mv examples/gcmc to mc, add 2 scripts for fix mol/swap
This commit is contained in:
Steve Plimpton
@ -75,7 +75,6 @@ eim: NaCl using the EIM potential
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ellipse: ellipsoidal particles in spherical solvent, 2d system
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flow: Couette and Poiseuille flow in a 2d channel
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friction: frictional contact of spherical asperities between 2d surfaces
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gcmc: Grand Canonical MC with fix gcmc, Widom insertion with fix widom
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gjf: use of fix langevin Gronbech-Jensen/Farago option
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granregion: use of fix wall/region/gran as boundary on granular particles
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hugoniostat: Hugoniostat shock dynamics
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@ -83,6 +82,7 @@ hyper: global and local hyperdynamics of diffusion on Pt surface
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indent: spherical indenter into a 2d solid
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kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
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latte: use of LATTE density-functional tight-binding quantum code
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mc: MC package models: GCMC, Widom, fix mol/swap
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meam: MEAM test for SiC and shear (same as shear examples)
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melt: rapid melt of 3d LJ system
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message: client/server coupling of 2 codes
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11733
examples/mc/data.bead
Executable file
11733
examples/mc/data.bead
Executable file
File diff suppressed because it is too large
Load Diff
44
examples/mc/in.mixed
Executable file
44
examples/mc/in.mixed
Executable file
@ -0,0 +1,44 @@
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# test script for fix mol/swap
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# initial system is 50/50 chains of type 1 and type 2
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# b/c epsilon12 is set to 1.02 (weakly same as 1/1 or 1/2) the
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# system will stay in equilibrium as a mix of both chain types
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# fix mol/swap helps this happen quickly
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# see the last 2 columns of thermo output for counts of 2 chain types
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units lj
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atom_style angle
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neighbor 0.36 bin
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neigh_modify delay 0
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pair_style lj/cut 1.1224620483
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bond_style fene
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angle_style cosine
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special_bonds lj 0.0 1.0 1.0
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read_data data.bead
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pair_coeff * * 1.0 1.0 1.1224620483
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pair_coeff 1 2 1.02 1.0 1.1224620483
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bond_coeff 1 30.0 1.5 1.0 1.0
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angle_coeff 1 1.500
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pair_modify shift yes
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variable vt1 atom type==1
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variable vt2 atom type==2
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group g1 dynamic all var vt1 every 100
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group g2 dynamic all var vt2 every 100
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variable count1 equal count(g1)
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variable count2 equal count(g2)
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timestep 0.010
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fix 1 all langevin 1.0 1.0 100.0 702547
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fix 2 all nve
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fix 3 all mol/swap 100 1 1 2 482794 1.0
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compute p all pressure thermo_temp
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thermo 1000
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thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2
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run 50000
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44
examples/mc/in.pure
Executable file
44
examples/mc/in.pure
Executable file
@ -0,0 +1,44 @@
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# test script for fix mol/swap
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# initial system is 50/50 chains of type 1 and type 2
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# b/c epsilon12 is set to 1.1 (stronger than 1/1 or 2/2) the
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# system will go to equilibrium as mostly one type or the other
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# fix mol/swap helps this happen quickly
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# see the last 2 columns of thermo output for counts of 2 chain types
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units lj
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atom_style angle
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neighbor 0.36 bin
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neigh_modify delay 0
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pair_style lj/cut 1.1224620483
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bond_style fene
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angle_style cosine
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special_bonds lj 0.0 1.0 1.0
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read_data data.bead
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pair_coeff * * 1.0 1.0 1.1224620483
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pair_coeff 1 2 1.1 1.0 1.1224620483
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bond_coeff 1 30.0 1.5 1.0 1.0
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angle_coeff 1 1.500
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pair_modify shift yes
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variable vt1 atom type==1
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variable vt2 atom type==2
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group g1 dynamic all var vt1 every 100
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group g2 dynamic all var vt2 every 100
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variable count1 equal count(g1)
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variable count2 equal count(g2)
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timestep 0.010
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fix 1 all langevin 1.0 1.0 100.0 702547
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fix 2 all nve
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fix 3 all mol/swap 100 1 1 2 482794 1.0
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compute p all pressure thermo_temp
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thermo 1000
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thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2
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run 50000
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164
examples/mc/log.13Oct21.mixed.g++.4
Normal file
164
examples/mc/log.13Oct21.mixed.g++.4
Normal file
@ -0,0 +1,164 @@
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LAMMPS (29 Sep 2021)
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# test script for fix mol/swap
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# initial system is 50/50 chains of type 1 and type 2
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# b/c epsilon12 is set to 1.02 (weakly same as 1/1 or 1/2) the
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# system will stay in equilibrium as a mix of both chain types
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# fix mol/swap helps this happen quickly
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# see the last 2 columns of thermo output for counts of 2 chain types
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units lj
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atom_style angle
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neighbor 0.36 bin
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neigh_modify delay 0
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pair_style lj/cut 1.1224620483
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bond_style fene
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angle_style cosine
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special_bonds lj 0.0 1.0 1.0
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read_data data.bead
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Reading data file ...
