Merge pull request #3161 from athomps/gcmc-relax-mol-mpi-error
Relaxed the error check on molecule moves in parallel. Molecule excha…
This commit is contained in:
Axel Kohlmeyer
@ -444,8 +444,15 @@ doc page for more info.
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Do not set "neigh_modify once yes" or else this fix will never be
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Do not set "neigh_modify once yes" or else this fix will never be
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called. Reneighboring is required.
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called. Reneighboring is required.
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Only usable for 3D simulations.
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Can be run in parallel, but aspects of the GCMC part will not scale
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Can be run in parallel, but aspects of the GCMC part will not scale
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well in parallel. Only usable for 3D simulations.
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well in parallel. Currently, molecule translations and rotations
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are not supported with more than one MPI process.
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It is still possible to do parallel molecule exchange without
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translation and rotation moves by setting MC moves to zero
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and/or by using mcmoves keyword with *Pmoltrans*=*Pmolrotate*=0.
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When using fix gcmc in combination with fix shake or fix rigid,
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When using fix gcmc in combination with fix shake or fix rigid,
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only GCMC exchange moves are supported, so the argument
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only GCMC exchange moves are supported, so the argument
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198
examples/mc/log.03Mar22.gcmc.co2.g++.4
Normal file
198
examples/mc/log.03Mar22.gcmc.co2.g++.4
Normal file
@ -0,0 +1,198 @@
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LAMMPS (17 Feb 2022)
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# GCMC for CO2 molecular fluid, rigid/small dynamics
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# Rigid CO2 TraPPE model
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# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
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# mixtures containing alkanes, carbon dioxide and
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# nitrogen AIChE J., 47,1676-1682 (2001)].
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# variables available on command line
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variable mu index -8.1
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variable disp index 0.5
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variable temp index 338.0
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variable lbox index 10.0
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variable spacing index 5.0
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# global model settings
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units real
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atom_style full
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boundary p p p
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pair_style lj/cut/coul/long 14
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pair_modify mix arithmetic tail yes
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kspace_style ewald 0.0001
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bond_style harmonic
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angle_style harmonic
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# box, start molecules on simple cubic lattice
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lattice sc ${spacing}
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lattice sc 5.0
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Lattice spacing in x,y,z = 5 5 5
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region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
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region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
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region box block 0 10.0 0 10.0 0 ${lbox} units box
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region box block 0 10.0 0 10.0 0 10.0 units box
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create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
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Created orthogonal box = (0 0 0) to (10 10 10)
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1 by 2 by 2 MPI processor grid
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molecule co2mol CO2.txt
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Read molecule template co2mol:
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1 molecules
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0 fragments
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3 atoms with max type 2
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2 bonds with max type 1
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1 angles with max type 1
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0 dihedrals with max type 0
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0 impropers with max type 0
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create_atoms 0 box mol co2mol 464563 units box
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Created 24 atoms
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using box units in orthogonal box = (0 0 0) to (10 10 10)
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create_atoms CPU = 0.002 seconds
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# rigid CO2 TraPPE model
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pair_coeff 1 1 0.053649 2.8
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pair_coeff 2 2 0.156973 3.05
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bond_coeff 1 0 1.16
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angle_coeff 1 0 180
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# masses
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mass 1 12.0107
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mass 2 15.9994
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# MD settings
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group co2 type 1 2
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24 atoms in group co2
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neighbor 2.0 bin
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neigh_modify every 1 delay 10 check yes
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velocity all create ${temp} 54654
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velocity all create 338.0 54654
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timestep 1.0
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# rigid constraints with thermostat
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fix myrigid co2 rigid/small molecule mol co2mol
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create bodies CPU = 0.000 seconds
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8 rigid bodies with 24 atoms
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1.16 = max distance from body owner to body atom
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# dynamically update fix rigid/nvt/small temperature ndof
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fix_modify myrigid dynamic/dof yes
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# gcmc
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variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
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fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigid
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fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigid
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fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigid
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fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigid
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fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigid
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# atom counts
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variable carbon atom "type==1"
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variable oxygen atom "type==2"
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group carbon dynamic co2 var carbon
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dynamic group carbon defined
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group oxygen dynamic co2 var oxygen
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dynamic group oxygen defined
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variable nC equal count(carbon)
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variable nO equal count(oxygen)
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# output
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variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
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variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
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variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
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variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
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# dynamically update default temperature ndof
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compute_modify thermo_temp dynamic/dof yes
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thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
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thermo 1000
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# run
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run 20000
