forked from lijiext/lammps
new example scripts for fix gcmc
This commit is contained in:
Steve Plimpton
parent
f2dc764d1d
commit
dde94c28a7
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@ -67,6 +67,15 @@ variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
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fix mygcmc all 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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# 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 all var carbon
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group oxygen dynamic all var oxygen
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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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@ -74,7 +83,7 @@ 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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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
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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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@ -72,6 +72,15 @@ variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
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fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
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h2omol tfac_insert ${tfac} group h2o shake wshake
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# atom counts
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variable oxygen atom "type==1"
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variable hydrogen atom "type==2"
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group oxygen dynamic all var oxygen
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group hydrogen dynamic all var hydrogen
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variable nO equal count(oxygen)
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variable nH equal count(hydrogen)
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# output
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variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
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@ -79,7 +88,7 @@ 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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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
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thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
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thermo 1000
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# run
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@ -33,6 +33,12 @@ mass * 1.0
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fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
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# atom count
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variable type1 atom "type==1"
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group type1 dynamic all var type1
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variable n1 equal count(type1)
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# averaging
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variable rho equal density
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@ -40,10 +46,11 @@ variable p equal press
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variable nugget equal 1.0e-8
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variable lambda equal 1.0
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variable muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
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fix ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
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fix ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
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variable rhoav equal f_ave[1]
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variable pav equal f_ave[2]
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variable muexav equal f_ave[3]
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variable n1av equal f_ave[4]
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# output
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@ -51,7 +58,7 @@ variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
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variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
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variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
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compute_modify thermo_temp dynamic yes
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thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
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thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
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thermo 1000
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# run
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@ -1,4 +1,5 @@
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LAMMPS (6 Jul 2017)
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LAMMPS (22 Sep 2017)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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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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@ -46,6 +47,7 @@ Read molecule co2mol:
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0 impropers with 0 types
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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 = 0.00136113 secs
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# rigid CO2 TraPPE model
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@ -87,6 +89,17 @@ fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol
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fix mygcmc all 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 all 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 all var carbon
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dynamic group carbon defined
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group oxygen dynamic all 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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@ -94,7 +107,7 @@ 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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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
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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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@ -110,7 +123,7 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
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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 (../neighbor.cpp:472)
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WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:476)
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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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@ -124,57 +137,57 @@ Neighbor list info ...
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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
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0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0
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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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WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
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1000 420.43475 1722.4052 -9.6956123 15.456579 0.5846359 24 0.20879341 0.20713005 0 0
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2000 302.29516 -547.83641 -22.017674 14.11699 0.73079488 30 0.1742478 0.1678018 0 0
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3000 316.6934 -1080.2672 -8.2218891 10.069364 0.51155641 21 0.13544917 0.13720634 0 0
