simplify multi-replica run by passing per-replica parameters as variables on the command line
This commit is contained in:
Axel Kohlmeyer
@ -1,22 +0,0 @@
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# LJ particles
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variable T0 equal 300.0
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variable press equal 0.0
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units real
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atom_style full
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pair_style lj/cut 5.0
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read_data "restart_file"
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thermo 10
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thermo_style custom step temp pe etotal press vol
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velocity all create ${T0} 12427
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timestep 1.0
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fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
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fix fxgREM all grem 405 -.01 -30000 fxnvt
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thermo_modify press fxgREM_press
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run 10000
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write_data final_restart_file
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@ -1,22 +0,0 @@
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# LJ particles
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variable T0 equal 300.0
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variable press equal 0.0
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units real
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atom_style full
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pair_style lj/cut 5.0
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read_data "restart_file"
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thermo 10
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thermo_style custom step temp pe etotal press vol
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velocity all create ${T0} 12427
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timestep 1.0
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fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
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fix fxgREM all grem 410 -.01 -30000 fxnvt
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thermo_modify press fxgREM_press
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run 10000
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write_data final_restart_file
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@ -1,22 +0,0 @@
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# LJ particles
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variable T0 equal 300.0
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variable press equal 0.0
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units real
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atom_style full
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pair_style lj/cut 5.0
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read_data "restart_file"
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thermo 10
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thermo_style custom step temp pe etotal press vol
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velocity all create ${T0} 12427
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timestep 1.0
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fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
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fix fxgREM all grem 415 -.01 -30000 fxnvt
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thermo_modify press fxgREM_press
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run 10000
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write_data final_restart_file
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@ -1,22 +0,0 @@
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# LJ particles
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variable T0 equal 300.0
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variable press equal 0.0
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units real
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atom_style full
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pair_style lj/cut 5.0
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read_data "restart_file"
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thermo 10
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thermo_style custom step temp pe etotal press vol
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velocity all create ${T0} 12427
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timestep 1.0
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fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
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fix fxgREM all grem 420 -.01 -30000 fxnvt
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thermo_modify press fxgREM_press
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run 10000
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write_data final_restart_file
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@ -1,22 +0,0 @@
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# LJ particles
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variable T0 equal 300.0
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variable press equal 0.0
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units real
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atom_style full
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pair_style lj/cut 5.0
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read_data "restart_file"
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thermo 10
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thermo_style custom step temp pe etotal press vol
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velocity all create ${T0} 12427
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timestep 1.0
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fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
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fix fxgREM all grem 425 -.01 -30000 fxnvt
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thermo_modify press fxgREM_press
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run 10000
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write_data final_restart_file
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@ -51,9 +51,9 @@ for exchange in arange(starting_ex,max_exchange):
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os.chdir(path+"/%s" % lambdas[l])
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#os.system("cp restart_file restart_file%d" % exchange)
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if (nproc > 1):
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os.system("mpirun -np %d " + lmp + " -in " + inp + " > output" % nproc)
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os.system("mpirun -np %d " + lmp + " -in ../" + inp + " -var lambda %g -var eta %g -var enthalpy %g > output" % (nproc, lambdas[l], eta, H))
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if (nproc == 1):
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os.system(lmp + " -in " + inp + " > output")
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os.system(lmp + " -in ../" + inp + " -var lambda %g -var eta %g -var enthalpy %g > output" % (lambdas[l], eta, H))
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os.system("grep -v '[a-zA-Z]' output | awk '{if(NF==6 && NR>19)print $0}' | awk '{print $3}' >ent")
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enthalpy[l] = os.popen("tail -n 1 ent").read()
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ee = loadtxt("ent")
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@ -1,6 +1,9 @@
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# LJ particles
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variable T0 equal 300.0
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variable press equal 0.0
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variable T0 index 300.0
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variable press index 0.0
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variable lambda index 400.0
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variable eta index -0.01
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variable enthalpy index -30000.0
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units real
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atom_style full
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@ -15,7 +18,7 @@ velocity all create ${T0} 12427
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timestep 1.0
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fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
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fix fxgREM all grem 400 -.01 -30000 fxnvt
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fix fxgREM all grem ${lambda} ${eta} ${enthalpy} fxnvt
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thermo_modify press fxgREM_press
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run 10000
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@ -1,5 +1,4 @@
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LAMMPS (9 Nov 2016)
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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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# LJ particles
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variable T0 equal 300.0
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@ -26,16 +25,13 @@ thermo_style custom step temp pe etotal press vol
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timestep 1.0
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fix fxgREM all grem 400 -.01 -30000 ${T0} ${press}
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fix fxgREM all grem 400 -.01 -30000 300 ${press}
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fix fxgREM all grem 400 -.01 -30000 300 0
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fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
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fix fxnvt all npt temp 300 ${T0} 1000.0 iso ${press} ${press} 10000.0
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fix fxnvt all npt temp 300 300 1000.0 iso ${press} ${press} 10000.0
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fix fxnvt all npt temp 300 300 1000.0 iso 0 ${press} 10000.0
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fix fxnvt all npt temp 300 300 1000.0 iso 0 0 10000.0
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fix fxgREM all grem 400 -.01 -30000 fxnvt
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thermo_modify press fxgREM_press
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fix_modify fxnvt press fxgREM_press
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run 1000
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Neighbor list info ...