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Ewald initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
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G vector (1/distance) = 0.16463644
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estimated absolute RMS force accuracy = 0.033206372
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estimated relative force accuracy = 0.0001
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KSpace vectors: actual max1d max3d = 16 2 62
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kxmax kymax kzmax = 2 2 2
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generated 1 of 1 mixed pair_coeff terms from arithmetic mixing rule
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WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:486)
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0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
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0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
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WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:635)
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 16
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ghost atom cutoff = 16
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binsize = 8, bins = 2 2 2
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/coul/long, 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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Per MPI rank memory allocation (min/avg/max) = 15.98 | 15.98 | 15.98 Mbytes
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Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
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0 386.52184 23582.465 -3.2433417 14.209828 0.5846359 24 0 0 0 0 8 16
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1000 384.36044 168.85423 -23.23758 19.858894 0.80387436 33 0.066251757 0.059749054 0 0 11 22
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2000 259.20275 79.927114 -7.8419025 6.9537074 0.43847693 18 0.051929539 0.052057755 0 0 6 12
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3000 302.33017 445.51546 -13.370306 12.616643 0.65771539 27 0.047267159 0.046725853 0 0 9 18
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4000 311.19874 -941.64049 -29.224589 17.624862 0.87695385 36 0.054172258 0.052814245 0 0 12 24
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5000 357.15913 -643.8797 -23.716174 18.453474 0.80387436 33 0.044110118 0.044289139 0 0 11 22
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6000 343.81577 816.03183 -23.966196 17.764058 0.80387436 33 0.042107357 0.041553567 0 0 11 22
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7000 360.66228 -396.06153 -12.261373 13.259144 0.5846359 24 0.046352562 0.047370093 0 0 8 16
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8000 536.38773 97.164555 -1.3308134 6.3954798 0.21923846 9 0.088510977 0.090746839 0 0 3 6
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9000 768.3631 251.53458 -0.87836731 5.3441371 0.14615898 6 0.11093712 0.11396968 0 0 2 4
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10000 219.20608 -312.87929 -18.365974 9.1477634 0.65771539 27 0.117446 0.11875767 0 0 9 18
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11000 380.32873 -455.7618 -19.955783 17.761107 0.73079488 30 0.11798452 0.11947738 0 0 10 20
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12000 379.24355 197.4359 -2.1821544 4.521812 0.21923846 9 0.12913146 0.13205423 0 0 3 6
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13000 396.07556 137.32879 -13.038496 14.561054 0.5846359 24 0.14552187 0.14709749 0 0 8 16
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14000 324.11748 156.7682 -7.5905299 8.6951939 0.43847693 18 0.14458311 0.14598959 0 0 6 12
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15000 355.07055 -171.07765 -14.067188 14.81757 0.65771539 27 0.14061899 0.14191715 0 0 9 18
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16000 303.99764 -48.184319 -22.94389 15.70676 0.80387436 33 0.13709205 0.13778218 0 0 11 22
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17000 233.8048 -12.817441 -10.840623 8.5954415 0.5846359 24 0.13670252 0.13812514 0 0 8 16
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18000 288.74916 157.63378 -6.0604526 7.7463575 0.43847693 18 0.14212703 0.14298282 0 0 6 12
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19000 285.23652 -41.79006 -1.0403841 1.9838837 0.14615898 6 0.1500458 0.15058244 0 0 2 4
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20000 537.62536 77.091199 -3.9443433 9.0811682 0.29231795 12 0.15563619 0.1561609 0 0 4 8
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Loop time of 8.33966 on 4 procs for 20000 steps with 12 atoms
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Performance: 207.203 ns/day, 0.116 hours/ns, 2398.178 timesteps/s
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99.9% 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 | 0.23792 | 0.33196 | 0.40407 | 10.7 | 3.98
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Bond | 0.0061255 | 0.0062467 | 0.0063458 | 0.1 | 0.07