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4000 246.81618 -679.83642 -14.577244 10.29997 0.65771539 27 0.1568939 0.15860229 0 0
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5000 260.22849 -896.29914 -16.097593 10.859684 0.65771539 27 0.13138744 0.13547049 0 0
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6000 291.70796 -1521.99 -22.303136 13.622574 0.73079488 30 0.12615476 0.12717694 0 0
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7000 236.02638 -599.92186 -27.580831 13.367447 0.87695385 36 0.119703 0.12145398 0 0
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8000 321.45341 688.10577 -10.09204 11.817696 0.5846359 24 0.10917411 0.11032646 0 0
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9000 502.85382 -302.31056 -0.22330142 0.99927447 0.073079488 3 0.1254105 0.12905828 0 0
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10000 249.98239 -510.0091 -32.815145 15.399767 0.95003334 39 0.1274504 0.12875623 0 0
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11000 247.59424 -1129.0274 -25.320205 12.792544 0.80387436 33 0.11739076 0.11916784 0 0
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12000 0 -20.39554 -0.14872889 -0 0 0 0.1254933 0.12920375 0 0
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13000 1272.2738 -474.79484 -0.29450485 8.8489483 0.14615898 6 0.13767133 0.14112496 0 0
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14000 516.54246 -36.296516 -5.0012009 11.291243 0.36539744 15 0.15632744 0.15955377 0 0
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15000 307.09233 1951.9301 -14.820362 12.815375 0.65771539 27 0.15393544 0.15716192 0 0
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16000 198.31989 -559.48443 -30.459487 11.231925 0.87695385 36 0.1482565 0.15025652 0 0
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17000 246.99311 657.85683 -18.579206 11.53442 0.73079488 30 0.14143958 0.14375423 0 0
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18000 467.13468 167.03738 -1.0945268 5.569759 0.21923846 9 0.13847359 0.14098533 0 0
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19000 359.54027 -1413.5407 -12.156233 13.217895 0.5846359 24 0.15169146 0.15294205 0 0
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20000 227.79597 -1204.5652 -23.24144 10.637925 0.73079488 30 0.14917199 0.15022946 0 0
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Loop time of 20.153 on 1 procs for 20000 steps with 30 atoms
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1000 420.43475 1722.4052 -9.6956122 15.456579 0.5846359 24 0.20879341 0.20713005 0 0 8 16
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2000 302.29516 -547.83642 -22.017674 14.11699 0.73079488 30 0.1742478 0.1678018 0 0 10 20
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3000 316.6934 -1080.2673 -8.2218902 10.069364 0.51155641 21 0.13544917 0.13720634 0 0 7 14
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4000 246.81614 -679.83628 -14.57724 10.299968 0.65771539 27 0.1568939 0.15860229 0 0 9 18
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5000 260.23291 -896.27949 -16.097524 10.859868 0.65771539 27 0.13138744 0.13547049 0 0 9 18
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6000 291.64889 -1524.1007 -22.306243 13.619816 0.73079488 30 0.12615476 0.12717694 0 0 10 20
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7000 235.90417 -565.40879 -27.600934 13.360525 0.87695385 36 0.119703 0.12145398 0 0 12 24
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8000 483.381 2017.6258 -7.1315833 15.369247 0.51155641 21 0.10942279 0.11082908 0 0 7 14
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9000 468.87446 -285.22545 -0.22330095 0.93175047 0.073079488 3 0.13029748 0.13349433 0 0 1 2
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10000 245.34708 -254.65444 -16.192443 11.457551 0.73079488 30 0.15023549 0.15176828 0 0 10 20
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11000 233.27704 523.81197 -24.29051 12.052812 0.80387436 33 0.1438083 0.14547187 0 0 11 22
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12000 230.75966 -2161.9134 -23.812352 11.922746 0.80387436 33 0.1338274 0.13534617 0 0 11 22
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13000 216.09982 -930.72014 -23.138263 11.16531 0.80387436 33 0.12480714 0.12612138 0 0 11 22
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14000 343.12403 -327.36241 -16.995149 16.023672 0.73079488 30 0.12006081 0.12108416 0 0 10 20
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15000 369.60805 581.40471 -11.495738 13.588021 0.5846359 24 0.11372814 0.11534691 0 0 8 16
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16000 221.23125 -918.58249 -30.702491 12.529519 0.87695385 36 0.11489536 0.11560548 0 0 12 24
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17000 301.82269 -450.56586 -14.373996 12.595466 0.65771539 27 0.11226626 0.11350321 0 0 9 18
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18000 1065.1385 474.31881 -0.45476519 7.4082761 0.14615898 6 0.11419593 0.11580815 0 0 2 4
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19000 217.29422 -1111.0114 -12.048289 7.988458 0.5846359 24 0.12564213 0.1261457 0 0 8 16
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20000 353.35515 465.29269 -6.8428553 9.4795613 0.43847693 18 0.12529827 0.12590018 0 0 6 12
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Loop time of 14.604 on 1 procs for 20000 steps with 18 atoms
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Performance: 85.744 ns/day, 0.280 hours/ns, 992.408 timesteps/s
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99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
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Performance: 118.323 ns/day, 0.203 hours/ns, 1369.484 timesteps/s
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99.9% 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 | 2.5352 | 2.5352 | 2.5352 | 0.0 | 12.58
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Bond | 0.026112 | 0.026112 | 0.026112 | 0.0 | 0.13
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Kspace | 0.25 | 0.25 | 0.25 | 0.0 | 1.24
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Neigh | 0.10364 | 0.10364 | 0.10364 | 0.0 | 0.51
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Comm | 0.22907 | 0.22907 | 0.22907 | 0.0 | 1.14
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Output | 0.0013065 | 0.0013065 | 0.0013065 | 0.0 | 0.01
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Modify | 16.957 | 16.957 | 16.957 | 0.0 | 84.14
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Other | | 0.05061 | | | 0.25
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Pair | 1.8966 | 1.8966 | 1.8966 | 0.0 | 12.99
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Bond | 0.019538 | 0.019538 | 0.019538 | 0.0 | 0.13
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Kspace | 0.14784 | 0.14784 | 0.14784 | 0.0 | 1.01
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Neigh | 0.070002 | 0.070002 | 0.070002 | 0.0 | 0.48
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Comm | 0.15055 | 0.15055 | 0.15055 | 0.0 | 1.03
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Output | 0.0017672 | 0.0017672 | 0.0017672 | 0.0 | 0.01
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Modify | 12.287 | 12.287 | 12.287 | 0.0 | 84.13
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Other | | 0.03089 | | | 0.21
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Nlocal: 30 ave 30 max 30 min
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Nlocal: 18 ave 18 max 18 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2310 ave 2310 max 2310 min
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Nghost: 1335 ave 1335 max 1335 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 7736 ave 7736 max 7736 min
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Neighs: 2797 ave 2797 max 2797 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 7736
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Ave neighs/atom = 257.867
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Total # of neighbors = 2797
