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minor changes to example

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tomswinburne
2020-09-01 17:02:24 +02:00
parent 75b3bbd657
commit ae3a7d8901
4 changed files with 370 additions and 245 deletions
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7
examples/USER/misc/pafi/README
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@ -30,4 +30,11 @@ To run the example from this folder:
mpirun -np NPROCS /path/to/lammps/src/lmp_machine -in in.pafi mpirun -np NPROCS /path/to/lammps/src/lmp_machine -in in.pafi
``` ```
This example executes a hyperplane constrained overdamped Langevin simulation
whilst recording the projected free energy gradient, then minimizes in-plane,
then removes the hyperplane constraint and minimizes the whole system.
If the temperature is too high the system will leave the local minima of
the constrained system; PAFI checks for this also.
To generate your own path, please see the LAMMPS documentation for more details To generate your own path, please see the LAMMPS documentation for more details

40
examples/USER/misc/pafi/in.pafi
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@ -48,35 +48,39 @@ variable apf equal f_af[1]
run 1000 run 1000
minimize 0 0 1000 1000 minimize 0 0 1000 1000
variable s_pe equal ${pe}
variable s_apf equal ${apf}
variable s_adn equal ${adn}
variable s_maxjump equal ${maxjump}
unfix hp
unfix pa
unfix af
minimize 0 0 1000 1000
print """ print """
---------- PAFI RESULTS -------- ---------- PAFI RESULTS --------
During run: During run:
Average Distance From Hyperplane = ${adn} A, Average Distance From Hyperplane = ${s_adn}A (Should be very small, around 1e-5A),
Average Force Projection Along MFEP = ${apf} eV/A Average Force Projection Along MFEP = ${s_apf} eV/A
""" """
print """ print """
In-plane minimization post-run: In-plane minimization post-run:
energy = ${pe} eV energy = ${s_pe} eV
""" """
if "${maxjump} > 0.1" then & if "${s_maxjump} > 0.1" then &
"print 'Max Atomic Displacement = ${maxjump}A > 0.1A'" & "print 'Max Atomic Displacement = ${s_maxjump}A > 0.1A'" &
"print ' => Possible shallow in-plane metastability: Reduce time in basin and/or decrease tdamp'" & "print ' => Possible shallow in-plane metastability: Reduce time in basin and/or decrease tdamp'" &
else & else &
"print 'Max Atomic Displacement = ${maxjump}A < 0.1A => No in-plane jumps'" "print 'Max Atomic Displacement = ${s_maxjump}A < 0.1A => No in-plane jumps'"
print """ print """
Full minimization after removal of PAFI fixes:
energy = ${pe} eV
----- END PAFI ---- ----- END PAFI ----
""" """
# disable fix and minimize full system
# unfix hp
# unfix pa
# unfix af
# minimize 0 0 1000 1000
# print """
# Full minimization post-run:
# energy = ${pe} eV
# """

291
examples/USER/misc/pafi/log.15Apr20.pafi.g++.1
View File

@ -1,6 +1,4 @@
LAMMPS (15 Apr 2020) LAMMPS (24 Aug 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 units metal
atom_style atomic atom_style atomic
atom_modify map array sort 0 0.0 atom_modify map array sort 0 0.0
@ -9,16 +7,17 @@ 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 ## 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 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 read_data pafipath.4.data fix pa NULL PafiPath
orthogonal box = (0 0 0) to (19.9872 19.9872 19.9872) Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (19.987184 19.987184 19.987184)
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
reading atoms ... reading atoms ...
687 atoms 687 atoms
read_data CPU = 0.00261545 secs read_data CPU = 0.007 seconds
## EAM potential ## EAM potential
pair_style eam/fs pair_style eam/fs
pair_coeff * * Fe_mm.eam.fs Fe pair_coeff * * ../../../../potentials/Fe_mm.eam.fs Fe
Reading potential file Fe_mm.eam.fs with DATE: 2007-06-11 Reading eam/fs potential file ../../../../potentials/Fe_mm.eam.fs with DATE: 2007-06-11
mass * 55.85 mass * 55.85
thermo 100 thermo 100
@ -43,9 +42,9 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 6.903 | 6.903 | 6.903 Mbytes Per MPI rank memory allocation (min/avg/max) = 6.903 | 6.903 | 6.903 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -2828.2492 0 -2828.2492 3015.2014 0 0 -2828.2492 0 -2828.2492 3015.2014
Loop time of 7.15256e-07 on 1 procs for 0 steps with 687 atoms Loop time of 6.88e-07 on 1 procs for 0 steps with 687 atoms
139.8% CPU use with 1 MPI tasks x 1 OpenMP threads 290.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
@ -55,17 +54,17 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 7.153e-07 | | |100.00 Other | | 6.88e-07 | | |100.00
Nlocal: 687 ave 687 max 687 min Nlocal: 687.000 ave 687 max 687 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3239 ave 3239 max 3239 min Nghost: 3239.00 ave 3239 max 3239 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 46843 ave 46843 max 46843 min Neighs: 46843.0 ave 46843 max 46843 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46843 Total # of neighbors = 46843
Ave neighs/atom = 68.1849 Ave neighs/atom = 68.184862
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
print "energy=${pe}" print "energy=${pe}"
@ -77,9 +76,9 @@ run 0
Per MPI rank memory allocation (min/avg/max) = 6.903 | 6.903 | 6.903 Mbytes Per MPI rank memory allocation (min/avg/max) = 6.903 | 6.903 | 6.903 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -2828.2492 0 -2828.2492 3015.2014 0 0 -2828.2492 0 -2828.2492 3015.2014