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Kspace | 0.1676 | 0.2404 | 0.33413 | 12.6 | 2.88
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Neigh | 0.019046 | 0.019101 | 0.01916 | 0.0 | 0.23
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Comm | 0.67736 | 0.68025 | 0.68266 | 0.3 | 8.16
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Output | 0.00081757 | 0.00087737 | 0.0010462 | 0.0 | 0.01
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Modify | 7.0053 | 7.0093 | 7.0134 | 0.1 | 84.05
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Other | | 0.05152 | | | 0.62
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Nlocal: 3 ave 5 max 0 min
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Histogram: 1 0 0 0 1 0 0 0 0 2
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Nghost: 711 ave 750 max 671 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Neighs: 321.25 ave 568 max 0 min
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Histogram: 1 0 0 1 0 0 0 0 1 1
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Total # of neighbors = 1285
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Ave neighs/atom = 107.08333
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Ave special neighs/atom = 2
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Neighbor list builds = 20160
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Dangerous builds = 0
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Total wall time: 0:00:08
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296
examples/mc/log.03Mar22.gcmc.h2o.g++.4
Normal file
296
examples/mc/log.03Mar22.gcmc.h2o.g++.4
Normal file
@ -0,0 +1,296 @@
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LAMMPS (17 Feb 2022)
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# fix gcmc example with fix shake
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|
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# variables available on command line
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|
|
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variable mu index -8.1
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variable disp index 0.5
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variable temp index 338.0
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variable lbox index 10.0
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variable spacing index 5.0
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# global model settings
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|
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units real
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atom_style full
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boundary p p p
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pair_style lj/cut/coul/long 14
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pair_modify mix arithmetic tail yes
|
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kspace_style ewald 0.0001
|
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bond_style harmonic
|
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angle_style harmonic
|
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|
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# box, start molecules on simple cubic lattice
|
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|
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lattice sc ${spacing}
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lattice sc 5.0
|
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Lattice spacing in x,y,z = 5 5 5
|
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region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
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region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
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region box block 0 10.0 0 10.0 0 ${lbox} units box
|
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region box block 0 10.0 0 10.0 0 10.0 units box
|
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create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
|
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Created orthogonal box = (0 0 0) to (10 10 10)
|
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1 by 2 by 2 MPI processor grid
|
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|
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molecule h2omol H2O.txt
|
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Read molecule template h2omol:
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1 molecules
|
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0 fragments
|
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|
3 atoms with max type 2
|
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2 bonds with max type 1
|
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1 angles with max type 1
|
||||||
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0 dihedrals with max type 0
|
||||||
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0 impropers with max type 0
|
||||||
