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update PAFI example: remove unused data, replace potential with existing one, update logs

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This commit is contained in:
Axel Kohlmeyer
2020-04-29 16:35:45 -04:00
parent 595bb30e14
commit 46739329c4
17 changed files with 476 additions and 15418 deletions
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examples/USER/misc/pafi/Fe_SIA_NEB/pafipath.1.data
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examples/USER/misc/pafi/Fe_SIA_NEB/pafipath.10.data
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examples/USER/misc/pafi/Fe_SIA_NEB/pafipath.11.data
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examples/USER/misc/pafi/Fe_SIA_NEB/pafipath.2.data
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examples/USER/misc/pafi/Fe_SIA_NEB/pafipath.3.data
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examples/USER/misc/pafi/Fe_mm.eam.fs Symbolic link
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@ -0,0 +1 @@
/home/akohlmey/compile/lammps/potentials/Fe_mm.eam.fs

1
examples/USER/misc/pafi/README
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@ -21,7 +21,6 @@ To compile:
make yes-user-misc # for PAFI
make yes-manybody # for EAM potential
make machine mode=lib # for PAFI++ compilation
make machine # for binary (machine= e.g. mpi)
To run the example from this folder:

4
examples/USER/misc/pafi/in.pafi.lammps
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@ -5,11 +5,11 @@ neigh_modify every 2 delay 10 check yes page 1000000 one 100000
## read in path data using fix property/atom- here 4th image of a NEB
fix pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_ddnz
read_data Fe_SIA_NEB/pafipath.4.data fix pa NULL PafiPath
read_data pafipath.4.data fix pa NULL PafiPath
## EAM potential
pair_style eam/fs
pair_coeff * * Fe_M07.eam.fs Fe
pair_coeff * * Fe_mm.eam.fs Fe
mass * 55.85
thermo 100

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examples/USER/misc/pafi/log.pafi → examples/USER/misc/pafi/log.15Apr20.pafi.g++.1
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@ -1,4 +1,6 @@
LAMMPS (19 Mar 2020)
LAMMPS (15 Apr 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style atomic
atom_modify map array sort 0 0.0
@ -6,16 +8,17 @@ neigh_modify every 2 delay 10 check yes page 1000000 one 100000
## read in path data using fix property/atom- here 4th image of a NEB
fix pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_ddnz
read_data Fe_SIA_NEB/pafipath.4.data fix pa NULL PafiPath
read_data pafipath.4.data fix pa NULL PafiPath
orthogonal box = (0 0 0) to (19.9872 19.9872 19.9872)
1 by 1 by 1 MPI processor grid
reading atoms ...
687 atoms
read_data CPU = 0.00426539 secs
read_data CPU = 0.00261545 secs
## EAM potential
pair_style eam/fs
pair_coeff * * Fe_M07.eam.fs Fe
pair_coeff * * Fe_mm.eam.fs Fe
Reading potential file Fe_mm.eam.fs with DATE: 2007-06-11
mass * 55.85
thermo 100
@ -28,9 +31,9 @@ run 0
Neighbor list info ...