Loop time of 4.76837e-07 on 1 procs for 0 steps with 687 atoms Loop time of 9.41e-07 on 1 procs for 0 steps with 687 atoms
209.7% CPU use with 1 MPI tasks x 1 OpenMP threads 106.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
@ -89,31 +88,31 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 4.768e-07 | | |100.00 Other | | 9.41e-07 | | |100.00
Nlocal: 687 ave 687 max 687 min Nlocal: 687.000 ave 687 max 687 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3239 ave 3239 max 3239 min Nghost: 3239.00 ave 3239 max 3239 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 46843 ave 46843 max 46843 min Neighs: 46843.0 ave 46843 max 46843 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46843 Total # of neighbors = 46843
Ave neighs/atom = 68.1849 Ave neighs/atom = 68.184862
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
## fix name group-id pafi compute-id temperature tdamp seed overdamped 0/1 com 0/1 ## fix name group-id pafi 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 all pafi pa 500.0 0.01 434 overdamped no com yes
fix pafi compute name,style: pa,property/atom fix pafi compute name,style: pa,property/atom
run 0 run 0
Per MPI rank memory allocation (min/avg/max) = 8.403 | 8.403 | 8.403 Mbytes Per MPI rank memory allocation (min/avg/max) = 8.403 | 8.403 | 8.403 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -2828.2492 0 -2828.2492 3015.2014 0 0 -2828.2492 0 -2828.2492 3015.2014
Loop time of 4.76837e-07 on 1 procs for 0 steps with 687 atoms Loop time of 5.53002e-07 on 1 procs for 0 steps with 687 atoms
209.7% CPU use with 1 MPI tasks x 1 OpenMP threads 361.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
@ -123,21 +122,21 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 4.768e-07 | | |100.00 Other | | 5.53e-07 | | |100.00
Nlocal: 687 ave 687 max 687 min Nlocal: 687.000 ave 687 max 687 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3239 ave 3239 max 3239 min Nghost: 3239.00 ave 3239 max 3239 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 46843 ave 46843 max 46843 min Neighs: 46843.0 ave 46843 max 46843 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46843 Total # of neighbors = 46843
Ave neighs/atom = 68.1849 Ave neighs/atom = 68.184862
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
minimize 0 0 1000 1000 # best if using NEB path 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) WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:186)
Parameters for fire: Parameters for fire:
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback 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 0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes
@ -145,47 +144,47 @@ Per MPI rank memory allocation (min/avg/max) = 8.403 | 8.403 | 8.403 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -2828.2492 0 -2828.2492 3015.2014 0 0 -2828.2492 0 -2828.2492 3015.2014
100 9.5973821e-06 -2828.3565 0 -2828.3565 3092.936 100 9.5973821e-06 -2828.3565 0 -2828.3565 3092.936
200 1.501052e-13 -2828.3565 0 -2828.3565 3092.8883 200 1.5010519e-13 -2828.3565 0 -2828.3565 3092.8883
300 5.4507203e-14 -2828.3565 0 -2828.3565 3092.8883 300 5.4507205e-14 -2828.3565 0 -2828.3565 3092.8883
400 5.0283346e-14 -2828.3565 0 -2828.3565 3092.8883 400 5.0283348e-14 -2828.3565 0 -2828.3565 3092.8883
500 4.9056961e-14 -2828.3565 0 -2828.3565 3092.8883 500 4.9056964e-14 -2828.3565 0 -2828.3565 3092.8883
600 4.8645522e-14 -2828.3565 0 -2828.3565 3092.8883 600 4.8645525e-14 -2828.3565 0 -2828.3565 3092.8883
700 4.8498897e-14 -2828.3565 0 -2828.3565 3092.8882 700 4.8498912e-14 -2828.3565 0 -2828.3565 3092.8882
800 4.8444578e-14 -2828.3565 0 -2828.3565 3092.8882 800 4.8444552e-14 -2828.3565 0 -2828.3565 3092.8882
900 4.8424662e-14 -2828.3565 0 -2828.3565 3092.8882 900 4.8424643e-14 -2828.3565 0 -2828.3565 3092.8882
1000 4.8416874e-14 -2828.3565 0 -2828.3565 3092.8882 1000 4.84169e-14 -2828.3565 0 -2828.3565 3092.8882
Loop time of 1.07709 on 1 procs for 1000 steps with 687 atoms Loop time of 1.23105 on 1 procs for 1000 steps with 687 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads 100.0% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats: Minimization stats:
Stopping criterion = max iterations Stopping criterion = max iterations
Energy initial, next-to-last, final = Energy initial, next-to-last, final =
-2828.24917967 -2828.35645844 -2828.35645844 -2828.24917967199 -2828.35645843665 -2828.35645844395
Force two-norm initial, final = 1.2831 7.46892e-07 Force two-norm initial, final = 1.2831004431533395 7.468917431980592e-07
Force max component initial, final = 0.333171 2.93217e-07 Force max component initial, final = 0.3331705829071986 2.93217567864934e-07
Final line search alpha, max atom move = 0 0 Final line search alpha, max atom move = 0.0 0.0
Iterations, force evaluations = 1000 1007 Iterations, force evaluations = 1000 1007
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 1.0319 | 1.0319 | 1.0319 | 0.0 | 95.80 Pair | 1.1849 | 1.1849 | 1.1849 | 0.0 | 96.25
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0099187 | 0.0099187 | 0.0099187 | 0.0 | 0.92 Comm | 0.010743 | 0.010743 | 0.010743 | 0.0 | 0.87
Output | 0.00012374 | 0.00012374 | 0.00012374 | 0.0 | 0.01 Output | 0.00013686 | 0.00013686 | 0.00013686 | 0.0 | 0.01