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Ave neighs/atom = 155.389
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Ave special neighs/atom = 2
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Neighbor list builds = 20349
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Neighbor list builds = 20401
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Dangerous builds = 0
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Total wall time: 0:00:20
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Total wall time: 0:00:14
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@ -1,4 +1,5 @@
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LAMMPS (6 Jul 2017)
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LAMMPS (22 Sep 2017)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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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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@ -46,6 +47,7 @@ Read molecule co2mol:
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0 impropers with 0 types
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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 = 0.00223303 secs
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# rigid CO2 TraPPE model
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@ -87,6 +89,17 @@ fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol
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fix mygcmc all 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 all 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 all var carbon
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dynamic group carbon defined
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group oxygen dynamic all 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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@ -94,7 +107,7 @@ 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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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
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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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@ -110,7 +123,7 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
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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 (../neighbor.cpp:472)
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WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:476)
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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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@ -124,57 +137,57 @@ Neighbor list info ...
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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) = 15.41 | 15.41 | 15.41 Mbytes
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Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc
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0 386.52184 23582.465 -3.2433417 14.209828 0.5846359 24 0 0 0 0
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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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WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
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1000 335.66829 -3.7743052 -4.6268612 7.3374649 0.36539744 15 0.20601899 0.20787963 0 0
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2000 459.73529 238.91592 -0.42937831 5.4815343 0.21923846 9 0.30392058 0.30105616 0 0
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3000 255.47773 -479.67802 -36.850434 15.738299 0.95003334 39 0.22220744 0.2197582 0 0
|
||||
4000 182.70803 -1059.2262 -43.044833 12.163134 1.0231128 42 0.16781689 0.16716177 0 0
|
||||
5000 234.00907 -1821.0444 -46.04795 15.578317 1.0231128 42 0.13498091 0.13704201 0 0
|
||||
6000 163.42759 -774.67294 -49.686261 11.691518 1.0961923 45 0.11401677 0.11296973 0 0
|
||||
7000 171.64616 -355.23516 -49.323434 12.27947 1.0961923 45 0.098302308 0.098552065 0 0
|
||||
8000 251.29791 -905.47863 -37.841209 15.480807 0.95003334 39 0.086856972 0.08638658 0 0
|
||||
9000 143.69498 -849.95393 -49.073188 10.279858 1.0961923 45 0.078261061 0.077955243 0 0
|
||||
10000 239.35727 -1158.1879 -43.562047 15.934355 1.0231128 42 0.070789792 0.070807529 0 0
|
||||
11000 169.51213 -1574.7885 -51.125228 12.126803 1.0961923 45 0.065008734 0.06498871 0 0
|
||||
12000 181.39739 160.11631 -46.850937 12.977068 1.0961923 45 0.059648717 0.059514803 0 0
|
||||
13000 164.14601 -1107.7629 -50.726722 11.742914 1.0961923 45 0.055207333 0.055097701 0 0
|
||||
14000 287.26285 418.51463 -41.664766 19.123497 1.0231128 42 0.051346789 0.051222285 0 0
|
||||
15000 256.94593 -532.36615 -41.651618 17.105257 1.0231128 42 0.047870301 0.047861685 0 0
|
||||
16000 166.92132 151.15933 -39.957018 11.11219 1.0231128 42 0.045205599 0.045042211 0 0
|
||||
17000 163.22452 -1299.8119 -42.677558 10.866089 1.0231128 42 0.043122086 0.042993687 0 0
|
||||
18000 158.01154 475.77329 -48.803162 11.304057 1.0961923 45 0.041016683 0.040647229 0 0
|
||||
19000 138.49297 -1585.1508 -47.517099 9.9077098 1.0961923 45 0.038929287 0.038436764 0 0
|
||||
20000 173.84439 -1362.6301 -53.002743 12.436731 1.0961923 45 0.036973919 0.036523816 0 0
|
||||
Loop time of 31.8386 on 4 procs for 20000 steps with 45 atoms
|
||||
1000 335.66829 -3.7743052 -4.6268612 7.3374649 0.36539744 15 0.20601899 0.20787963 0 0 5 10
|
||||
2000 459.73529 238.91592 -0.42937831 5.4815343 0.21923846 9 0.30392058 0.30105616 0 0 3 6
|
||||
3000 255.47773 -479.67802 -36.850434 15.738299 0.95003334 39 0.22220744 0.2197582 0 0 13 26
|
||||
4000 182.70803 -1059.2265 -43.04484 12.163134 1.0231128 42 0.16781689 0.16716177 0 0 14 28
|
||||
5000 234.00901 -1821.0459 -46.047939 15.578313 1.0231128 42 0.13498091 0.13704201 0 0 14 28
|
||||
6000 163.42358 -774.64962 -49.686149 11.691232 1.0961923 45 0.11401677 0.11296973 0 0 15 30
|
||||
7000 171.36765 -359.28792 -49.34022 12.259546 1.0961923 45 0.098302308 0.098552065 0 0 15 30
|
||||
8000 215.2905 -905.73479 -38.206404 13.262629 0.95003334 39 0.086608098 0.086135456 0 0 13 26
|
||||
9000 185.19905 -2320.8255 -52.964346 13.249037 1.0961923 45 0.077379246 0.077059206 0 0 15 30
|
||||
10000 241.5783 -1410.8134 -51.37248 17.282377 1.0961923 45 0.069600048 0.069395413 0 0 15 30
|
||||
11000 153.38332 -2647.9572 -53.967244 10.972957 1.0961923 45 0.063207938 0.06315287 0 0 15 30
|
||||
12000 188.93059 -1639.9304 -52.218219 13.515989 1.0961923 45 0.05816163 0.058001715 0 0 15 30
|
||||
13000 243.39974 -1127.2881 -44.54519 16.203468 1.0231128 42 0.053682268 0.053700858 0 0 14 28
|
||||
14000 200.88474 -272.11992 -41.725507 13.373183 1.0231128 42 0.050212054 0.050071222 0 0 14 28
|
||||
15000 204.6505 -1616.9057 -44.631997 13.623875 1.0231128 42 0.046944632 0.046920585 0 0 14 28
|
||||
16000 169.22546 105.40991 -42.46103 11.26558 1.0231128 42 0.044460451 0.044287314 0 0 14 28
|
||||
17000 163.55389 -783.34837 -36.841459 10.075477 0.95003334 39 0.042304052 0.042283048 0 0 13 26
|
||||
18000 499.48334 -503.24838 -8.94456 15.881226 0.51155641 21 0.04035334 0.040870565 0 0 7 14
|
||||
19000 658.81004 391.68747 -2.6979013 11.12813 0.29231795 12 0.055391781 0.056188676 0 0 4 8
|
||||
20000 489.87356 -122.40743 -13.636951 18.00938 0.5846359 24 0.061378424 0.061821941 0 0 8 16
|
||||
Loop time of 17.1274 on 4 procs for 20000 steps with 24 atoms
|
||||
|
||||
Performance: 54.274 ns/day, 0.442 hours/ns, 628.168 timesteps/s
|
||||
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 100.891 ns/day, 0.238 hours/ns, 1167.718 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1546 | 1.6687 | 2.1338 | 29.5 | 5.24
|
||||
Bond | 0.019769 | 0.020369 | 0.02132 | 0.4 | 0.06
|
||||
Kspace | 0.53392 | 0.99911 | 1.5116 | 37.8 | 3.14
|
||||
Neigh | 0.06737 | 0.067842 | 0.068412 | 0.2 | 0.21
|
||||
Comm | 1.9408 | 1.9582 | 1.9733 | 1.1 | 6.15
|
||||
Output | 0.0019503 | 0.0020472 | 0.0022476 | 0.3 | 0.01
|
||||
Modify | 26.974 | 26.99 | 27.001 | 0.2 | 84.77
|
