3789 | 1.3789 | 0.0 | 0.20
|
||||
Comm | 9.412 | 9.412 | 9.412 | 0.0 | 1.33
|
||||
Output | 0.092 | 0.092 | 0.092 | 0.0 | 0.01
|
||||
Modify | 8.3026 | 8.3026 | 8.3026 | 0.0 | 1.17
|
||||
Other | | 2.458 | | | 0.35
|
||||
|
||||
Nlocal: 3072 ave 3072 max 3072 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8370 ave 8370 max 8370 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
|
||||
|
||||
Total # of neighbors = -1
|
||||
Ave neighs/atom = -0.00032552083
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 14698
|
||||
Dangerous builds = 21
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
variable gamma_v equal 100*(pzz-0.5*(pxx+pyy))/2/100 # surface tension via the mechanical route
|
||||
|
||||
fix FEP all ave/time 100 1000 100000 c_TA[*] v_gamma_v ave running file spce.fep.ta
|
||||
|
||||
run 2000000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
|
||||
G vector (1/distance) = 0.24270009
|
||||
grid = 20 20 50
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0037271514
|
||||
estimated relative force accuracy = 1.1224206e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 40824 20000
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.61 | 10.61 | 10.61 Mbytes
|
||||
Step Temp Press TotEng PotEng c_TA[1] c_TA[2] c_TA[3]
|
||||
0 302.48853 186.71327 -8655.8918 -11424.892 0.20325452 0.71110271 0.45
|
||||
5000 296.71986 -573.544 -8510.0832 -11226.277 0.43636365 0.48096787 0.45
|
||||
10000 302.58189 314.36295 -8636.8139 -11406.669 0.005932853 0.99009761 0.45
|
||||
15000 296.98096 -950.66627 -8635.9066 -11354.49 0.48058674 0.44658101 0.45
|
||||
20000 297.11923 -474.65836 -8666.9864 -11386.836 0.27933535 0.62590536 0.45
|
||||
25000 302.26474 -621.83271 -8655.4227 -11422.375 0.01931686 0.96811729 0.45
|
||||
30000 300.37645 -358.95128 -8568.7732 -11318.44 0.25415456 0.65290873 0.45
|
||||
35000 296.5436 179.71411 -8665.0335 -11379.614 0.1911473 0.72569185 0.45
|
||||
40000 300.79459 92.193193 -8617.7807 -11371.275 0.27587113 0.629553 0.45
|
||||
45000 298.87827 220.06674 -8695.83 -11431.782 0.28715816 0.61774591 0.45
|
||||
50000 304.4095 -375.31266 -8614.4396 -11401.025 -0.18683272 1.3680584 0.45
|
||||
55000 305.11287 128.51602 -8559.8245 -11352.848 0.24122754 0.66722084 0.45
|
||||
60000 296.56241 302.30371 -8725.6357 -11440.388 -0.27104279 1.5756158 0.45
|
||||
65000 295.78468 -393.18931 -8716.4616 -11424.095 0.39132466 0.51871194 0.45
|
||||
70000 297.67504 155.75977 -8641.2451 -11366.182 0.031194864 0.94901929 0.45
|
||||
75000 298.81381 -207.51201 -8622.9859 -11358.348 -0.11330086 1.2093106 0.45
|
||||
80000 296.17928 -360.65589 -8679.0048 -11390.25 0.68794433 0.31538684 0.45
|
||||
85000 303.90294 488.01134 -8643.2028 -11425.151 0.41330713 0.49993365 0.45
|
||||
90000 296.49425 14.901201 -8636.0539 -11350.182 -0.21538319 1.4351695 0.45
|
||||
95000 308.63505 137.10659 -8570.395 -11395.661 0.51407684 0.42218544 0.45
|
||||
100000 302.56638 -402.80803 -8635.0157 -11404.729 0.1552006 0.77079493 0.45
|
||||
105000 293.79289 -417.74599 -8626.2538 -11315.654 -0.13491963 1.253969 0.45
|
||||
110000 293.52504 -808.94658 -8684.9259 -11371.874 0.20573374 0.70815164 0.45
|
||||
115000 307.6821 132.78071 -8639.817 -11456.36 -0.67060193 3.0798018 0.45
|
||||
120000 303.22974 121.87128 -8714.7295 -11490.515 0.3675961 0.5397742 0.45
|
||||
125000 303.8202 -34.518279 -8625.1384 -11406.329 0.17151619 0.74998608 0.45
|
||||
130000 294.5718 -508.86133 -8684.9608 -11381.491 0.23323323 0.67622827 0.45
|
||||
135000 302.79866 -445.99091 -8627.6163 -11399.456 0.3300839 0.57482965 0.45
|
||||
140000 297.84052 -78.442467 -8621.5234 -11347.976 0.39157424 0.51849484 0.45
|
||||
145000 303.64247 463.89678 -8673.8591 -11453.423 0.39692857 0.51385891 0.45
|
||||
150000 288.38239 28.567607 -8789.6464 -11429.518 -0.045509865 1.0793274 0.45
|
||||
155000 296.02581 -111.35664 -8674.295 -11384.135 0.23313764 0.67633671 0.45
|
||||
160000 307.72004 -410.73956 -8578.8169 -11395.707 0.28485416 0.62013794 0.45
|
||||
165000 300.42279 -483.56039 -8598.0354 -11348.126 0.38342507 0.52563101 0.45
|
||||
170000 302.51326 -150.99512 -8626.2426 -11395.469 0.2439355 0.66419697 0.45
|
||||
175000 295.41161 -554.9058 -8760.0201 -11464.238 0.38186652 0.52700696 0.45
|
||||
180000 296.21987 -194.97724 -8645.4143 -11357.031 0.098453456 0.84777037 0.45
|
||||
185000 296.52352 -186.85833 -8690.0538 -11404.45 0.6348999 0.34473516 0.45
|
||||
190000 304.72799 -60.2868 -8667.2005 -11456.701 0.1885985 0.72880108 0.45
|
||||
195000 306.65221 -871.17267 -8679.3434 -11486.458 0.56138735 0.38997638 0.45
|
||||
200000 301.07509 362.96369 -8616.9867 -11373.048 -0.53126323 2.4379049 0.45
|
||||
205000 303.65587 -216.8767 -8564.3182 -11344.005 0.11046546 0.83085967 0.45
|
||||
210000 296.20891 -474.08356 -8698.3778 -11409.894 -0.11237476 1.2074335 0.45
|
||||
215000 295.37276 422.46284 -8714.4636 -11418.326 0.042757549 0.93079022 0.45
|
||||
220000 301.20663 -202.20616 -8577.1827 -11334.449 0.30387837 0.60066105 0.45
|
||||
225000 306.20481 -90.566175 -8503.5134 -11306.533 0.29188403 0.6128683 0.45
|
||||
230000 303.54253 -24.255163 -8641.8724 -11420.521 -0.38522168 1.9082173 0.45
|
||||
235000 300.29265 -572.08074 -8664.2779 -11413.177 0.48055356 0.44660587 0.45
|
||||
240000 302.90712 -226.88617 -8636.6962 -11409.528 -0.15295452 1.2924832 0.45
|
||||
245000 305.05222 -68.241521 -8591.0885 -11383.557 -0.19850824 1.3951152 0.45
|
||||
250000 300.27784 -46.680162 -8746.7288 -11495.492 -0.0098493376 1.0166585 0.45
|
||||
255000 308.23091 -424.64171 -8573.7405 -11395.307 0.1366107 0.79520901 0.45
|
||||
260000 296.11619 4.6901264 -8742.1916 -11452.859 -0.12450429 1.2322516 0.45
|
||||
265000 301.62359 134.42152 -8565.5323 -11326.615 -0.028534957 1.0490284 0.45
|
||||
270000 306.71999 -62.484213 -8690.7983 -11498.534 0.28432443 0.62068922 0.45
|
||||
275000 292.91982 532.15442 -8779.2684 -11460.676 -0.40898808 1.9858264 0.45
|
||||
280000 306.88024 -339.05165 -8557.2761 -11366.479 0.12573772 0.80984534 0.45
|
||||
285000 303.38798 617.66326 -8630.5787 -11407.813 -0.1310487 1.2458532 0.45
|
||||
290000 299.66094 302.90333 -8692.267 -11435.383 0.65063395 0.33575584 0.45
|
||||
295000 304.49009 656.72392 -8710.7918 -11498.115 -0.16849302 1.3266137 0.45
|
||||
300000 303.80861 -221.66912 -8688.9465 -11470.031 -0.24985266 1.5205954 0.45
|
||||
305000 300.67136 -498.92059 -8669.6648 -11422.031 0.19219443 0.72441833 0.45
|
||||
310000 305.7021 -521.59218 -8505.6751 -11304.093 0.52013748 0.4179152 0.45
|
||||
315000 302.66313 -359.25677 -8682.4925 -11453.091 -0.26135382 1.5502155 0.45
|
||||
320000 304.5646 441.04962 -8610.9569 -11398.962 0.41662005 0.49716319 0.45
|
||||
325000 300.04934 -142.59053 -8698.3246 -11444.997 -0.23029219 1.4715132 0.45
|
||||
330000 305.55522 -212.47771 -8576.3678 -11373.441 0.091594168 0.85758093 0.45
|
||||
335000 294.79439 -151.62761 -8762.4565 -11461.024 0.14345357 0.78613362 0.45
|
||||
340000 302.4373 463.41717 -8643.2588 -11411.79 0.36279978 0.54413438 0.45
|
||||
345000 295.91624 -272.3623 -8678.9725 -11387.81 0.1032874 0.84092407 0.45
|
||||
350000 300.60829 62.418773 -8633.2343 -11385.023 -0.040578988 1.0704371 0.45
|
||||
355000 301.41802 -860.82496 -8573.5867 -11332.788 0.04947461 0.9203617 0.45
|
||||
360000 298.03103 -265.05516 -8619.4232 -11347.619 -0.20903224 1.4199617 0.45
|
||||
365000 298.08727 -359.76277 -8612.4898 -11341.201 0.040109682 0.93493354 0.45
|
||||
370000 301.55162 -339.05976 -8687.3746 -11447.799 0.1705358 0.75122045 0.45
|
||||
375000 299.3933 -290.38029 -8723.9515 -11464.618 -0.1476 1.2809266 0.45
|
||||
380000 303.02442 -1104.7914 -8626.7252 -11400.631 0.3211992 0.58346059 0.45
|
||||
385000 301.49421 -613.53228 -8662.2479 -11422.146 -0.42642873 2.0447796 0.45
|
||||
390000 302.01134 -351.23257 -8662.4664 -11427.099 0.23747904 0.67142935 0.45
|
||||
395000 307.32962 -443.86959 -8624.8646 -11438.181 0.17359502 0.74737541 0.45
|
||||
400000 301.67955 -253.92045 -8690.6143 -11452.209 -0.43779134 2.0841261 0.45
|
||||
405000 302.60773 -97.544471 -8646.8281 -11416.92 0.071259831 0.88733652 0.45
|
||||
410000 302.48853 -630.99507 -8710.4497 -11479.45 0.28763517 0.61725182 0.45
|
||||
415000 296.46562 -443.33457 -8763.0661 -11476.932 0.088532948 0.86199583 0.45
|
||||
420000 295.37803 -70.515081 -8720.0027 -11423.913 0.06359365 0.89882065 0.45
|
||||
425000 299.31069 -48.284153 -8678.6115 -11418.522 0.063520704 0.89893064 0.45
|
||||
430000 296.37918 -651.48627 -8784.4246 -11497.5 -0.0094249768 1.0159351 0.45
|
||||
435000 303.07145 -284.10404 -8558.3149 -11332.651 0.034731239 0.94340646 0.45
|
||||
440000 293.1823 -280.18182 -8707.2432 -11391.054 0.14151034 0.78870025 0.45
|
||||
445000 305.55617 -286.4858 -8646.9315 -11444.013 0.26166889 0.64473078 0.45
|
||||
450000 300.67206 102.89156 -8705.2376 -11457.61 0.88202179 0.2277515 0.45
|
||||
455000 304.23258 9.5792632 -8571.8771 -11356.843 -0.42835558 2.0513992 0.45
|
||||
460000 292.30355 265.8009 -8707.4453 -11383.212 0.20592758 0.70792142 0.45
|
||||
465000 297.62746 193.66269 -8716.5132 -11441.015 0.36938368 0.53815813 0.45
|
||||
470000 292.53483 -75.549804 -8728.3188 -11406.202 0.49993961 0.43231669 0.45
|
||||
475000 296.10181 -202.26042 -8657.5804 -11368.116 -0.29829888 1.6493239 0.45
|
||||
480000 300.24953 249.20038 -8688.6705 -11437.175 0.4372485 0.48025452 0.45
|
||||
485000 296.41241 -73.46156 -8558.9344 -11272.314 -0.15947631 1.3067001 0.45
|
||||
490000 302.51379 -654.60188 -8571.28 -11340.512 0.36608136 0.54114742 0.45
|
||||
495000 300.50497 -127.55361 -8724.7069 -11475.55 0.029571506 0.95160701 0.45
|
||||
500000 303.60879 183.79306 -8568.3539 -11347.609 0.050255275 0.91915729 0.45
|
||||
505000 303.19721 -181.45226 -8614.403 -11389.891 0.32941264 0.57547725 0.45
|
||||
510000 296.74554 -22.844257 -8659.5977 -11376.026 0.017555998 0.97098101 0.45
|
||||
515000 304.94785 184.89151 -8657.5502 -11449.063 0.36892431 0.53857296 0.45
|
||||
520000 297.55996 -618.66865 -8737.5039 -11461.388 0.0057510291 0.99039963 0.45
|
||||
525000 301.79028 298.59479 -8629.0889 -11391.698 0.34316268 0.56235619 0.45
|
||||
530000 309.73127 127.43322 -8551.5448 -11386.846 0.76278829 0.27817682 0.45
|
||||
535000 296.10155 231.50902 -8700.9183 -11411.452 0.44398766 0.47485618 0.45
|
||||
540000 299.71005 -102.1096 -8655.905 -11399.471 0.76085637 0.27907974 0.45
|
||||
545000 300.14982 -206.19313 -8714.8486 -11462.44 0.22627441 0.68416793 0.45
|
||||
550000 294.79885 -643.7432 -8605.2486 -11303.857 -0.057557071 1.1013603 0.45
|
||||
555000 294.17638 -19.930168 -8726.0381 -11418.949 0.40954478 0.50309869 0.45
|
||||
560000 297.03199 -369.45853 -8470.404 -11189.455 -0.6540448 2.9954437 0.45
|
||||
565000 291.48707 -349.3956 -8714.1576 -11382.45 0.16175418 0.76236802 0.45
|
||||
570000 310.66906 -63.356318 -8637.4971 -11481.383 0.025729917 0.95775884 0.45
|
||||
575000 300.62447 -741.10788 -8620.5725 -11372.509 0.16003059 0.76457532 0.45
|
||||
580000 303.7169 -69.625554 -8649.3106 -11429.556 0.13011667 0.80391862 0.45
|
||||
585000 296.8583 22.033506 -8781.0388 -11498.5 0.05826221 0.9068948 0.45
|
||||
590000 295.12104 251.36802 -8661.2354 -11362.793 0.0042041083 0.99297285 0.45
|
||||
595000 291.91551 264.01646 -8784.286 -11456.5 -0.3176707 1.7037977 0.45
|
||||
600000 299.51751 -425.6209 -8680.4016 -11422.205 0.063170047 0.89945954 0.45
|
||||
605000 296.04489 -702.56187 -8648.8336 -11358.848 0.44150563 0.47683729 0.45
|
||||
610000 293.08062 387.21018 -8636.9022 -11319.782 0.430424 0.48578377 0.45
|
||||
615000 300.1062 -406.07366 -8651.5383 -11398.731 0.16393273 0.75958719 0.45
|
||||
620000 304.45492 -717.77411 -8466.6335 -11253.634 0.14754207 0.78076073 0.45
|
||||
625000 300.25467 394.44177 -8545.7468 -11294.298 -0.098814662 1.1802796 0.45