update every 2 steps, delay 10 steps, check yes
max neighbors/atom: 100000, page size: 1000000
master list distance cutoff = 7.8
ghost atom cutoff = 7.8
binsize = 3.9, bins = 6 6 6
master list distance cutoff = 7.3
ghost atom cutoff = 7.3
binsize = 3.65, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/fs, perpetual
attributes: half, newton on
@ -39,10 +42,10 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.903 | 6.903 | 6.903 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2828.1883 0 -2828.1883 3563.9027
Loop time of 1.333e-06 on 1 procs for 0 steps with 687 atoms
0 0 -2828.2492 0 -2828.2492 3015.2014
Loop time of 7.15256e-07 on 1 procs for 0 steps with 687 atoms
225.1% CPU use with 1 MPI tasks x no OpenMP threads
139.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -52,31 +55,31 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.333e-06 | | |100.00
Other | | 7.153e-07 | | |100.00
Nlocal: 687 ave 687 max 687 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3239 ave 3239 max 3239 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 57796 ave 57796 max 57796 min
Neighs: 46843 ave 46843 max 46843 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 57796
Ave neighs/atom = 84.1281
Total # of neighbors = 46843
Ave neighs/atom = 68.1849
Neighbor list builds = 0
Dangerous builds = 0
print "energy=${pe}"
energy=-2828.18831312874
energy=-2828.24917967199
## compute property/atom to access relevant fields
compute pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_ddnz
run 0
Per MPI rank memory allocation (min/avg/max) = 6.903 | 6.903 | 6.903 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2828.1883 0 -2828.1883 3563.9027
Loop time of 1.42e-06 on 1 procs for 0 steps with 687 atoms
0 0 -2828.2492 0 -2828.2492 3015.2014
Loop time of 4.76837e-07 on 1 procs for 0 steps with 687 atoms
140.8% CPU use with 1 MPI tasks x no OpenMP threads
209.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -86,31 +89,31 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.42e-06 | | |100.00
Other | | 4.768e-07 | | |100.00
Nlocal: 687 ave 687 max 687 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3239 ave 3239 max 3239 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 57796 ave 57796 max 57796 min
Neighs: 46843 ave 46843 max 46843 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 57796
Ave neighs/atom = 84.1281
Total # of neighbors = 46843
Ave neighs/atom = 68.1849
Neighbor list builds = 0
Dangerous builds = 0
## fix name group-id hp compute-id temperature tdamp seed overdamped 0/1 com 0/1
fix hp all pafi pa 500.0 0.01 434 overdamped 0 com 1
fix hp compute name,style: pa,property/atom
fix pafi compute name,style: pa,property/atom
run 0
Per MPI rank memory allocation (min/avg/max) = 8.403 | 8.403 | 8.403 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2828.1883 0 -2828.1883 3563.9027
Loop time of 1.305e-06 on 1 procs for 0 steps with 687 atoms
0 0 -2828.2492 0 -2828.2492 3015.2014
Loop time of 4.76837e-07 on 1 procs for 0 steps with 687 atoms
229.9% CPU use with 1 MPI tasks x no OpenMP threads
209.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -120,69 +123,69 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.305e-06 | | |100.00
Other | | 4.768e-07 | | |100.00
Nlocal: 687 ave 687 max 687 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3239 ave 3239 max 3239 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 57796 ave 57796 max 57796 min
Neighs: 46843 ave 46843 max 46843 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 57796
Ave neighs/atom = 84.1281
Total # of neighbors = 46843
Ave neighs/atom = 68.1849
Neighbor list builds = 0
Dangerous builds = 0