||||
Other | | 0.1322 | | | 0.42
|
||||
Pair | 0.81646 | 1.1504 | 1.4937 | 23.0 | 6.72
|
||||
Bond | 0.011878 | 0.012255 | 0.013296 | 0.5 | 0.07
|
||||
Kspace | 0.23802 | 0.58086 | 0.91304 | 32.3 | 3.39
|
||||
Neigh | 0.04321 | 0.043291 | 0.043372 | 0.0 | 0.25
|
||||
Comm | 0.90855 | 0.90959 | 0.91112 | 0.1 | 5.31
|
||||
Output | 0.0011697 | 0.0012506 | 0.001482 | 0.4 | 0.01
|
||||
Modify | 14.362 | 14.365 | 14.367 | 0.1 | 83.87
|
||||
Other | | 0.06436 | | | 0.38
|
||||
|
||||
Nlocal: 11.25 ave 14 max 8 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Nghost: 2639.75 ave 2656 max 2617 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 4320 ave 5824 max 2201 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Nlocal: 6 ave 8 max 4 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 1465.25 ave 1556 max 1376 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 1243.5 ave 1726 max 748 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 17280
|
||||
Ave neighs/atom = 384
|
||||
Total # of neighbors = 4974
|
||||
Ave neighs/atom = 207.25
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 20394
|
||||
Neighbor list builds = 20375
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:31
|
||||
Total wall time: 0:00:17
|
||||
|
|
|
|||
|
|
@ -1,4 +1,5 @@
|
|||
LAMMPS (6 Jul 2017)
|
||||
LAMMPS (22 Sep 2017)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# fix gcmc example with fix shake
|
||||
|
||||
|
|
@ -51,6 +52,7 @@ Read molecule h2omol:
|
|||
0 impropers with 0 types
|
||||
create_atoms 0 box mol h2omol 464563 units box
|
||||
Created 24 atoms
|
||||
Time spent = 0.00136209 secs
|
||||
|
||||
# rigid SPC/E water model
|
||||
|
||||
|
|
@ -99,41 +101,41 @@ Neighbor list info ...
|
|||
Per MPI rank memory allocation (min/avg/max) = 11.88 | 11.88 | 11.88 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 338 -4.1890564 9.2628112e-06 18.98377 739.06991
|
||||
100 338 -30.182886 0.85607237 -6.1539961 -2535.3207
|
||||
Loop time of 0.0525794 on 1 procs for 100 steps with 24 atoms
|
||||
100 338 -27.771871 0.61137788 -3.9876753 -2259.9107
|
||||
Loop time of 0.0333829 on 1 procs for 100 steps with 24 atoms
|
||||
|
||||
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-4.18904713252 -28.9258064504 -29.3268133965
|
||||
Force two-norm initial, final = 18.0027 42.4511
|
||||
Force max component initial, final = 5.8993 16.0523
|
||||
Final line search alpha, max atom move = 0.00353207 0.056698
|
||||
Iterations, force evaluations = 100 238
|
||||
-4.18904713252 -26.8589493819 -27.1604926722
|
||||
Force two-norm initial, final = 18.0027 28.6823
|
||||
Force max component initial, final = 5.8993 11.77
|
||||
Final line search alpha, max atom move = 0.00301381 0.0354725
|
||||
Iterations, force evaluations = 100 239
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.044199 | 0.044199 | 0.044199 | 0.0 | 84.06
|
||||
Bond | 0.00049019 | 0.00049019 | 0.00049019 | 0.0 | 0.93
|
||||
Kspace | 0.0031631 | 0.0031631 | 0.0031631 | 0.0 | 6.02
|
||||
Neigh | 0.00046444 | 0.00046444 | 0.00046444 | 0.0 | 0.88
|
||||
Comm | 0.0034101 | 0.0034101 | 0.0034101 | 0.0 | 6.49
|
||||
Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.04
|
||||
Pair | 0.028252 | 0.028252 | 0.028252 | 0.0 | 84.63
|
||||
Bond | 0.00025415 | 0.00025415 | 0.00025415 | 0.0 | 0.76
|
||||
Kspace | 0.0017328 | 0.0017328 | 0.0017328 | 0.0 | 5.19
|
||||
Neigh | 0.00038004 | 0.00038004 | 0.00038004 | 0.0 | 1.14
|
||||
Comm | 0.0022359 | 0.0022359 | 0.0022359 | 0.0 | 6.70
|
||||
Output | 2.1935e-05 | 2.1935e-05 | 2.1935e-05 | 0.0 | 0.07
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0008333 | | | 1.58
|
||||
Other | | 0.0005062 | | | 1.52
|
||||
|
||||
Nlocal: 24 ave 24 max 24 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2047 ave 2047 max 2047 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4936 ave 4936 max 4936 min
|
||||
Neighs: 4939 ave 4939 max 4939 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4936
|
||||
Ave neighs/atom = 205.667
|
||||
Total # of neighbors = 4939
|
||||
Ave neighs/atom = 205.792
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
|
@ -162,36 +164,36 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
|||
kxmax kymax kzmax = 2 2 2
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 518.26667 -30.182886 0 -7.0100684 993.1985
|
||||
1000 326.9865 -62.258445 0 -47.638175 -5.3440813
|
||||
Loop time of 0.14263 on 1 procs for 1000 steps with 24 atoms
|
||||
0 518.26667 -27.771871 0 -4.5990532 3.1322213
|
||||
1000 277.5448 -45.272615 0 -32.86299 -1575.2641
|
||||
Loop time of 0.101694 on 1 procs for 1000 steps with 24 atoms
|
||||
|
||||
Performance: 605.764 ns/day, 0.040 hours/ns, 7011.155 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 849.609 ns/day, 0.028 hours/ns, 9833.435 timesteps/s
|
||||
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.10849 | 0.10849 | 0.10849 | 0.0 | 76.07
|
||||
Bond | 0.00015426 | 0.00015426 | 0.00015426 | 0.0 | 0.11
|
||||
Kspace | 0.01205 | 0.01205 | 0.01205 | 0.0 | 8.45
|
||||
Neigh | 0.0046577 | 0.0046577 | 0.0046577 | 0.0 | 3.27
|
||||
Comm | 0.011531 | 0.011531 | 0.011531 | 0.0 | 8.08
|
||||
Output | 1.6212e-05 | 1.6212e-05 | 1.6212e-05 | 0.0 | 0.01
|
||||
Modify | 0.0037699 | 0.0037699 | 0.0037699 | 0.0 | 2.64
|
||||
Other | | 0.001957 | | | 1.37
|
||||
Pair | 0.078345 | 0.078345 | 0.078345 | 0.0 | 77.04
|
||||
Bond | 0.00010109 | 0.00010109 | 0.00010109 | 0.0 | 0.10
|
||||
Kspace | 0.0079424 | 0.0079424 | 0.0079424 | 0.0 | 7.81
|
||||
Neigh | 0.003454 | 0.003454 | 0.003454 | 0.0 | 3.40
|
||||
Comm | 0.0080469 | 0.0080469 | 0.0080469 | 0.0 | 7.91
|
||||
Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.02
|
||||
Modify | 0.0026064 | 0.0026064 | 0.0026064 | 0.0 | 2.56
|
||||
Other | | 0.001179 | | | 1.16
|
||||
|
||||
Nlocal: 24 ave 24 max 24 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1660 ave 1660 max 1660 min
|
||||
Nghost: 1688 ave 1688 max 1688 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 5112 ave 5112 max 5112 min
|
||||
Neighs: 4952 ave 4952 max 4952 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 5112
|
||||
Ave neighs/atom = 213
|
||||
Total # of neighbors = 4952
|
||||
Ave neighs/atom = 206.333
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 25
|
||||
Neighbor list builds = 26
|
||||
Dangerous builds = 0
|
||||
|
||||
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
|
||||
|
|
@ -201,6 +203,17 @@ fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol
|
|||
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
|
||||
fix mygcmc all 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)
|
||||
|
|
@ -208,7 +221,7 @@ 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)
|
||||
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
|
||||
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
|
||||
|
|
@ -224,58 +237,58 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
|||
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
|
||||
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 (../neighbor.cpp:472)
|
||||
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:476)
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc
|
||||
1000 326.9865 -4.3509713 -62.258445 14.62027 0.23910963 24 0 0 0 0
|
||||
2000 116.99793 -5344.1527 -286.61595 17.088682 0.74721761 75 0.048183096 0.013941446 0 0
|
||||
3000 106.86746 -3920.4926 -361.60598 18.794545 0.89666113 90 0.035637919 0.012768883 0 0
|
||||
4000 75.002668 540.46846 -414.8511 14.531966 0.98632724 99 0.025963651 0.0093451705 0 0
|
||||
5000 79.924788 -2131.1173 -437.21216 15.962121 1.0162159 102 0.019879728 0.0070418993 0 0
|
||||
6000 95.552773 -3647.0233 -438.24276 19.083253 1.0162159 102 0.015753613 0.0056885133 0 0
|
||||
7000 79.501736 -2071.5369 -440.77351 15.877631 1.0162159 102 0.01326216 0.0046915318 0 0
|
||||
8000 62.567091 -3102.9616 -442.21884 12.495541 1.0162159 102 0.011305503 0.0040437885 0 0
|
||||
9000 68.324047 -3812.7866 -440.46835 13.645287 1.0162159 102 0.0099549538 0.0035157329 0 0
|
||||
10000 83.857631 -2158.2659 -444.8183 16.747566 1.0162159 102 0.0088200922 0.0031354281 0 0