|
||||
630000 301.25687 315.97468 -8555.4413 -11313.167 -0.30209606 1.6598626 0.45
|
||||
635000 296.62552 -313.8236 -8661.4264 -11376.756 0.82351209 0.25123759 0.45
|
||||
640000 300.49659 458.65236 -8648.2545 -11399.021 -0.2575 1.5402266 0.45
|
||||
645000 299.08458 -40.905776 -8589.4621 -11327.303 0.07180479 0.88652576 0.45
|
||||
650000 299.78807 286.71966 -8663.8862 -11408.166 -0.10586303 1.1943167 0.45
|
||||
655000 300.2646 175.76273 -8685.9588 -11434.601 -0.4131303 1.9996722 0.45
|
||||
660000 296.01304 69.482635 -8722.0849 -11431.808 0.65234529 0.33479341 0.45
|
||||
665000 307.08179 -192.78965 -8554.9636 -11366.011 0.37228163 0.53554848 0.45
|
||||
670000 298.81489 46.512873 -8651.3386 -11386.71 -0.34071772 1.7709545 0.45
|
||||
675000 298.09695 -320.42123 -8744.4868 -11473.286 0.21787637 0.6938739 0.45
|
||||
680000 291.73582 -346.08326 -8809.3602 -11479.93 0.35114775 0.55487414 0.45
|
||||
685000 299.8583 -53.573198 -8742.9543 -11487.877 -0.032502983 1.056034 0.45
|
||||
690000 299.56857 -129.53024 -8600.751 -11343.022 0.11604588 0.82311864 0.45
|
||||
695000 287.63895 77.534045 -8889.5114 -11522.578 0.16150699 0.76268419 0.45
|
||||
700000 294.71917 -187.77101 -8824.4116 -11522.291 0.33093056 0.57401387 0.45
|
||||
705000 301.78978 -269.32554 -8594.7858 -11357.39 -0.098783804 1.1802185 0.45
|
||||
710000 305.58313 -214.43945 -8518.1241 -11315.453 -0.03149037 1.0542418 0.45
|
||||
715000 306.30354 -121.41526 -8617.5112 -11421.435 0.10640694 0.83653526 0.45
|
||||
720000 304.94559 91.460869 -8587.9126 -11379.405 -0.4078455 1.982024 0.45
|
||||
725000 295.36839 -505.69412 -8724.4826 -11428.305 0.71800645 0.29987744 0.45
|
||||
730000 298.79826 -9.9970862 -8716.023 -11451.242 0.59730469 0.36717499 0.45
|
||||
735000 300.95964 286.58072 -8641.7744 -11396.779 0.23910326 0.66960256 0.45
|
||||
740000 298.32007 -198.81619 -8685.7142 -11416.556 0.16840724 0.75390743 0.45
|
||||
745000 296.06461 157.22083 -8605.3591 -11315.555 0.3149783 0.58958082 0.45
|
||||
750000 297.27956 -277.36948 -8673.9548 -11395.272 0.058965185 0.90582605 0.45
|
||||
755000 296.79569 203.4854 -8671.4835 -11388.371 0.097863507 0.84860972 0.45
|
||||
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||||
1660000 305.65546 522.2866 -8702.2765 -11500.267 -0.093142651 1.1691034 0.45
|
||||
1665000 296.92311 -22.202256 -8648.9808 -11367.035 0.21695848 0.69494306 0.45
|
||||
1670000 293.71721 -216.98365 -8726.8596 -11415.567 0.062675713 0.90020567 0.45
|
||||
1675000 302.06866 69.039243 -8665.567 -11430.724 0.0012561112 0.99789522 0.45
|
||||
1680000 292.51483 -764.83087 -8759.3069 -11437.007 0.0022259364 0.99627318 0.45
|
||||
1685000 300.70748 -239.98915 -8682.5295 -11435.226 0.21854685 0.69309397 0.45
|
||||
1690000 303.31754 36.443117 -8554.7105 -11331.3 0.18904617 0.72825402 0.45
|
||||
1695000 300.96783 -365.40002 -8606.9996 -11362.08 0.21317894 0.69936284 0.45
|
||||
1700000 301.78038 -460.56572 -8703.0763 -11465.594 -0.074311844 1.1327524 0.45
|
||||
1705000 299.08328 224.74817 -8680.6969 -11418.526 0.14954235 0.77814547 0.45
|
||||
1710000 303.24064 298.73582 -8637.4191 -11413.304 -0.11628651 1.2153822 0.45
|
||||
1715000 299.1988 535.86954 -8722.2318 -11461.118 0.51289768 0.42302132 0.45
|
||||
1720000 300.88716 -11.654893 -8624.0905 -11378.432 0.62281958 0.35179195 0.45
|
||||
1725000 306.59581 -286.69581 -8574.7957 -11381.394 0.3964476 0.51427364 0.45
|
||||
1730000 302.58784 590.55523 -8670.9964 -11440.906 -0.28655798 1.6171597 0.45
|
||||
1735000 295.17235 -60.036989 -8631.671 -11333.699 0.72231294 0.29771902 0.45
|
||||
1740000 290.06228 -254.79282 -8715.6619 -11370.912 0.35583392 0.55052961 0.45
|
||||
1745000 306.47487 418.58552 -8590.4226 -11395.914 -0.04975774 1.0870455 0.45
|
||||
1750000 296.74674 -73.367187 -8727.0183 -11443.458 -0.27066543 1.5746188 0.45
|
||||
1755000 299.03541 551.77198 -8712.6905 -11450.081 -0.35865936 1.8250619 0.45
|
||||
1760000 288.98684 -380.17132 -8775.8546 -11421.26 -0.17754854 1.3469184 0.45
|
||||
1765000 300.76459 -662.80282 -8671.5414 -11424.761 0.078118597 0.87718632 0.45
|
||||
1770000 301.47287 -498.34628 -8675.582 -11435.285 0.57886218 0.37871122 0.45
|
||||
1775000 307.18565 -70.676548 -8554.9531 -11366.951 0.38766498 0.52190597 0.45
|
||||
1780000 302.58164 -329.49774 -8638.9781 -11408.831 0.53149245 0.41003059 0.45
|
||||
1785000 307.4086 294.59322 -8586.4793 -11400.518 0.34963097 0.55628768 0.45
|
||||
1790000 295.81491 -366.57154 -8756.8143 -11464.724 0.61653346 0.35552098 0.45
|
||||
1795000 296.46712 18.92361 -8640.9928 -11354.873 0.21158778 0.70123194 0.45
|
||||
1800000 290.9851 -805.74081 -8636.1049 -11299.802 0.36361854 0.54338759 0.45
|
||||
1805000 291.6313 -58.207903 -8707.0768 -11376.689 0.2659117 0.6401586 0.45
|
||||
1810000 299.14324 327.45026 -8613.3385 -11351.716 0.58264334 0.37631684 0.45
|
||||
1815000 295.3441 37.594139 -8747.5577 -11451.158 0.10312363 0.84115511 0.45
|
||||
1820000 297.19616 596.87014 -8601.4315 -11321.985 0.11690702 0.82193051 0.45
|
||||
1825000 305.23709 -229.45704 -8586.9328 -11381.094 -0.070794327 1.1260885 0.45
|
||||
1830000 308.48265 -50.225625 -8595.8609 -11419.732 0.28577292 0.61918297 0.45
|
||||
1835000 301.67215 30.600339 -8561.9509 -11323.478 0.67464985 0.32249901 0.45
|
||||
1840000 297.44022 -46.915689 -8760.5329 -11483.321 0.20308399 0.71130615 0.45
|
||||
1845000 294.56439 121.7989 -8819.2766 -11515.739 -0.13859762 1.2617292 0.45
|
||||
1850000 303.92475 63.511256 -8655.7131 -11437.861 -0.064617898 1.1144821 0.45
|
||||
1855000 302.36347 -403.0262 -8663.1963 -11431.052 0.63223295 0.34628081 0.45
|
||||
1860000 292.88227 124.53259 -8622.4528 -11303.517 0.21782313 0.69393587 0.45
|
||||
1865000 299.49141 1.3922328 -8592.8243 -11334.389 0.024359522 0.95996296 0.45
|
||||
1870000 295.36403 -1.848842 -8534.7607 -11238.543 0.53331666 0.40877784 0.45
|
||||
1875000 299.5254 -303.35635 -8642.4199 -11384.296 0.12049946 0.8169925 0.45
|
||||
1880000 302.15027 -233.4192 -8607.1984 -11373.102 0.42967343 0.48639576 0.45
|
||||
1885000 293.78387 -312.31798 -8576.6303 -11265.948 0.62050206 0.35316217 0.45
|
||||
1890000 296.33987 227.42925 -8675.0988 -11387.814 -0.2387251 1.4924762 0.45
|
||||
1895000 296.4116 -297.41585 -8695.6693 -11409.041 0.1899345 0.72716967 0.45
|
||||
1900000 305.04631 -744.8928 -8495.6073 -11288.022 -0.092917858 1.1686627 0.45
|
||||
1905000 299.13767 -233.05542 -8771.8955 -11510.222 -0.053515786 1.0939196 0.45
|
||||
1910000 301.18529 391.32364 -8594.238 -11351.309 0.17761387 0.74235415 0.45
|
||||
1915000 304.53139 -205.26743 -8615.1863 -11402.887 -0.65441918 2.9973254 0.45
|
||||
1920000 304.46794 75.506851 -8696.0461 -11483.166 0.28757039 0.6173189 0.45
|
||||
1925000 295.83229 -40.226799 -8677.0683 -11385.137 0.34338584 0.56214572 0.45
|
||||
1930000 298.91694 72.305481 -8662.7622 -11399.068 -0.45255095 2.1363683 0.45
|
||||
1935000 297.28693 -277.78411 -8678.223 -11399.608 0.32165864 0.58301111 0.45
|
||||
1940000 295.22194 -153.48885 -8737.0529 -11439.534 0.47753767 0.4488709 0.45
|
||||
1945000 298.41366 0.98105216 -8615.733 -11347.432 0.061208942 0.90242323 0.45
|
||||
1950000 298.47932 -461.39566 -8587.8993 -11320.199 0.41883297 0.49532116 0.45
|
||||
1955000 293.30456 -530.72887 -8712.242 -11397.172 -0.052983042 1.0929425 0.45
|
||||
1960000 307.27812 -609.68084 -8563.1295 -11375.974 0.10863685 0.83341209 0.45
|
||||
1965000 309.21876 -661.65884 -8619.5376 -11450.147 -0.00074060514 1.0012431 0.45
|
||||
1970000 294.16474 130.9219 -8662.5966 -11355.4 -0.048761848 1.0852311 0.45
|
||||
1975000 293.87023 -652.42226 -8587.2681 -11277.376 -0.42701916 2.0468057 0.45
|
||||
1980000 302.66906 -396.94893 -8576.3291 -11346.982 0.55938449 0.39128874 0.45
|
||||
1985000 304.00863 167.22102 -8525.9503 -11308.866 -0.12417188 1.2315647 0.45
|
||||
1990000 299.53376 -234.11494 -8528.8821 -11270.834 0.58392743 0.37550715 0.45
|
||||
1995000 296.20959 -99.022727 -8599.3854 -11310.908 0.10920765 0.83261451 0.45
|
||||
2000000 307.40367 -179.44965 -8545.6064 -11359.6 0.485016 0.44327537 0.45
|
||||
Loop time of 4787.7 on 1 procs for 2000000 steps with 3072 atoms
|
||||
|
||||
Performance: 36.092 ns/day, 0.665 hours/ns, 417.737 timesteps/s
|
||||
95.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1015.1 | 1015.1 | 1015.1 | 0.0 | 21.20
|
||||
Bond | 121.19 | 121.19 | 121.19 | 0.0 | 2.53
|
||||
Kspace | 3455.1 | 3455.1 | 3455.1 | 0.0 | 72.17
|
||||
Neigh | 8.7475 | 8.7475 | 8.7475 | 0.0 | 0.18
|
||||
Comm | 58.679 | 58.679 | 58.679 | 0.0 | 1.23
|
||||
Output | 0.60209 | 0.60209 | 0.60209 | 0.0 | 0.01
|
||||
Modify | 81.328 | 81.328 | 81.328 | 0.0 | 1.70
|
||||
Other | | 46.88 | | | 0.98
|
||||
|
||||
Nlocal: 3072 ave 3072 max 3072 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8395 ave 8395 max 8395 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
|
||||
|
||||
Total # of neighbors = -1
|
||||
Ave neighs/atom = -0.00032552083
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 93794
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 1:31:34
|
||||
22
examples/PACKAGES/fep/ta/spce.fep.ta
Normal file
22
examples/PACKAGES/fep/ta/spce.fep.ta
Normal file
@ -0,0 +1,22 @@
|
||||
# Time-averaged data for fix FEP
|
||||
# TimeStep c_TA[1] c_TA[2] c_TA[3] v_gamma_v
|
||||
100000 0.168677 0.863546 0.45 65.7437
|
||||
200000 0.169722 0.861354 0.45 66.6859
|
||||
300000 0.165507 0.868407 0.45 63.1899
|
||||
400000 0.162311 0.875704 0.45 60.7859
|
||||
500000 0.165468 0.872729 0.45 63.2053
|
||||
600000 0.165267 0.873825 0.45 63.1828
|
||||
700000 0.167824 0.869356 0.45 65.1722
|
||||
800000 0.170332 0.866538 0.45 67.0749
|
||||
900000 0.164396 0.875043 0.45 62.4639
|
||||
1000000 0.164738 0.87663 0.45 62.5659
|
||||
1100000 0.168395 0.870496 0.45 65.415
|
||||
1200000 0.170147 0.867104 0.45 66.7132
|
||||
1300000 0.170509 0.866709 0.45 66.9833
|
||||
1400000 0.171152 0.865294 0.45 67.5598
|
||||
1500000 0.172363 0.863433 0.45 68.547
|
||||
1600000 0.171538 0.864062 0.45 67.8359
|
||||
1700000 0.171662 0.864029 0.45 67.9145
|
||||
1800000 0.170202 0.866069 0.45 66.7697
|
||||
1900000 0.171403 0.864162 0.45 67.6313
|
||||
2000000 0.170962 0.864753 0.45 67.2314
|
||||
1
examples/PACKAGES/tmd/data.peptide
Symbolic link
1
examples/PACKAGES/tmd/data.peptide
Symbolic link
@ -0,0 +1 @@
|
||||
../../peptide/data.peptide
|
||||
45
examples/PACKAGES/tmd/in.tmd
Normal file
45
examples/PACKAGES/tmd/in.tmd
Normal file
@ -0,0 +1,45 @@
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
thermo_style multi
|
||||
thermo 50
|
||||
|
||||
group tmd id 1:6
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
fix 0 tmd tmd 0.1 tmd.target 100 tmd.log
|
||||
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
|
||||
group peptide type <= 12
|
||||
|
||||
#dump 1 peptide atom 10 dump.peptide
|
||||
|
||||
#dump 2 peptide image 25 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30 bond atom 0.5
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 peptide movie 25 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30 bond atom 0.5
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
#compute bnd all property/local btype batom1 batom2
|
||||
#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
|
||||
|
||||
run 300
|
||||
|
||||
210
examples/PACKAGES/tmd/log.31Mar22.tmd.g++.1
Normal file
210
examples/PACKAGES/tmd/log.31Mar22.tmd.g++.1
Normal file
@ -0,0 +1,210 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.011 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
thermo_style multi
|
||||
thermo 50
|
||||
|
||||
group tmd id 1:6
|
||||
6 atoms in group tmd
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
fix 0 tmd tmd 0.1 tmd.target 100 tmd.log
|
||||
Reading TMD target file tmd.target ...