Modify | 0.023141 | 0.023141 | 0.023141 | 0.0 | 2.15 Modify | 0.02476 | 0.02476 | 0.02476 | 0.0 | 2.01
Other | | 0.01203 | | | 1.12 Other | | 0.01055 | | | 0.86
Nlocal: 687 ave 687 max 687 min Nlocal: 687.000 ave 687 max 687 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3239 ave 3239 max 3239 min Nghost: 3239.00 ave 3239 max 3239 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 46843 ave 46843 max 46843 min Neighs: 46843.0 ave 46843 max 46843 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46843 Total # of neighbors = 46843
Ave neighs/atom = 68.1849 Ave neighs/atom = 68.184862
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
compute dx all displace/atom compute dx all displace/atom
@ -207,7 +206,7 @@ variable apf equal f_af[1]
run 1000 run 1000
Per MPI rank memory allocation (min/avg/max) = 8.778 | 8.778 | 8.778 Mbytes Per MPI rank memory allocation (min/avg/max) = 8.778 | 8.778 | 8.778 Mbytes
Step PotEng Temp v_maxjump Step PotEng Temp v_maxjump
1000 -2828.3565 4.8416874e-14 0 1000 -2828.3565 4.84169e-14 3.9400009e-08
1100 -2788.9297 505.16169 0.53846275 1100 -2788.9297 505.16169 0.53846275
1200 -2784.1274 471.52773 0.5820714 1200 -2784.1274 471.52773 0.5820714
1300 -2782.7071 503.23183 0.57990998 1300 -2782.7071 503.23183 0.57990998
@ -218,34 +217,34 @@ Step PotEng Temp v_maxjump
1800 -2781.6555 512.32986 0.58277945 1800 -2781.6555 512.32986 0.58277945
1900 -2782.1648 486.16736 0.58913114 1900 -2782.1648 486.16736 0.58913114
2000 -2781.1942 493.15046 0.56962281 2000 -2781.1942 493.15046 0.56962281
Loop time of 1.12102 on 1 procs for 1000 steps with 687 atoms Loop time of 1.3463 on 1 procs for 1000 steps with 687 atoms
Performance: 77.072 ns/day, 0.311 hours/ns, 892.043 timesteps/s Performance: 64.176 ns/day, 0.374 hours/ns, 742.778 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads 100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 1.0281 | 1.0281 | 1.0281 | 0.0 | 91.71 Pair | 1.2429 | 1.2429 | 1.2429 | 0.0 | 92.32
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0097873 | 0.0097873 | 0.0097873 | 0.0 | 0.87 Comm | 0.011341 | 0.011341 | 0.011341 | 0.0 | 0.84
Output | 0.00018072 | 0.00018072 | 0.00018072 | 0.0 | 0.02 Output | 0.0001418 | 0.0001418 | 0.0001418 | 0.0 | 0.01
Modify | 0.080336 | 0.080336 | 0.080336 | 0.0 | 7.17 Modify | 0.089655 | 0.089655 | 0.089655 | 0.0 | 6.66
Other | | 0.002599 | | | 0.23 Other | | 0.002248 | | | 0.17
Nlocal: 687 ave 687 max 687 min Nlocal: 687.000 ave 687 max 687 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3239 ave 3239 max 3239 min Nghost: 3239.00 ave 3239 max 3239 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 46844 ave 46844 max 46844 min Neighs: 46844.0 ave 46844 max 46844 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46844 Total # of neighbors = 46844
Ave neighs/atom = 68.1863 Ave neighs/atom = 68.186317
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
minimize 0 0 1000 1000 minimize 0 0 1000 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:186)
Parameters for fire: Parameters for fire:
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback 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 0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes
@ -254,91 +253,149 @@ Step PotEng Temp v_maxjump
2000 -2781.1942 0 0.56962281 2000 -2781.1942 0 0.56962281
2100 -2828.3564 2.3533517e-06 0.028829312 2100 -2828.3564 2.3533517e-06 0.028829312
2200 -2828.3565 2.3166114e-09 0.0015098779 2200 -2828.3565 2.3166114e-09 0.0015098779
2300 -2828.3565 5.7159207e-14 0.0017926087 2300 -2828.3565 5.7159208e-14 0.0017926087
2400 -2828.3565 5.0928432e-14 0.0020264648 2400 -2828.3565 5.0928429e-14 0.0020264648
2500 -2828.3565 4.9253427e-14 0.0022344754 2500 -2828.3565 4.9253427e-14 0.0022344754
2600 -2828.3565 4.8706709e-14 0.0024243813 2600 -2828.3565 4.8706717e-14 0.0024243813
2700 -2828.3565 4.8513394e-14 0.0026003645 2700 -2828.3565 4.8513392e-14 0.0026003645
2800 -2828.3565 4.8442921e-14 0.0027651416 2800 -2828.3565 4.8442915e-14 0.0027651416
2900 -2828.3565 4.8417392e-14 0.0029206277 2900 -2828.3565 4.8417422e-14 0.0029206277
3000 -2828.3565 4.8407328e-14 0.0030682417 3000 -2828.3565 4.840734e-14 0.0030682417
Loop time of 1.10285 on 1 procs for 1000 steps with 687 atoms Loop time of 1.24896 on 1 procs for 1000 steps with 687 atoms
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads 100.0% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats: Minimization stats:
Stopping criterion = max iterations Stopping criterion = max iterations
Energy initial, next-to-last, final = Energy initial, next-to-last, final =
-2781.19422469 -2828.35646618 -2828.35646619 -2781.19422468903 -2828.35646618005 -2828.35646618733
Force two-norm initial, final = 29.0662 7.46923e-07 Force two-norm initial, final = 29.0662462838641 7.469228601686482e-07
Force max component initial, final = 2.29107 2.93233e-07 Force max component initial, final = 2.2910705425983147 2.932332034966123e-07
Final line search alpha, max atom move = 0 0 Final line search alpha, max atom move = 0.0 0.0
Iterations, force evaluations = 1000 1008 Iterations, force evaluations = 1000 1008
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 1.0574 | 1.0574 | 1.0574 | 0.0 | 95.88 Pair | 1.2027 | 1.2027 | 1.2027 | 0.0 | 96.30
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0099056 | 0.0099056 | 0.0099056 | 0.0 | 0.90 Comm | 0.010706 | 0.010706 | 0.010706 | 0.0 | 0.86