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1 neighbor list requests
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@ -147,21 +143,21 @@ Step Temp PotEng TotEng Press Volume
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980 303.93331 -3178.9891 -2726.9114 -88.434034 11953.723
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990 307.36223 -3180.7316 -2723.5535 -145.46208 11953.849
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1000 310.09574 -3181.101 -2719.8571 -180.39125 11953.972
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Loop time of 0.248474 on 1 procs for 1000 steps with 500 atoms
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Loop time of 0.303645 on 1 procs for 1000 steps with 500 atoms
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Performance: 347.722 ns/day, 0.069 hours/ns, 4024.566 timesteps/s
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99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
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Performance: 284.542 ns/day, 0.084 hours/ns, 3293.315 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 | 0.20529 | 0.20529 | 0.20529 | 0.0 | 82.62
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Bond | 8.4e-05 | 8.4e-05 | 8.4e-05 | 0.0 | 0.03
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Neigh | 0.004163 | 0.004163 | 0.004163 | 0.0 | 1.68
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Comm | 0.007817 | 0.007817 | 0.007817 | 0.0 | 3.15
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Output | 0.001142 | 0.001142 | 0.001142 | 0.0 | 0.46
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Modify | 0.026383 | 0.026383 | 0.026383 | 0.0 | 10.62
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Other | | 0.003598 | | | 1.45
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Pair | 0.25029 | 0.25029 | 0.25029 | 0.0 | 82.43
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Bond | 7.0572e-05 | 7.0572e-05 | 7.0572e-05 | 0.0 | 0.02
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Neigh | 0.0042012 | 0.0042012 | 0.0042012 | 0.0 | 1.38
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Comm | 0.010247 | 0.010247 | 0.010247 | 0.0 | 3.37
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Output | 0.0013516 | 0.0013516 | 0.0013516 | 0.0 | 0.45
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Modify | 0.033518 | 0.033518 | 0.033518 | 0.0 | 11.04
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Other | | 0.003969 | | | 1.31
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Nlocal: 500 ave 500 max 500 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -1,5 +1,4 @@
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LAMMPS (9 Nov 2016)
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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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# LJ particles
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variable T0 equal 300.0
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@ -26,16 +25,13 @@ thermo_style custom step temp pe etotal press vol
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timestep 1.0
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fix fxgREM all grem 400 -.01 -30000 ${T0} ${press}
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fix fxgREM all grem 400 -.01 -30000 300 ${press}
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fix fxgREM all grem 400 -.01 -30000 300 0
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fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
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fix fxnvt all npt temp 300 ${T0} 1000.0 iso ${press} ${press} 10000.0
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fix fxnvt all npt temp 300 300 1000.0 iso ${press} ${press} 10000.0
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fix fxnvt all npt temp 300 300 1000.0 iso 0 ${press} 10000.0
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fix fxnvt all npt temp 300 300 1000.0 iso 0 0 10000.0
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fix fxgREM all grem 400 -.01 -30000 fxnvt
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thermo_modify press fxgREM_press
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fix_modify fxnvt press fxgREM_press
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run 1000
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Neighbor list info ...
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1 neighbor list requests
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@ -147,21 +143,21 @@ Step Temp PotEng TotEng Press Volume
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980 303.93331 -3178.9891 -2726.9114 -88.434034 11953.723
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990 307.36223 -3180.7316 -2723.5535 -145.46208 11953.849
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1000 310.09574 -3181.101 -2719.8571 -180.39125 11953.972
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Loop time of 0.203733 on 4 procs for 1000 steps with 500 atoms
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Loop time of 0.143976 on 4 procs for 1000 steps with 500 atoms
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Performance: 424.084 ns/day, 0.057 hours/ns, 4908.379 timesteps/s
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84.1% CPU use with 4 MPI tasks x 1 OpenMP threads
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Performance: 600.102 ns/day, 0.040 hours/ns, 6945.623 timesteps/s
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97.3% CPU use with 4 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 | 0.09278 | 0.097682 | 0.10458 | 1.4 | 47.95
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Bond | 8.1e-05 | 0.00010075 | 0.000116 | 0.1 | 0.05
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Neigh | 0.001528 | 0.001553 | 0.00159 | 0.1 | 0.76
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Comm | 0.03798 | 0.045863 | 0.050976 | 2.4 | 22.51
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Output | 0.001655 | 0.0066915 | 0.021705 | 10.6 | 3.28
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Modify | 0.033916 | 0.047091 | 0.053775 | 3.7 | 23.11
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Other | | 0.004751 | | | 2.33
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Pair | 0.068275 | 0.070354 | 0.073701 | 0.8 | 48.87
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Bond | 5.2452e-05 | 7.9632e-05 | 0.00014615 | 0.4 | 0.06
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Neigh | 0.0011015 | 0.0011383 | 0.0011773 | 0.1 | 0.79
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Comm | 0.031418 | 0.034908 | 0.037399 | 1.2 | 24.25
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Output | 0.0017476 | 0.00189 | 0.0022433 | 0.5 | 1.31
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Modify | 0.029245 | 0.029931 | 0.030481 | 0.3 | 20.79
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Other | | 0.005674 | | | 3.94
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Nlocal: 125 ave 127 max 123 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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