|
||||
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
|
||||
#dump 1 peptide atom 10 dump.peptide
|
||||
|
||||
#dump 2 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
#compute bnd all property/local btype batom1 batom2
|
||||
#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
|
||||
|
||||
run 300
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 9
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.78 | 19.78 | 19.78 Mbytes
|
||||
------------ Step 0 ----- CPU = 0 (sec) -------------
|
||||
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
|
||||
PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
|
||||
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
|
||||
E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112
|
||||
------------ Step 50 ----- CPU = 0.6301453 (sec) -------------
|
||||
TotEng = -5001.6799 KinEng = 1319.3760 Temp = 327.9501
|
||||
PotEng = -6321.0559 E_bond = 17.4415 E_angle = 42.4509
|
||||
E_dihed = 25.0839 E_impro = 4.4025 E_vdwl = 725.7619
|
||||
E_coul = 26771.0015 E_long = -33907.1980 Press = -1.1409
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11096 0.000146572 9
|
||||
Bond: 6 0.996997 7.55911e-06 6
|
||||
Bond: 8 1.08 8.22449e-06 9
|
||||
Bond: 10 1.11099 3.00424e-05 8
|
||||
Bond: 12 1.08 6.53505e-06 9
|
||||
Bond: 14 0.95999 0 1
|
||||
Bond: 18 0.957195 4.74892e-05 1280
|
||||
Angle: 31 104.52 0.00446577 640
|
||||
------------ Step 100 ----- CPU = 1.251267 (sec) -------------
|
||||
TotEng = -5114.3221 KinEng = 1168.2996 Temp = 290.3979
|
||||
PotEng = -6282.6217 E_bond = 45.5470 E_angle = 87.5725
|
||||
E_dihed = 26.1332 E_impro = 1.8662 E_vdwl = 791.5291
|
||||
E_coul = 26670.6791 E_long = -33905.9488 Press = -29.3446
|
||||
------------ Step 150 ----- CPU = 1.869158 (sec) -------------
|
||||
TotEng = -5302.3058 KinEng = 1211.4300 Temp = 301.1186
|
||||
PotEng = -6513.7358 E_bond = 51.4069 E_angle = 82.5752
|
||||
E_dihed = 31.1298 E_impro = 4.3390 E_vdwl = 764.0550
|
||||
E_coul = 26461.8974 E_long = -33909.1392 Press = -1204.2714
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 4 1.11094 0.000292869 9
|
||||
Bond: 6 0.996989 3.13206e-05 6
|
||||
Bond: 8 1.07999 4.4723e-05 9
|
||||
Bond: 10 1.111 1.08895e-05 8
|
||||
Bond: 12 1.07999 1.42694e-05 9
|
||||
Bond: 14 0.959976 0 1
|
||||
Bond: 18 0.957195 8.58256e-05 1280
|
||||
Angle: 31 104.52 0.00597861 640
|
||||
------------ Step 200 ----- CPU = 2.48933 (sec) -------------
|
||||
TotEng = -5785.4658 KinEng = 1048.7220 Temp = 260.6751
|
||||
PotEng = -6834.1879 E_bond = 21.7304 E_angle = 48.3249
|
||||
E_dihed = 20.5973 E_impro = 2.0603 E_vdwl = 818.9175
|
||||
E_coul = 26165.9672 E_long = -33911.7854 Press = -1228.5741
|
||||
------------ Step 250 ----- CPU = 3.119859 (sec) -------------
|
||||
TotEng = -6108.4578 KinEng = 828.5247 Temp = 205.9419
|
||||
PotEng = -6936.9825 E_bond = 26.5971 E_angle = 68.2771
|
||||
E_dihed = 36.1232 E_impro = 5.2092 E_vdwl = 884.1147
|
||||
E_coul = 25955.7300 E_long = -33913.0338 Press = -1365.4744
|
||||
SHAKE stats (type/ave/delta/count) on step 300
|
||||
Bond: 4 1.11174 0.0109853 9
|
||||
Bond: 6 0.996999 1.94772e-06 6
|
||||
Bond: 8 1.08 3.97091e-06 9
|
||||
Bond: 10 1.111 2.52635e-06 8
|
||||
Bond: 12 1.08 1.24444e-06 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.9572 1.22873e-05 1280
|
||||
Angle: 31 104.52 0.00134864 640
|
||||
------------ Step 300 ----- CPU = 3.74524 (sec) -------------
|
||||
TotEng = -5492.5012 KinEng = 1315.6902 Temp = 327.0339
|
||||
PotEng = -6808.1914 E_bond = 88.7967 E_angle = 104.4231
|
||||
E_dihed = 28.2383 E_impro = 43.5062 E_vdwl = 992.5311
|
||||
E_coul = 25849.1502 E_long = -33914.8370 Press = 268.8004
|
||||
Loop time of 3.74527 on 1 procs for 300 steps with 2004 atoms
|
||||
|
||||
Performance: 13.841 ns/day, 1.734 hours/ns, 80.101 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.9399 | 2.9399 | 2.9399 | 0.0 | 78.50
|
||||
Bond | 0.0069522 | 0.0069522 | 0.0069522 | 0.0 | 0.19
|
||||
Kspace | 0.25203 | 0.25203 | 0.25203 | 0.0 | 6.73
|
||||
Neigh | 0.48624 | 0.48624 | 0.48624 | 0.0 | 12.98
|
||||
Comm | 0.016948 | 0.016948 | 0.016948 | 0.0 | 0.45
|
||||
Output | 0.00023689 | 0.00023689 | 0.00023689 | 0.0 | 0.01
|
||||
Modify | 0.039476 | 0.039476 | 0.039476 | 0.0 | 1.05
|
||||
Other | | 0.003502 | | | 0.09
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11242 ave 11242 max 11242 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 710782 ave 710782 max 710782 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 710782
|
||||
Ave neighs/atom = 354.68164
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 32
|
||||
Dangerous builds = 1
|
||||
|
||||
Total wall time: 0:00:03
|
||||
210
examples/PACKAGES/tmd/log.31Mar22.tmd.g++.4
Normal file
210
examples/PACKAGES/tmd/log.31Mar22.tmd.g++.4
Normal file
@ -0,0 +1,210 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.017 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
thermo_style multi
|
||||
thermo 50
|
||||
|
||||
group tmd id 1:6
|
||||
6 atoms in group tmd
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
fix 0 tmd tmd 0.1 tmd.target 100 tmd.log
|
||||
Reading TMD target file tmd.target ...
|
||||
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
|
||||
#dump 1 peptide atom 10 dump.peptide
|
||||
|
||||
#dump 2 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
#compute bnd all property/local btype batom1 batom2
|
||||
#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
|
||||
|
||||
run 300
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 6
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.78 | 16.97 | 17.16 Mbytes
|
||||
------------ Step 0 ----- CPU = 0 (sec) -------------
|
||||
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
|
||||
PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
|
||||
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
|
||||
E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112
|
||||
------------ Step 50 ----- CPU = 0.1916178 (sec) -------------
|
||||
TotEng = -5001.6799 KinEng = 1319.3760 Temp = 327.9501
|
||||
PotEng = -6321.0559 E_bond = 17.4415 E_angle = 42.4509
|
||||
E_dihed = 25.0839 E_impro = 4.4025 E_vdwl = 725.7619
|
||||
E_coul = 26771.0015 E_long = -33907.1980 Press = -1.1409
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11096 0.000146572 9
|
||||
Bond: 6 0.996997 7.55911e-06 6
|
||||
Bond: 8 1.08 8.22449e-06 6
|
||||
Bond: 10 1.11099 3.00424e-05 8
|
||||
Bond: 12 1.08 6.53505e-06 9
|
||||
Bond: 14 0.95999 0 1
|
||||
Bond: 18 0.957195 4.74892e-05 1280
|
||||
Angle: 31 104.52 0.00446577 640
|
||||
------------ Step 100 ----- CPU = 0.3672111 (sec) -------------
|
||||
TotEng = -5114.3221 KinEng = 1168.2996 Temp = 290.3979
|
||||
PotEng = -6282.6217 E_bond = 45.5470 E_angle = 87.5725
|
||||
E_dihed = 26.1332 E_impro = 1.8662 E_vdwl = 791.5291
|
||||
E_coul = 26670.6792 E_long = -33905.9488 Press = -29.3446
|
||||
------------ Step 150 ----- CPU = 0.5543252 (sec) -------------
|
||||
TotEng = -5302.3058 KinEng = 1211.4300 Temp = 301.1186
|
||||
PotEng = -6513.7358 E_bond = 51.4069 E_angle = 82.5752
|
||||
E_dihed = 31.1298 E_impro = 4.3390 E_vdwl = 764.0550
|
||||
E_coul = 26461.8975 E_long = -33909.1392 Press = -1204.2714
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 4 1.11094 0.000292869 9
|
||||
Bond: 6 0.996989 3.13206e-05 6
|
||||
Bond: 8 1.07999 4.4723e-05 6
|
||||
Bond: 10 1.111 1.08895e-05 8
|
||||
Bond: 12 1.07999 1.42694e-05 9
|
||||
Bond: 14 0.959976 0 1
|
||||
Bond: 18 0.957195 8.58257e-05 1280
|
||||
Angle: 31 104.52 0.00597861 640
|
||||
------------ Step 200 ----- CPU = 0.7449468 (sec) -------------
|
||||
TotEng = -5785.4658 KinEng = 1048.7220 Temp = 260.6751
|
||||
PotEng = -6834.1878 E_bond = 21.7304 E_angle = 48.3249
|
||||
E_dihed = 20.5973 E_impro = 2.0603 E_vdwl = 818.9173
|
||||
E_coul = 26165.9673 E_long = -33911.7854 Press = -1228.5754
|
||||
------------ Step 250 ----- CPU = 0.9417257 (sec) -------------
|
||||
TotEng = -6108.4577 KinEng = 828.5246 Temp = 205.9418
|
||||
PotEng = -6936.9823 E_bond = 26.5971 E_angle = 68.2771
|
||||
E_dihed = 36.1232 E_impro = 5.2092 E_vdwl = 884.1146
|
||||
E_coul = 25955.7302 E_long = -33913.0338 Press = -1365.4736
|
||||
SHAKE stats (type/ave/delta/count) on step 300
|
||||
Bond: 4 1.11174 0.0109854 9
|
||||
Bond: 6 0.996999 1.94775e-06 6
|
||||
Bond: 8 1.08 3.97089e-06 6
|
||||
Bond: 10 1.111 2.52634e-06 8
|
||||
Bond: 12 1.08 1.24445e-06 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.9572 1.22873e-05 1280
|
||||
Angle: 31 104.52 0.0013486 640
|
||||
------------ Step 300 ----- CPU = 1.137003 (sec) -------------
|
||||
TotEng = -5492.5016 KinEng = 1315.6899 Temp = 327.0339
|
||||
PotEng = -6808.1915 E_bond = 88.7968 E_angle = 104.4228
|
||||
E_dihed = 28.2384 E_impro = 43.5061 E_vdwl = 992.5315
|
||||
E_coul = 25849.1499 E_long = -33914.8370 Press = 268.8010
|
||||
Loop time of 1.13706 on 4 procs for 300 steps with 2004 atoms
|
||||
|
||||
Performance: 45.591 ns/day, 0.526 hours/ns, 263.838 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.75407 | 0.80373 | 0.84144 | 3.6 | 70.68
|
||||
Bond | 0.0010088 | 0.0024668 | 0.0045274 | 2.6 | 0.22
|
||||
Kspace | 0.095468 | 0.13434 | 0.18276 | 8.9 | 11.81
|
||||
Neigh | 0.13509 | 0.13515 | 0.13522 | 0.0 | 11.89
|
||||
Comm | 0.024217 | 0.025086 | 0.026404 | 0.5 | 2.21
|
||||
Output | 0.00020952 | 0.00023591 | 0.00031389 | 0.0 | 0.02
|
||||
Modify | 0.033319 | 0.033374 | 0.033436 | 0.0 | 2.94
|
||||
Other | | 0.00268 | | | 0.24
|
||||
|
||||
Nlocal: 501 ave 530 max 459 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Nghost: 6562.75 ave 6755 max 6370 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 177696 ave 195050 max 158403 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 710782
|
||||
Ave neighs/atom = 354.68164
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 32
|
||||
Dangerous builds = 1
|
||||
|
||||
Total wall time: 0:00:01
|
||||
4
examples/PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.1
Normal file
4
examples/PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.1
Normal file
@ -0,0 +1,4 @@
|
||||
# Step rho_target rho_old gamma_back gamma_forward lambda work_lambda work_analytical
|
||||
100 11.580338717125848 11.637740410711476 0.00432656530431019 -0.0006058453921097923 1295.0393774041895 -7808.460018545273 562.4687334224966
|
||||
200 5.840169358562925 5.897571052148553 0.009256742629063092 -0.0004765379201060169 1404.114149312145 -15441.509720360129 1352.9255849946983
|
||||
300 0.10000000000000142 0.15740169358562994 -0.030035833473071705 -0.5643261296323345 -121.59623659080042 -22929.738462520727 2299.6676396746325
|
||||
4
examples/PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.4
Normal file
4
examples/PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.4
Normal file
@ -0,0 +1,4 @@
|
||||
# Step rho_target rho_old gamma_back gamma_forward lambda work_lambda work_analytical
|
||||
100 11.580338717125848 11.637740410711476 0.004326565303381905 -0.0006058453930379918 1295.0393771263327 -7808.46001855425 562.4687334073235
|
||||
200 5.840169358562925 5.897571052148553 0.009256742652188668 -0.0004765378969710561 1404.114152819961 -15441.50972264099 1352.9255825827688
|
||||
300 0.10000000000000142 0.15740169358562994 -0.03003651537895091 -0.5643268572640833 -121.59899719968097 -22929.73877163682 2299.6674130478946
|
||||
13
examples/PACKAGES/tmd/tmd.target
Normal file
13
examples/PACKAGES/tmd/tmd.target
Normal file
@ -0,0 +1,13 @@
|
||||
# pull a few peptide atoms across the box
|
||||
36.840194 64.211560 xlo xhi
|
||||
41.013691 68.385058 ylo yhi
|
||||
29.768095 57.139462 zlo zhi # comment
|
||||
# comment
|
||||
1 53.99993 48.52678 46.78550 0 0 0
|
||||
2 55.10395 48.23499 45.86693 0 0 0
|
||||
3 53.81519 49.54928 47.43995 0 0 0
|
||||
4 55.71714 47.34797 46.13434 0 0 0
|
||||
5 55.72261 49.13657 45.67007 0 0 0
|
