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minor changes to example

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This commit is contained in:
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
View File

@ -30,4 +30,11 @@ To run the example from this folder:
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

40
examples/USER/misc/pafi/in.pafi
View File

@ -48,35 +48,39 @@ variable apf equal f_af[1]
run 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 """
---------- PAFI RESULTS --------
During run:
Average Distance From Hyperplane = ${adn} A,
Average Force Projection Along MFEP = ${apf} eV/A
Average Distance From Hyperplane = ${s_adn}A (Should be very small, around 1e-5A),
Average Force Projection Along MFEP = ${s_apf} eV/A
"""
print """
In-plane minimization post-run:
energy = ${pe} eV
energy = ${s_pe} eV
"""
if "${maxjump} > 0.1" then &
"print 'Max Atomic Displacement = ${maxjump}A > 0.1A'" &
if "${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 = ${maxjump}A < 0.1A => No in-plane jumps'"
"print 'Max Atomic Displacement = ${s_maxjump}A < 0.1A => No in-plane jumps'"
print """
Full minimization after removal of PAFI fixes:
energy = ${pe} eV
----- 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)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
LAMMPS (24 Aug 2020)
units metal
atom_style atomic
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
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)
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
reading atoms ...
687 atoms
read_data CPU = 0.00261545 secs
read_data CPU = 0.007 seconds
## 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
pair_coeff * * ../../../../potentials/Fe_mm.eam.fs Fe
Reading eam/fs potential file ../../../../potentials/Fe_mm.eam.fs with DATE: 2007-06-11
mass * 55.85
thermo 100
@ -43,9 +42,9 @@ Neighbor list info ...
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 -2828.2492 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:
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
Output | 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
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
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
Total # of neighbors = 46843
Ave neighs/atom = 68.1849
Ave neighs/atom = 68.184862
Neighbor list builds = 0
Dangerous builds = 0
print "energy=${pe}"
@ -77,9 +76,9 @@ 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 -2828.2492 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:
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
Output | 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
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
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
Total # of neighbors = 46843
Ave neighs/atom = 68.1849
Ave neighs/atom = 68.184862
Neighbor list builds = 0
Dangerous builds = 0
## 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
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 -2828.2492 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:
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
Output | 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
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
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
Total # of neighbors = 46843
Ave neighs/atom = 68.1849
Ave neighs/atom = 68.184862
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)
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
@ -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
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
200 1.5010519e-13 -2828.3565 0 -2828.3565 3092.8883
300 5.4507205e-14 -2828.3565 0 -2828.3565 3092.8883
400 5.0283348e-14 -2828.3565 0 -2828.3565 3092.8883
500 4.9056964e-14 -2828.3565 0 -2828.3565 3092.8883
600 4.8645525e-14 -2828.3565 0 -2828.3565 3092.8883
700 4.8498912e-14 -2828.3565 0 -2828.3565 3092.8882
800 4.8444552e-14 -2828.3565 0 -2828.3565 3092.8882
900 4.8424643e-14 -2828.3565 0 -2828.3565 3092.8882
1000 4.84169e-14 -2828.3565 0 -2828.3565 3092.8882
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:
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 2.93217e-07
Final line search alpha, max atom move = 0 0
-2828.24917967199 -2828.35645843665 -2828.35645844395
Force two-norm initial, final = 1.2831004431533395 7.468917431980592e-07
Force max component initial, final = 0.3331705829071986 2.93217567864934e-07
