Fix the compatibility issue with latest LAMMPS. Add examples.
This commit is contained in:
Zheng Gong
@ -1,8 +1,8 @@
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Example simulations of polarizable systems using Drude oscillators
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==================================================================
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Each example comes in two versions for demonstrating the use of
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Nosé-Hoover or Langevin thermostats.
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Each example comes in several versions for demonstrating the use of
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Langevin, Nosé-Hoover and temperature-grouped Nosé-Hoover thermostats.
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* `butane` -- simulation in NVT ensemble with Thole damping
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57
examples/USER/drude/butane/in.butane.tgnh
Normal file
57
examples/USER/drude/butane/in.butane.tgnh
Normal file
@ -0,0 +1,57 @@
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# 250 butane system for drude polarizability example (Langevin)
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units real
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boundary p p p
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atom_style full
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bond_style harmonic
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angle_style harmonic
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dihedral_style opls
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special_bonds lj/coul 0.0 0.0 0.5
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pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
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pair_modify mix geometric tail yes
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kspace_style pppm 1.0e-4
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read_data data.butane
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comm_modify vel yes
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group gBUTANE molecule 1:250
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group gCORES type 1 2 3
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group gDRUDES type 4 5
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pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
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pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
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pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
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pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
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pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H
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pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
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pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
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pair_coeff 1 * thole 1.368000
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pair_coeff 2 * thole 1.368000
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pair_coeff 4 * thole 1.368000
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pair_coeff 5 * thole 1.368000
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neighbor 2.0 bin
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variable vTEMP equal 260.0
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variable vTEMP_D equal 1.0
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variable vPRESS equal 1.0
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velocity gCORES create ${vTEMP} 12345
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velocity gDRUDES create ${vTEMP_D} 12345
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fix fDRUDE all drude C C N D D
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fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
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fix fNVT all tgnvt/drude temp ${vTEMP} ${vTEMP} 100.0 ${vTEMP_D} 20.0
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compute cTEMP all temp/drude
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thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] f_fNVT[1] f_fNVT[2] f_fNVT[3]
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thermo 50
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timestep 0.5
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run 2000
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203
examples/USER/drude/butane/log.12Nov20.butane.tgnh.g++.1
Normal file
203
examples/USER/drude/butane/log.12Nov20.butane.tgnh.g++.1
Normal file
@ -0,0 +1,203 @@
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LAMMPS (29 Oct 2020)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
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using 1 OpenMP thread(s) per MPI task
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# 250 butane system for drude polarizability example (Langevin)
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units real
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boundary p p p
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atom_style full
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bond_style harmonic
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angle_style harmonic
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dihedral_style opls
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special_bonds lj/coul 0.0 0.0 0.5
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pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
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pair_modify mix geometric tail yes
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kspace_style pppm 1.0e-4
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read_data data.butane
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Reading data file ...
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orthogonal box = (-19.099988 -19.099913 -19.099998) to (19.099998 19.099999 19.099987)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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4500 atoms
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scanning bonds ...
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5 = max bonds/atom
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scanning angles ...
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6 = max angles/atom
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scanning dihedrals ...
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9 = max dihedrals/atom
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reading bonds ...
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4250 bonds
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reading angles ...
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6000 angles
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reading dihedrals ...