Output | 0.00018358 | 0.00018358 | 0.00018358 | 0.0 | 0.02 Output | 0.00016364 | 0.00016364 | 0.00016364 | 0.0 | 0.01
Modify | 0.023358 | 0.023358 | 0.023358 | 0.0 | 2.12 Modify | 0.024873 | 0.024873 | 0.024873 | 0.0 | 1.99
Other | | 0.012 | | | 1.09 Other | | 0.01053 | | | 0.84
Nlocal: 687 ave 687 max 687 min Nlocal: 687.000 ave 687 max 687 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3209 ave 3209 max 3209 min Nghost: 3209.00 ave 3209 max 3209 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 48576 ave 48576 max 48576 min Neighs: 48576.0 ave 48576 max 48576 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 48576 Total # of neighbors = 48576
Ave neighs/atom = 70.7074 Ave neighs/atom = 70.707424
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
variable s_pe equal ${pe}
variable s_pe equal -2828.35646618733
variable s_apf equal ${apf}
variable s_apf equal -0.117797263023891
variable s_adn equal ${adn}
variable s_adn equal 1.36645874805011e-05
variable s_maxjump equal ${maxjump}
variable s_maxjump equal 0.00306824174470598
unfix hp
unfix pa
unfix af
minimize 0 0 1000 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:186)
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) = 8.778 | 8.778 | 8.778 Mbytes
Step PotEng Temp v_maxjump
3000 -2828.3565 0 0.0030682417
3100 -2828.5793 0.00016081731 0.54349309
3200 -2828.5793 1.1620454e-14 0.54386121
3300 -2828.5793 4.4699993e-19 0.54386124
3400 -2828.5793 1.0681196e-23 0.54386124
3500 -2828.5793 2.046642e-25 0.54386124
3600 -2828.5793 1.4539039e-25 0.54386124
3700 -2828.5793 2.0152508e-25 0.54386124
3800 -2828.5793 1.3593174e-25 0.54386124
3900 -2828.5793 1.8155665e-25 0.54386124
4000 -2828.5793 1.2308872e-25 0.54386124
Loop time of 1.20543 on 1 procs for 1000 steps with 687 atoms
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-2828.35646618733 -2828.57925588226 -2828.57925588226
Force two-norm initial, final = 0.5639141583763609 2.3523921777846766e-13
Force max component initial, final = 0.22089321768110187 2.037953139577553e-14
Final line search alpha, max atom move = 0.0 0.0
Iterations, force evaluations = 1000 1017
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1843 | 1.1843 | 1.1843 | 0.0 | 98.25
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.010469 | 0.010469 | 0.010469 | 0.0 | 0.87
Output | 0.00012213 | 0.00012213 | 0.00012213 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01051 | | | 0.87
Nlocal: 687.000 ave 687 max 687 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3239.00 ave 3239 max 3239 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 46844.0 ave 46844 max 46844 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46844
Ave neighs/atom = 68.186317
Neighbor list builds = 0
Dangerous builds = 0
print """ print """
---------- PAFI RESULTS -------- ---------- PAFI RESULTS --------
During run: During run:
Average Distance From Hyperplane = ${adn} A, Average Distance From Hyperplane = ${s_adn}A (Should be very small, around 1e-5A),
Average Force Projection Along MFEP = ${apf} eV/A Average Force Projection Along MFEP = ${s_apf} eV/A
""" """
---------- PAFI RESULTS -------- ---------- PAFI RESULTS --------
During run: During run:
Average Distance From Hyperplane = 1.36645874707752e-05 A, Average Distance From Hyperplane = 1.36645874805011e-05A (Should be very small, around 1e-5A),
Average Force Projection Along MFEP = -0.117797263023877 eV/A Average Force Projection Along MFEP = -0.117797263023891 eV/A
print """ print """
In-plane minimization post-run: In-plane minimization post-run:
energy = ${s_pe} eV
"""
In-plane minimization post-run:
energy = -2828.35646618733 eV
if "${s_maxjump} > 0.1" then "print 'Max Atomic Displacement = ${s_maxjump}A > 0.1A'" "print ' => Possible shallow in-plane metastability: Reduce time in basin and/or decrease tdamp'" else "print 'Max Atomic Displacement = ${s_maxjump}A < 0.1A => No in-plane jumps'"
print 'Max Atomic Displacement = ${s_maxjump}A < 0.1A => No in-plane jumps'
Max Atomic Displacement = 0.00306824174470598A < 0.1A => No in-plane jumps
print """
Full minimization after removal of PAFI fixes:
energy = ${pe} eV energy = ${pe} eV
"""
In-plane minimization post-run:
energy = -2828.35646618732 eV
if "${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 = 0.00306824174700518A < 0.1A => No in-plane jumps
print """
----- END PAFI ---- ----- END PAFI ----
""" """
Full minimization after removal of PAFI fixes:
energy = -2828.57925588226 eV
----- 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 Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03 Total wall time: 0:00:05

277
examples/USER/misc/pafi/log.15Apr20.pafi.g++.4
View File

@ -1,6 +1,4 @@
LAMMPS (15 Apr 2020) LAMMPS (24 Aug 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 units metal
atom_style atomic atom_style atomic
atom_modify map array sort 0 0.0 atom_modify map array sort 0 0.0
@ -9,16 +7,17 @@ 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 ## 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 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 read_data pafipath.4.data fix pa NULL PafiPath
orthogonal box = (0 0 0) to (19.9872 19.9872 19.9872) Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (19.987184 19.987184 19.987184)
2 by 1 by 2 MPI processor grid 2 by 1 by 2 MPI processor grid
reading atoms ... reading atoms ...