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orthogonal box = (-8.2115700 -8.2115700 -8.2115700) to (8.2115700 8.2115700 8.2115700)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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4000 atoms
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scanning bonds ...
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1 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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3900 bonds
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reading angles ...
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3800 angles
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 1 1
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special bond factors coul: 0 0 0
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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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4 = max # of 1-4 neighbors
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6 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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read_data CPU = 0.028 seconds
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pair_coeff * * 1.0 1.0 1.1224620483
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pair_coeff 1 2 1.02 1.0 1.1224620483
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bond_coeff 1 30.0 1.5 1.0 1.0
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angle_coeff 1 1.500
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pair_modify shift yes
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variable vt1 atom type==1
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variable vt2 atom type==2
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group g1 dynamic all var vt1 every 100
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dynamic group g1 defined
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group g2 dynamic all var vt2 every 100
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dynamic group g2 defined
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variable count1 equal count(g1)
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variable count2 equal count(g2)
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timestep 0.010
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fix 1 all langevin 1.0 1.0 100.0 702547
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fix 2 all nve
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fix 3 all mol/swap 100 1 1 2 482794 1.0
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compute p all pressure thermo_temp
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thermo 1000
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thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2
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run 50000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.482462
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ghost atom cutoff = 1.482462
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binsize = 0.74123102, bins = 23 23 23
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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WARNING: Communication cutoff 1.4824620483 is shorter than a bond length based estimate of 1.815. This may lead to errors. (../comm.cpp:728)
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Per MPI rank memory allocation (min/avg/max) = 5.313 | 5.314 | 5.314 Mbytes
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Step Temp TotEng Press f_3[1] f_3[2] v_count1 v_count2
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0 0 21.451627 5.079399 0 0 2000 2000
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1000 0.49011138 21.59359 4.2337989 10 10 2000 2000
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2000 0.55288866 21.724374 4.4596786 20 20 2080 1920
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3000 0.59299724 21.844178 4.6112243 30 29 2280 1720
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4000 0.64746348 21.964318 4.9463669 40 39 2280 1720
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5000 0.67853936 22.053147 5.1950218 50 48 2320 1680
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6000 0.70751144 22.147453 5.0636869 60 58 2240 1760
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7000 0.73570064 22.233705 5.4872622 70 68 2160 1840
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8000 0.7677554 22.312938 5.4283736 80 77 2360 1640
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9000 0.78493237 22.383155 5.8547233 90 87 2440 1560
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10000 0.80634514 22.449402 5.8785731 100 96 2400 1600
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11000 0.82563194 22.475286 5.8193738 110 104 2400 1600
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12000 0.81684024 22.527492 6.0323967 120 114 2320 1680
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13000 0.84497155 22.567888 6.0488755 130 122 2240 1760
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14000 0.85452242 22.606908 6.1983634 140 132 2080 1920
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15000 0.88109242 22.654336 6.1408279 150 141 1960 2040
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16000 0.88925915 22.707597 6.1560975 160 150 2000 2000
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17000 0.91598439 22.762791 6.1071728 170 160 2000 2000
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18000 0.92453211 22.778304 6.3330693 180 170 2240 1760
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19000 0.92839551 22.797316 6.2917909 190 180 2000 2000
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20000 0.93054033 22.819289 6.091701 200 189 2200 1800
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21000 0.93955351 22.844135 6.5833013 210 198 2000 2000
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22000 0.94454858 22.856272 6.5661753 220 207 2200 1800
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23000 0.95446407 22.878735 6.5957294 230 216 2160 1840
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24000 0.94748257 22.894539 6.6187447 240 226 1920 2080