||||
6 54.66624 48.09539 44.85538 0 0 0
|
||||
7 53.28193 47.47427 46.91953 0 0 0
|
||||
8 52.07157 47.45486 47.62418 0 0 0
|
||||
@ -83,6 +83,7 @@ indent: spherical indenter into a 2d solid
|
||||
kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
|
||||
latte: use of LATTE density-functional tight-binding quantum code
|
||||
mc: MC package models: GCMC, Widom, fix mol/swap
|
||||
mdi: use of the MDI package and MolSSI MDI code coupling library
|
||||
meam: MEAM test for SiC and shear (same as shear examples)
|
||||
melt: rapid melt of 3d LJ system
|
||||
micelle: self-assembly of small lipid-like molecules into 2d bilayers
|
||||
@ -117,6 +118,7 @@ ttm: two-temeperature model examples
|
||||
vashishta: models using the Vashishta potential
|
||||
voronoi: Voronoi tesselation via compute voronoi/atom command
|
||||
wall: use of reflective walls with different stochastic models
|
||||
yaml: demonstrates use of yaml thermo and dump styles
|
||||
|
||||
Here is how you might run and visualize one of the sample problems:
|
||||
|
||||
|
||||
99
examples/kim/plugin/CMakeLists.txt
Normal file
99
examples/kim/plugin/CMakeLists.txt
Normal file
@ -0,0 +1,99 @@
|
||||
##########################################
|
||||
# CMake build system for plugin examples.
|
||||
# The is meant to be used as a template for plugins that are
|
||||
# distributed independent from the LAMMPS package.
|
||||
##########################################
|
||||
|
||||
cmake_minimum_required(VERSION 3.10)
|
||||
|
||||
# enforce out-of-source build
|
||||
if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
|
||||
message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. "
|
||||
"Please remove CMakeCache.txt and CMakeFiles first.")
|
||||
endif()
|
||||
|
||||
project(kimplugin VERSION 1.0 LANGUAGES CXX)
|
||||
|
||||
set(LAMMPS_SOURCE_DIR "" CACHE PATH "Location of LAMMPS sources folder")
|
||||
if(NOT LAMMPS_SOURCE_DIR)
|
||||
message(FATAL_ERROR "Must set LAMMPS_SOURCE_DIR")
|
||||
endif()
|
||||
|
||||
# by default, install into $HOME/.local (not /usr/local),
|
||||
# so that no root access (and sudo) is needed
|
||||
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
|
||||
set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
|
||||
endif()
|
||||
|
||||
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
|
||||
# and prints lots of pointless warnings about "unsafe" functions
|
||||
if(MSVC)
|
||||
add_compile_options(/Zc:__cplusplus)
|
||||
add_compile_options(/wd4244)
|
||||
add_compile_options(/wd4267)
|
||||
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
|
||||
endif()
|
||||
|
||||
# C++11 is required
|
||||
set(CMAKE_CXX_STANDARD 11)
|
||||
set(CMAKE_CXX_STANDARD_REQUIRED ON)
|
||||
|
||||
# Need -restrict with Intel compilers
|
||||
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
|
||||
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
|
||||
endif()
|
||||
|
||||
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
|
||||
include(CheckIncludeFileCXX)
|
||||
include(LAMMPSInterfaceCXX)
|
||||
|
||||
##########################
|
||||
# building the plugins
|
||||
|
||||
add_library(kimplugin MODULE kimplugin.cpp ${LAMMPS_SOURCE_DIR}/KIM/pair_kim.cpp
|
||||
${LAMMPS_SOURCE_DIR}/KIM/fix_store_kim.cpp ${LAMMPS_SOURCE_DIR}/KIM/kim_command.cpp
|
||||
${LAMMPS_SOURCE_DIR}/KIM/kim_init.cpp ${LAMMPS_SOURCE_DIR}/KIM/kim_interactions.cpp
|
||||
${LAMMPS_SOURCE_DIR}/KIM/kim_param.cpp ${LAMMPS_SOURCE_DIR}/KIM/kim_property.cpp
|
||||
${LAMMPS_SOURCE_DIR}/KIM/kim_query.cpp ${LAMMPS_SOURCE_DIR}/KIM/kim_units.cpp)
|
||||
target_link_libraries(kimplugin PRIVATE lammps)
|
||||
target_include_directories(kimplugin PRIVATE ${LAMMPS_SOURCE_DIR}/KIM)
|
||||
set_target_properties(kimplugin PROPERTIES PREFIX "" SUFFIX ".so")
|
||||
|
||||
find_package(KIM-API 2.2.0 CONFIG REQUIRED)
|
||||
target_link_libraries(kimplugin PRIVATE KIM-API::kim-api)
|
||||
|
||||
##########################
|
||||
# need libcurl
|
||||
find_package(CURL)
|
||||
if(CURL_FOUND)
|
||||
if(CMAKE_VERSION VERSION_LESS 3.12)
|
||||
target_include_directories(kimplugin PRIVATE ${CURL_INCLUDE_DIRS})
|
||||
target_link_libraries(kimplugin PRIVATE ${CURL_LIBRARIES})
|
||||
else()
|
||||
target_link_libraries(kimplugin PRIVATE CURL::libcurl)
|
||||
endif()
|
||||
target_compile_definitions(kimplugin PRIVATE -DLMP_KIM_CURL)
|
||||
set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
|
||||
mark_as_advanced(LMP_DEBUG_CURL)
|
||||
if(LMP_DEBUG_CURL)
|
||||
target_compile_definitions(kimplugin PRIVATE -DLMP_DEBUG_CURL)
|
||||
endif()
|
||||
set(LMP_NO_SSL_CHECK OFF CACHE STRING "Tell libcurl to not verify the peer. If on, the connection succeeds regardless of the names in the certificate. Insecure - Use with caution!")
|
||||
mark_as_advanced(LMP_NO_SSL_CHECK)
|
||||
if(LMP_NO_SSL_CHECK)
|
||||
target_compile_definitions(kimplugin PRIVATE -DLMP_NO_SSL_CHECK)
|
||||
endif()
|
||||
endif()
|
||||
|
||||
# MacOS seems to need this
|
||||
if(CMAKE_SYSTEM_NAME STREQUAL Darwin)
|
||||
set_target_properties(kimplugin PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup")
|
||||
elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows")
|
||||
# tell CMake to export all symbols to a .dll on Windows with special case for MinGW cross-compilers
|
||||
set_target_properties(kimplugin.so PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
|
||||
if(CMAKE_CROSSCOMPILING)
|
||||
set_target_properties(kimplugin PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
|
||||
endif()
|
||||
else()
|
||||
set_target_properties(kimplugin PROPERTIES LINK_FLAGS "-rdynamic")
|
||||
endif()
|
||||
88
examples/kim/plugin/LAMMPSInterfaceCXX.cmake
Normal file
88
examples/kim/plugin/LAMMPSInterfaceCXX.cmake
Normal file
@ -0,0 +1,88 @@
|
||||
# Cmake script code to define the LAMMPS C++ interface
|
||||
# settings required for building LAMMPS plugins
|
||||
|
||||
################################################################################
|
||||
# helper function
|
||||
function(validate_option name values)
|
||||
string(TOLOWER ${${name}} needle_lower)
|
||||
string(TOUPPER ${${name}} needle_upper)
|
||||
list(FIND ${values} ${needle_lower} IDX_LOWER)
|
||||
list(FIND ${values} ${needle_upper} IDX_UPPER)
|
||||
if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0)
|
||||
list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}})
|
||||
message(FATAL_ERROR "\n########################################################################\n"
|
||||
"Invalid value '${${name}}' for option ${name}\n"
|
||||
"\n"
|
||||
"Possible values are:\n"
|
||||
"${POSSIBLE_VALUE_LIST}"
|
||||
"########################################################################")
|
||||
endif()
|
||||
endfunction(validate_option)
|
||||
|
||||
#################################################################################
|
||||
# LAMMPS C++ interface. We only need the header related parts.
|
||||
add_library(lammps INTERFACE)
|
||||
target_include_directories(lammps INTERFACE ${LAMMPS_SOURCE_DIR})
|
||||
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
|
||||
target_link_libraries(lammps INTERFACE ${CMAKE_BINARY_DIR}/../liblammps.dll.a)
|
||||
endif()
|
||||
################################################################################
|
||||
# MPI configuration
|
||||
if(NOT CMAKE_CROSSCOMPILING)
|
||||
set(MPI_CXX_SKIP_MPICXX TRUE)
|
||||
find_package(MPI QUIET)
|
||||
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
|
||||
else()
|
||||
option(BUILD_MPI "Build MPI version" OFF)
|
||||
endif()
|
||||
|
||||
if(BUILD_MPI)
|
||||
find_package(MPI REQUIRED)
|
||||
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
|
||||
if(LAMMPS_LONGLONG_TO_LONG)
|
||||
target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG)
|
||||
endif()
|
||||
target_link_libraries(lammps INTERFACE MPI::MPI_CXX)
|
||||
else()
|
||||
target_include_directories(lammps INTERFACE "${LAMMPS_SOURCE_DIR}/STUBS")
|
||||
endif()
|
||||
|
||||
set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
|
||||
set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
|
||||
set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
|
||||
validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
|
||||
string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
|
||||
target_compile_definitions(lammps INTERFACE -DLAMMPS_${LAMMPS_SIZES})
|
||||
|
||||
################################################################################
|
||||
# detect if we may enable OpenMP support by default
|
||||
set(BUILD_OMP_DEFAULT OFF)
|
||||
find_package(OpenMP QUIET)
|
||||
if(OpenMP_FOUND)
|
||||
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
|
||||
if(HAVE_OMP_H_INCLUDE)
|
||||
set(BUILD_OMP_DEFAULT ON)
|
||||
endif()
|
||||
endif()
|
||||
|
||||
option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
|
||||
|
||||
if(BUILD_OMP)
|
||||
find_package(OpenMP REQUIRED)
|
||||
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
|
||||
if(NOT HAVE_OMP_H_INCLUDE)
|
||||
message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
|
||||
endif()
|
||||
|
||||
if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
|
||||
(CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR
|
||||
((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
|
||||
((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
|
||||
# GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
|
||||
# Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
|
||||
target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=4)
|
||||
else()
|
||||
target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=3)
|
||||
endif()
|
||||
target_link_libraries(lammps INTERFACE OpenMP::OpenMP_CXX)
|
||||
endif()
|
||||
54
examples/kim/plugin/kimplugin.cpp
Normal file
54
examples/kim/plugin/kimplugin.cpp
Normal file
@ -0,0 +1,54 @@
|
||||
|
||||
#include "lammpsplugin.h"
|
||||
#include "version.h"
|
||||
|
||||
#include "pair_kim.h"
|
||||
#include "fix_store_kim.h"
|
||||
#include "kim_command.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
static Pair *pair_kim_creator(LAMMPS *lmp)
|
||||
{
|
||||
return new PairKIM(lmp);
|
||||
}
|
||||
|
||||
static Fix *fix_store_kim_creator(LAMMPS *lmp, int argc, char **argv)
|
||||
{
|
||||
return new FixStoreKIM(lmp, argc, argv);
|
||||
}
|
||||
|
||||
static Command *kim_command_creator(LAMMPS *lmp)
|
||||
{
|
||||
return new KimCommand(lmp);
|
||||
}
|
||||
|
||||
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
|
||||
{
|
||||
lammpsplugin_t plugin;
|
||||
lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
|
||||
|
||||
// register kim pair style
|
||||
plugin.version = LAMMPS_VERSION;
|
||||
plugin.style = "pair";
|
||||
plugin.name = "kim";
|
||||
plugin.info = "KIM plugin pair style v1.0";
|
||||
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
|
||||
plugin.creator.v1 = (lammpsplugin_factory1 *) &pair_kim_creator;
|
||||
plugin.handle = handle;
|
||||
(*register_plugin)(&plugin, lmp);
|
||||
|
||||
// register fix STORE/KIM only need to update changed fields
|
||||
plugin.style = "fix";
|
||||
plugin.name = "STORE/KIM";
|
||||
plugin.info = "Internal settings storage for KIM fix style v1.0";
|
||||
plugin.creator.v2 = (lammpsplugin_factory2 *) &fix_store_kim_creator;
|
||||
(*register_plugin)(&plugin, lmp);
|
||||
|
||||
// register KIM command
|
||||
plugin.style = "command";
|
||||
plugin.name = "kim";
|
||||
plugin.info = "kim command style v1.0";
|
||||
plugin.creator.v1 = (lammpsplugin_factory1 *) &kim_command_creator;
|
||||
(*register_plugin)(&plugin, lmp);
|
||||
}
|
||||
228
examples/mdi/README
Normal file
228
examples/mdi/README
Normal file
@ -0,0 +1,228 @@
|
||||
These are examples that work the MDI package in LAMMPS which uses the
|
||||
MolSSI MDI library for coupling codes together and communicating
|
||||
between them with MDI messages.