687 atoms 687 atoms
read_data CPU = 0.00148988 secs read_data CPU = 0.007 seconds
## EAM potential ## EAM potential
pair_style eam/fs pair_style eam/fs
pair_coeff * * Fe_mm.eam.fs Fe pair_coeff * * ../../../../potentials/Fe_mm.eam.fs Fe
Reading potential file Fe_mm.eam.fs with DATE: 2007-06-11 Reading eam/fs potential file ../../../../potentials/Fe_mm.eam.fs with DATE: 2007-06-11
mass * 55.85 mass * 55.85
thermo 100 thermo 100
@ -43,9 +42,9 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 6.844 | 6.844 | 6.844 Mbytes Per MPI rank memory allocation (min/avg/max) = 6.844 | 6.844 | 6.844 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -2828.2492 0 -2828.2492 3015.2014 0 0 -2828.2492 0 -2828.2492 3015.2014
Loop time of 9.17912e-06 on 4 procs for 0 steps with 687 atoms Loop time of 2.82e-06 on 4 procs for 0 steps with 687 atoms
59.9% CPU use with 4 MPI tasks x 1 OpenMP threads 97.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
@ -55,17 +54,17 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.179e-06 | | |100.00 Other | | 2.82e-06 | | |100.00
Nlocal: 171.75 ave 187 max 163 min Nlocal: 171.750 ave 187 max 163 min
Histogram: 1 1 1 0 0 0 0 0 0 1 Histogram: 1 1 1 0 0 0 0 0 0 1
Nghost: 1854.25 ave 1863 max 1839 min Nghost: 1854.25 ave 1863 max 1839 min
Histogram: 1 0 0 0 0 0 0 1 1 1 Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 11710.8 ave 12319 max 10647 min Neighs: 11710.8 ave 12319 max 10647 min
Histogram: 1 0 0 0 0 0 0 1 1 1 Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 46843 Total # of neighbors = 46843
Ave neighs/atom = 68.1849 Ave neighs/atom = 68.184862
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
print "energy=${pe}" print "energy=${pe}"
@ -77,9 +76,9 @@ run 0
Per MPI rank memory allocation (min/avg/max) = 6.844 | 6.844 | 6.844 Mbytes Per MPI rank memory allocation (min/avg/max) = 6.844 | 6.844 | 6.844 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -2828.2492 0 -2828.2492 3015.2014 0 0 -2828.2492 0 -2828.2492 3015.2014
Loop time of 9.11951e-06 on 4 procs for 0 steps with 687 atoms Loop time of 2.667e-06 on 4 procs for 0 steps with 687 atoms
52.1% CPU use with 4 MPI tasks x 1 OpenMP threads 37.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
@ -89,31 +88,31 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.12e-06 | | |100.00 Other | | 2.667e-06 | | |100.00
Nlocal: 171.75 ave 187 max 163 min Nlocal: 171.750 ave 187 max 163 min
Histogram: 1 1 1 0 0 0 0 0 0 1 Histogram: 1 1 1 0 0 0 0 0 0 1
Nghost: 1854.25 ave 1863 max 1839 min Nghost: 1854.25 ave 1863 max 1839 min
Histogram: 1 0 0 0 0 0 0 1 1 1 Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 11710.8 ave 12319 max 10647 min Neighs: 11710.8 ave 12319 max 10647 min
Histogram: 1 0 0 0 0 0 0 1 1 1 Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 46843 Total # of neighbors = 46843
Ave neighs/atom = 68.1849 Ave neighs/atom = 68.184862
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
## fix name group-id pafi compute-id temperature tdamp seed overdamped 0/1 com 0/1 ## fix name group-id pafi 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 all pafi pa 500.0 0.01 434 overdamped no com yes
fix pafi compute name,style: pa,property/atom fix pafi compute name,style: pa,property/atom
run 0 run 0
Per MPI rank memory allocation (min/avg/max) = 8.344 | 8.344 | 8.344 Mbytes Per MPI rank memory allocation (min/avg/max) = 8.344 | 8.344 | 8.344 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -2828.2492 0 -2828.2492 3015.2014 0 0 -2828.2492 0 -2828.2492 3015.2014
Loop time of 9.17912e-06 on 4 procs for 0 steps with 687 atoms Loop time of 2.52725e-06 on 4 procs for 0 steps with 687 atoms
84.4% CPU use with 4 MPI tasks x 1 OpenMP threads 108.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
@ -123,21 +122,21 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.179e-06 | | |100.00 Other | | 2.527e-06 | | |100.00
Nlocal: 171.75 ave 187 max 163 min Nlocal: 171.750 ave 187 max 163 min
Histogram: 1 1 1 0 0 0 0 0 0 1 Histogram: 1 1 1 0 0 0 0 0 0 1
Nghost: 1854.25 ave 1863 max 1839 min Nghost: 1854.25 ave 1863 max 1839 min
Histogram: 1 0 0 0 0 0 0 1 1 1 Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 11710.8 ave 12319 max 10647 min Neighs: 11710.8 ave 12319 max 10647 min
Histogram: 1 0 0 0 0 0 0 1 1 1 Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 46843 Total # of neighbors = 46843
Ave neighs/atom = 68.1849 Ave neighs/atom = 68.184862
