From 1751a27ff6c6fbcc19c15a97b9c7c952f7aaf975 Mon Sep 17 00:00:00 2001 From: wverestek Date: Wed, 22 Apr 2020 14:07:11 +0200 Subject: [PATCH] removing example script from nylon melt and adding to tiny nylon --- .../in.large_nylon_melt_variable_probability | 55 ----- ...tiny_nylon.stabilized_variable_probability | 56 +++++ .../log.22Apr20.tiny_nylon.unstabilized.g++ | 199 ++++++++++++++++++ 3 files changed, 255 insertions(+), 55 deletions(-) delete mode 100644 examples/USER/reaction/nylon,6-6_melt/in.large_nylon_melt_variable_probability create mode 100644 examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability create mode 100644 examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.unstabilized.g++ diff --git a/examples/USER/reaction/nylon,6-6_melt/in.large_nylon_melt_variable_probability b/examples/USER/reaction/nylon,6-6_melt/in.large_nylon_melt_variable_probability deleted file mode 100644 index f169f19504..0000000000 --- a/examples/USER/reaction/nylon,6-6_melt/in.large_nylon_melt_variable_probability +++ /dev/null @@ -1,55 +0,0 @@ -# 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 diff --git a/examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability b/examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability new file mode 100644 index 0000000000..2c101ac77c --- /dev/null +++ b/examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability @@ -0,0 +1,56 @@ +# 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 diff --git a/examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.unstabilized.g++ b/examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.unstabilized.g++ new file mode 100644 index 0000000000..9fbd807c85 --- /dev/null +++ b/examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.unstabilized.g++ @@ -0,0 +1,199 @@ +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