minimize 0 0 1000 1000 # best if using NEB path
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:190)
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190)
Parameters for fire:
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback
0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes
Per MPI rank memory allocation (min/avg/max) = 8.403 | 8.403 | 8.403 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2828.1883 0 -2828.1883 3563.9027
100 1.9938996e-07 -2828.1886 0 -2828.1886 3561.199
200 7.8041956e-13 -2828.1886 0 -2828.1886 3561.1945
300 3.4605594e-16 -2828.1886 0 -2828.1886 3561.1949
400 3.6528471e-16 -2828.1886 0 -2828.1886 3561.1955
500 3.7404973e-16 -2828.1886 0 -2828.1886 3561.1963
600 3.7779115e-16 -2828.1886 0 -2828.1886 3561.197
700 3.7919033e-16 -2828.1886 0 -2828.1886 3561.1977
800 3.7972651e-16 -2828.1886 0 -2828.1886 3561.1984
900 3.7992772e-16 -2828.1886 0 -2828.1886 3561.1992
1000 3.7999216e-16 -2828.1886 0 -2828.1886 3561.1999
Loop time of 1.85272 on 1 procs for 1000 steps with 687 atoms
0 0 -2828.2492 0 -2828.2492 3015.2014
100 9.5973821e-06 -2828.3565 0 -2828.3565 3092.936
200 1.501052e-13 -2828.3565 0 -2828.3565 3092.8883
300 5.4507203e-14 -2828.3565 0 -2828.3565 3092.8883
400 5.0283346e-14 -2828.3565 0 -2828.3565 3092.8883
500 4.9056961e-14 -2828.3565 0 -2828.3565 3092.8883
600 4.8645522e-14 -2828.3565 0 -2828.3565 3092.8883
700 4.8498897e-14 -2828.3565 0 -2828.3565 3092.8882
800 4.8444578e-14 -2828.3565 0 -2828.3565 3092.8882
900 4.8424662e-14 -2828.3565 0 -2828.3565 3092.8882
1000 4.8416874e-14 -2828.3565 0 -2828.3565 3092.8882
Loop time of 1.07709 on 1 procs for 1000 steps with 687 atoms
100.0% CPU use with 1 MPI tasks x no OpenMP threads
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-2828.18831313 -2828.18858696 -2828.18858696
Force two-norm initial, final = 0.0423352 5.03778e-07
Force max component initial, final = 0.013445 1.97768e-07
-2828.24917967 -2828.35645844 -2828.35645844
Force two-norm initial, final = 1.2831 7.46892e-07
Force max component initial, final = 0.333171 2.93217e-07
Final line search alpha, max atom move = 0 0
Iterations, force evaluations = 1000 1011
Iterations, force evaluations = 1000 1007
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.7948 | 1.7948 | 1.7948 | 0.0 | 96.87
Pair | 1.0319 | 1.0319 | 1.0319 | 0.0 | 95.80
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0131 | 0.0131 | 0.0131 | 0.0 | 0.71
Output | 0.00024421 | 0.00024421 | 0.00024421 | 0.0 | 0.01
Modify | 0.029904 | 0.029904 | 0.029904 | 0.0 | 1.61
Other | | 0.01468 | | | 0.79
Comm | 0.0099187 | 0.0099187 | 0.0099187 | 0.0 | 0.92
Output | 0.00012374 | 0.00012374 | 0.00012374 | 0.0 | 0.01
Modify | 0.023141 | 0.023141 | 0.023141 | 0.0 | 2.15
Other | | 0.01203 | | | 1.12
Nlocal: 687 ave 687 max 687 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3239 ave 3239 max 3239 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 57796 ave 57796 max 57796 min
Neighs: 46843 ave 46843 max 46843 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 57796
Ave neighs/atom = 84.1281
Total # of neighbors = 46843
Ave neighs/atom = 68.1849
Neighbor list builds = 0
Dangerous builds = 0
compute dx all displace/atom
@ -197,100 +200,100 @@ variable dn equal f_hp[4]*f_hp[4] # should be zero to float precision
fix af all ave/time 1 1000 1000 f_hp[1] f_hp[2] f_hp[3] v_dn
variable adn equal sqrt(f_af[4]) # should be zero to float precision (approx. 1e-14)
variable adn equal sqrt(f_af[4]) # should be very small (approx. 1e-6 A)
variable apf equal f_af[1]
run 1000
Per MPI rank memory allocation (min/avg/max) = 8.778 | 8.778 | 8.778 Mbytes
Step PotEng Temp v_maxjump
1000 -2828.1886 3.7999216e-16 3.4278728e-08