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
minimize 0 0 1000 1000 # best if using NEB path 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) WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:186)
Parameters for fire: Parameters for fire:
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback 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 0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes
@ -145,47 +144,47 @@ Per MPI rank memory allocation (min/avg/max) = 8.344 | 8.344 | 8.344 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -2828.2492 0 -2828.2492 3015.2014 0 0 -2828.2492 0 -2828.2492 3015.2014
100 9.5973821e-06 -2828.3565 0 -2828.3565 3092.936 100 9.5973821e-06 -2828.3565 0 -2828.3565 3092.936
200 1.5010519e-13 -2828.3565 0 -2828.3565 3092.8883 200 1.501052e-13 -2828.3565 0 -2828.3565 3092.8883
300 5.4507205e-14 -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 400 5.0283344e-14 -2828.3565 0 -2828.3565 3092.8883
500 4.905696e-14 -2828.3565 0 -2828.3565 3092.8883 500 4.9056968e-14 -2828.3565 0 -2828.3565 3092.8883
600 4.8645524e-14 -2828.3565 0 -2828.3565 3092.8883 600 4.8645528e-14 -2828.3565 0 -2828.3565 3092.8883
700 4.8498896e-14 -2828.3565 0 -2828.3565 3092.8882 700 4.8498892e-14 -2828.3565 0 -2828.3565 3092.8882
800 4.8444558e-14 -2828.3565 0 -2828.3565 3092.8882 800 4.8444568e-14 -2828.3565 0 -2828.3565 3092.8882
900 4.8424652e-14 -2828.3565 0 -2828.3565 3092.8882 900 4.8424653e-14 -2828.3565 0 -2828.3565 3092.8882
1000 4.8416883e-14 -2828.3565 0 -2828.3565 3092.8882 1000 4.8416878e-14 -2828.3565 0 -2828.3565 3092.8882
Loop time of 0.378521 on 4 procs for 1000 steps with 687 atoms Loop time of 0.43333 on 4 procs for 1000 steps with 687 atoms
94.6% CPU use with 4 MPI tasks x 1 OpenMP threads 95.4% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats: Minimization stats:
Stopping criterion = max iterations Stopping criterion = max iterations
Energy initial, next-to-last, final = Energy initial, next-to-last, final =
-2828.24917967 -2828.35645844 -2828.35645844 -2828.24917967201 -2828.35645843663 -2828.3564584439
Force two-norm initial, final = 1.2831 7.46892e-07 Force two-norm initial, final = 1.2831004431533406 7.468917439994878e-07
Force max component initial, final = 0.333171 2.93218e-07 Force max component initial, final = 0.33317058290719853 2.9321733663323357e-07
Final line search alpha, max atom move = 0 0 Final line search alpha, max atom move = 0.0 0.0
Iterations, force evaluations = 1000 1007 Iterations, force evaluations = 1000 1007
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.28507 | 0.30427 | 0.3132 | 2.1 | 80.38 Pair | 0.3303 | 0.34246 | 0.35813 | 1.7 | 79.03
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.041108 | 0.050675 | 0.070478 | 5.2 | 13.39 Comm | 0.046971 | 0.062117 | 0.073961 | 3.9 | 14.33
Output | 0.00013185 | 0.00025684 | 0.00063133 | 0.0 | 0.07 Output | 0.00013746 | 0.00014874 | 0.00016997 | 0.0 | 0.03
Modify | 0.012176 | 0.01298 | 0.013903 | 0.7 | 3.43 Modify | 0.0099064 | 0.01077 | 0.011612 | 0.6 | 2.49
Other | | 0.01034 | | | 2.73 Other | | 0.01784 | | | 4.12
Nlocal: 171.75 ave 187 max 163 min Nlocal: 171.750 ave 187 max 163 min
Histogram: 1 1 1 0 0 0 0 0 0 1 Histogram: 1 1 1 0 0 0 0 0 0 1
Nghost: 1854.25 ave 1863 max 1839 min Nghost: 1854.25 ave 1863 max 1839 min
Histogram: 1 0 0 0 0 0 0 1 1 1 Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 11710.8 ave 12319 max 10647 min Neighs: 11710.8 ave 12319 max 10647 min
Histogram: 1 0 0 0 0 0 0 1 1 1 Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 46843 Total # of neighbors = 46843
Ave neighs/atom = 68.1849 Ave neighs/atom = 68.184862
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
compute dx all displace/atom compute dx all displace/atom
@ -207,7 +206,7 @@ variable apf equal f_af[1]
run 1000 run 1000
Per MPI rank memory allocation (min/avg/max) = 8.719 | 8.719 | 8.719 Mbytes Per MPI rank memory allocation (min/avg/max) = 8.719 | 8.719 | 8.719 Mbytes
Step PotEng Temp v_maxjump Step PotEng Temp v_maxjump
1000 -2828.3565 4.8416883e-14 0 1000 -2828.3565 4.8416878e-14 3.9625012e-08
1100 -2787.3877 503.1749 0.53858794 1100 -2787.3877 503.1749 0.53858794
1200 -2783.8463 508.91879 0.57609619 1200 -2783.8463 508.91879 0.57609619
1300 -2782.5288 533.03961 0.64090828 1300 -2782.5288 533.03961 0.64090828
@ -218,34 +217,34 @@ Step PotEng Temp v_maxjump
1800 -2780.4909 519.01911 0.60204913 1800 -2780.4909 519.01911 0.60204913