|
||||
|
||||
In MDI lingo, one code is the driver and another code is the engine.
|
||||
The 2 codes can be written in any language; C++ (LAMMPS) and Python
|
||||
are illustrated here. The 2 codes can each be stand-alone codes, in
|
||||
which case they can be run on different numbers of processors. The 2
|
||||
codes can communicate either via TCP (sockets) or via MPI. For the
|
||||
TCP case, the driver and engine need to be launched separately,
|
||||
e.g. in 2 windows on your desktop machine. For the MPI case, a single
|
||||
mpirun command launches both codes.
|
||||
|
||||
Alternatively the engine code can be a plugin library which the driver
|
||||
code loads, in which case the driver and engine run on the same
|
||||
processors.
|
||||
|
||||
LAMMPS supports operating in all these MDI modes. It can be an engine
|
||||
operating either as a stand-alone code or as a plugin. It can also be
|
||||
a driver and couple to an engine that is either a stand-alone code or
|
||||
a plugin. Examples for all these use cases are in this directory.
|
||||
The example commands below illustrate how to run all the variants.
|
||||
|
||||
To use LAMMPS as a plugin engine, you must build it as a shared library.
|
||||
Something like this, which also builds the normal LAMMPS executable
|
||||
lmp_mpi:
|
||||
|
||||
cd src
|
||||
make yes-mdi
|
||||
make mode=shlib mpi
|
||||
|
||||
To use the serial_driver.py example you will need Python 3 with Numpy
|
||||
and mpi4py available in your Python. Make sure LAMMPS and Python are
|
||||
using same the same version of MPI.
|
||||
|
||||
-------------------------------------------------
|
||||
-------------------------------------------------
|
||||
|
||||
* Example #1 = run ab inito MD (AIMD)
|
||||
Two instances of LAMMPS operate as a driver and engine
|
||||
As an engine, LAMMPS is a surrogate for a quantum code
|
||||
|
||||
Note that the 2 input scripts in.aimd.alone and in.aimd.driver
|
||||
have an option for running in NVE vs NPT mode. Comment in/out
|
||||
the appropriate line to change modes. Nothing needs to be
|
||||
changed in the in.aimd.engine or in.aimd.engine.plugin scripts.
|
||||
|
||||
---
|
||||
|
||||
Run the entire calculation with a single instance of LAMMPS by itself
|
||||
results should be identical to running this example with MDI
|
||||
|
||||
% lmp_mpi < in.aimd.alone
|
||||
|
||||
With MDI, the thermo output of the driver should match the thermo
|
||||
output of the in.aimd.alone script.
|
||||
|
||||
---
|
||||
|
||||
Run with TCP: 1 proc each
|
||||
|
||||
% lmp_mpi -mdi "-name aimd -role DRIVER -method TCP -port 8021" -log log.aimd.driver -in in.aimd.driver
|
||||
|
||||
% lmp_mpi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine -in in.aimd.engine
|
||||
|
||||
---
|
||||
|
||||
Run with TCP: 3 procs + 4 procs
|
||||
|
||||
% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method TCP -port 8021" -log log.aimd.driver -in in.aimd.driver
|
||||
|
||||
% mpirun -np 4 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine -in in.aimd.engine
|
||||
|
||||
---
|
||||
|
||||
Run with MPI: 1 proc each
|
||||
|
||||
% mpirun -np 1 lmp_mpi -mdi "-name aimd -role DRIVER -method MPI" -log log.aimd.driver -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method MPI" -log log.aimd.engine -in in.aimd.engine
|
||||
|
||||
---
|
||||
|
||||
Run with MPI: 3 procs + 4 procs
|
||||
|
||||
% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method MPI" -log log.aimd.driver -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method MPI" -log log.aimd.engine -in in.aimd.engine
|
||||
|
||||
---
|
||||
|
||||
Run in plugin mode: 1 proc
|
||||
|
||||
% lmp_mpi -mdi "-name aimd -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
|
||||
|
||||
---
|
||||
|
||||
Run in plugin mode: 3 procs
|
||||
|
||||
% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
|
||||
|
||||
-------------------------------------------------
|
||||
-------------------------------------------------
|
||||
|
||||
* Example #2 = Python driver runs a sequence of unrelated LAMMPS calculations
|
||||
Each calculation can be a single-point evaluation, MD run, or minimization
|
||||
|
||||
The sequence_driver.py code allows for optional switches in addition
|
||||
to -mdi (required) and the -plugin and -plugin_args switches which are
|
||||
used to link to an engine as a plugin library. The example run
|
||||
commands below just use the default values of the optional switches.
|
||||
The switches are also explained at the top of the file; the info is
|
||||
copied here:
|
||||
|
||||
# -n 3
|
||||
# number of calculations to perform, default = 3
|
||||
# -mode eval/run/min
|
||||
# style of calculations: single snapshot evals, dynamics, minimization
|
||||
# default = run
|
||||
# -size Nx Ny Nz
|
||||
# cubic lattice, default = 2 2 2
|
||||
# -rho 0.75 0.1
|
||||
# reduced density and random variation thereof, default = 0.75 0.1
|
||||
# -delta 0.1
|
||||
# randomly perturb atoms initially by this distance, default 0.1
|
||||
# -nsteps 100
|
||||
# number of timesteps in dynamics runs, default = 100
|
||||
# -temp 1.0
|
||||
# initial temperature in dynamics runs, default = 1.0
|
||||
# -tol 0.001
|
||||
# tolerance for minimizations, default = 0.001
|
||||
# -seed 12345
|
||||
# random number seed > 0, default = 12345
|
||||
|
||||
---
|
||||
|
||||
Run with TCP: 1 proc each
|
||||
|
||||
% python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
|
||||
|
||||
% lmp_mpi -mdi "-role ENGINE -name LAMMPS -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence
|
||||
|
||||
---
|
||||
|
||||
Run with TCP: 2 proc + 4 procs
|
||||
|
||||
% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
|
||||
|
||||
% mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence
|
||||
|
||||
---
|
||||
|
||||
Run with MPI: 1 proc each
|
||||
|
||||
% mpirun -np 1 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence
|
||||
|
||||
---
|
||||
|
||||
Run with MPI: 2 procs + 4 procs
|
||||
|
||||
% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence
|
||||
|
||||
---
|
||||
|
||||
Run in plugin mode: 1 proc
|
||||
|
||||
% python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence"
|
||||
|
||||
---
|
||||
|
||||
Run in plugin mode: 3 procs
|
||||
|
||||
% mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence"
|
||||
|
||||
-------------------------------------------------
|
||||
-------------------------------------------------
|
||||
|
||||
* Example #3 = run AIMD with Python driver code and 2 LAMMPS instances as engines
|
||||
First LAMMPS instance performs the MD timestepping
|
||||
Second LAMMPS instance is surrogate QM = computes forces
|
||||
|
||||
The aimd_driver.py code allows for an optional switch in addition to
|
||||
-mdi (required) and the -plugin and -plugin_args swiches which are
|
||||
used to link to the 2 engines as a plugin libraries. The example run
|
||||
commands below use the default values of the optional switch. The
|
||||
switch is also explained the top of the file; the info is copied
|
||||
here:
|
||||
|
||||
# -nsteps 5
|
||||
# number of timesteps in dynamics runs, default = 5
|
||||
|
||||
---
|
||||
|
||||
Run the entire calculation with a single instance of LAMMPS by itself
|
||||
results should be identical to running this example with MDI
|
||||
|
||||
% lmp_mpi < in.aimd.alone
|
||||
|
||||
With MDI, the driver prints the QM and Total energies. These should
|
||||
match the PotEng and TotEng output of the in.aimd.alone script.
|
||||
|
||||
---
|
||||
|
||||
Run with TCP: 1 proc each
|
||||
|
||||
% python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021"
|
||||
|
||||
% lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm
|
||||
|
||||
% lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm
|
||||
|
||||
---
|
||||
|
||||
Run with TCP: 2 procs + 2 procs + 3 procs
|
||||
|
||||
% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021"
|
||||
|
||||
% mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm
|
||||
|
||||
% mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm
|
||||
|
||||
---
|
||||
|
||||
Run with MPI: 1 proc each
|
||||
|
||||
% mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm
|
||||
|
||||
---
|
||||
|
||||
Run with MPI: 2 procs + 2 procs + 3 procs
|
||||
|
||||
% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm
|
||||
255
examples/mdi/aimd_driver.py
Normal file
255
examples/mdi/aimd_driver.py
Normal file
@ -0,0 +1,255 @@
|
||||
# MDI driver to perform an AIMD simulation
|
||||
# using one instance of LAMMPS as the MD timestepper
|
||||
# using second instance of LAMMPS as a QM surrogate to compute forces
|
||||
|
||||
# NOTE: this script is derived from the MDI_AIMD_Driver.cpp code
|
||||
# included in the MDI distribution
|
||||
# it alters the timestepping to match a velocity Verlet algorithm
|
||||
# forces are computed once before timestepping beings
|
||||
# both the @COORDS and @FORCES nodes are triggered in the MM code
|
||||
# as the appropriate places to extract COORDS and provide FORCES
|
||||
|
||||
# Syntax: python3 aimd_driver.py switch arg switch arg ...
|
||||
# possible switches:
|
||||
# -mdi "-role DRIVER ..."
|
||||
# required switch
|
||||
# example for stand-alone mode:
|
||||
# -mdi "-role DRIVER -name sequence -method TCP -port 8021"
|
||||
# example for plugin mode:
|
||||
# -mdi "-role DRIVER -name sequemce -method LINK
|
||||
# -plugin_path /home/sjplimp/lammps/src/"
|
||||
# -plugin name
|
||||
# name of plugin library, only when using plugin mode
|
||||
# -plugin_args arglist
|
||||
# args to add when launching plugin library, only when using plugin mode
|
||||
# enclose arglist in quotes if multiple words
|
||||
# -nsteps 5
|
||||
# number of timesteps, default = 5
|
||||
|
||||
import sys,math,random
|
||||
import mdi
|
||||
import numpy as np
|
||||
from mpi4py import MPI
|
||||
|
||||
# error message
|
||||
|
||||
def error(txt=None):
|
||||
if txt: raise Exception(txt)
|
||||
raise Exception("Syntax: python3 aimd_driver.py switch arg switch arg ...")