1100 -2789.8905 505.0196 0.5339377
1200 -2786.4812 475.87154 0.60507378
1300 -2785.0896 503.35831 0.56457282
1400 -2782.9099 531.27274 0.61644994
1500 -2783.9471 490.65163 0.5535807
1600 -2785.7798 515.06521 0.64570403
1700 -2782.4161 492.14884 0.56823928
1800 -2783.7633 513.6031 0.55073614
1900 -2784.6075 488.34035 0.56023518
2000 -2783.6017 492.46418 0.55443537
Loop time of 2.72875 on 1 procs for 1000 steps with 687 atoms
1000 -2828.3565 4.8416874e-14 0
1100 -2788.9297 505.16169 0.53846275
1200 -2784.1274 471.52773 0.5820714
1300 -2782.7071 503.23183 0.57990998
1400 -2780.7259 531.16141 0.61955057
1500 -2781.512 490.9404 0.58663715
1600 -2783.4961 513.37777 0.65062082
1700 -2780.0312 492.76259 0.5785296
1800 -2781.6555 512.32986 0.58277945
1900 -2782.1648 486.16736 0.58913114
2000 -2781.1942 493.15046 0.56962281
Loop time of 1.12102 on 1 procs for 1000 steps with 687 atoms
Performance: 31.663 ns/day, 0.758 hours/ns, 366.468 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 77.072 ns/day, 0.311 hours/ns, 892.043 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 | 2.5784 | 2.5784 | 2.5784 | 0.0 | 94.49
Pair | 1.0281 | 1.0281 | 1.0281 | 0.0 | 91.71
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.016643 | 0.016643 | 0.016643 | 0.0 | 0.61
Output | 0.00038734 | 0.00038734 | 0.00038734 | 0.0 | 0.01
Modify | 0.12857 | 0.12857 | 0.12857 | 0.0 | 4.71
Other | | 0.004711 | | | 0.17
Comm | 0.0097873 | 0.0097873 | 0.0097873 | 0.0 | 0.87
Output | 0.00018072 | 0.00018072 | 0.00018072 | 0.0 | 0.02
Modify | 0.080336 | 0.080336 | 0.080336 | 0.0 | 7.17
Other | | 0.002599 | | | 0.23
Nlocal: 687 ave 687 max 687 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3239 ave 3239 max 3239 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 57797 ave 57797 max 57797 min
Neighs: 46844 ave 46844 max 46844 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 57797
Ave neighs/atom = 84.1295
Total # of neighbors = 46844
Ave neighs/atom = 68.1863
Neighbor list builds = 0
Dangerous builds = 0
minimize 0 0 1000 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:190)
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190)
Parameters for fire:
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback
0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes
Per MPI rank memory allocation (min/avg/max) = 9.278 | 9.278 | 9.278 Mbytes
Step PotEng Temp v_maxjump
2000 -2783.6017 0 0.55443537
2100 -2828.1879 0.0086616241 0.052304638
2200 -2828.1886 2.0746651e-09 0.0029841667
2300 -2828.1886 2.1913323e-11 0.001058494
2400 -2828.1886 3.870467e-16 0.001183855
2500 -2828.1886 3.6687627e-16 0.0013411719
2600 -2828.1886 3.7514402e-16 0.0014886111
2700 -2828.1886 3.7835629e-16 0.0016249577
2800 -2828.1886 3.7928875e-16 0.0017514793
2900 -2828.1886 3.7984492e-16 0.0018697188
3000 -2828.1886 3.8006665e-16 0.0019810034
Loop time of 1.91057 on 1 procs for 1000 steps with 687 atoms
2000 -2781.1942 0 0.56962281
2100 -2828.3564 2.3533517e-06 0.028829312
2200 -2828.3565 2.3166114e-09 0.0015098779
2300 -2828.3565 5.7159207e-14 0.0017926087
2400 -2828.3565 5.0928432e-14 0.0020264648
2500 -2828.3565 4.9253427e-14 0.0022344754
2600 -2828.3565 4.8706709e-14 0.0024243813
2700 -2828.3565 4.8513394e-14 0.0026003645
2800 -2828.3565 4.8442921e-14 0.0027651416
2900 -2828.3565 4.8417392e-14 0.0029206277
3000 -2828.3565 4.8407328e-14 0.0030682417
Loop time of 1.10285 on 1 procs for 1000 steps with 687 atoms
100.0% CPU use with 1 MPI tasks x no OpenMP threads
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-2783.60173619 -2828.18858999 -2828.18858999
Force two-norm initial, final = 30.2396 5.03784e-07
Force max component initial, final = 2.42484 1.97774e-07