1900 -2782.0825 512.3441 0.6071772 1900 -2782.0825 512.3441 0.6071772
2000 -2779.5449 526.21838 0.58247597 2000 -2779.5449 526.21838 0.58247597
Loop time of 0.358743 on 4 procs for 1000 steps with 687 atoms Loop time of 0.446418 on 4 procs for 1000 steps with 687 atoms
Performance: 240.841 ns/day, 0.100 hours/ns, 2787.512 timesteps/s Performance: 193.541 ns/day, 0.124 hours/ns, 2240.053 timesteps/s
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads 95.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.2806 | 0.29275 | 0.30044 | 1.4 | 81.60 Pair | 0.34383 | 0.35018 | 0.35655 | 0.9 | 78.44
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.028289 | 0.035765 | 0.047713 | 4.0 | 9.97 Comm | 0.049244 | 0.055398 | 0.061404 | 2.2 | 12.41
Output | 0.00016427 | 0.00046188 | 0.001353 | 0.0 | 0.13 Output | 0.00015376 | 0.00016326 | 0.00018954 | 0.0 | 0.04
Modify | 0.02722 | 0.027855 | 0.02832 | 0.2 | 7.76 Modify | 0.034111 | 0.034443 | 0.03473 | 0.1 | 7.72
Other | | 0.001914 | | | 0.53 Other | | 0.006229 | | | 1.40
Nlocal: 171.75 ave 183 max 165 min Nlocal: 171.750 ave 183 max 165 min
Histogram: 1 1 0 1 0 0 0 0 0 1 Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 1854.25 ave 1861 max 1843 min Nghost: 1854.25 ave 1861 max 1843 min
Histogram: 1 0 0 0 0 0 1 0 1 1 Histogram: 1 0 0 0 0 0 1 0 1 1
Neighs: 11711 ave 12115 max 10983 min Neighs: 11711.0 ave 12115 max 10983 min
Histogram: 1 0 0 0 0 0 1 0 1 1 Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 46844 Total # of neighbors = 46844
Ave neighs/atom = 68.1863 Ave neighs/atom = 68.186317
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
minimize 0 0 1000 1000 minimize 0 0 1000 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:186)
Parameters for fire: Parameters for fire:
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback 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 0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes
@ -254,91 +253,149 @@ Step PotEng Temp v_maxjump
2000 -2779.5449 0 0.58247597 2000 -2779.5449 0 0.58247597
2100 -2828.3564 5.5901288e-06 0.022258122 2100 -2828.3564 5.5901288e-06 0.022258122
2200 -2828.3565 2.5724945e-11 0.0014462408 2200 -2828.3565 2.5724945e-11 0.0014462408
2300 -2828.3565 5.8980022e-14 0.0018217607 2300 -2828.3565 5.8980018e-14 0.0018217607
2400 -2828.3565 5.1597338e-14 0.0020531463 2400 -2828.3565 5.1597335e-14 0.0020531463
2500 -2828.3565 4.9451625e-14 0.0022588465 2500 -2828.3565 4.9451623e-14 0.0022588465
2600 -2828.3565 4.8775183e-14 0.0024468988 2600 -2828.3565 4.8775183e-14 0.0024468988
2700 -2828.3565 4.8538712e-14 0.0026213819 2700 -2828.3565 4.8538707e-14 0.0026213819
2800 -2828.3565 4.8450182e-14 0.0027849194 2800 -2828.3565 4.8450209e-14 0.0027849194
2900 -2828.3565 4.8421015e-14 0.0029393609 2900 -2828.3565 4.8421002e-14 0.0029393609
3000 -2828.3565 4.8409029e-14 0.0030860795 3000 -2828.3565 4.8409037e-14 0.0030860795
Loop time of 0.358516 on 4 procs for 1000 steps with 687 atoms Loop time of 0.432206 on 4 procs for 1000 steps with 687 atoms
97.2% CPU use with 4 MPI tasks x 1 OpenMP threads 91.9% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats: Minimization stats:
Stopping criterion = max iterations Stopping criterion = max iterations
Energy initial, next-to-last, final = Energy initial, next-to-last, final =
-2779.54493573 -2828.35646627 -2828.35646628 -2779.54493572831 -2828.35646627033 -2828.3564662776
Force two-norm initial, final = 29.3013 7.46923e-07 Force two-norm initial, final = 29.30132707276523 7.469232246845132e-07
Force max component initial, final = 2.07903 2.93237e-07 Force max component initial, final = 2.0790292865239595 2.9323707292916446e-07
Final line search alpha, max atom move = 0 0 Final line search alpha, max atom move = 0.0 0.0
Iterations, force evaluations = 1000 1008 Iterations, force evaluations = 1000 1008
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.28555 | 0.30143 | 0.30793 | 1.7 | 84.08 Pair | 0.33828 | 0.34752 | 0.35566 | 1.1 | 80.41
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.029324 | 0.035806 | 0.051662 | 4.9 | 9.99 Comm | 0.04768 | 0.056242 | 0.065447 | 2.8 | 13.01
Output | 0.00016069 | 0.00043958 | 0.0012667 | 0.0 | 0.12 Output | 0.00016892 | 0.00018009 | 0.00020427 | 0.0 | 0.04
Modify | 0.0087969 | 0.0089234 | 0.0090258 | 0.1 | 2.49 Modify | 0.010016 | 0.010698 | 0.011316 | 0.4 | 2.48
Other | | 0.01192 | | | 3.32 Other | | 0.01756 | | | 4.06
Nlocal: 171.75 ave 184 max 165 min Nlocal: 171.750 ave 184 max 165 min
