update gcmc example to use fix rigid/small
This commit is contained in:
Axel Kohlmeyer
@ -1,4 +1,4 @@
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# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
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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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@ -58,16 +58,16 @@ timestep 1.0
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# rigid constraints with thermostat
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fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
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fix myrigid co2 rigid/small molecule mol co2mol
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# dynamically update fix rigid/nvt/small temperature ndof
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fix_modify myrigidnvt dynamic/dof yes
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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 &
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co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
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co2mol tfac_insert ${tfac} group co2 rigid myrigid
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# atom counts
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@ -1,196 +0,0 @@
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# GCMC for CO2 molecular fluid, rigid/small/nvt 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 1 by 1 MPI processor grid
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molecule co2mol CO2.txt
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Read molecule co2mol:
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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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Time spent = 0.00134993 secs
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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 myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
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fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
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fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
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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 myrigidnvt 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 myrigidnvt
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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 myrigidnvt
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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 myrigidnvt
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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 myrigidnvt
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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 myrigidnvt
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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:321)
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G vector (1/distance) = 0.164636
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estimated absolute RMS force accuracy = 0.0332064
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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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WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:487)
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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:471)
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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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 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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0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16
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1000 267.9799 -73.919548 -3.6735999 5.8578459 0.36539744 15 0.23663972 0.2494423 0 0 5 10
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2000 409.06596 -98.033864 -6.7570039 10.974131 0.43847693 18 0.29379544 0.29816284 0 0 6 12
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3000 279.3225 -836.47758 -26.434976 15.819539 0.87695385 36 0.23798567 0.24203908 0 0 12 24
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4000 333.6181 606.63478 -30.35312 18.894592 0.87695385 36 0.19121778 0.19481508 0 0 12 24
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5000 405.98741 -103.97582 -14.180277 16.942399 0.65771539 27 0.15272841 0.15982952 0 0 9 18
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6000 283.5835 -240.01076 -6.7198093 7.607777 0.43847693 18 0.1606796 0.16536735 0 0 6 12
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7000 142.00717 154.95914 -0.74192319 0.98769159 0.14615898 6 0.19501993 0.20103405 0 0 2 4
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8000 376.67702 -118.12474 -10.774631 13.847899 0.5846359 24 0.20133396 0.20468352 0 0 8 16
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9000 305.43166 -1095.8633 -10.388279 9.7112935 0.51155641 21 0.19445239 0.19869334 0 0 7 14
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10000 244.08225 -179.31274 -12.974988 8.9732748 0.5846359 24 0.19098971 0.19586397 0 0 8 16
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11000 305.03389 -568.94714 -21.745425 14.244887 0.73079488 30 0.18517522 0.18978828 0 0 10 20
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12000 318.29735 767.76579 -37.184231 21.189508 1.0231128 42 0.17256426 0.17580267 0 0 14 28
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13000 411.21707 433.01125 -4.5149215 8.9889065 0.36539744 15 0.16329385 0.16767604 0 0 5 10
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14000 304.29535 148.28607 -2.3505844 6.6516754 0.36539744 15 0.17435868 0.17897674 0 0 5 10
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15000 338.00555 2384.1424 -21.438264 17.463859 0.80387436 33 0.17237066 0.17634112 0 0 11 22
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16000 613.56062 610.93867 -0.057364228 1.2192718 0.073079488 3 0.17128158 0.1758886 0 0 1 2
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17000 432.63323 -980.52384 -15.79844 18.054365 0.65771539 27 0.17145651 0.17504846 0 0 9 18
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18000 181.74572 -352.81765 -1.8617959 2.1669979 0.21923846 9 0.17292463 0.17654774 0 0 3 6
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19000 208.55292 -248.38735 -4.2287767 4.5588154 0.36539744 15 0.18168324 0.18454331 0 0 5 10
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20000 304.73317 -649.9896 -16.532405 12.716924 0.65771539 27 0.18085983 0.18345574 0 0 9 18
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Loop time of 21.0434 on 1 procs for 20000 steps with 27 atoms
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Performance: 82.116 ns/day, 0.292 hours/ns, 950.415 timesteps/s