-2781.19422469 -2828.35646618 -2828.35646619
Force two-norm initial, final = 29.0662 7.46923e-07
Force max component initial, final = 2.29107 2.93233e-07
Final line search alpha, max atom move = 0 0
Iterations, force evaluations = 1000 1016
Iterations, force evaluations = 1000 1008
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.8515 | 1.8515 | 1.8515 | 0.0 | 96.91
Pair | 1.0574 | 1.0574 | 1.0574 | 0.0 | 95.88
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013356 | 0.013356 | 0.013356 | 0.0 | 0.70
Output | 0.00034649 | 0.00034649 | 0.00034649 | 0.0 | 0.02
Modify | 0.030632 | 0.030632 | 0.030632 | 0.0 | 1.60
Other | | 0.01471 | | | 0.77
Comm | 0.0099056 | 0.0099056 | 0.0099056 | 0.0 | 0.90
Output | 0.00018358 | 0.00018358 | 0.00018358 | 0.0 | 0.02
Modify | 0.023358 | 0.023358 | 0.023358 | 0.0 | 2.12
Other | | 0.012 | | | 1.09
Nlocal: 687 ave 687 max 687 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3239 ave 3239 max 3239 min
Nghost: 3209 ave 3209 max 3209 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 57816 ave 57816 max 57816 min
Neighs: 48576 ave 48576 max 48576 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 57816
Ave neighs/atom = 84.1572
Total # of neighbors = 48576
Ave neighs/atom = 70.7074
Neighbor list builds = 0
Dangerous builds = 0
print """
@ -302,9 +305,8 @@ During run:
---------- PAFI RESULTS --------
During run:
Average Distance From Hyperplane = 8.14961490182052e-06 A,
Average Force Projection Along MFEP = -0.250816030478286 eV/A
Average Distance From Hyperplane = 1.36645874707752e-05 A,
Average Force Projection Along MFEP = -0.117797263023877 eV/A
print """
In-plane minimization post-run:
@ -312,11 +314,11 @@ energy = ${pe} eV
"""
In-plane minimization post-run:
energy = -2828.18858999199 eV
energy = -2828.35646618732 eV
if "${maxjump} > 0.1" then "print 'sup|X_t-X_0| = ${maxjump}A > 0.1A'" "print ' => Possible shallow in-plane metastability: Reduce time in basin and/or decrease tdamp'" else "print 'sup|X_t-X_0| = ${maxjump}A < 0.1A => No in-plane jumps'"
print 'sup|X_t-X_0| = ${maxjump}A < 0.1A => No in-plane jumps'
sup|X_t-X_0| = 0.0019810034288544A < 0.1A => No in-plane jumps
if "${maxjump} > 0.1" then "print 'Max Atomic Displacement = ${maxjump}A > 0.1A'" "print ' => Possible shallow in-plane metastability: Reduce time in basin and/or decrease tdamp'" else "print 'Max Atomic Displacement = ${maxjump}A < 0.1A => No in-plane jumps'"
print 'Max Atomic Displacement = ${maxjump}A < 0.1A => No in-plane jumps'
Max Atomic Displacement = 0.00306824174700518A < 0.1A => No in-plane jumps
print """
----- END PAFI ----
"""
@ -324,6 +326,19 @@ print """
----- END PAFI ----
#unfix hp
#unfix pa
#unfix af
#minimize 0 0 1000 1000
#print """
#Full minimization post-run:
#energy = ${pe} eV
#"""
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:06
Total wall time: 0:00:03

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@ -0,0 +1,344 @@
LAMMPS (15 Apr 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style atomic
atom_modify map array sort 0 0.0
neigh_modify every 2 delay 10 check yes page 1000000 one 100000
## read in path data using fix property/atom- here 4th image of a NEB
fix pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_ddnz
read_data pafipath.4.data fix pa NULL PafiPath
orthogonal box = (0 0 0) to (19.9872 19.9872 19.9872)
2 by 1 by 2 MPI processor grid
reading atoms ...
687 atoms
read_data CPU = 0.00148988 secs
## EAM potential
pair_style eam/fs
pair_coeff * * Fe_mm.eam.fs Fe
Reading potential file Fe_mm.eam.fs with DATE: 2007-06-11
mass * 55.85
thermo 100
min_style fire
compute pe all pe
variable pe equal pe
run 0
Neighbor list info ...