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create_atoms 0 box mol h2omol 464563 units box
|
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Created 24 atoms
|
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|
using box units in orthogonal box = (0 0 0) to (10 10 10)
|
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|
create_atoms CPU = 0.002 seconds
|
||||||
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|
||||||
|
# rigid SPC/E water model
|
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|
|
||||||
|
pair_coeff 1 1 0.15535 3.166
|
||||||
|
pair_coeff * 2 0.0000 0.0000
|
||||||
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|
||||||
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bond_coeff 1 1000 1.0
|
||||||
|
angle_coeff 1 100 109.47
|
||||||
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|
||||||
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# masses
|
||||||
|
|
||||||
|
mass 1 15.9994
|
||||||
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mass 2 1.0
|
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|
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|
# MD settings
|
||||||
|
|
||||||
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group h2o type 1 2
|
||||||
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24 atoms in group h2o
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
velocity all create ${temp} 54654
|
||||||
|
velocity all create 338.0 54654
|
||||||
|
timestep 1.0
|
||||||
|
|
||||||
|
minimize 0.0 0.0 100 1000
|
||||||
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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
|
||||||
|
Ewald initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
|
||||||
|
G vector (1/distance) = 0.17044845
|
||||||
|
estimated absolute RMS force accuracy = 0.033206374
|
||||||
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estimated relative force accuracy = 0.00010000001
|
||||||
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KSpace vectors: actual max1d max3d = 16 2 62
|
||||||
|
kxmax kymax kzmax = 2 2 2
|
||||||
|
generated 0 of 1 mixed pair_coeff terms from arithmetic mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 16
|
||||||
|
ghost atom cutoff = 16
|
||||||
|
binsize = 8, bins = 2 2 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut/coul/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 11.85 | 11.85 | 11.85 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 338 -4.9610706 9.2628112e-06 18.211756 730.90791
|
||||||
|
100 338 -15.815905 0.10936727 7.4662793 -278.75864
|
||||||
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Loop time of 0.0318772 on 4 procs for 100 steps with 24 atoms
|
||||||
|
|
||||||
|
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = max iterations
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
-4.96106135392776 -15.6966371009978 -15.7065379926413
|
||||||
|
Force two-norm initial, final = 15.47396 4.3807065
|
||||||
|
Force max component initial, final = 5.8004229 2.0143175
|
||||||
|
Final line search alpha, max atom move = 0.0046871063 0.00944132
|
||||||
|
Iterations, force evaluations = 100 346
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0044502 | 0.008939 | 0.014884 | 4.0 | 28.04
|
||||||
|
Bond | 0.00010079 | 0.00013115 | 0.0001615 | 0.0 | 0.41
|
||||||
|
Kspace | 0.0015161 | 0.0073496 | 0.011723 | 4.3 | 23.06
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.013957 | 0.014086 | 0.01416 | 0.1 | 44.19
|
||||||
|
Output | 1.1416e-05 | 1.2871e-05 | 1.6202e-05 | 0.0 | 0.04
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 0.001359 | | | 4.26
|
||||||
|
|
||||||
|
Nlocal: 6 ave 8 max 3 min
|
||||||
|
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||||
|
Nghost: 1722 ave 1725 max 1720 min
|
||||||
|
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||||
|
Neighs: 1256.75 ave 2101 max 667 min
|
||||||
|
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 5027
|
||||||
|
Ave neighs/atom = 209.45833
|
||||||
|
Ave special neighs/atom = 2
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
reset_timestep 0
|
||||||
|
|
||||||
|
# rigid constraints with thermostat
|
||||||
|
|
||||||
|
fix mynvt h2o nvt temp ${temp} ${temp} 100
|
||||||
|
fix mynvt h2o nvt temp 338.0 ${temp} 100
|
||||||
|
fix mynvt h2o nvt temp 338.0 338.0 100
|
||||||
|
fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol
|
||||||
|
0 = # of size 2 clusters
|
||||||
|
0 = # of size 3 clusters
|
||||||
|
0 = # of size 4 clusters
|
||||||
|
8 = # of frozen angles
|
||||||
|
find clusters CPU = 0.001 seconds
|
||||||
|
|
||||||
|
# important to make temperature dofs dynamic
|
||||||
|
|
||||||
|
compute_modify thermo_temp dynamic/dof yes
|
||||||
|
compute_modify mynvt_temp dynamic/dof yes
|
||||||
|
|
||||||
|
run 1000
|
||||||
|
Ewald initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
|
||||||
|
G vector (1/distance) = 0.17044845
|
||||||
|
estimated absolute RMS force accuracy = 0.033206374
|
||||||
|
estimated relative force accuracy = 0.00010000001
|
||||||
|
KSpace vectors: actual max1d max3d = 16 2 62
|
||||||
|
kxmax kymax kzmax = 2 2 2
|
||||||
|