|
||||
11000 68.350984 -2084.0789 -440.14081 13.650667 1.0162159 102 0.0081331455 0.0030247424 0 0
|
||||
12000 76.867315 -1585.6723 -443.36199 15.3515 1.0162159 102 0.0073845932 0.0027532534 0 0
|
||||
13000 59.74266 -2211.0211 -446.07791 11.931462 1.0162159 102 0.0067756276 0.0025213898 0 0
|
||||
14000 81.154979 -907.0176 -441.53368 16.207808 1.0162159 102 0.0062527642 0.0023280719 0 0
|
||||
15000 66.814346 -2804.5134 -455.80704 13.7421 1.0461046 105 0.0059590528 0.0021576214 0 0
|
||||
16000 71.42983 -3930.4004 -458.43218 14.691394 1.0461046 105 0.0055547473 0.0020163729 0 0
|
||||
17000 89.624855 -3569.8136 -455.18164 18.433672 1.0461046 105 0.0052173265 0.0018867687 0 0
|
||||
18000 63.519962 -1882.8157 -456.58939 13.064525 1.0461046 105 0.0049082049 0.0017765986 0 0
|
||||
19000 71.872698 -2243.5046 -454.93359 14.782481 1.0461046 105 0.0046439115 0.0016748361 0 0
|
||||
20000 73.660765 -2285.3173 -476.35473 15.589381 1.0759934 108 0.0045124933 0.0015837653 0 0
|
||||
21000 95.675868 987.92089 -475.46736 20.248603 1.0759934 108 0.004285814 0.0015049513 0 0
|
||||
Loop time of 226.155 on 1 procs for 20000 steps with 108 atoms
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
|
||||
1000 277.5448 -1575.1516 -45.272615 12.409625 0.23910963 24 0 0 0 0 8 16
|
||||
2000 84.31104 -7419.6538 -330.36966 13.319705 0.80699501 81 0.048183096 0.0099581757 0 0 27 54
|
||||
3000 79.654082 -7034.6542 -345.84563 13.058853 0.83688372 84 0.027492109 0.0068755525 0 0 28 56
|
||||
4000 73.831702 -3905.1456 -380.27757 12.984619 0.89666113 90 0.020637774 0.0060076096 0 0 30 60
|
||||
5000 95.397292 -3523.6886 -414.9618 18.483479 0.98632724 99 0.016897769 0.0045269353 0 0 33 66
|
||||
6000 74.46018 -4913.3009 -425.33102 14.426857 0.98632724 99 0.013390571 0.0036569014 0 0 33 66
|
||||
7000 59.601812 -3108.7781 -425.91441 11.548009 0.98632724 99 0.01160439 0.0033510941 0 0 33 66
|
||||
8000 74.104787 -1710.7687 -444.03326 14.799784 1.0162159 102 0.010174953 0.0028884203 0 0 34 68
|
||||
9000 92.497957 -1255.2193 -435.57266 18.473162 1.0162159 102 0.0089594585 0.0025112378 0 0 34 68
|
||||
10000 71.075249 -3191.4633 -454.19438 14.618465 1.0461046 105 0.0081585853 0.0022395915 0 0 35 70
|
||||
11000 60.402203 -2011.6602 -461.68383 12.423277 1.0461046 105 0.0073396679 0.0020164949 0 0 35 70
|
||||
12000 92.903919 -3023.4452 -462.20701 19.108096 1.0461046 105 0.0066641451 0.0018355023 0 0 35 70
|
||||
13000 51.285407 -1016.3672 -466.29402 10.548172 1.0461046 105 0.0061145907 0.0016809265 0 0 35 70
|
||||
14000 72.733554 -3284.3632 -463.38578 14.959539 1.0461046 105 0.0056427384 0.0015520479 0 0 35 70
|
||||
15000 76.324778 -1795.0839 -477.59722 16.153186 1.0759934 108 0.005391524 0.0014384143 0 0 36 72
|
||||
16000 78.185379 345.92387 -481.1903 16.546959 1.0759934 108 0.0050257238 0.0013442486 0 0 36 72
|
||||
17000 79.868226 -3095.839 -478.59141 16.903113 1.0759934 108 0.0047204383 0.0012578458 0 0 36 72
|
||||
18000 69.578814 -1884.4164 -482.28013 14.725487 1.0759934 108 0.0044407568 0.0011843991 0 0 36 72
|
||||
19000 73.973471 -1943.8906 -480.82986 15.655561 1.0759934 108 0.0042016342 0.0011165574 0 0 36 72
|
||||
20000 59.614528 -2439.1076 -485.78451 12.616671 1.0759934 108 0.0040927265 0.0011614279 0 0 36 72
|
||||
21000 89.393596 -728.94872 -484.62787 18.919038 1.0759934 108 0.0038871336 0.0011036309 0 0 36 72
|
||||
Loop time of 148.361 on 1 procs for 20000 steps with 108 atoms
|
||||
|
||||
Performance: 7.641 ns/day, 3.141 hours/ns, 88.435 timesteps/s
|
||||
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 11.647 ns/day, 2.061 hours/ns, 134.806 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 38.053 | 38.053 | 38.053 | 0.0 | 16.83
|
||||
Bond | 0.089673 | 0.089673 | 0.089673 | 0.0 | 0.04
|
||||
Kspace | 0.92778 | 0.92778 | 0.92778 | 0.0 | 0.41
|
||||
Neigh | 1.2619 | 1.2619 | 1.2619 | 0.0 | 0.56
|
||||
Comm | 0.97483 | 0.97483 | 0.97483 | 0.0 | 0.43
|
||||
Output | 0.0013306 | 0.0013306 | 0.0013306 | 0.0 | 0.00
|
||||
Modify | 184.68 | 184.68 | 184.68 | 0.0 | 81.66
|
||||
Other | | 0.171 | | | 0.08
|
||||
Pair | 26.404 | 26.404 | 26.404 | 0.0 | 17.80
|
||||
Bond | 0.058909 | 0.058909 | 0.058909 | 0.0 | 0.04
|
||||
Kspace | 0.58222 | 0.58222 | 0.58222 | 0.0 | 0.39
|
||||
Neigh | 0.81976 | 0.81976 | 0.81976 | 0.0 | 0.55
|
||||
Comm | 0.60514 | 0.60514 | 0.60514 | 0.0 | 0.41
|
||||
Output | 0.00070596 | 0.00070596 | 0.00070596 | 0.0 | 0.00
|
||||
Modify | 119.77 | 119.77 | 119.77 | 0.0 | 80.73
|
||||
Other | | 0.1157 | | | 0.08
|
||||
|
||||
Nlocal: 108 ave 108 max 108 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7850 ave 7850 max 7850 min
|
||||
Nghost: 7908 ave 7908 max 7908 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 99828 ave 99828 max 99828 min
|
||||
Neighs: 99854 ave 99854 max 99854 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 99828
|
||||
Ave neighs/atom = 924.333
|
||||
Total # of neighbors = 99854
|
||||
Ave neighs/atom = 924.574
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 20439
|
||||
Neighbor list builds = 20442
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:03:46
|
||||
Total wall time: 0:02:28
|
||||
|
|
|
|||
|
|
@ -1,4 +1,5 @@
|
|||
LAMMPS (6 Jul 2017)
|
||||
LAMMPS (22 Sep 2017)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# fix gcmc example with fix shake
|
||||
|
||||
|
|
@ -51,6 +52,7 @@ Read molecule h2omol:
|
|||
0 impropers with 0 types
|
||||
create_atoms 0 box mol h2omol 464563 units box
|
||||
Created 24 atoms
|
||||
Time spent = 0.00236797 secs
|
||||
|
||||
# rigid SPC/E water model
|
||||
|
||||
|
|
@ -99,31 +101,31 @@ Neighbor list info ...
|
|||
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 -15.742442 0.14954269 7.579918 -637.49568
|
||||
Loop time of 0.0828406 on 4 procs for 100 steps with 24 atoms
|
||||
100 338 -15.815905 0.10936727 7.4662793 -278.75864
|
||||
Loop time of 0.0389402 on 4 procs for 100 steps with 24 atoms
|
||||
|
||||
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-4.96106135393 -15.5388622715 -15.592899346
|
||||
Force two-norm initial, final = 15.474 18.1478
|
||||
Force max component initial, final = 5.80042 7.56514
|
||||
Final line search alpha, max atom move = 0.00151131 0.0114333
|
||||
Iterations, force evaluations = 100 328
|
||||
-4.96106135393 -15.696637101 -15.7065379926
|
||||
Force two-norm initial, final = 15.474 4.38071
|
||||
Force max component initial, final = 5.80042 2.01432
|
||||
Final line search alpha, max atom move = 0.00468711 0.00944132
|
||||
Iterations, force evaluations = 100 346
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.012844 | 0.025471 | 0.047008 | 8.1 | 30.75
|
||||
Bond | 0.00038934 | 0.00046468 | 0.00054336 | 0.0 | 0.56
|
||||
Kspace | 0.0061138 | 0.027556 | 0.04014 | 7.8 | 33.26
|
||||
Pair | 0.0067904 | 0.012084 | 0.019882 | 4.5 | 31.03
|
||||
Bond | 0.0001657 | 0.00019389 | 0.00022459 | 0.0 | 0.50
|
||||
Kspace | 0.0032685 | 0.010629 | 0.015032 | 4.4 | 27.30
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.023276 | 0.023636 | 0.023804 | 0.1 | 28.53
|
||||
Output | 3.171e-05 | 3.3557e-05 | 3.8147e-05 | 0.0 | 0.04
|
||||
Comm | 0.013826 | 0.014182 | 0.015051 | 0.4 | 36.42
|
||||
Output | 2.0027e-05 | 2.2769e-05 | 3.0994e-05 | 0.0 | 0.06
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.00568 | | | 6.86
|
||||
Other | | 0.001829 | | | 4.70
|
||||
|
||||
Nlocal: 6 ave 8 max 3 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
|
@ -162,36 +164,36 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
|||
kxmax kymax kzmax = 2 2 2
|
||||
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 -15.742442 0 7.4303753 -613.0781
|
||||
1000 369.81793 -54.202686 0 -37.667331 294.98823
|
||||
Loop time of 0.199641 on 4 procs for 1000 steps with 24 atoms
|
||||
0 518.26667 -15.815905 0 7.3569121 -385.7767
|
||||
1000 240.84589 -44.723106 0 -33.954368 61.365522
|
||||
Loop time of 0.0971818 on 4 procs for 1000 steps with 24 atoms
|
||||
|
||||
Performance: 432.777 ns/day, 0.055 hours/ns, 5008.996 timesteps/s
|
||||