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25000 0.95732202 22.912292 6.4795471 250 236 1680 2320
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26000 0.96970172 22.908988 6.537366 260 245 1720 2280
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27000 0.96032166 22.924899 6.6238248 270 255 1960 2040
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28000 0.96197769 22.9358 6.8926097 280 264 1920 2080
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29000 0.98745595 22.964694 6.5839025 290 271 2040 1960
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30000 0.99264869 22.947884 6.3893499 300 280 1920 2080
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31000 0.96953069 22.957927 6.6616047 310 289 1800 2200
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32000 0.99955117 22.963979 6.5958456 320 298 1680 2320
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33000 0.97090103 22.969029 6.9087296 330 307 1800 2200
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34000 0.99818457 22.988477 6.6471994 340 316 1920 2080
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35000 0.9965288 22.992883 6.9691785 350 325 2040 1960
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36000 0.99533174 22.983774 6.6585089 360 334 2000 2000
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37000 0.98819278 22.995387 6.618802 370 344 2080 1920
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38000 0.99598576 22.991892 6.7536669 380 354 2080 1920
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39000 0.99312702 22.989239 6.4028165 390 364 2080 1920
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40000 1.0035821 23.001944 6.9307671 400 374 1920 2080
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41000 0.99914733 23.00134 6.6251677 410 383 1880 2120
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42000 0.98054536 22.981781 6.5918554 420 393 1880 2120
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43000 0.99413829 23.008 6.7390795 430 403 1720 2280
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44000 0.98867961 23.00521 6.8505543 440 412 1600 2400
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45000 0.99626811 23.019995 6.827741 450 421 1640 2360
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46000 1.0186043 23.020759 6.6195562 460 430 1680 2320
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47000 1.0121335 23.019271 6.6022102 470 439 1800 2200
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48000 0.99883756 23.013973 6.5255522 480 448 1920 2080
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49000 0.99425223 23.022708 6.609746 490 458 2240 1760
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50000 0.99505489 23.012641 6.4592863 500 468 2240 1760
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Loop time of 19.4175 on 4 procs for 50000 steps with 4000 atoms
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Performance: 2224796.830 tau/day, 2574.996 timesteps/s
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95.0% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 2.5467 | 2.6684 | 2.7896 | 6.3 | 13.74
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Bond | 2.3037 | 2.4117 | 2.5085 | 5.3 | 12.42
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Neigh | 7.3597 | 7.3633 | 7.3673 | 0.1 | 37.92
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Comm | 3.0482 | 3.2694 | 3.4997 | 10.2 | 16.84
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Output | 0.0014609 | 0.0017069 | 0.0021793 | 0.7 | 0.01
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Modify | 2.9624 | 3.0581 | 3.1424 | 4.7 | 15.75
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Other | | 0.6447 | | | 3.32
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Nlocal: 1000.00 ave 1013 max 986 min
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Histogram: 1 0 0 1 0 0 0 1 0 1
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Nghost: 1186.25 ave 1198 max 1178 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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Neighs: 4927.00 ave 5028 max 4790 min
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Histogram: 1 0 0 0 0 1 0 1 0 1
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Total # of neighbors = 19708
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Ave neighs/atom = 4.9270000
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Ave special neighs/atom = 5.7000000
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Neighbor list builds = 10721
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Dangerous builds = 0
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Total wall time: 0:00:19
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164
examples/mc/log.13Oct21.pure.g++.4
Normal file
164
examples/mc/log.13Oct21.pure.g++.4
Normal file
@ -0,0 +1,164 @@
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LAMMPS (29 Sep 2021)
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# test script for fix mol/swap
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# initial system is 50/50 chains of type 1 and type 2
|
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# b/c epsilon12 is set to 1.1 (stronger than 1/1 or 2/2) the
|
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# system will go to equilibrium as mostly one type or the other
|
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# fix mol/swap helps this happen quickly
|
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# see the last 2 columns of thermo output for counts of 2 chain types
|
||||
|
||||
units lj
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atom_style angle
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neighbor 0.36 bin
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neigh_modify delay 0
|
||||
|
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pair_style lj/cut 1.1224620483
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bond_style fene
|
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angle_style cosine
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special_bonds lj 0.0 1.0 1.0
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read_data data.bead
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Reading data file ...