Final line search alpha, max atom move = 0.0 0.0
Iterations, force evaluations = 1000 1007
MPI task timing breakdown:
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
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
Comm | 0.010743 | 0.010743 | 0.010743 | 0.0 | 0.87
Output | 0.00013686 | 0.00013686 | 0.00013686 | 0.0 | 0.01
Modify | 0.02476 | 0.02476 | 0.02476 | 0.0 | 2.01
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
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
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
Total # of neighbors = 46843
Ave neighs/atom = 68.1849
Ave neighs/atom = 68.184862
Neighbor list builds = 0
Dangerous builds = 0
compute dx all displace/atom
@ -207,7 +206,7 @@ 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 -2828.3565 4.8416874e-14 0
1000 -2828.3565 4.84169e-14 3.9400009e-08
1100 -2788.9297 505.16169 0.53846275
1200 -2784.1274 471.52773 0.5820714
1300 -2782.7071 503.23183 0.57990998
@ -218,34 +217,34 @@ Step PotEng Temp v_maxjump
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
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
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 64.176 ns/day, 0.374 hours/ns, 742.778 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
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
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
Comm | 0.011341 | 0.011341 | 0.011341 | 0.0 | 0.84
Output | 0.0001418 | 0.0001418 | 0.0001418 | 0.0 | 0.01
Modify | 0.089655 | 0.089655 | 0.089655 | 0.0 | 6.66
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
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
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
Total # of neighbors = 46844
Ave neighs/atom = 68.1863
Ave neighs/atom = 68.186317
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)
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
@ -254,91 +253,149 @@ Step PotEng Temp v_maxjump
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
2300 -2828.3565 5.7159208e-14 0.0017926087
2400 -2828.3565 5.0928429e-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
2600 -2828.3565 4.8706717e-14 0.0024243813
2700 -2828.3565 4.8513392e-14 0.0026003645
2800 -2828.3565 4.8442915e-14 0.0027651416
2900 -2828.3565 4.8417422e-14 0.0029206277
3000 -2828.3565 4.840734e-14 0.0030682417
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:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-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
-2781.19422468903 -2828.35646618005 -2828.35646618733
Force two-norm initial, final = 29.0662462838641 7.469228601686482e-07
Force max component initial, final = 2.2910705425983147 2.932332034966123e-07
Final line search alpha, max atom move = 0.0 0.0
Iterations, force evaluations = 1000 1008
MPI task timing breakdown:
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
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
Comm | 0.010706 | 0.010706 | 0.010706 | 0.0 | 0.86
Output | 0.00016364 | 0.00016364 | 0.00016364 | 0.0 | 0.01
Modify | 0.024873 | 0.024873 | 0.024873 | 0.0 | 1.99
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
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
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
Total # of neighbors = 48576
Ave neighs/atom = 70.7074
Ave neighs/atom = 70.707424
Neighbor list 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 """
---------- PAFI RESULTS --------
During run:
Average Distance From Hyperplane = ${adn} A,
Average Force Projection Along MFEP = ${apf} eV/A
Average Distance From Hyperplane = ${s_adn}A (Should be very small, around 1e-5A),
Average Force Projection Along MFEP = ${s_apf} eV/A
"""
---------- PAFI RESULTS --------
During run:
Average Distance From Hyperplane = 1.36645874707752e-05 A,
Average Force Projection Along MFEP = -0.117797263023877 eV/A
Average Distance From Hyperplane = 1.36645874805011e-05A (Should be very small, around 1e-5A),
Average Force Projection Along MFEP = -0.117797263023891 eV/A
print """
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 = ${pe} eV
"""
In-plane minimization post-run:
energy = -2828.35646618732 eV
if "${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 ----
"""
Full minimization after removal of PAFI fixes:
energy = -2828.57925588226 eV
----- 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: 0:00:03
Total wall time: 0:00:05