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 889.055 ns/day, 0.027 hours/ns, 10289.993 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.017161 | 0.034988 | 0.05833 | 8.0 | 17.53
|
||||
Bond | 0.00017357 | 0.00021374 | 0.00027347 | 0.0 | 0.11
|
||||
Kspace | 0.018025 | 0.044624 | 0.065613 | 8.4 | 22.35
|
||||
Neigh | 0.0029755 | 0.0033154 | 0.0036366 | 0.6 | 1.66
|
||||
Comm | 0.059933 | 0.06537 | 0.070709 | 1.5 | 32.74
|
||||
Output | 3.4571e-05 | 3.6657e-05 | 4.22e-05 | 0.0 | 0.02
|
||||
Modify | 0.043458 | 0.045628 | 0.04767 | 0.9 | 22.86
|
||||
Other | | 0.005465 | | | 2.74
|
||||
Pair | 0.010939 | 0.020819 | 0.033432 | 5.8 | 21.42
|
||||
Bond | 9.5129e-05 | 0.00010997 | 0.0001266 | 0.0 | 0.11
|
||||
Kspace | 0.0058987 | 0.017954 | 0.027383 | 5.9 | 18.47
|
||||
Neigh | 0.0018289 | 0.001851 | 0.0018759 | 0.0 | 1.90
|
||||
Comm | 0.033144 | 0.033717 | 0.034395 | 0.3 | 34.69
|
||||
Output | 1.3113e-05 | 1.6809e-05 | 2.5988e-05 | 0.0 | 0.02
|
||||
Modify | 0.020795 | 0.020843 | 0.020866 | 0.0 | 21.45
|
||||
Other | | 0.001872 | | | 1.93
|
||||
|
||||
Nlocal: 6 ave 8 max 3 min
|
||||
Nlocal: 6 ave 9 max 1 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 1331.5 ave 1369 max 1290 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 1259.75 ave 1642 max 428 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
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 = 5039
|
||||
Ave neighs/atom = 209.958
|
||||
Total # of neighbors = 5053
|
||||
Ave neighs/atom = 210.542
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 27
|
||||
Neighbor list builds = 30
|
||||
Dangerous builds = 0
|
||||
|
||||
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
|
||||
|
|
@ -201,6 +203,17 @@ fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol
|
|||
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
|
||||
fix mygcmc all 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)
|
||||
|
|
@ -208,7 +221,7 @@ 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)
|
||||
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
|
||||
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
|
||||
|
|
@ -224,58 +237,58 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
|||
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
|
||||
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 (../neighbor.cpp:472)
|
||||
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:476)
|
||||
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
|
||||
1000 369.81793 295.32434 -54.202686 16.535355 0.23910963 24 0 0 0 0
|
||||
2000 84.544466 -2810.9047 -344.81664 14.364627 0.86677242 87 0.052198354 0.0099581757 0 0
|
||||
3000 75.188527 -3688.256 -425.02228 14.567977 0.98632724 99 0.030546787 0.0049111089 0 0
|
||||
4000 75.019396 -5669.3063 -427.69454 14.535207 0.98632724 99 0.019972039 0.0033375609 0 0
|
||||
5000 90.415371 -2141.7596 -434.65925 17.518218 0.98632724 99 0.014909796 0.002514964 0 0
|
||||
6000 78.212628 -943.75125 -428.80584 15.153904 0.98632724 99 0.01181521 0.0020316119 0 0
|
||||
7000 71.754139 -2028.5122 -435.2139 13.902555 0.98632724 99 0.0099466198 0.0016755471 0 0
|
||||
8000 84.446231 -1969.1657 -428.27313 16.361681 0.98632724 99 0.0084791272 0.0014442102 0 0
|
||||
9000 70.952348 -2476.9812 -446.33824 14.170197 1.0162159 102 0.0077150892 0.0012556189 0 0
|
||||
10000 71.418543 -1875.7083 -443.7214 14.263302 1.0162159 102 0.0068355714 0.0011197957 0 0
|
||||
11000 86.094994 -4508.7581 -444.82687 17.194399 1.0162159 102 0.0061494515 0.0010082475 0 0
|
||||
12000 81.906091 -1547.8105 -442.36719 16.357815 1.0162159 102 0.0055834729 0.00091775114 0 0
|
||||
13000 57.221548 -4607.6222 -448.30939 11.42796 1.0162159 102 0.0051230355 0.00084046326 0 0
|
||||
14000 61.288344 -2518.1779 -445.70636 12.240157 1.0162159 102 0.0047276997 0.00077602396 0 0
|
||||
15000 85.787669 -2407.7111 -443.3834 17.133022 1.0162159 102 0.0043983485 0.00071920715 0 0
|
||||
16000 74.845939 -3288.3403 -445.8247 14.947802 1.0162159 102 0.0042321884 0.00080654918 0 0
|
||||
17000 73.835431 -1926.9566 -445.67476 14.745989 1.0162159 102 0.0039751059 0.00075470749 0 0
|
||||
18000 72.634985 -3997.552 -447.2351 14.506243 1.0162159 102 0.0037395847 0.00071063946 0 0
|
||||
19000 96.776472 -714.44132 -453.65552 19.904587 1.0461046 105 0.0036487876 0.00066993446 0 0
|
||||
20000 75.470786 183.16972 -464.04688 15.522521 1.0461046 105 0.0034630763 0.00063350614 0 0
|
||||
21000 65.658309 -773.41266 -466.27068 13.504331 1.0461046 105 0.003289113 0.00060198052 0 0
|
||||
Loop time of 93.8859 on 4 procs for 20000 steps with 105 atoms
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
|
||||
1000 240.84589 61.724018 -44.723106 10.768738 0.23910963 24 0 0 0 0 8 16
|
||||
2000 90.409434 -6561.5238 -333.25624 14.822134 0.83688372 84 0.050190725 0.0099581757 0 0 28 56
|
||||
3000 67.305679 -341.32154 -396.19372 12.238152 0.92654983 93 0.030546787 0.0068755525 0 0 31 62
|
||||
4000 70.339514 -2575.9146 -419.94752 13.628467 0.98632724 99 0.021303508 0.0046725853 0 0 33 66
|
||||
5000 85.676845 -3904.0268 -427.45932 17.110889 1.0162159 102 0.016400775 0.0035209497 0 0 34 68
|
||||
6000 55.817537 -2067.5498 -448.02732 11.147559 1.0162159 102 0.012996731 0.0028442566 0 0 34 68
|
||||
7000 87.59123 -3931.0089 -442.0299 17.493219 1.0162159 102 0.01160439 0.0030159847 0 0 34 68
|
||||
8000 77.695862 -1684.9299 -461.16897 15.980166 1.0461046 105 0.010174953 0.0025995783 0 0 35 70
|
||||
9000 70.375873 -6250.5951 -467.15813 14.474621 1.0461046 105 0.0089594585 0.002260114 0 0 35 70
|
||||
10000 85.004974 -3406.0315 -464.23871 17.483474 1.0461046 105 0.007938083 0.0020156323 0 0 35 70
|
||||
11000 55.459986 -3437.3858 -470.38117 11.406782 1.0461046 105 0.0071412985 0.0018148454 0 0 35 70
|
||||
12000 80.59057 -2145.2149 -464.5658 16.575538 1.0461046 105 0.0064840331 0.0016519521 0 0 35 70
|
||||
13000 52.183725 -3956.875 -470.42779 10.732934 1.0461046 105 0.0059493315 0.0015128339 0 0 35 70
|
||||
14000 78.482417 -4895.8977 -465.0452 16.141941 1.0461046 105 0.005490232 0.0013968431 0 0 35 70
|
||||
15000 61.802226 -6148.8506 -469.41496 12.711228 1.0461046 105 0.0051077595 0.0012945729 0 0 35 70
|
||||
16000 69.59917 -5755.4737 -462.37636 14.314872 1.0461046 105 0.004761212 0.0012098238 0 0 35 70
|
||||
17000 78.44382 -4103.8449 -461.5505 16.134003 1.0461046 105 0.0044719941 0.0011320612 0 0 35 70
|
||||
18000 76.04971 -3994.5995 -464.26842 15.641592 1.0461046 105 0.0042070328 0.0010659592 0 0 35 70
|
||||
19000 70.676514 -4558.507 -463.40477 14.536455 1.0461046 105 0.0039804956 0.0010049017 0 0 35 70
|
||||
20000 79.682951 -3876.5977 -462.70391 16.388862 1.0461046 105 0.0037779014 0.00095025921 0 0 35 70
|
||||
21000 56.755378 -4224.8128 -465.66199 11.673213 1.0461046 105 0.0035881233 0.00090297077 0 0 35 70
|
||||
Loop time of 63.5274 on 4 procs for 20000 steps with 105 atoms
|
||||
|
||||
Performance: 18.405 ns/day, 1.304 hours/ns, 213.024 timesteps/s
|
||||
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 27.201 ns/day, 0.882 hours/ns, 314.825 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.7882 | 10.264 | 14.758 | 93.2 | 10.93
|
||||
Bond | 0.028286 | 0.034218 | 0.039038 | 2.5 | 0.04
|
||||
Kspace | 0.57255 | 5.2227 | 8.8493 | 133.8 | 5.56
|
||||
Neigh | 0.3635 | 0.36915 | 0.37473 | 0.9 | 0.39
|
||||
Comm | 2.9961 | 3.2542 | 3.509 | 11.4 | 3.47
|
||||
Output | 0.0011675 | 0.0012342 | 0.001375 | 0.2 | 0.00
|
||||
Modify | 74.428 | 74.499 | 74.571 | 0.7 | 79.35
|
||||
Other | | 0.2411 | | | 0.26
|
||||
Pair | 6.7399 | 8.4644 | 10.565 | 49.0 | 13.32
|
||||
Bond | 0.021824 | 0.024522 | 0.0278 | 1.4 | 0.04
|
||||
Kspace | 0.47207 | 2.5646 | 4.286 | 88.8 | 4.04
|
||||
Neigh | 0.25299 | 0.2535 | 0.25374 | 0.1 | 0.40
|
||||
Comm | 2.011 | 2.0187 | 2.0311 | 0.5 | 3.18
|
||||
Output | 0.00063848 | 0.00072688 | 0.00099015 | 0.0 | 0.00
|
||||
Modify | 50.025 | 50.035 | 50.051 | 0.1 | 78.76
|
||||
Other | | 0.166 | | | 0.26
|
||||
|
||||
Nlocal: 26.25 ave 31 max 22 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 6049.25 ave 6133 max 5962 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 23613 ave 35083 max 14025 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Nlocal: 26.25 ave 30 max 24 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 5965 ave 6026 max 5911 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Neighs: 23614.8 ave 29343 max 16281 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