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orthogonal box = (-8.2115700 -8.2115700 -8.2115700) to (8.2115700 8.2115700 8.2115700)
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1 by 2 by 2 MPI processor grid
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||||
reading atoms ...
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||||
4000 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
3900 bonds
|
||||
reading angles ...
|
||||
3800 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 0 0
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||||
2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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4 = max # of 1-4 neighbors
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6 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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read_data CPU = 0.034 seconds
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pair_coeff * * 1.0 1.0 1.1224620483
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pair_coeff 1 2 1.1 1.0 1.1224620483
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bond_coeff 1 30.0 1.5 1.0 1.0
|
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angle_coeff 1 1.500
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pair_modify shift yes
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variable vt1 atom type==1
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variable vt2 atom type==2
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group g1 dynamic all var vt1 every 100
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dynamic group g1 defined
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group g2 dynamic all var vt2 every 100
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dynamic group g2 defined
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variable count1 equal count(g1)
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variable count2 equal count(g2)
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timestep 0.010
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fix 1 all langevin 1.0 1.0 100.0 702547
|
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fix 2 all nve
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fix 3 all mol/swap 100 1 1 2 482794 1.0
|
||||
|
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compute p all pressure thermo_temp
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||||
thermo 1000
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||||
thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2
|
||||
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
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||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.482462
|
||||
ghost atom cutoff = 1.482462
|
||||
binsize = 0.74123102, bins = 23 23 23
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||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
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attributes: half, newton on
|
||||
pair build: half/bin/newton
|
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stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Communication cutoff 1.4824620483 is shorter than a bond length based estimate of 1.815. This may lead to errors. (../comm.cpp:728)
|
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Per MPI rank memory allocation (min/avg/max) = 5.313 | 5.314 | 5.314 Mbytes
|
||||
Step Temp TotEng Press f_3[1] f_3[2] v_count1 v_count2
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0 0 21.4699 5.230121 0 0 2000 2000
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1000 0.50228459 21.61044 4.3659303 10 9 1960 2040
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2000 0.55721903 21.75955 4.5695439 20 17 1960 2040
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3000 0.61139287 21.892943 4.6514755 30 26 2240 1760
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4000 0.65767189 22.002303 5.1854503 40 33 2280 1720
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5000 0.69383416 22.110271 5.3803498 50 41 2280 1720
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6000 0.72692038 22.205887 5.1756569 60 49 2280 1720
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7000 0.77151336 22.306777 5.5743555 70 56 2240 1760
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8000 0.78606858 22.37036 5.7745208 80 64 2560 1440