update every 2 steps, delay 10 steps, check yes
max neighbors/atom: 100000, page size: 1000000
master list distance cutoff = 7.3
ghost atom cutoff = 7.3
binsize = 3.65, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/fs, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.844 | 6.844 | 6.844 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2828.2492 0 -2828.2492 3015.2014
Loop time of 9.17912e-06 on 4 procs for 0 steps with 687 atoms
59.9% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.179e-06 | | |100.00
Nlocal: 171.75 ave 187 max 163 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Nghost: 1854.25 ave 1863 max 1839 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 11710.8 ave 12319 max 10647 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 46843
Ave neighs/atom = 68.1849
Neighbor list builds = 0
Dangerous builds = 0
print "energy=${pe}"
energy=-2828.24917967201
## compute property/atom to access relevant fields
compute pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_ddnz
run 0
Per MPI rank memory allocation (min/avg/max) = 6.844 | 6.844 | 6.844 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2828.2492 0 -2828.2492 3015.2014
Loop time of 9.11951e-06 on 4 procs for 0 steps with 687 atoms
52.1% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.12e-06 | | |100.00
Nlocal: 171.75 ave 187 max 163 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Nghost: 1854.25 ave 1863 max 1839 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 11710.8 ave 12319 max 10647 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 46843
Ave neighs/atom = 68.1849
Neighbor list builds = 0
Dangerous builds = 0
## fix name group-id hp compute-id temperature tdamp seed overdamped 0/1 com 0/1
fix hp all pafi pa 500.0 0.01 434 overdamped 0 com 1
fix pafi compute name,style: pa,property/atom
run 0
Per MPI rank memory allocation (min/avg/max) = 8.344 | 8.344 | 8.344 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2828.2492 0 -2828.2492 3015.2014
Loop time of 9.17912e-06 on 4 procs for 0 steps with 687 atoms
84.4% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.179e-06 | | |100.00
Nlocal: 171.75 ave 187 max 163 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Nghost: 1854.25 ave 1863 max 1839 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 11710.8 ave 12319 max 10647 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 46843
Ave neighs/atom = 68.1849
Neighbor list builds = 0
Dangerous builds = 0
minimize 0 0 1000 1000 # best if using NEB path
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190)
Parameters for fire:
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback
0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes
Per MPI rank memory allocation (min/avg/max) = 8.344 | 8.344 | 8.344 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2828.2492 0 -2828.2492 3015.2014
100 9.5973821e-06 -2828.3565 0 -2828.3565 3092.936
200 1.5010519e-13 -2828.3565 0 -2828.3565 3092.8883
300 5.4507205e-14 -2828.3565 0 -2828.3565 3092.8883
400 5.028334e-14 -2828.3565 0 -2828.3565 3092.8883
500 4.905696e-14 -2828.3565 0 -2828.3565 3092.8883
600 4.8645524e-14 -2828.3565 0 -2828.3565 3092.8883
700 4.8498896e-14 -2828.3565 0 -2828.3565 3092.8882
800 4.8444558e-14 -2828.3565 0 -2828.3565 3092.8882
900 4.8424652e-14 -2828.3565 0 -2828.3565 3092.8882
1000 4.8416883e-14 -2828.3565 0 -2828.3565 3092.8882
Loop time of 0.378521 on 4 procs for 1000 steps with 687 atoms
94.6% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-2828.24917967 -2828.35645844 -2828.35645844
Force two-norm initial, final = 1.2831 7.46892e-07
Force max component initial, final = 0.333171 2.93218e-07
Final line search alpha, max atom move = 0 0
Iterations, force evaluations = 1000 1007
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.28507 | 0.30427 | 0.3132 | 2.1 | 80.38
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.041108 | 0.050675 | 0.070478 | 5.2 | 13.39
Output | 0.00013185 | 0.00025684 | 0.00063133 | 0.0 | 0.07
Modify | 0.012176 | 0.01298 | 0.013903 | 0.7 | 3.43
Other | | 0.01034 | | | 2.73
Nlocal: 171.75 ave 187 max 163 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Nghost: 1854.25 ave 1863 max 1839 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 11710.8 ave 12319 max 10647 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 46843
Ave neighs/atom = 68.1849
Neighbor list builds = 0
Dangerous builds = 0
compute dx all displace/atom
compute dmag all reduce max c_dx[4]
variable maxjump equal sqrt(c_dmag)
thermo_style custom step pe temp v_maxjump
variable dn equal f_hp[4]*f_hp[4] # should be zero to float precision