|
||||
|
||||
# run an AIMD simulation
|
||||
|
||||
def perform_aimd(world,mm_comm,qm_comm):
|
||||
|
||||
me = world.Get_rank()
|
||||
nprocs = world.Get_size()
|
||||
|
||||
# receive number of atoms from the MM engine
|
||||
|
||||
mdi.MDI_Send_command("<NATOMS",mm_comm)
|
||||
natoms = mdi.MDI_Recv(1,mdi.MDI_INT,mm_comm)
|
||||
natoms = world.bcast(natoms,root=0)
|
||||
|
||||
# allocate arrays for coordinates and forces
|
||||
|
||||
coords = np.zeros(3*natoms,dtype=np.float64)
|
||||
forces = np.zeros(3*natoms,dtype=np.float64)
|
||||
|
||||
# MM engine initializes a new MD simulation
|
||||
|
||||
mdi.MDI_Send_command("@INIT_MD",mm_comm)
|
||||
|
||||
# -----------------
|
||||
# compute initial forces for Verlet timestepping
|
||||
# and initial energy for output on step 0
|
||||
# -----------------
|
||||
|
||||
# MM engine proceeds to @FORCES node in setup()
|
||||
|
||||
mdi.MDI_Send_command("@FORCES",mm_comm)
|
||||
|
||||
# get coords from MM engine
|
||||
|
||||
mdi.MDI_Send_command("<COORDS",mm_comm)
|
||||
mdi.MDI_Recv(3*natoms,mdi.MDI_DOUBLE,mm_comm,buf=coords)
|
||||
world.Bcast(coords,root=0)
|
||||
|
||||
# send coords to QM engine
|
||||
|
||||
mdi.MDI_Send_command(">COORDS",qm_comm)
|
||||
mdi.MDI_Send(coords,3*natoms,mdi.MDI_DOUBLE,qm_comm)
|
||||
|
||||
# get QM potential energy
|
||||
|
||||
mdi.MDI_Send_command("<PE",qm_comm)
|
||||
qm_pe = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,qm_comm)
|
||||
qm_pe = world.bcast(qm_pe,root=0)
|
||||
|
||||
# get forces from QM engine
|
||||
|
||||
mdi.MDI_Send_command("<FORCES",qm_comm)
|
||||
mdi.MDI_Recv(3*natoms,mdi.MDI_DOUBLE,qm_comm,buf=forces)
|
||||
world.Bcast(forces,root=0)
|
||||
|
||||
# send forces to MM engine
|
||||
|
||||
mdi.MDI_Send_command(">FORCES",mm_comm)
|
||||
mdi.MDI_Send(forces,3*natoms,mdi.MDI_DOUBLE,mm_comm)
|
||||
|
||||
# get MM kinetic energy
|
||||
|
||||
mdi.MDI_Send_command("<KE",mm_comm)
|
||||
mm_ke = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,mm_comm)
|
||||
mm_ke = world.bcast(mm_ke,root=0)
|
||||
|
||||
# output by driver
|
||||
# normalize energies by atom count
|
||||
|
||||
if me == 0:
|
||||
print("Step %d: MM energy %g, QM energy %g, Total energy %g" % \
|
||||
(0,mm_ke/natoms,qm_pe/natoms,(mm_ke+qm_pe)/natoms))
|
||||
|
||||
# -----------------
|
||||
# timestepping loop
|
||||
# -----------------
|
||||
|
||||
for istep in range(nsteps):
|
||||
|
||||
# MM engine proceeds to @FORCES node
|
||||
|
||||
mdi.MDI_Send_command("@FORCES",mm_comm)
|
||||
|
||||
# get coords from MM engine
|
||||
|
||||
mdi.MDI_Send_command("<COORDS",mm_comm)
|
||||
mdi.MDI_Recv(3*natoms,mdi.MDI_DOUBLE,mm_comm,buf=coords)
|
||||
world.Bcast(coords,root=0)
|
||||
|
||||
# send coords to QM engine
|
||||
|
||||
mdi.MDI_Send_command(">COORDS",qm_comm)
|
||||
mdi.MDI_Send(coords,3*natoms,mdi.MDI_DOUBLE,qm_comm)
|
||||
|
||||
# get QM potential energy
|
||||
|
||||
mdi.MDI_Send_command("<PE",qm_comm)
|
||||
qm_pe = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,qm_comm)
|
||||
qm_pe = world.bcast(qm_pe,root=0)
|
||||
|
||||
# get forces from QM engine
|
||||
|
||||
mdi.MDI_Send_command("<FORCES",qm_comm)
|
||||
mdi.MDI_Recv(3*natoms,mdi.MDI_DOUBLE,qm_comm,buf=forces)
|
||||
world.Bcast(forces,root=0)
|
||||
|
||||
# send forces to MM engine
|
||||
|
||||
mdi.MDI_Send_command(">FORCES",mm_comm)
|
||||
mdi.MDI_Send(forces,3*natoms,mdi.MDI_DOUBLE,mm_comm)
|
||||
|
||||
# MM engine proceeds to @ENDSTEP node
|
||||
# so that KE will be for fully updated velocity
|
||||
|
||||
mdi.MDI_Send_command("@ENDSTEP",mm_comm)
|
||||
|
||||
# get MM kinetic energy
|
||||
|
||||
mdi.MDI_Send_command("<KE",mm_comm)
|
||||
mm_ke = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,mm_comm)
|
||||
mm_ke = world.bcast(mm_ke,root=0)
|
||||
|
||||
# output by driver
|
||||
# normalize energies by atom count
|
||||
|
||||
if me == 0:
|
||||
print("Step %d: MM energy %g, QM energy %g, Total energy %g" % \
|
||||
(istep+1,mm_ke/natoms,qm_pe/natoms,(mm_ke+qm_pe)/natoms))
|
||||
|
||||
# send EXIT to each engine
|
||||
|
||||
mdi.MDI_Send_command("EXIT",mm_comm)
|
||||
mdi.MDI_Send_command("EXIT",qm_comm)
|
||||
|
||||
# ------------------------
|
||||
# main program
|
||||
# ------------------------
|
||||
|
||||
args = sys.argv[1:]
|
||||
narg = len(args)
|
||||
|
||||
# defaults for command-line args
|
||||
|
||||
mdiarg = ""
|
||||
plugin = ""
|
||||
plugin_args = ""
|
||||
|
||||
nsteps = 5
|
||||
|
||||
# parse command-line args
|
||||
|
||||
iarg = 0
|
||||
while iarg < narg:
|
||||
if args[iarg] == "-mdi":
|
||||
if iarg+2 > narg: error()
|
||||
mdiarg = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-plugin":
|
||||
if iarg+2 > narg: error()
|
||||
plugin = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-plugin_args":
|
||||
if iarg+2 > narg: error()
|
||||
plugin_args = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-nsteps":
|
||||
if iarg+2 > narg: error()
|
||||
nsteps = int(args[iarg+1])
|
||||
if nsteps < 0: error()
|
||||
iarg += 2
|
||||
else: error()
|
||||
|
||||
if not mdiarg: error()
|
||||
|
||||
# LAMMPS engines are stand-alone codes
|
||||
# world = MPI communicator for just this driver
|
||||
# invoke perform_tasks() directly
|
||||
|
||||
if not plugin:
|
||||
mdi.MDI_Init(mdiarg)
|
||||
world = mdi.MDI_MPI_get_world_comm()
|
||||
|
||||
# connect to 2 engines, determine which is MM vs QM
|
||||
|
||||
mdicomm1 = mdi.MDI_Accept_Communicator()
|
||||
mdicomm2 = mdi.MDI_Accept_Communicator()
|
||||
|
||||
mdi.MDI_Send_command("<NAME",mdicomm1)
|
||||
name1 = mdi.MDI_Recv(mdi.MDI_NAME_LENGTH,mdi.MDI_CHAR,mdicomm1)
|
||||
name1 = world.bcast(name1,root=0)
|
||||
mdi.MDI_Send_command("<NAME",mdicomm2)
|
||||
name2 = mdi.MDI_Recv(mdi.MDI_NAME_LENGTH,mdi.MDI_CHAR,mdicomm2)
|
||||
name2 = world.bcast(name2,root=0)
|
||||
|
||||
if name1 == "MM" and name2 == "QM":
|
||||
mm_comm = mdicomm1
|
||||
qm_comm = mdicomm2
|
||||
elif name1 == "QM" and name2 == "MM":
|
||||
mm_comm = mdicomm2
|
||||
qm_comm = mdicomm1
|
||||
else: error("Two engines have invalid names")
|
||||
|
||||
perform_aimd(world,mm_comm,qm_comm)
|
||||
|
||||
# LAMMPS engines are plugin libraries
|
||||
# launch plugins
|
||||
# NOTE: need to run driver on 2 or more procs
|
||||
# partition driver into 2 MPI comms
|
||||
# launch one plugin on each partition
|
||||
# each with their own callback function
|
||||
|
||||
if plugin:
|
||||
error("Cannot yet run in plugin mode")
|
||||
mdi.MDI_Init(mdiarg)
|
||||
world = MPI.COMM_WORLD
|
||||
plugin_args += " -mdi \"-role ENGINE -name lammps -method LINK\""
|
||||
mdi.MDI_Launch_plugin(plugin,plugin_args,world,perform_tasks,None)
|
||||
32
examples/mdi/in.aimd.alone
Normal file
32
examples/mdi/in.aimd.alone
Normal file
@ -0,0 +1,32 @@
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
32
examples/mdi/in.aimd.driver
Normal file
32
examples/mdi/in.aimd.driver
Normal file
@ -0,0 +1,32 @@
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
34
examples/mdi/in.aimd.driver.plugin
Normal file
34
examples/mdi/in.aimd.driver.plugin
Normal file
@ -0,0 +1,34 @@
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd plugin
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" &
|
||||
infile in.aimd.engine extra "-log log.aimd.engine.plugin" &
|
||||
command "run 5"
|
||||
22
examples/mdi/in.aimd.engine
Normal file
22
examples/mdi/in.aimd.engine
Normal file
@ -0,0 +1,22 @@
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
23
examples/mdi/in.aimd.mm
Normal file
23
examples/mdi/in.aimd.mm
Normal file
@ -0,0 +1,23 @@
|
||||
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
mdi engine
|
||||
22
examples/mdi/in.aimd.qm
Normal file
22
examples/mdi/in.aimd.qm
Normal file
@ -0,0 +1,22 @@
|
||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
21
examples/mdi/in.sequence
Normal file
21
examples/mdi/in.sequence
Normal file
@ -0,0 +1,21 @@
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
90
examples/mdi/log.7Apr22.mdi.aimd.alone.g++.1
Normal file
90
examples/mdi/log.7Apr22.mdi.aimd.alone.g++.1
Normal file
@ -0,0 +1,90 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, 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) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 0.00427098 on 1 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 505739.085 tau/day, 1170.692 timesteps/s
|
||||
73.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0038665 | 0.0038665 | 0.0038665 | 0.0 | 90.53
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0001297 | 0.0001297 | 0.0001297 | 0.0 | 3.04
|
||||
Output | 0.00014902 | 0.00014902 | 0.00014902 | 0.0 | 3.49
|
||||
Modify | 6.5249e-05 | 6.5249e-05 | 6.5249e-05 | 0.0 | 1.53
|
||||
Other | | 6.054e-05 | | | 1.42
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1956 ave 1956 max 1956 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19500 ave 19500 max 19500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19500
|
||||
Ave neighs/atom = 39
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
79
examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.1
Normal file
79
examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.1
Normal file
@ -0,0 +1,79 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 0.0029525 on 1 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 731582.413 tau/day, 1693.478 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.2632e-05 | 1.2632e-05 | 1.2632e-05 | 0.0 | 0.43
|
||||
Output | 0.00010561 | 0.00010561 | 0.00010561 | 0.0 | 3.58
|
||||
Modify | 0.0028043 | 0.0028043 | 0.0028043 | 0.0 | 94.98
|
||||
Other | | 3e-05 | | | 1.02
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 166 ave 166 max 166 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
|
||||
|
||||
Total # of neighbors = -1
|
||||
Ave neighs/atom = -0.002
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
79
examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.3
Normal file
79
examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.3
Normal file
@ -0,0 +1,79 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 0.00315597 on 3 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 684416.574 tau/day, 1584.298 timesteps/s
|
||||
99.5% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.769e-05 | 3.7059e-05 | 4.7808e-05 | 0.0 | 1.17
|
||||
Output | 0.00011556 | 0.00015516 | 0.00021954 | 0.0 | 4.92
|
||||
Modify | 0.002819 | 0.0028366 | 0.0028599 | 0.0 | 89.88
|
||||
Other | | 0.0001272 | | | 4.03
|
||||
|
||||
Nlocal: 166.667 ave 200 max 150 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 55.3333 ave 92 max 32 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = -3
|
||||
Ave neighs/atom = -0.006
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
80
examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.1
Normal file
80
examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.1
Normal file
@ -0,0 +1,80 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd plugin
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 5"
|
||||
run 5
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 0.00396559 on 1 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 544685.246 tau/day, 1260.845 timesteps/s
|
||||
98.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.5936e-05 | 1.5936e-05 | 1.5936e-05 | 0.0 | 0.40
|
||||
Output | 0.00011527 | 0.00011527 | 0.00011527 | 0.0 | 2.91
|
||||
Modify | 0.0038025 | 0.0038025 | 0.0038025 | 0.0 | 95.89
|
||||
Other | | 3.184e-05 | | | 0.80
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 166 ave 166 max 166 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
|
||||
|
||||
Total # of neighbors = -1
|
||||
Ave neighs/atom = -0.002
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
80
examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.3
Normal file
80
examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.3
Normal file
@ -0,0 +1,80 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd plugin
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 5"
|
||||
run 5
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 0.00287217 on 3 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 752045.581 tau/day, 1740.846 timesteps/s
|
||||
99.1% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.6368e-05 | 3.9139e-05 | 5.1029e-05 | 0.0 | 1.36
|
||||
Output | 9.6932e-05 | 0.00012081 | 0.00016442 | 0.0 | 4.21
|
||||
Modify | 0.0026109 | 0.0026258 | 0.0026494 | 0.0 | 91.42
|
||||
Other | | 8.637e-05 | | | 3.01
|
||||
|
||||
Nlocal: 166.667 ave 200 max 150 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 55.3333 ave 92 max 32 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = -3
|
||||
Ave neighs/atom = -0.006
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
79
examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.1
Normal file
79
examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.1
Normal file
@ -0,0 +1,79 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 1.20486 on 1 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 1792.736 tau/day, 4.150 timesteps/s
|
||||
0.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 2.4487e-05 | 2.4487e-05 | 2.4487e-05 | 0.0 | 0.00
|
||||
Output | 0.00026499 | 0.00026499 | 0.00026499 | 0.0 | 0.02
|
||||
Modify | 1.2045 | 1.2045 | 1.2045 | 0.0 | 99.97
|
||||
Other | | 6.184e-05 | | | 0.01
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 166 ave 166 max 166 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
|
||||
|
||||
Total # of neighbors = -1
|
||||
Ave neighs/atom = -0.002
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:08
|
||||
79
examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.3
Normal file
79
examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.3
Normal file
@ -0,0 +1,79 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 1.19983 on 3 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 1800.259 tau/day, 4.167 timesteps/s
|
||||
66.7% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 4.604e-06 | 4.8462e-05 | 7.527e-05 | 0.0 | 0.00