Histogram: 1 0 2 0 0 0 0 0 0 1 Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 1828.25 ave 1835 max 1815 min Nghost: 1828.25 ave 1835 max 1815 min
Histogram: 1 0 0 0 0 0 0 1 0 2 Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 12157.5 ave 12578 max 11155 min Neighs: 12157.5 ave 12578 max 11155 min
Histogram: 1 0 0 0 0 0 0 0 0 3 Histogram: 1 0 0 0 0 0 0 0 0 3
Total # of neighbors = 48630 Total # of neighbors = 48630
Ave neighs/atom = 70.786 Ave neighs/atom = 70.786026
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
variable s_pe equal ${pe}
variable s_pe equal -2828.3564662776
variable s_apf equal ${apf}
variable s_apf equal -0.44222069537824
variable s_adn equal ${adn}
variable s_adn equal 1.36645875188617e-05
variable s_maxjump equal ${maxjump}
variable s_maxjump equal 0.00308607949485962
unfix hp
unfix pa
unfix af
minimize 0 0 1000 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:186)
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) = 8.719 | 8.719 | 8.719 Mbytes
Step PotEng Temp v_maxjump
3000 -2828.3565 0 0.0030860795
3100 -2828.5793 0.00016081696 0.5434931
3200 -2828.5793 1.1620338e-14 0.54386121
3300 -2828.5793 4.4708247e-19 0.54386124
3400 -2828.5793 1.0642423e-23 0.54386124
3500 -2828.5793 1.9858026e-25 0.54386124
3600 -2828.5793 1.395464e-25 0.54386124
3700 -2828.5793 2.0687121e-25 0.54386124
3800 -2828.5793 1.3586688e-25 0.54386124
3900 -2828.5793 2.0485828e-25 0.54386124
4000 -2828.5793 1.3803592e-25 0.54386124
Loop time of 0.427843 on 4 procs for 1000 steps with 687 atoms
96.5% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-2828.3564662776 -2828.57925588218 -2828.57925588218
Force two-norm initial, final = 0.5639144322930092 2.34573110665124e-13
Force max component initial, final = 0.22089332498188619 2.0969337377607644e-14
Final line search alpha, max atom move = 0.0 0.0
Iterations, force evaluations = 1000 1017
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.34748 | 0.35476 | 0.3611 | 0.9 | 82.92
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.049149 | 0.054906 | 0.062132 | 2.2 | 12.83
Output | 0.00015435 | 0.00016534 | 0.00018687 | 0.0 | 0.04
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01801 | | | 4.21
Nlocal: 171.750 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: 11711.0 ave 12115 max 10983 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 46844
Ave neighs/atom = 68.186317
Neighbor list builds = 0
Dangerous builds = 0
print """ print """
---------- PAFI RESULTS -------- ---------- PAFI RESULTS --------
During run: During run:
Average Distance From Hyperplane = ${adn} A, Average Distance From Hyperplane = ${s_adn}A (Should be very small, around 1e-5A),
Average Force Projection Along MFEP = ${apf} eV/A Average Force Projection Along MFEP = ${s_apf} eV/A
""" """
---------- PAFI RESULTS -------- ---------- PAFI RESULTS --------
During run: During run:
Average Distance From Hyperplane = 1.3664587498043e-05 A, Average Distance From Hyperplane = 1.36645875188617e-05A (Should be very small, around 1e-5A),
Average Force Projection Along MFEP = -0.442220695378227 eV/A Average Force Projection Along MFEP = -0.44222069537824 eV/A
print """ print """
In-plane minimization post-run: In-plane minimization post-run:
energy = ${pe} eV energy = ${s_pe} eV
""" """
In-plane minimization post-run: In-plane minimization post-run:
energy = -2828.3564662776 eV energy = -2828.3564662776 eV
if "${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 = ${maxjump}A < 0.1A => No in-plane jumps'" if "${s_maxjump} > 0.1" then "print 'Max Atomic Displacement = ${s_maxjump}A > 0.1A'" "print ' => Possible shallow in-plane metastability: Reduce time in basin and/or decrease tdamp'" else "print 'Max Atomic Displacement = ${s_maxjump}A < 0.1A => No in-plane jumps'"
print 'Max Atomic Displacement = ${maxjump}A < 0.1A => No in-plane jumps' print 'Max Atomic Displacement = ${s_maxjump}A < 0.1A => No in-plane jumps'
Max Atomic Displacement = 0.00308607949101158A < 0.1A => No in-plane jumps Max Atomic Displacement = 0.00308607949485962A < 0.1A => No in-plane jumps
print """ print """
Full minimization after removal of PAFI fixes:
energy = ${pe} eV
----- END PAFI ---- ----- END PAFI ----
""" """
Full minimization after removal of PAFI fixes:
energy = -2828.57925588218 eV
----- 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 Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:01 Total wall time: 0:00:01