fix af all ave/time 1 1000 1000 f_hp[1] f_hp[2] f_hp[3] v_dn
variable adn equal sqrt(f_af[4]) # should be very small (approx. 1e-6 A)
variable apf equal f_af[1]
run 1000
Per MPI rank memory allocation (min/avg/max) = 8.719 | 8.719 | 8.719 Mbytes
Step PotEng Temp v_maxjump
1000 -2828.3565 4.8416883e-14 0
1100 -2787.3877 503.1749 0.53858794
1200 -2783.8463 508.91879 0.57609619
1300 -2782.5288 533.03961 0.64090828
1400 -2782.4551 508.05688 0.61706248
1500 -2784.0499 538.34202 0.56379358
1600 -2786.4068 487.9633 0.57600511
1700 -2780.7727 489.2309 0.61048418
1800 -2780.4909 519.01911 0.60204913
1900 -2782.0825 512.3441 0.6071772
2000 -2779.5449 526.21838 0.58247597
Loop time of 0.358743 on 4 procs for 1000 steps with 687 atoms
Performance: 240.841 ns/day, 0.100 hours/ns, 2787.512 timesteps/s
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.2806 | 0.29275 | 0.30044 | 1.4 | 81.60
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.028289 | 0.035765 | 0.047713 | 4.0 | 9.97
Output | 0.00016427 | 0.00046188 | 0.001353 | 0.0 | 0.13
Modify | 0.02722 | 0.027855 | 0.02832 | 0.2 | 7.76
Other | | 0.001914 | | | 0.53
Nlocal: 171.75 ave 183 max 165 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 1854.25 ave 1861 max 1843 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Neighs: 11711 ave 12115 max 10983 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 46844
Ave neighs/atom = 68.1863
Neighbor list builds = 0
Dangerous builds = 0
minimize 0 0 1000 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190)
Parameters for fire:
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback
0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes
Per MPI rank memory allocation (min/avg/max) = 9.219 | 9.219 | 9.219 Mbytes
Step PotEng Temp v_maxjump
2000 -2779.5449 0 0.58247597
2100 -2828.3564 5.5901288e-06 0.022258122
2200 -2828.3565 2.5724945e-11 0.0014462408
2300 -2828.3565 5.8980022e-14 0.0018217607
2400 -2828.3565 5.1597338e-14 0.0020531463
2500 -2828.3565 4.9451625e-14 0.0022588465
2600 -2828.3565 4.8775183e-14 0.0024468988
2700 -2828.3565 4.8538712e-14 0.0026213819
2800 -2828.3565 4.8450182e-14 0.0027849194
2900 -2828.3565 4.8421015e-14 0.0029393609
3000 -2828.3565 4.8409029e-14 0.0030860795
Loop time of 0.358516 on 4 procs for 1000 steps with 687 atoms
97.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-2779.54493573 -2828.35646627 -2828.35646628
Force two-norm initial, final = 29.3013 7.46923e-07
Force max component initial, final = 2.07903 2.93237e-07
Final line search alpha, max atom move = 0 0
Iterations, force evaluations = 1000 1008
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.28555 | 0.30143 | 0.30793 | 1.7 | 84.08
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.029324 | 0.035806 | 0.051662 | 4.9 | 9.99
Output | 0.00016069 | 0.00043958 | 0.0012667 | 0.0 | 0.12
Modify | 0.0087969 | 0.0089234 | 0.0090258 | 0.1 | 2.49
Other | | 0.01192 | | | 3.32
Nlocal: 171.75 ave 184 max 165 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 1828.25 ave 1835 max 1815 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 12157.5 ave 12578 max 11155 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Total # of neighbors = 48630
Ave neighs/atom = 70.786
Neighbor list builds = 0
Dangerous builds = 0
print """
---------- PAFI RESULTS --------
During run:
Average Distance From Hyperplane = ${adn} A,
Average Force Projection Along MFEP = ${apf} eV/A
"""
---------- PAFI RESULTS --------
During run:
Average Distance From Hyperplane = 1.3664587498043e-05 A,
Average Force Projection Along MFEP = -0.442220695378227 eV/A
print """
In-plane minimization post-run:
energy = ${pe} eV
"""
In-plane minimization post-run:
energy = -2828.3564662776 eV
if "${maxjump} > 0.1" then "print 'Max Atomic Displacement = ${maxjump}A > 0.1A'" "print ' => Possible shallow in-plane metastability: Reduce time in basin and/or decrease tdamp'" else "print 'Max Atomic Displacement = ${maxjump}A < 0.1A => No in-plane jumps'"
print 'Max Atomic Displacement = ${maxjump}A < 0.1A => No in-plane jumps'
Max Atomic Displacement = 0.00308607949101158A < 0.1A => No in-plane jumps
print """
----- END PAFI ----
"""
----- END PAFI ----
#unfix hp
#unfix pa
#unfix af
#minimize 0 0 1000 1000
#print """
#Full minimization post-run:
#energy = ${pe} eV
#"""
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:01

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examples/USER/misc/pafi/pafi.data
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examples/USER/misc/pafi/Fe_SIA_NEB/pafipath.4.data → examples/USER/misc/pafi/pafipath.4.data
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