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removing example script from nylon melt and adding to tiny nylon

This commit is contained in:
wverestek 2020-04-22 14:07:11 +02:00
parent 0288bb4b6b
commit 1751a27ff6
3 changed files with 255 additions and 55 deletions
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55
examples/USER/reaction/nylon,6-6_melt/in.large_nylon_melt_variable_probability
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# 35,000 atom nylon melt example
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data large_nylon_melt.data.gz
variable runsteps equal 200
varaible prob equal step/v_runsteps
velocity all create 800.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
molecule mol2 rxn1_stp1_reacted.data_template
molecule mol3 rxn1_stp2_unreacted.data_template
molecule mol4 rxn1_stp2_reacted.data_template
thermo 50
# dump 1 all xyz 100 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
# stable at 800K
fix 1 statted_grp_REACT nvt temp 800 800 100
# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
# restart 100 restart1 restart2
run 200
# write_restart restart_longrun
# write_data restart_longrun.data

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examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability Normal file
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# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data
variable runsteps equal 1000
variable prob1 equal step/v_runsteps*2
variable prob2 equal (step/v_runsteps)>0.5
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
molecule mol2 rxn1_stp1_reacted.data_template
molecule mol3 rxn1_stp2_unreacted.data_template
molecule mol4 rxn1_stp2_reacted.data_template
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 &
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234
fix 1 statted_grp_REACT nvt temp 300 300 100
# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run ${runsteps}
# write_restart restart_longrun
# write_data restart_longrun.data

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examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.unstabilized.g++ Normal file
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LAMMPS (15 Apr 2020)
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000278722 secs
read_data CPU = 0.0146239 secs
variable runsteps equal 1000
variable prob1 equal step/v_runsteps*2
variable prob2 equal (step/v_runsteps)>0.5
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule template mol1:
1 molecules
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule template mol2:
1 molecules
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
molecule mol3 rxn1_stp2_unreacted.data_template
Read molecule template mol3:
1 molecules
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
molecule mol4 rxn1_stp2_reacted.data_template
Read molecule template mol4:
1 molecules
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
thermo 50
dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:2052)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:2052)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
fix 1 statted_grp_REACT nvt temp 300 300 100
# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run ${runsteps}
run 1000
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:332)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision KISS FFT
3d grid and FFT values/proc = 343 8
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Inconsistent image flags (../domain.cpp:812)
Per MPI rank memory allocation (min/avg/max) = 34.78 | 34.78 | 34.78 Mbytes
Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0 0 0
50 262.63913 -492.10749 0.0034851739 0.1 0 1 0
100 766.52962 -29.714349 0.0034851739 0.2 0 1 0
150 503.86837 50.220304 0.0034851739 0.3 0 1 0
200 456.51295 12.312892 0.0034851739 0.4 0 1 0
250 391.54928 9.2335844 0.0034851739 0.5 0 1 0
300 336.6988 -47.193937 0.0034851739 0.6 0 1 0
350 254.06985 -9.2867898 0.0034851739 0.7 0 1 0
400 259.41098 -25.657321 0.0034851739 0.8 0 1 0
450 258.10364 22.5086 0.0034851739 0.9 0 1 0
500 272.13412 -6.5391448 0.0034851739 1 0 1 0
550 202.75504 54.658731 0.0034851739 1.1 1 1 1
600 344.79887 23.798478 0.0034851739 1.2 1 1 1
650 328.44488 -29.908484 0.0034851739 1.3 1 1 1
700 280.13593 -8.3223255 0.0034851739 1.4 1 1 1
750 300.67624 1.0632669 0.0034851739 1.5 1 1 1
800 376.64234 12.488392 0.0034851739 1.6 1 1 1
850 321.07642 19.814074 0.0034851739 1.7 1 1 1
900 332.23751 30.814079 0.0034851739 1.8 1 1 1
950 311.14029 5.7853136 0.0034851739 1.9 1 1 1
1000 253.14634 -37.560642 0.0034851739 2 1 1 1
Loop time of 0.580684 on 1 procs for 1000 steps with 44 atoms
Performance: 148.790 ns/day, 0.161 hours/ns, 1722.106 timesteps/s
95.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.090707 | 0.090707 | 0.090707 | 0.0 | 15.62
Bond | 0.18541 | 0.18541 | 0.18541 | 0.0 | 31.93
Kspace | 0.065715 | 0.065715 | 0.065715 | 0.0 | 11.32
Neigh | 0.085003 | 0.085003 | 0.085003 | 0.0 | 14.64
Comm | 0.0068229 | 0.0068229 | 0.0068229 | 0.0 | 1.17
Output | 0.096583 | 0.096583 | 0.096583 | 0.0 | 16.63
Modify | 0.047377 | 0.047377 | 0.047377 | 0.0 | 8.16
Other | | 0.00307 | | | 0.53
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 722 ave 722 max 722 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 722
Ave neighs/atom = 16.4091
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00