255
examples/USER/misc/pafi/log.15Apr20.pafi.g++.4
View File

@ -1,6 +1,4 @@
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
LAMMPS (24 Aug 2020)
units metal
atom_style atomic
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
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)
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
reading atoms ...
687 atoms
read_data CPU = 0.00148988 secs
read_data CPU = 0.007 seconds
## 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
pair_coeff * * ../../../../potentials/Fe_mm.eam.fs Fe
Reading eam/fs potential file ../../../../potentials/Fe_mm.eam.fs with DATE: 2007-06-11
mass * 55.85
thermo 100
@ -43,9 +42,9 @@ Neighbor list info ...
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
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:
Section | min time | avg time | max time |%varavg| %total
@ -55,9 +54,9 @@ 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
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
Nghost: 1854.25 ave 1863 max 1839 min
Histogram: 1 0 0 0 0 0 0 1 1 1
@ -65,7 +64,7 @@ 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
Ave neighs/atom = 68.184862
Neighbor list builds = 0
Dangerous builds = 0
print "energy=${pe}"
@ -77,9 +76,9 @@ 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
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:
Section | min time | avg time | max time |%varavg| %total
@ -89,9 +88,9 @@ 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
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
Nghost: 1854.25 ave 1863 max 1839 min
Histogram: 1 0 0 0 0 0 0 1 1 1
@ -99,21 +98,21 @@ 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
Ave neighs/atom = 68.184862
Neighbor list builds = 0
Dangerous builds = 0
## 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
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
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:
Section | min time | avg time | max time |%varavg| %total
@ -123,9 +122,9 @@ 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
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
Nghost: 1854.25 ave 1863 max 1839 min
Histogram: 1 0 0 0 0 0 0 1 1 1
@ -133,11 +132,11 @@ 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
Ave neighs/atom = 68.184862
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)
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
@ -145,39 +144,39 @@ 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
200 1.501052e-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
400 5.0283344e-14 -2828.3565 0 -2828.3565 3092.8883
500 4.9056968e-14 -2828.3565 0 -2828.3565 3092.8883
600 4.8645528e-14 -2828.3565 0 -2828.3565 3092.8883
700 4.8498892e-14 -2828.3565 0 -2828.3565 3092.8882
800 4.8444568e-14 -2828.3565 0 -2828.3565 3092.8882
900 4.8424653e-14 -2828.3565 0 -2828.3565 3092.8882
1000 4.8416878e-14 -2828.3565 0 -2828.3565 3092.8882
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:
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
-2828.24917967201 -2828.35645843663 -2828.3564584439
Force two-norm initial, final = 1.2831004431533406 7.468917439994878e-07
Force max component initial, final = 0.33317058290719853 2.9321733663323357e-07
Final line search alpha, max atom move = 0.0 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
Pair | 0.3303 | 0.34246 | 0.35813 | 1.7 | 79.03
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
Comm | 0.046971 | 0.062117 | 0.073961 | 3.9 | 14.33
Output | 0.00013746 | 0.00014874 | 0.00016997 | 0.0 | 0.03
Modify | 0.0099064 | 0.01077 | 0.011612 | 0.6 | 2.49
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
Nghost: 1854.25 ave 1863 max 1839 min
Histogram: 1 0 0 0 0 0 0 1 1 1
@ -185,7 +184,7 @@ 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
Ave neighs/atom = 68.184862
Neighbor list builds = 0
Dangerous builds = 0
compute dx all displace/atom
@ -207,7 +206,7 @@ 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
1000 -2828.3565 4.8416878e-14 3.9625012e-08
1100 -2787.3877 503.1749 0.53858794
1200 -2783.8463 508.91879 0.57609619
1300 -2782.5288 533.03961 0.64090828
@ -218,34 +217,34 @@ Step PotEng Temp v_maxjump
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
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
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 193.541 ns/day, 0.124 hours/ns, 2240.053 timesteps/s
95.8% CPU use with 4 MPI tasks x no 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
Pair | 0.34383 | 0.35018 | 0.35655 | 0.9 | 78.44
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
Comm | 0.049244 | 0.055398 | 0.061404 | 2.2 | 12.41
Output | 0.00015376 | 0.00016326 | 0.00018954 | 0.0 | 0.04
Modify | 0.034111 | 0.034443 | 0.03473 | 0.1 | 7.72
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
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
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 = 68.1863
Ave neighs/atom = 68.186317
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)
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
@ -254,38 +253,38 @@ 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
2300 -2828.3565 5.8980018e-14 0.0018217607
2400 -2828.3565 5.1597335e-14 0.0020531463
2500 -2828.3565 4.9451623e-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
2700 -2828.3565 4.8538707e-14 0.0026213819
2800 -2828.3565 4.8450209e-14 0.0027849194
2900 -2828.3565 4.8421002e-14 0.0029393609
3000 -2828.3565 4.8409037e-14 0.0030860795
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:
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
-2779.54493572831 -2828.35646627033 -2828.3564662776
Force two-norm initial, final = 29.30132707276523 7.469232246845132e-07
Force max component initial, final = 2.0790292865239595 2.9323707292916446e-07
Final line search alpha, max atom move = 0.0 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
Pair | 0.33828 | 0.34752 | 0.35566 | 1.1 | 80.41
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
Comm | 0.04768 | 0.056242 | 0.065447 | 2.8 | 13.01
Output | 0.00016892 | 0.00018009 | 0.00020427 | 0.0 | 0.04
Modify | 0.010016 | 0.010698 | 0.011316 | 0.4 | 2.48
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
Nghost: 1828.25 ave 1835 max 1815 min
Histogram: 1 0 0 0 0 0 0 1 0 2
@ -293,52 +292,110 @@ 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
Ave neighs/atom = 70.786026
Neighbor list 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 """
---------- PAFI RESULTS --------
During run:
Average Distance From Hyperplane = ${adn} A,
Average Force Projection Along MFEP = ${apf} eV/A
Average Distance From Hyperplane = ${s_adn}A (Should be very small, around 1e-5A),
Average Force Projection Along MFEP = ${s_apf} eV/A
"""
---------- PAFI RESULTS --------
During run:
Average Distance From Hyperplane = 1.3664587498043e-05 A,
Average Force Projection Along MFEP = -0.442220695378227 eV/A
Average Distance From Hyperplane = 1.36645875188617e-05A (Should be very small, around 1e-5A),
Average Force Projection Along MFEP = -0.44222069537824 eV/A
print """
In-plane minimization post-run:
energy = ${pe} eV
energy = ${s_pe} eV
"""
In-plane minimization post-run:
energy = -2828.3564662776 eV
if "${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 = ${maxjump}A < 0.1A => No in-plane jumps'
Max Atomic Displacement = 0.00308607949101158A < 0.1A => No in-plane jumps
if "${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 = 0.00308607949485962A < 0.1A => No in-plane jumps
print """
Full minimization after removal of PAFI fixes:
energy = ${pe} eV
----- END PAFI ----
"""
Full minimization after removal of PAFI fixes:
energy = -2828.57925588218 eV
----- 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