generated 0 of 1 mixed pair_coeff terms from arithmetic mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 518.26667 -15.815905 0 7.3569121 -385.7767
|
||||||
|
1000 240.84589 -44.723106 0 -33.954368 61.365522
|
||||||
|
Loop time of 0.0928135 on 4 procs for 1000 steps with 24 atoms
|
||||||
|
|
||||||
|
Performance: 930.900 ns/day, 0.026 hours/ns, 10774.300 timesteps/s
|
||||||
|
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0079337 | 0.014647 | 0.023202 | 4.8 | 15.78
|
||||||
|
Bond | 7.45e-05 | 9.0251e-05 | 0.00012098 | 0.0 | 0.10
|
||||||
|
Kspace | 0.0044849 | 0.012865 | 0.019419 | 5.0 | 13.86
|
||||||
|
Neigh | 0.0015513 | 0.0015789 | 0.0016063 | 0.1 | 1.70
|
||||||
|
Comm | 0.038145 | 0.038416 | 0.038704 | 0.1 | 41.39
|
||||||
|
Output | 9.084e-06 | 1.0765e-05 | 1.546e-05 | 0.0 | 0.01
|
||||||
|
Modify | 0.023572 | 0.023646 | 0.023723 | 0.0 | 25.48
|
||||||
|
Other | | 0.00156 | | | 1.68
|
||||||
|
|
||||||
|
Nlocal: 6 ave 9 max 1 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||||
|
Nghost: 1375.25 ave 1495 max 1251 min
|
||||||
|
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||||
|
Neighs: 1263.25 ave 2045 max 122 min
|
||||||
|
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 5053
|
||||||
|
Ave neighs/atom = 210.54167
|
||||||
|
Ave special neighs/atom = 2
|
||||||
|
Neighbor list builds = 30
|
||||||
|
Dangerous builds = 0
|
||||||
|
reset_timestep 0
|
||||||
|
|
||||||
|
# gcmc
|
||||||
|
|
||||||
|
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
|
||||||
|
fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
|
||||||
|
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
|
||||||
|
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
|
||||||
|
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
|
||||||
|
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
|
||||||
|
|
||||||
|
# atom counts
|
||||||
|
|
||||||
|
variable oxygen atom "type==1"
|
||||||
|
variable hydrogen atom "type==2"
|
||||||
|
group oxygen dynamic all var oxygen
|
||||||
|
dynamic group oxygen defined
|
||||||
|
group hydrogen dynamic all var hydrogen
|
||||||
|
dynamic group hydrogen defined
|
||||||
|
variable nO equal count(oxygen)
|
||||||
|
variable nH equal count(hydrogen)
|
||||||
|
|
||||||
|
# output
|
||||||
|
|
||||||
|
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
|
||||||
|
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
|
||||||
|
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
|
||||||
|
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
|
||||||
|
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
# run
|
||||||
|
|
||||||
|
run 20000
|
||||||
|
Ewald initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
|
||||||
|
G vector (1/distance) = 0.17044845
|
||||||
|
estimated absolute RMS force accuracy = 0.033206374
|
||||||
|
estimated relative force accuracy = 0.00010000001
|
||||||
|
KSpace vectors: actual max1d max3d = 16 2 62
|
||||||
|
kxmax kymax kzmax = 2 2 2
|
||||||
|
generated 0 of 1 mixed pair_coeff terms from arithmetic mixing rule
|
||||||
|
WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:486)
|
||||||
|
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
|
||||||
|
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
|
||||||
|
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:635)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
|
||||||
|
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
|
||||||
|
0 240.84589 61.724018 -44.723106 10.768738 0.23910963 24 0 0 0 0 8 16
|
||||||
|
1000 345.18281 -1439.9493 -275.72969 56.590842 0.83688372 84 0.054205983 0.013941446 0 0 28 56
|
||||||
|
2000 345.18939 -1776.1886 -334.1935 66.88136 0.98632724 99 0.03258324 0.0068755525 0 0 33 66
|
||||||
|
3000 371.00685 1611.457 -344.8868 71.883561 0.98632724 99 0.021303508 0.0046725853 0 0 33 66
|
||||||
|
4000 333.39448 -779.09163 -363.7251 66.583637 1.0162159 102 0.016400775 0.0035209497 0 0 34 68
|
||||||
|
5000 313.43793 1752.7257 -366.08712 62.598028 1.0162159 102 0.012996731 0.0028442566 0 0 34 68
|
||||||
|
6000 372.34785 3089.6885 -378.09103 74.36318 1.0162159 102 0.011272836 0.0026808753 0 0 34 68
|
||||||
|
7000 393.56304 1095.6551 -359.16911 78.600157 1.0162159 102 0.0096096775 0.0023107363 0 0 34 68
|
||||||
|
8000 378.04525 -1933.9224 -346.54153 75.501032 1.0162159 102 0.0084617108 0.0020089902 0 0 34 68
|
||||||
|
9000 297.05101 4804.6743 -367.61786 59.325326 1.0162159 102 0.0074970783 0.0017916732 0 0 34 68
|
||||||
|
10000 379.5212 -951.43658 -368.99713 78.058362 1.0461046 105 0.0069429291 0.0016131959 0 0 35 70
|
||||||
|
11000 308.54229 1335.2452 -378.61796 63.459711 1.0461046 105 0.006303921 0.0014684018 0 0 35 70
|
||||||
|
12000 375.19931 2791.9525 -368.98209 79.406248 1.0759934 108 0.0059493315 0.0013447412 0 0 36 72
|
||||||
|
13000 392.21002 4857.5806 -386.58586 83.006354 1.0759934 108 0.005490232 0.0012416383 0 0 36 72
|
||||||
|
14000 327.23916 3472.146 -393.65093 69.256081 1.0759934 108 0.0051077595 0.0011507314 0 0 36 72
|
||||||
|
15000 330.63194 5995.4662 -389.36253 69.974121 1.0759934 108 0.004761212 0.0010753989 0 0 36 72
|
||||||
|
16000 329.25034 694.90103 -387.21725 69.681723 1.0759934 108 0.0044719941 0.0010062767 0 0 36 72
|
||||||
|