|
||||
Output | 0.00015266 | 0.00020593 | 0.00031177 | 0.0 | 0.02
|
||||
Modify | 1.1993 | 1.1994 | 1.1994 | 0.0 | 99.96
|
||||
Other | | 0.0002123 | | | 0.02
|
||||
|
||||
Nlocal: 166.667 ave 200 max 150 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 55.3333 ave 92 max 32 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = -3
|
||||
Ave neighs/atom = -0.006
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:08
|
||||
55
examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.1
Normal file
55
examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.1
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, 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) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:00
|
||||
55
examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.4
Normal file
55
examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.4
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, 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) = 3.109 | 3.109 | 3.109 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:00
|
||||
55
examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.1
Normal file
55
examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.1
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, 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) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:00
|
||||
55
examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.3
Normal file
55
examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.3
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, 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) = 3.124 | 3.13 | 3.133 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:00
|
||||
55
examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.1
Normal file
55
examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.1
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, 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) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:01
|
||||
55
examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.4
Normal file
55
examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.4
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, 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) = 3.109 | 3.109 | 3.109 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:01
|
||||
5
examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.1
Normal file
5
examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.1
Normal file
@ -0,0 +1,5 @@
|
||||
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
|
||||
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||
5
examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.2
Normal file
5
examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.2
Normal file
@ -0,0 +1,5 @@
|
||||
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
|
||||
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||
6
examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.1
Normal file
6
examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.1
Normal file
@ -0,0 +1,6 @@
|
||||
Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769
|
||||
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
|
||||
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||
6
examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.2
Normal file
6
examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.2
Normal file
@ -0,0 +1,6 @@
|
||||
Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769
|
||||
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
|
||||
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||
44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.1
Normal file
44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.1
Normal file
@ -0,0 +1,44 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
mdi engine
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 2.15568 1.2132167
|
||||
1 1.4377309 0 0 2.1522832 1.211305
|
||||
2 1.430825 0 0 2.141945 1.2054866
|
||||
3 1.4189655 0 0 2.1241913 1.1954949
|
||||
4 1.4016029 0 0 2.0981995 1.1808667
|
||||
5 1.3779738 0 0 2.0628267 1.1609589
|
||||
Total wall time: 0:00:00
|
||||
44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.2
Normal file
44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.2
Normal file
@ -0,0 +1,44 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
mdi engine
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 2.15568 1.2132167
|
||||
1 1.4377309 0 0 2.1522832 1.211305
|
||||
2 1.430825 0 0 2.141945 1.2054866
|
||||
3 1.4189655 0 0 2.1241913 1.1954949
|
||||
4 1.4016029 0 0 2.0981995 1.1808667
|
||||
5 1.3779738 0 0 2.0628267 1.1609589
|
||||
Total wall time: 0:00:00
|
||||
44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.1
Normal file
44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.1
Normal file
@ -0,0 +1,44 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
mdi engine
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 2.15568 1.2132167
|
||||
1 1.4377309 0 0 2.1522832 1.211305
|
||||
2 1.430825 0 0 2.141945 1.2054866
|
||||
3 1.4189655 0 0 2.1241913 1.1954949
|
||||
4 1.4016029 0 0 2.0981995 1.1808667
|
||||
5 1.3779738 0 0 2.0628267 1.1609589
|
||||
Total wall time: 0:00:11
|
||||
44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.2
Normal file
44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.2
Normal file
@ -0,0 +1,44 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
mdi engine
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 2.15568 1.2132167
|
||||
1 1.4377309 0 0 2.1522832 1.211305
|
||||
2 1.430825 0 0 2.141945 1.2054866
|
||||
3 1.4189655 0 0 2.1241913 1.1954949
|
||||
4 1.4016029 0 0 2.0981995 1.1808667
|
||||
5 1.3779738 0 0 2.0628267 1.1609589
|
||||
Total wall time: 0:00:11
|
||||
55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.1
Normal file
55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.1
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, 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) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:00
|
||||
55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.3
Normal file
55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.3
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, 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) = 3.124 | 3.13 | 3.133 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:00
|
||||
55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.1
Normal file
55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.1
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, 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) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:01
|
||||
55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.3
Normal file
55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.3
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, 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) = 3.124 | 3.13 | 3.133 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:01
|
||||
3
examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.1
Normal file
3
examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.1
Normal file
@ -0,0 +1,3 @@
|
||||
Calc 1: eng -4.5209 pressure 0.98188 aveForce 4.4409e-16 -1.1102e-16 6.6613e-16
|
||||
Calc 2: eng -4.5432 pressure -0.53137 aveForce 7.0083e-16 1.1796e-16 5.4384e-16
|
||||
Calc 3: eng -4.501 pressure 2.0049 aveForce 0 2.0817e-16 -4.3021e-16
|
||||
3
examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.2
Normal file
3
examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.2
Normal file
@ -0,0 +1,3 @@
|
||||
Calc 1: eng -4.5209 pressure 0.98188 aveForce -2.2204e-16 0 2.2204e-16
|
||||
Calc 2: eng -4.5432 pressure -0.53137 aveForce -2.498e-16 -1.8735e-16 -3.4001e-16
|
||||
Calc 3: eng -4.501 pressure 2.0049 aveForce -7.9103e-16 3.4694e-16 4.0246e-16
|
||||
3
examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.1
Normal file
3
examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.1
Normal file
@ -0,0 +1,3 @@
|
||||
Calc 1: eng -4.5209 pressure 0.98188 aveForce 4.4409e-16 -1.1102e-16 6.6613e-16
|
||||
Calc 2: eng -4.5432 pressure -0.53137 aveForce 7.0083e-16 1.1796e-16 5.4384e-16
|
||||
Calc 3: eng -4.501 pressure 2.0049 aveForce 0 2.0817e-16 -4.3021e-16
|
||||
3
examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.3
Normal file
3
examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.3
Normal file
@ -0,0 +1,3 @@
|
||||
Calc 1: eng -4.5209 pressure 0.98188 aveForce -1.1102e-16 8.3267e-16 1.9429e-16
|
||||
Calc 2: eng -4.5432 pressure -0.53137 aveForce 9.0206e-17 4.996e-16 1.5959e-16
|
||||
Calc 3: eng -4.501 pressure 2.0049 aveForce -1.4849e-15 -8.1879e-16 -1.7347e-16
|
||||
3
examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.1
Normal file
3
examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.1
Normal file
@ -0,0 +1,3 @@
|
||||
Calc 1: eng -4.5209 pressure 0.98188 aveForce 4.4409e-16 -1.1102e-16 6.6613e-16
|
||||
Calc 2: eng -4.5432 pressure -0.53137 aveForce 7.0083e-16 1.1796e-16 5.4384e-16
|
||||
Calc 3: eng -4.501 pressure 2.0049 aveForce 0 2.0817e-16 -4.3021e-16
|
||||
3
examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.2
Normal file
3
examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.2
Normal file
@ -0,0 +1,3 @@
|
||||
Calc 1: eng -4.5209 pressure 0.98188 aveForce -2.2204e-16 0 2.2204e-16
|
||||
Calc 2: eng -4.5432 pressure -0.53137 aveForce -2.498e-16 -1.8735e-16 -3.4001e-16
|
||||
Calc 3: eng -4.501 pressure 2.0049 aveForce -7.9103e-16 3.4694e-16 4.0246e-16
|
||||
89
examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.1
Normal file
89
examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.1
Normal file
@ -0,0 +1,89 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, 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) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
Total wall time: 0:00:00
|
||||
89
examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.4
Normal file
89
examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.4
Normal file
@ -0,0 +1,89 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, 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) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
Total wall time: 0:00:00
|
||||
89
examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.1
Normal file
89
examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.1
Normal file
@ -0,0 +1,89 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, 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) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
Total wall time: 0:00:00
|
||||
89
examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.3
Normal file
89
examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.3
Normal file
@ -0,0 +1,89 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 3 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, 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) = 3.07 | 3.07 | 3.071 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 3 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
3 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
Total wall time: 0:00:00
|
||||
89
examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.1
Normal file
89
examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.1
Normal file
@ -0,0 +1,89 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, 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) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
Total wall time: 0:00:00
|
||||
89
examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.4
Normal file
89
examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.4
Normal file
@ -0,0 +1,89 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, 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) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
Total wall time: 0:00:00
|
||||
311
examples/mdi/sequence_driver.py
Normal file
311
examples/mdi/sequence_driver.py
Normal file
@ -0,0 +1,311 @@
|
||||
# MDI driver to perform a series of independent calculations
|
||||
# using LAMMPS (or a QM code with MDI support) as an MDI engine,
|
||||
# the engine can be either a standalone code or a plugin library
|
||||
|
||||
# Syntax: python3 series_driver.py switch arg switch arg ...
|
||||
# possible switches:
|
||||
# -mdi "-role DRIVER ..."
|
||||
# required switch
|
||||
# example for stand-alone mode:
|
||||
# -mdi "-role DRIVER -name sequence -method TCP -port 8021"
|
||||
# example for plugin mode:
|
||||
# -mdi "-role DRIVER -name sequemce -method LINK
|
||||
# -plugin_path /home/sjplimp/lammps/src/"
|
||||
# -plugin name
|
||||
# name of plugin library, only when using plugin mode
|
||||
# -plugin_args arglist
|
||||
# args to add when launching plugin library, only when using plugin mode
|
||||
# enclose arglist in quotes if multiple words
|
||||
# -n 3
|
||||
# number of calculations to perform, default = 3
|
||||
# -mode eval/run/min
|
||||
# style of calculations: single snapshot evals, dynamics, minimization
|
||||
# default = run
|
||||
# -size Nx Ny Nz
|
||||
# cubic lattice, default = 4 4 4
|
||||
# -rho 0.75 0.1
|
||||
# reduced density and random variation thereof, default = 0.75 0.1
|
||||
# -delta 0.1
|
||||
# randomly perturb atoms initially by this distance, default 0.1
|
||||
# -nsteps 100
|
||||
# number of timesteps in dynamics runs, default = 100
|
||||
# -temp 1.0
|
||||
# initial temperature in dynamics runs, default = 1.0
|
||||
# -tol 0.001
|
||||
# tolerance for minimizations, default = 0.001
|
||||
# -seed 12345
|
||||
# random number seed > 0, default = 12345
|
||||
|
||||
import sys,math,random
|
||||
import mdi
|
||||
import numpy as np
|
||||
from mpi4py import MPI
|
||||
|
||||
# error message
|
||||
|
||||
def error(txt=None):
|
||||
if txt: raise Exception(txt)
|
||||
raise Exception("Syntax: python3 series_driver.py switch arg switch arg ...")