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98.5% CPU use with 1 MPI tasks x 1 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 | 2.2373 | 2.2373 | 2.2373 | 0.0 | 10.63
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Bond | 0.022895 | 0.022895 | 0.022895 | 0.0 | 0.11
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Kspace | 0.16756 | 0.16756 | 0.16756 | 0.0 | 0.80
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Neigh | 0.11436 | 0.11436 | 0.11436 | 0.0 | 0.54
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Comm | 0.26988 | 0.26988 | 0.26988 | 0.0 | 1.28
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Output | 0.0014684 | 0.0014684 | 0.0014684 | 0.0 | 0.01
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Modify | 18.193 | 18.193 | 18.193 | 0.0 | 86.45
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Other | | 0.03692 | | | 0.18
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Nlocal: 27 ave 27 max 27 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2081 ave 2081 max 2081 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 6264 ave 6264 max 6264 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 6264
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Ave neighs/atom = 232
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Ave special neighs/atom = 2
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Neighbor list builds = 20177
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Dangerous builds = 0
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Total wall time: 0:00:21
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196
examples/gcmc/log.31Mar21.gcmc.co2.g++.1
Normal file
196
examples/gcmc/log.31Mar21.gcmc.co2.g++.1
Normal file
@ -0,0 +1,196 @@
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LAMMPS (10 Mar 2021)
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using 1 OpenMP thread(s) per MPI task
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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 = 5.0000000 5.0000000 5.0000000
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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 = (0.0000000 0.0000000 0.0000000) to (10.000000 10.000000 10.000000)
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1 by 1 by 1 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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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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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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1.1600000 = 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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||||
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# dynamically update default temperature ndof
|
||||
compute_modify thermo_temp dynamic/dof yes
|
||||
|
||||
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:339)
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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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WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:482)
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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:486)
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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
|
||||
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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
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0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16
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1000 261.50949 -204.60974 -9.6459249 8.3147747 0.51155641 21 0.096366192 0.097590121 0 0 7 14
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2000 479.39697 231.28436 -7.0089345 10.47927 0.36539744 15 0.085531005 0.085453295 0 0 5 10
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3000 318.31766 -433.17133 -7.3680951 8.5396005 0.43847693 18 0.078556687 0.080101462 0 0 6 12
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4000 357.40776 -186.78 -16.453111 14.915105 0.65771539 27 0.082003877 0.08249082 0 0 9 18
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||||
5000 399.94731 1524.2909 -16.624678 18.677282 0.73079488 30 0.071285101 0.072731705 0 0 10 20
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6000 354.71736 60.134827 -18.988979 16.565073 0.73079488 30 0.071615663 0.071713414 0 0 10 20
|
||||
7000 483.32057 966.32174 -5.7393251 10.565037 0.36539744 15 0.087027775 0.089855826 0 0 5 10
|
||||
8000 547.68562 494.96891 -4.125626 11.97201 0.36539744 15 0.11738082 0.11937373 0 0 5 10
|
||||
9000 433.76488 390.91467 -0.85312985 5.1718828 0.21923846 9 0.13265238 0.13513212 0 0 3 6
|
||||
10000 330.01685 -862.07457 -26.494645 18.690633 0.87695385 36 0.13775034 0.13905403 0 0 12 24
|
||||
11000 334.26318 -578.48274 -13.236965 12.288625 0.5846359 24 0.13713936 0.13960485 0 0 8 16
|
||||
12000 243.68657 -1244.7156 -25.757644 12.590645 0.80387436 33 0.1339588 0.13588739 0 0 11 22
|
||||
13000 307.66758 -429.66928 -17.864639 14.367878 0.73079488 30 0.12604721 0.1278094 0 0 10 20
|
||||
14000 330.91434 495.97112 -15.374248 13.809499 0.65771539 27 0.12011756 0.12145865 0 0 9 18
|
||||
15000 564.87966 982.72332 -14.810525 26.379517 0.73079488 30 0.12164324 0.12343521 0 0 10 20
|
||||
16000 342.63867 -54.776299 -2.2580523 5.7875978 0.29231795 12 0.13535812 0.13790758 0 0 4 8
|
||||
17000 461.07005 -2.4317694 -1.145154 3.2068452 0.14615898 6 0.1444739 0.14730804 0 0 2 4
|
||||
18000 197.21207 -40.124433 -7.0857418 5.2906654 0.43847693 18 0.14403997 0.14574329 0 0 6 12
|
||||
19000 393.36395 -420.49802 -11.172739 14.461366 0.5846359 24 0.15005606 0.15142063 0 0 8 16
|
||||
20000 356.48539 56.071962 -1.7861789 4.2504609 0.21923846 9 0.15422732 0.15627984 0 0 3 6
|
||||
Loop time of 19.5982 on 1 procs for 20000 steps with 9 atoms
|
||||
|
||||
Performance: 88.171 ns/day, 0.272 hours/ns, 1020.502 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.3404 | 2.3404 | 2.3404 | 0.0 | 11.94
|
||||
Bond | 0.033919 | 0.033919 | 0.033919 | 0.0 | 0.17
|
||||
Kspace | 0.19974 | 0.19974 | 0.19974 | 0.0 | 1.02
|
||||
Neigh | 0.11478 | 0.11478 | 0.11478 | 0.0 | 0.59
|
||||
Comm | 0.22538 | 0.22538 | 0.22538 | 0.0 | 1.15
|
||||
Output | 0.00096536 | 0.00096536 | 0.00096536 | 0.0 | 0.00
|
||||
Modify | 16.627 | 16.627 | 16.627 | 0.0 | 84.84
|
||||
Other | | 0.05594 | | | 0.29
|
||||
|
||||
Nlocal: 9.00000 ave 9 max 9 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 703.000 ave 703 max 703 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 719.000 ave 719 max 719 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 719
|
||||
Ave neighs/atom = 79.888889
|
||||
Ave special neighs/atom = 2.0000000
|
||||
Neighbor list builds = 20196
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:19
|
||||
Reference in New Issue
Block a user