17000 368.22282 -3340.8134 -399.58632 77.929761 1.0759934 108 0.0042070328 0.00094751928 0 0 36 72
|
||||||
|
18000 270.78376 1831.8085 -388.15376 57.308002 1.0759934 108 0.0039804956 0.00089324594 0 0 36 72
|
||||||
|
19000 337.54827 1211.6625 -387.9744 71.437877 1.0759934 108 0.0037779014 0.00084467485 0 0 36 72
|
||||||
|
20000 382.5465 5070.3639 -399.03603 83.241787 1.1058821 111 0.0036877934 0.00080264069 0 0 37 74
|
||||||
|
Loop time of 47.6346 on 4 procs for 20000 steps with 111 atoms
|
||||||
|
|
||||||
|
Performance: 36.276 ns/day, 0.662 hours/ns, 419.863 timesteps/s
|
||||||
|
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 4.3783 | 5.9819 | 7.7932 | 52.3 | 12.56
|
||||||
|
Bond | 0.014825 | 0.015376 | 0.016097 | 0.4 | 0.03
|
||||||
|
Kspace | 0.27624 | 2.0815 | 3.68 | 88.4 | 4.37
|
||||||
|
Neigh | 0.60717 | 0.60731 | 0.60741 | 0.0 | 1.27
|
||||||
|
Comm | 1.6019 | 1.6072 | 1.6116 | 0.3 | 3.37
|
||||||
|
Output | 0.00049839 | 0.00055603 | 0.00072798 | 0.0 | 0.00
|
||||||
|
Modify | 37.253 | 37.253 | 37.253 | 0.0 | 78.21
|
||||||
|
Other | | 0.08782 | | | 0.18
|
||||||
|
|
||||||
|
Nlocal: 27.75 ave 31 max 26 min
|
||||||
|
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||||
|
Nghost: 6387 ave 6439 max 6327 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||||
|
Neighs: 26407 ave 33738 max 18362 min
|
||||||
|
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 105628
|
||||||
|
Ave neighs/atom = 951.6036
|
||||||
|
Ave special neighs/atom = 2
|
||||||
|
Neighbor list builds = 20923
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:47
|
||||||
@ -62,7 +62,7 @@ using namespace MathConst;
|
|||||||
#define MAXENERGYTEST 1.0e50
|
#define MAXENERGYTEST 1.0e50
|
||||||
|
|
||||||
enum{EXCHATOM,EXCHMOL}; // exchmode
|
enum{EXCHATOM,EXCHMOL}; // exchmode
|
||||||
enum{MOVEATOM,MOVEMOL}; // movemode
|
enum{NONE,MOVEATOM,MOVEMOL}; // movemode
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
@ -235,7 +235,7 @@ void FixGCMC::options(int narg, char **arg)
|
|||||||
// defaults
|
// defaults
|
||||||
|
|
||||||
exchmode = EXCHATOM;
|
exchmode = EXCHATOM;
|
||||||
movemode = MOVEATOM;
|
movemode = NONE;
|
||||||
patomtrans = 0.0;
|
patomtrans = 0.0;
|
||||||
pmoltrans = 0.0;
|
pmoltrans = 0.0;
|
||||||
pmolrotate = 0.0;
|
pmolrotate = 0.0;
|
||||||
@ -447,27 +447,29 @@ void FixGCMC::init()
|
|||||||
|
|
||||||
// set probabilities for MC moves
|
// set probabilities for MC moves
|
||||||
|
|
||||||
if (pmctot == 0.0)
|
if (nmcmoves > 0) {
|
||||||
if (exchmode == EXCHATOM) {
|
if (pmctot == 0.0)
|
||||||
movemode = MOVEATOM;
|
if (exchmode == EXCHATOM) {
|
||||||
patomtrans = 1.0;
|
movemode = MOVEATOM;
|
||||||
pmoltrans = 0.0;
|
patomtrans = 1.0;
|
||||||
pmolrotate = 0.0;
|
pmoltrans = 0.0;
|
||||||
} else {
|
pmolrotate = 0.0;
|
||||||
movemode = MOVEMOL;
|
} else {
|
||||||
patomtrans = 0.0;
|
movemode = MOVEMOL;
|
||||||
pmoltrans = 0.5;
|
patomtrans = 0.0;
|
||||||
pmolrotate = 0.5;
|
pmoltrans = 0.5;
|
||||||
}
|
pmolrotate = 0.5;
|
||||||
else {
|
}
|
||||||
if (pmoltrans == 0.0 && pmolrotate == 0.0)
|
else {
|
||||||
movemode = MOVEATOM;
|
if (pmoltrans == 0.0 && pmolrotate == 0.0)
|
||||||
else
|
movemode = MOVEATOM;
|
||||||
movemode = MOVEMOL;
|
else
|
||||||
patomtrans /= pmctot;
|
movemode = MOVEMOL;
|
||||||
pmoltrans /= pmctot;
|
patomtrans /= pmctot;
|
||||||
pmolrotate /= pmctot;
|
pmoltrans /= pmctot;
|
||||||
}
|
pmolrotate /= pmctot;
|
||||||
|
}
|
||||||
|
} else movemode = NONE;
|
||||||
|
|
||||||
// decide whether to switch to the full_energy option
|
// decide whether to switch to the full_energy option
|
||||||
|
|
||||||
@ -681,11 +683,13 @@ void FixGCMC::init()
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
// Current implementation is broken using
|
// current implementation is broken using
|
||||||
// full_flag on molecules on more than one processor.
|
// full_flag and translation/rotation of molecules
|
||||||
// Print error if this is the current mode
|
// on more than one processor.
|
||||||
if (full_flag && (exchmode == EXCHMOL || movemode == MOVEMOL) && comm->nprocs > 1)
|
|
||||||
error->all(FLERR,"fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process.");
|
if (full_flag && movemode == MOVEMOL && comm->nprocs > 1)
|
||||||
|
error->all(FLERR,"fix gcmc does currently not support full_energy "
|
||||||
|
"option with molecule MC moves on more than 1 MPI process.");
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -311,9 +311,10 @@ E: Could not find specified fix gcmc group ID
|
|||||||
|
|
||||||
Self-explanatory.
|
Self-explanatory.
|
||||||
|
|
||||||
E: fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process.
|
E: fix gcmc does currently not support full_energy option with molecule MC moves on more than 1 MPI process.
|
||||||
|
|
||||||
UNDOCUMENTED
|
It is still possible to do parallel molecule exchange without translation and rotation moves
|
||||||
|
by setting MC moves to zero and/or by using mcmoves keyword with Pmoltrans=Pmolrotate=0
|
||||||
|
|
||||||
W: Energy of old configuration in fix gcmc is > MAXENERGYTEST.
|
W: Energy of old configuration in fix gcmc is > MAXENERGYTEST.
|
||||||
|
|
||||||
|
|||||||
Reference in New Issue
Block a user