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9000 0.79363653 22.420931 5.7369418 90 71 2680 1320
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10000 0.82352629 22.488759 6.0238896 100 76 2720 1280
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11000 0.83867685 22.534887 6.1263771 110 82 2800 1200
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12000 0.85335127 22.590281 6.1499954 120 86 2800 1200
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13000 0.86430985 22.632068 6.1654016 130 89 2760 1240
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14000 0.88057592 22.680253 6.2162735 140 94 2800 1200
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15000 0.89326694 22.719731 6.4789839 150 97 2760 1240
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16000 0.90667644 22.737367 6.214481 160 101 2760 1240
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17000 0.91190336 22.758572 6.2293336 170 105 2600 1400
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18000 0.93182455 22.782019 6.2865382 180 111 2680 1320
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19000 0.93002139 22.797048 6.5579988 190 117 2600 1400
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20000 0.92396243 22.796108 6.6207461 200 122 2800 1200
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21000 0.92949808 22.802813 6.3753268 210 125 2920 1080
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22000 0.93415719 22.807112 6.4696121 220 130 3040 960
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23000 0.9214833 22.82116 6.4146288 230 131 3080 920
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24000 0.95693685 22.839738 6.4035728 240 135 2920 1080
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25000 0.95421851 22.865199 6.4510751 250 138 2880 1120
|
||||
26000 0.95476555 22.878082 6.4652888 260 145 3000 1000
|
||||
27000 0.95773535 22.880671 6.757952 270 149 3000 1000
|
||||
28000 0.95405332 22.896053 6.7425175 280 155 3080 920
|
||||
29000 0.95955713 22.904144 6.6672832 290 161 3240 760
|
||||
30000 0.95521498 22.886699 6.6197941 300 164 3360 640
|
||||
31000 0.96431176 22.91094 6.6373887 310 168 3440 560
|
||||
32000 0.96592495 22.903679 6.4245884 320 172 3520 480
|
||||
33000 0.96457971 22.922681 6.6987987 330 175 3480 520
|
||||
34000 0.96541889 22.92116 6.5992755 340 178 3600 400
|
||||
35000 0.96892691 22.923361 6.7973298 350 178 3600 400
|
||||
36000 0.97267726 22.923431 6.6577403 360 179 3640 360
|
||||
37000 0.97514714 22.939979 6.4028068 370 183 3640 360
|
||||
38000 0.98638599 22.952022 6.6518868 380 183 3640 360
|
||||
39000 0.97864891 22.962534 6.3906837 390 184 3680 320
|
||||
40000 0.9933016 22.975785 6.6819613 400 185 3720 280
|
||||
41000 0.9861477 22.977271 6.6747347 410 187 3800 200
|
||||
42000 0.98157369 22.963129 6.830028 420 187 3800 200
|
||||
43000 0.98202452 22.966947 6.5257905 430 187 3800 200
|
||||
44000 0.99540503 22.971262 6.5546513 440 187 3800 200
|
||||
45000 0.98433653 22.978028 6.4316725 450 189 3800 200
|
||||
46000 0.97912775 22.981328 6.9139851 460 189 3800 200
|
||||
47000 0.9791927 22.981131 6.6417971 470 190 3840 160
|
||||
48000 0.99601024 22.998536 6.6756953 480 191 3880 120
|
||||
49000 0.99589958 22.998489 6.9262843 490 191 3880 120
|
||||
50000 0.99294715 23.00399 6.6976013 500 192 3920 80
|
||||
Loop time of 19.5161 on 4 procs for 50000 steps with 4000 atoms
|
||||
|
||||
Performance: 2213556.537 tau/day, 2561.987 timesteps/s
|
||||
95.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.6256 | 2.7183 | 2.8265 | 5.2 | 13.93
|
||||
Bond | 2.3363 | 2.4406 | 2.5197 | 4.8 | 12.51
|
||||
Neigh | 7.382 | 7.3884 | 7.3936 | 0.2 | 37.86
|
||||
Comm | 3.014 | 3.2136 | 3.3994 | 9.4 | 16.47
|
||||
Output | 0.0014574 | 0.0017086 | 0.0020613 | 0.5 | 0.01
|
||||
Modify | 3.0282 | 3.1295 | 3.2034 | 4.1 | 16.04
|
||||
Other | | 0.624 | | | 3.20
|
||||
|
||||
Nlocal: 1000.00 ave 1011 max 993 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Nghost: 1187.25 ave 1202 max 1179 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 4939.25 ave 5067 max 4850 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 19757
|
||||
Ave neighs/atom = 4.9392500
|
||||
Ave special neighs/atom = 5.7000000
|
||||
Neighbor list builds = 10714
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:19
|
||||
Reference in New Issue
Block a user