|
||||
Total # of neighbors = 94452
|
||||
Ave neighs/atom = 899.543
|
||||
Total # of neighbors = 94459
|
||||
Ave neighs/atom = 899.61
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 20428
|
||||
Neighbor list builds = 20437
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:01:34
|
||||
Total wall time: 0:01:03
|
||||
|
|
|
|||
|
|
@ -1,4 +1,5 @@
|
|||
LAMMPS (6 Jul 2017)
|
||||
LAMMPS (22 Sep 2017)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# GCMC for LJ simple fluid, no dynamics
|
||||
# T = 2.0
|
||||
|
|
@ -43,6 +44,13 @@ fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
|
|||
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
|
||||
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
|
||||
|
||||
# atom count
|
||||
|
||||
variable type1 atom "type==1"
|
||||
group type1 dynamic all var type1
|
||||
dynamic group type1 defined
|
||||
variable n1 equal count(type1)
|
||||
|
||||
# averaging
|
||||
|
||||
variable rho equal density
|
||||
|
|
@ -54,10 +62,11 @@ variable muex equal -1.25-${temp}*ln(density*${lambda}+${nugget})
|
|||
variable muex equal -1.25-2.0*ln(density*${lambda}+${nugget})
|
||||
variable muex equal -1.25-2.0*ln(density*1+${nugget})
|
||||
variable muex equal -1.25-2.0*ln(density*1+1e-08)
|
||||
fix ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
|
||||
fix ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
|
||||
variable rhoav equal f_ave[1]
|
||||
variable pav equal f_ave[2]
|
||||
variable muexav equal f_ave[3]
|
||||
variable n1av equal f_ave[4]
|
||||
|
||||
# output
|
||||
|
||||
|
|
@ -68,7 +77,7 @@ variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
|
|||
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
|
||||
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08)
|
||||
compute_modify thermo_temp dynamic yes
|
||||
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
|
||||
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
|
||||
thermo 1000
|
||||
|
||||
# run
|
||||
|
|
@ -87,32 +96,32 @@ Neighbor list info ...
|
|||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 0.433 | 0.433 | 0.433 Mbytes
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
|
||||
0 0 0 0 -0 0 0 0 0 0 0 0 0
|
||||
1000 2.4038954 2.1735585 -2.7041368 3.5476844 0.496 62 0.064790036 0.06313096 0.1081294 0.54304 1.4513524 -0.025479219
|
||||
2000 2.0461168 1.1913842 -2.9880181 3.0212194 0.512 64 0.067416408 0.066335853 0.11306166 0.52736 1.3274665 0.034690004
|
||||
3000 1.7930436 1.3788681 -3.2212667 2.6505861 0.552 69 0.067733191 0.066877836 0.1133516 0.5344 1.3834744 0.0070582537
|
||||
4000 1.981449 1.2541054 -2.8222868 2.9217977 0.472 59 0.068546991 0.067856412 0.11442807 0.52504 1.3815629 0.043309657
|
||||
5000 2.0946818 1.0701629 -3.5213291 3.0977688 0.568 71 0.06813743 0.067567891 0.11342906 0.53824 1.4049567 -0.0054539777
|
||||
6000 1.9793484 0.68224187 -3.410211 2.9247088 0.536 67 0.067797628 0.067420108 0.11295333 0.5384 1.401683 -0.0066894359
|
||||
7000 2.1885798 1.6745012 -3.185499 3.2345922 0.544 68 0.068630201 0.068261832 0.11403705 0.5244 1.449239 0.045987399
|
||||
8000 2.2175324 1.5897263 -3.078898 3.2759002 0.528 66 0.068180395 0.067899629 0.11332691 0.53928 1.5488388 -0.01075766
|
||||
9000 1.8610779 1.0396231 -2.923262 2.7465908 0.496 62 0.068346453 0.068028117 0.1134132 0.52912 1.4352871 0.027082544
|
||||
10000 2.1079271 1.1746643 -2.9112062 3.1091925 0.48 60 0.068352878 0.068054948 0.11335434 0.5316 1.4462327 0.018503094
|
||||
Loop time of 20.6892 on 1 procs for 10000 steps with 60 atoms
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
|
||||
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
|
||||
1000 2.4038954 2.1735585 -2.7041368 3.5476844 0.496 62 0.064790036 0.06313096 0.1081294 0.54304 1.4513524 -0.025479219 64.98
|
||||
2000 2.0461168 1.1913842 -2.9880181 3.0212194 0.512 64 0.067416408 0.066335853 0.11306166 0.52736 1.3274665 0.034690004 62.97
|
||||
3000 1.7930436 1.3788681 -3.2212667 2.6505861 0.552 69 0.067733191 0.066877836 0.1133516 0.5344 1.3834744 0.0070582537 63.5
|
||||
4000 1.981449 1.2541054 -2.8222868 2.9217977 0.472 59 0.068546991 0.067856412 0.11442807 0.52504 1.3815629 0.043309657 62.17
|
||||
5000 2.0946818 1.0701629 -3.5213291 3.0977688 0.568 71 0.06813743 0.067567891 0.11342906 0.53824 1.4049567 -0.0054539777 64.15
|
||||
6000 1.9793484 0.68224187 -3.410211 2.9247088 0.536 67 0.067797628 0.067420108 0.11295333 0.5384 1.401683 -0.0066894359 64.37
|
||||
7000 2.1885798 1.6745012 -3.185499 3.2345922 0.544 68 0.068630201 0.068261832 0.11403705 0.5244 1.449239 0.045987399 62.33
|
||||
8000 2.2175324 1.5897263 -3.078898 3.2759002 0.528 66 0.068180395 0.067899629 0.11332691 0.53928 1.5488388 -0.01075766 64.29
|
||||
9000 1.8610779 1.0396231 -2.923262 2.7465908 0.496 62 0.068346453 0.068028117 0.1134132 0.52912 1.4352871 0.027082544 62.87
|
||||
10000 2.1079271 1.1746643 -2.9112062 3.1091925 0.48 60 0.068352878 0.068054948 0.11335434 0.5316 1.4462327 0.018503094 63.2
|
||||
Loop time of 13.1886 on 1 procs for 10000 steps with 60 atoms
|
||||
|
||||
Performance: 208804.611 tau/day, 483.344 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 327555.715 tau/day, 758.231 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.47227 | 0.47227 | 0.47227 | 0.0 | 2.28
|
||||
Neigh | 1.1729 | 1.1729 | 1.1729 | 0.0 | 5.67
|
||||
Comm | 0.17133 | 0.17133 | 0.17133 | 0.0 | 0.83
|
||||
Output | 0.00028253 | 0.00028253 | 0.00028253 | 0.0 | 0.00
|
||||
Modify | 18.852 | 18.852 | 18.852 | 0.0 | 91.12
|
||||
Other | | 0.02063 | | | 0.10
|
||||
Pair | 0.37102 | 0.37102 | 0.37102 | 0.0 | 2.81
|
||||
Neigh | 0.86986 | 0.86986 | 0.86986 | 0.0 | 6.60
|
||||
Comm | 0.10394 | 0.10394 | 0.10394 | 0.0 | 0.79
|
||||
Output | 0.00025702 | 0.00025702 | 0.00025702 | 0.0 | 0.00
|
||||
Modify | 11.833 | 11.833 | 11.833 | 0.0 | 89.72
|
||||
Other | | 0.01084 | | | 0.08
|
||||
|
||||
Nlocal: 60 ave 60 max 60 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
|
@ -125,4 +134,4 @@ Total # of neighbors = 2133
|
|||
Ave neighs/atom = 35.55
|
||||
Neighbor list builds = 10000
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:20
|
||||
Total wall time: 0:00:13
|
||||
|
|
|
|||
|
|
@ -1,4 +1,5 @@
|
|||
LAMMPS (6 Jul 2017)
|
||||
LAMMPS (22 Sep 2017)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# GCMC for LJ simple fluid, no dynamics
|
||||
# T = 2.0
|
||||
|
|
@ -43,6 +44,13 @@ fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
|
|||
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
|
||||
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
|
||||
|
||||
# atom count
|
||||
|
||||
variable type1 atom "type==1"
|
||||
group type1 dynamic all var type1
|
||||
dynamic group type1 defined
|
||||
variable n1 equal count(type1)
|
||||
|
||||
# averaging
|
||||
|
||||
variable rho equal density
|
||||
|
|
@ -54,10 +62,11 @@ variable muex equal -1.25-${temp}*ln(density*${lambda}+${nugget})
|
|||
variable muex equal -1.25-2.0*ln(density*${lambda}+${nugget})
|
||||
variable muex equal -1.25-2.0*ln(density*1+${nugget})
|
||||
variable muex equal -1.25-2.0*ln(density*1+1e-08)
|
||||
fix ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
|
||||
fix ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
|
||||
variable rhoav equal f_ave[1]
|
||||
variable pav equal f_ave[2]
|
||||
variable muexav equal f_ave[3]
|
||||
variable n1av equal f_ave[4]
|
||||
|
||||
# output
|
||||
|
||||
|
|
@ -68,7 +77,7 @@ variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
|
|||
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
|
||||
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08)
|
||||
compute_modify thermo_temp dynamic yes
|
||||
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
|
||||
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
|
||||
thermo 1000
|
||||
|
||||
# run
|
||||
|
|
@ -87,32 +96,32 @@ Neighbor list info ...