|
||||
|
||||
# loop over all the tasks to exchange MDI Sends/Receives with the engine
|
||||
# for standalone mode, this is called by main program below
|
||||
# for plugin mode, this is a callback function invoked by MDI
|
||||
|
||||
def perform_tasks(world,mdicomm,dummy):
|
||||
|
||||
me = world.Get_rank()
|
||||
nprocs = world.Get_size()
|
||||
|
||||
# allocate vectors for per-atom types, coords, vels, forces
|
||||
|
||||
natoms = nx * ny * nz
|
||||
atypes = np.zeros(natoms,dtype=np.int)
|
||||
coords = np.zeros(3*natoms,dtype=np.float64)
|
||||
vels = np.zeros(3*natoms,dtype=np.float64)
|
||||
forces = np.zeros(3*natoms,dtype=np.float64)
|
||||
|
||||
atypes[:] = 1
|
||||
|
||||
# initialize RN generator
|
||||
|
||||
random.seed(seed)
|
||||
|
||||
# loop over sequence of calculations
|
||||
|
||||
for icalc in range(ncalc):
|
||||
|
||||
# define simulation box
|
||||
|
||||
onerho = rho + (random.random()-0.5)*rhodelta;
|
||||
sigma = pow(1.0/onerho,1.0/3.0)
|
||||
|
||||
xlo = ylo = zlo = 0.0
|
||||
xhi = nx * sigma
|
||||
yhi = ny * sigma
|
||||
zhi = nz * sigma
|
||||
|
||||
# send simulation box to engine
|
||||
|
||||
vec = [xhi-xlo,0.0,0.0] + [0.0,yhi-ylo,0.0] + [0.0,0.0,zhi-zlo]
|
||||
mdi.MDI_Send_command(">CELL",mdicomm)
|
||||
mdi.MDI_Send(vec,9,mdi.MDI_DOUBLE,mdicomm)
|
||||
|
||||
# create atoms on perfect lattice
|
||||
|
||||
m = 0
|
||||
for k in range(nz):
|
||||
for j in range(ny):
|
||||
for i in range(nx):
|
||||
coords[m] = i * sigma
|
||||
coords[m+1] = j * sigma
|
||||
coords[m+2] = k * sigma
|
||||
m += 3
|
||||
|
||||
# perturb lattice
|
||||
|
||||
for m in range(3*natoms):
|
||||
coords[m] += 2.0*random.random()*delta - delta
|
||||
|
||||
# define initial velocities
|
||||
|
||||
for m in range(3*natoms):
|
||||
vels[m] = random.random() - 0.5
|
||||
|
||||
tcurrent = 0.0
|
||||
for m in range(3*natoms):
|
||||
tcurrent += vels[m]*vels[m]
|
||||
tcurrent /= 3*(natoms-1)
|
||||
|
||||
factor = math.sqrt(tinitial/tcurrent)
|
||||
|
||||
for m in range(3*natoms):
|
||||
vels[m] *= factor
|
||||
|
||||
# send atoms and their properties to engine
|
||||
|
||||
mdi.MDI_Send_command(">NATOMS",mdicomm)
|
||||
mdi.MDI_Send(natoms,1,mdi.MDI_INT,mdicomm)
|
||||
mdi.MDI_Send_command(">TYPES",mdicomm)
|
||||
mdi.MDI_Send(atypes,natoms,mdi.MDI_INT,mdicomm)
|
||||
mdi.MDI_Send_command(">COORDS",mdicomm)
|
||||
mdi.MDI_Send(coords,3*natoms,mdi.MDI_DOUBLE,mdicomm)
|
||||
mdi.MDI_Send_command(">VELOCITIES",mdicomm)
|
||||
mdi.MDI_Send(vels,3*natoms,mdi.MDI_DOUBLE,mdicomm)
|
||||
|
||||
# eval or run or minimize
|
||||
|
||||
if mode == "eval":
|
||||
pass
|
||||
elif mode == "run":
|
||||
mdi.MDI_Send_command(">NSTEPS",mdicomm)
|
||||
mdi.MDI_Send(nsteps,1,mdi.MDI_INT,mdicomm)
|
||||
mdi.MDI_Send_command("MD",mdicomm)
|
||||
elif mode == "min":
|
||||
mdi.MDI_Send_command(">TOLERANCE",mdicomm)
|
||||
params = [tol,tol,1000.0,1000.0]
|
||||
mdi.MDI_Send(params,4,mdi.MDI_DOUBLE,mdicomm)
|
||||
mdi.MDI_Send_command("OPTG",mdicomm)
|
||||
|
||||
# request potential energy
|
||||
|
||||
mdi.MDI_Send_command("<PE",mdicomm)
|
||||
pe = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,mdicomm)
|
||||
pe = world.bcast(pe,root=0)
|
||||
|
||||
# request virial tensor
|
||||
|
||||
mdi.MDI_Send_command("<STRESS",mdicomm)
|
||||
virial = mdi.MDI_Recv(6,mdi.MDI_DOUBLE,mdicomm)
|
||||
virial = world.bcast(virial,root=0)
|
||||
|
||||
# request forces
|
||||
|
||||
mdi.MDI_Send_command("<FORCES",mdicomm)
|
||||
mdi.MDI_Recv(3*natoms,mdi.MDI_DOUBLE,mdicomm,buf=forces)
|
||||
world.Bcast(forces,root=0)
|
||||
|
||||
# final output from each calculation
|
||||
# pressure = just virial component, no kinetic component
|
||||
|
||||
aveeng = pe/natoms
|
||||
pressure = (virial[0] + virial[1] + virial[2]) / 3.0
|
||||
|
||||
m = 0
|
||||
fx = fy = fz = 0.0
|
||||
for i in range(natoms):
|
||||
fx += forces[m]
|
||||
fy += forces[m+1]
|
||||
fz += forces[m+2]
|
||||
m += 3
|
||||
|
||||
fx /= natoms
|
||||
fy /= natoms
|
||||
fz /= natoms
|
||||
|
||||
line = "Calc %d: eng %7.5g pressure %7.5g aveForce %7.5g %7.5g %7.5g" % \
|
||||
(icalc+1,aveeng,pressure,fx,fy,fz)
|
||||
if me == 0: print(line)
|
||||
|
||||
# send EXIT command to engine
|
||||
# in plugin mode, removes the plugin library
|
||||
|
||||
mdi.MDI_Send_command("EXIT",mdicomm)
|
||||
|
||||
# return needed for plugin mode
|
||||
|
||||
return 0
|
||||
|
||||
# ------------------------
|
||||
# main program
|
||||
# ------------------------
|
||||
|
||||
args = sys.argv[1:]
|
||||
narg = len(args)
|
||||
|
||||
# defaults for command-line args
|
||||
|
||||
mdiarg = ""
|
||||
plugin = ""
|
||||
plugin_args = ""
|
||||
|
||||
ncalc = 3
|
||||
mode = "run"
|
||||
nx = ny = nz = 4
|
||||
rho = 0.75
|
||||
rhodelta = 0.1
|
||||
delta = 0.1
|
||||
nsteps = 100
|
||||
tinitial = 1.0
|
||||
tol = 0.001
|
||||
seed = 12345
|
||||
|
||||
# parse command-line args
|
||||
|
||||
iarg = 0
|
||||
while iarg < narg:
|
||||
if args[iarg] == "-mdi":
|
||||
if iarg+2 > narg: error()
|
||||
mdiarg = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-plugin":
|
||||
if iarg+2 > narg: error()
|
||||
plugin = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-plugin_args":
|
||||
if iarg+2 > narg: error()
|
||||
plugin_args = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-n":
|
||||
if iarg+2 > narg: error()
|
||||
ncalc = int(args[iarg+1])
|
||||
iarg += 2
|
||||
elif args[iarg] == "-mode":
|
||||
if iarg+2 > narg: error()
|
||||
mode = args[iarg+1]
|
||||
if mode != "eval" and mode != "run" and mode != "min": error()
|
||||
iarg += 2
|
||||
elif args[iarg] == "-size":
|
||||
if iarg+4 > narg: error()
|
||||
nx = int(args[iarg+1])
|
||||
ny = int(args[iarg+2])
|
||||
nz = int(args[iarg+3])
|
||||
if nx <= 0 or ny <= 0 or nz <= 0: error()
|
||||
iarg += 4
|
||||
elif args[iarg] == "-rho":
|
||||
if iarg+3 > narg: error()
|
||||
rho = float(args[iarg+1])
|
||||
rhodelta = float(args[iarg+2])
|
||||
if rho-rhodelta <= 0.0: error()
|
||||
iarg += 3
|
||||
elif args[iarg] == "-delta":
|
||||
if iarg+2 > narg: error()
|
||||
delta = float(args[iarg+1])
|
||||
if delta < 0.0: error()
|
||||
iarg += 2
|
||||
elif args[iarg] == "-nsteps":
|
||||
if iarg+2 > narg: error()
|
||||
nsteps = int(args[iarg+1])
|
||||
if nsteps < 0: error()
|
||||
iarg += 2
|
||||
elif args[iarg] == "-temp":
|
||||
if iarg+2 > narg: error()
|
||||
tinitial = float(args[iarg+1])
|
||||
if tinitial < 0.0: error()
|
||||
iarg += 2
|
||||
elif args[iarg] == "-tol":
|
||||
if iarg+2 > narg: error()
|
||||
tol = float(args[iarg+1])
|
||||
if tol < 0.0: error()
|
||||
iarg += 2
|
||||
elif args[iarg] == "-seed":
|
||||
if iarg+2 > narg: error()
|
||||
seed = int(args[iarg+1])
|
||||
if seed <= 0: error()
|
||||
iarg += 2
|
||||
else: error()
|
||||
|
||||
if not mdiarg: error()
|
||||
|
||||
# LAMMPS engine is a stand-alone code
|
||||
# world = MPI communicator for just this driver
|
||||
# invoke perform_tasks() directly
|
||||
|
||||
if not plugin:
|
||||
mdi.MDI_Init(mdiarg)
|
||||
world = mdi.MDI_MPI_get_world_comm()
|
||||
|
||||
# connect to engine
|
||||
|
||||
mdicomm = mdi.MDI_Accept_Communicator()
|
||||
|
||||
perform_tasks(world,mdicomm,None)
|
||||
|
||||
# LAMMPS engine is a plugin library
|
||||
# launch plugin
|
||||
# MDI will call back to perform_tasks()
|
||||
|
||||
if plugin:
|
||||
mdi.MDI_Init(mdiarg)
|
||||
world = MPI.COMM_WORLD
|
||||
plugin_args += " -mdi \"-role ENGINE -name lammps -method LINK\""
|
||||
mdi.MDI_Launch_plugin(plugin,plugin_args,world,perform_tasks,None)
|
||||
37
examples/yaml/in.yaml
Normal file
37
examples/yaml/in.yaml
Normal file
@ -0,0 +1,37 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable yy equal 20*$y
|
||||
variable zz equal 20*$z
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
thermo_style yaml
|
||||
thermo 10
|
||||
|
||||
#dump 1 all yaml 25 dump.yaml id type x y z ix iy iz vx vy vz
|
||||
#dump_modify 1 sort id thermo yes units yes time yes format 1 %5d format float "% 12.8e" format int %2d
|
||||
|
||||
run 100 post no
|
||||
|
||||
run 100 post no
|
||||
151
examples/yaml/log.7Apr22.yaml.g++.1
Normal file
151
examples/yaml/log.7Apr22.yaml.g++.1
Normal file
@ -0,0 +1,151 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (33.591924 33.591924 33.591924)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (33.591924 33.591924 33.591924)
|
||||
create_atoms CPU = 0.003 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
thermo_style yaml
|
||||
thermo 10
|
||||
|
||||
dump 1 all yaml 25 dump.yaml id type x y z ix iy iz vx vy vz
|
||||
dump_modify 1 sort id thermo yes units yes time yes format 1 %5d format float "% 12.8e" format int %2d
|
||||
|
||||
run 100
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 24 24 24
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, 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) = 20.56 | 20.56 | 20.56 Mbytes
|
||||
---
|
||||
keywords: [Step, Temp, KinEng, PotEng, E_bond, E_angle, E_dihed, E_impro, E_vdwl, E_coul, E_long, Press, ]
|
||||
data:
|
||||
- [0, 1.44000000000001, 2.15993250000001, -6.77336805323422, 0, 0, 0, 0, -6.77336805323422, 0, 0, -5.01970725908556, ]
|
||||
- [10, 1.12539487029313, 1.68803955255514, -6.30005271976029, 0, 0, 0, 0, -6.30005271976029, 0, 0, -2.55968522600129, ]
|
||||
- [20, 0.625793798302192, 0.938661363368992, -5.55655653922756, 0, 0, 0, 0, -5.55655653922756, 0, 0, 0.973517658007722, ]
|
||||
- [30, 0.745927295413064, 1.11885597777762, -5.73951278150759, 0, 0, 0, 0, -5.73951278150759, 0, 0, 0.339284096694852, ]
|
||||
- [40, 0.731026217827733, 1.09650505988764, -5.71764564663628, 0, 0, 0, 0, -5.71764564663628, 0, 0, 0.388973418756238, ]
|
||||
- [50, 0.740091517740786, 1.11010258482128, -5.73150426762886, 0, 0, 0, 0, -5.73150426762886, 0, 0, 0.335273324523691, ]
|
||||
- [60, 0.750500641591031, 1.12571578266897, -5.74713299283555, 0, 0, 0, 0, -5.74713299283555, 0, 0, 0.26343139026926, ]
|
||||
- [70, 0.755436366857812, 1.13311913920702, -5.75480059117447, 0, 0, 0, 0, -5.75480059117447, 0, 0, 0.224276619217515, ]
|
||||
- [80, 0.759974280364828, 1.13992579675285, -5.76187162670983, 0, 0, 0, 0, -5.76187162670983, 0, 0, 0.191626237124102, ]
|
||||
- [90, 0.760464250735042, 1.14066072934081, -5.76280209529731, 0, 0, 0, 0, -5.76280209529731, 0, 0, 0.189478083345243, ]
|
||||
- [100, 0.757453103239936, 1.13614414924569, -5.75850548601596, 0, 0, 0, 0, -5.75850548601596, 0, 0, 0.207261053624723, ]
|
||||
...
|
||||
Loop time of 1.89046 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 22851.622 tau/day, 52.897 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.2896 | 1.2896 | 1.2896 | 0.0 | 68.22
|
||||
Neigh | 0.17687 | 0.17687 | 0.17687 | 0.0 | 9.36
|
||||
Comm | 0.014543 | 0.014543 | 0.014543 | 0.0 | 0.77
|
||||
Output | 0.37678 | 0.37678 | 0.37678 | 0.0 | 19.93
|
||||
Modify | 0.028638 | 0.028638 | 0.028638 | 0.0 | 1.51
|
||||
Other | | 0.003975 | | | 0.21
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19657 ave 19657 max 19657 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1202833
|
||||
Ave neighs/atom = 37.588531
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
|
||||
run 100
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 20.57 | 20.57 | 20.57 Mbytes
|
||||
---
|
||||
keywords: [Step, Temp, KinEng, PotEng, E_bond, E_angle, E_dihed, E_impro, E_vdwl, E_coul, E_long, Press, ]
|
||||
data:
|
||||
- [100, 0.757453103239935, 1.13614414924569, -5.7585054860159, 0, 0, 0, 0, -5.7585054860159, 0, 0, 0.207261053624721, ]
|
||||
- [110, 0.759322359337036, 1.13894794576996, -5.7614668389562, 0, 0, 0, 0, -5.7614668389562, 0, 0, 0.194314975399602, ]
|
||||
- [120, 0.759372342462676, 1.13902291811546, -5.76149365656489, 0, 0, 0, 0, -5.76149365656489, 0, 0, 0.191600048851267, ]
|
||||
- [130, 0.756833027516501, 1.13521406472659, -5.75777334823494, 0, 0, 0, 0, -5.75777334823494, 0, 0, 0.208792327853067, ]
|
||||
- [140, 0.759725426691298, 1.13955252790757, -5.76208910746081, 0, 0, 0, 0, -5.76208910746081, 0, 0, 0.193895435346637, ]
|
||||
- [150, 0.760545839455106, 1.14078310859643, -5.7633284876011, 0, 0, 0, 0, -5.7633284876011, 0, 0, 0.187959630462945, ]
|
||||
- [160, 0.758404626168493, 1.13757138903589, -5.76023198892283, 0, 0, 0, 0, -5.76023198892283, 0, 0, 0.19692107984108, ]
|
||||
- [170, 0.758880300638885, 1.13828487844424, -5.76103232235402, 0, 0, 0, 0, -5.76103232235402, 0, 0, 0.197653518549842, ]
|
||||
- [180, 0.753691827878246, 1.13050241251294, -5.75304767384283, 0, 0, 0, 0, -5.75304767384283, 0, 0, 0.237041776410937, ]
|
||||
- [190, 0.757361226563721, 1.13600633853809, -5.75852399133222, 0, 0, 0, 0, -5.75852399133222, 0, 0, 0.219529562657488, ]
|
||||
- [200, 0.759531750132731, 1.13926202214831, -5.76188923485725, 0, 0, 0, 0, -5.76188923485725, 0, 0, 0.209105747192796, ]
|
||||
...
|
||||
Loop time of 1.93916 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 22277.687 tau/day, 51.569 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 | 1.3292 | 1.3292 | 1.3292 | 0.0 | 68.55
|
||||
Neigh | 0.18317 | 0.18317 | 0.18317 | 0.0 | 9.45
|
||||
Comm | 0.013626 | 0.013626 | 0.013626 | 0.0 | 0.70
|
||||
Output | 0.38206 | 0.38206 | 0.38206 | 0.0 | 19.70
|
||||
Modify | 0.027034 | 0.027034 | 0.027034 | 0.0 | 1.39
|
||||
Other | | 0.004028 | | | 0.21
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19570 ave 19570 max 19570 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.19982e+06 ave 1.19982e+06 max 1.19982e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1199821
|
||||
Ave neighs/atom = 37.494406
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:04
|
||||
Reference in New Issue
Block a user