|
|||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 0.4477 | 0.4477 | 0.4477 Mbytes
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
|
||||
0 0 0 0 -0 0 0 0 0 0 0 0 0
|
||||
1000 1.956397 1.7699101 -2.7889468 2.8864874 0.488 61 0.068894746 0.067229075 0.1141726 0.53288 1.3832798 0.013392866
|
||||
2000 2.040943 0.56060899 -2.8001647 3.0077055 0.456 57 0.069858594 0.068831934 0.11629114 0.5232 1.3587174 0.049995794
|
||||
3000 2.0004866 1.5736515 -3.3098044 2.9572411 0.552 69 0.069594029 0.068727791 0.11592543 0.53096 1.4129434 0.020022578
|
||||
4000 2.1127942 2.642809 -2.8865084 3.1211733 0.528 66 0.070268697 0.069533235 0.11693806 0.52424 1.3444615 0.046884078
|
||||
5000 2.3663648 1.354269 -3.1917346 3.4957662 0.528 66 0.070519633 0.069960064 0.11710321 0.52688 1.3595814 0.036270867
|
||||
6000 1.9224136 0.82756699 -3.1965 2.839257 0.52 65 0.06985018 0.069474645 0.11628632 0.536 1.47062 0.00141549
|
||||
7000 2.0266192 1.5593811 -2.9972341 2.9931606 0.52 65 0.070244693 0.069880791 0.11666541 0.52528 1.3246332 0.040754793
|
||||
8000 1.7790467 1.8680568 -2.8028819 2.6275151 0.52 65 0.070454494 0.070172368 0.11736806 0.524 1.4213649 0.047985191
|
||||
9000 1.7968847 1.3195587 -3.261001 2.6550983 0.536 67 0.069952011 0.069618327 0.11650087 0.53904 1.4624201 -0.01069837
|
||||
10000 2.1566109 1.1015729 -3.4999837 3.1880335 0.552 69 0.069603309 0.069284134 0.11625548 0.53128 1.3587249 0.02075238
|
||||
Loop time of 24.9916 on 4 procs for 10000 steps with 69 atoms
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
|
||||
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
|
||||
1000 1.956397 1.7699101 -2.7889468 2.8864874 0.488 61 0.068894746 0.067229075 0.1141726 0.53288 1.3832798 0.013392866 63.44
|
||||
2000 2.040943 0.56060899 -2.8001647 3.0077055 0.456 57 0.069858594 0.068831934 0.11629114 0.5232 1.3587174 0.049995794 62.19
|
||||
3000 2.0004866 1.5736515 -3.3098044 2.9572411 0.552 69 0.069594029 0.068727791 0.11592543 0.53096 1.4129434 0.020022578 63.23
|
||||
4000 2.1127942 2.642809 -2.8865084 3.1211733 0.528 66 0.070268697 0.069533235 0.11693806 0.52424 1.3444615 0.046884078 62.57
|
||||
5000 2.3663648 1.354269 -3.1917346 3.4957662 0.528 66 0.070519633 0.069960064 0.11710321 0.52688 1.3595814 0.036270867 62.56
|
||||
6000 1.9224136 0.82756699 -3.1965 2.839257 0.52 65 0.06985018 0.069474645 0.11628632 0.536 1.47062 0.00141549 63.76
|
||||
7000 2.0266192 1.5593811 -2.9972341 2.9931606 0.52 65 0.070244693 0.069880791 0.11666541 0.52528 1.3246332 0.040754793 62.2
|
||||
8000 1.7790467 1.8680568 -2.8028819 2.6275151 0.52 65 0.070454494 0.070172368 0.11736806 0.524 1.4213649 0.047985191 62.03
|
||||
9000 1.7968847 1.3195587 -3.261001 2.6550983 0.536 67 0.069952011 0.069618327 0.11650087 0.53904 1.4624201 -0.01069837 64.36
|
||||
10000 2.1566109 1.1015729 -3.4999837 3.1880335 0.552 69 0.069603309 0.069284134 0.11625548 0.53128 1.3587249 0.02075238 63.24
|
||||
Loop time of 13.089 on 4 procs for 10000 steps with 69 atoms
|
||||
|
||||
Performance: 172857.936 tau/day, 400.134 timesteps/s
|
||||
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 330047.561 tau/day, 763.999 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.11696 | 0.12516 | 0.1321 | 1.7 | 0.50
|
||||
Neigh | 0.34874 | 0.35644 | 0.36545 | 1.2 | 1.43
|
||||
Comm | 0.48531 | 0.51366 | 0.54755 | 3.8 | 2.06
|
||||
Output | 0.0005362 | 0.00069767 | 0.00076008 | 0.0 | 0.00
|
||||
Modify | 23.956 | 23.972 | 23.988 | 0.3 | 95.92
|
||||
Other | | 0.02376 | | | 0.10
|
||||
Pair | 0.088209 | 0.093632 | 0.098849 | 1.4 | 0.72
|
||||
Neigh | 0.25982 | 0.26669 | 0.27885 | 1.5 | 2.04
|
||||
Comm | 0.27092 | 0.28815 | 0.29998 | 2.1 | 2.20
|
||||
Output | 0.00030112 | 0.00035518 | 0.00037479 | 0.0 | 0.00
|
||||
Modify | 12.432 | 12.433 | 12.433 | 0.0 | 94.98
|
||||
Other | | 0.007692 | | | 0.06
|
||||
|
||||
Nlocal: 17.25 ave 23 max 10 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
|
|
@ -125,4 +134,4 @@ Total # of neighbors = 2823
|
|||
Ave neighs/atom = 40.913
|
||||
Neighbor list builds = 10000
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:24
|
||||
Total wall time: 0:00:13
|
||||
|
|
|
|||
Loading…
Reference in New Issue