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6750 dihedrals
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0.0 0.0 0.5
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special bond factors coul: 0.0 0.0 0.5
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5 = max # of 1-2 neighbors
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8 = max # of 1-3 neighbors
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12 = max # of 1-4 neighbors
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17 = max # of special neighbors
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special bonds CPU = 0.005 seconds
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read_data CPU = 0.107 seconds
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comm_modify vel yes
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group gBUTANE molecule 1:250
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4500 atoms in group gBUTANE
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group gCORES type 1 2 3
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3500 atoms in group gCORES
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group gDRUDES type 4 5
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1000 atoms in group gDRUDES
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pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
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pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
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pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
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pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
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pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H
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pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
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pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
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pair_coeff 1 * thole 1.368000
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pair_coeff 2 * thole 1.368000
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pair_coeff 4 * thole 1.368000
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pair_coeff 5 * thole 1.368000
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neighbor 2.0 bin
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variable vTEMP equal 260.0
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variable vTEMP_D equal 1.0
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variable vPRESS equal 1.0
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velocity gCORES create ${vTEMP} 12345
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velocity gCORES create 260 12345
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velocity gDRUDES create ${vTEMP_D} 12345
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velocity gDRUDES create 1 12345
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fix fDRUDE all drude C C N D D
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fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
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0 = # of size 2 clusters
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500 = # of size 3 clusters
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500 = # of size 4 clusters
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0 = # of frozen angles
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find clusters CPU = 0.002 seconds
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fix fNVT all tgnvt/drude temp ${vTEMP} ${vTEMP} 100.0 ${vTEMP_D} 20.0
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fix fNVT all tgnvt/drude temp 260 ${vTEMP} 100.0 ${vTEMP_D} 20.0
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fix fNVT all tgnvt/drude temp 260 260 100.0 ${vTEMP_D} 20.0
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fix fNVT all tgnvt/drude temp 260 260 100.0 1 20.0
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compute cTEMP all temp/drude
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thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] f_fNVT[1] f_fNVT[2] f_fNVT[3]
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thermo 50
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timestep 0.5
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run 2000
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
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G vector (1/distance) = 0.36786669
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grid = 36 36 36
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stencil order = 5
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estimated absolute RMS force accuracy = 0.031353958
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estimated relative force accuracy = 9.4421513e-05
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using double precision FFTW3
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3d grid and FFT values/proc = 79507 46656
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Rebuild special list taking Drude particles into account
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Old max number of 1-2 to 1-4 neighbors: 17
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New max number of 1-2 to 1-4 neighbors: 17 (+0)
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 10
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ghost atom cutoff = 10
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binsize = 5, bins = 8 8 8
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair lj/cut/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) pair thole, perpetual, skip from (1)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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TGNHC thermostat for Drude model
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DOFs of molecules, atoms and dipoles: 747.0 7250.0 3000.0
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Per MPI rank memory allocation (min/avg/max) = 26.74 | 26.74 | 26.74 Mbytes
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Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] f_fNVT[1] f_fNVT[2] f_fNVT[3]
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0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 4439.7916 55742.797 334.61375 18.435655 235.53872 344.96036 18.435655
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50 3.1687763 2088.2827 1463.7181 133.95847 624.56452 190.24602 660.52157 113.41252 0 -767.94561 595300.94 -594872.61 2824.2625 55742.797 183.94884 0.5168738 309.18564 171.12124 0.5168738
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100 6.392197 2119.741 1619.097 148.17863 500.64399 180.00042 696.41212 164.28885 0 -972.75524 595305.17 -594872.47 1212.6136 55742.797 203.63725 0.14080733 399.49069 183.54186 0.14080733
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150 9.5800587 2141.3837 1671.6283 152.98627 469.75531 135.1638 703.8743 168.6738 0 -966.11416 595300.45 -594872.29 4391.1694 55742.797 210.25781 0.10918071 418.15558 188.92417 0.10918071
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200 12.853705 2171.9506 1663.8326 152.27281 508.11794 189.68939 718.42616 166.2915 0 -990.53041 595295.36 -594871.12 2071.4055 55742.797 209.24314 0.19965091 435.49843 186.01763 0.19965091
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250 16.067977 2208.7064 1678.7069 153.6341 529.99951 152.56393 831.36872 167.05009 0 -1047.6813 595297.24 -594870.54 1092.2375 55742.797 210.84693 0.91289443 438.53468 187.47449 0.91289443
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300 19.290601 2251.9246 1764.9742 161.52921 486.95043 145.17235 805.81497 155.39025 0 -1045.9572 595297.21 -594870.68 2438.7801 55742.797 220.85043 3.177778 427.70756 199.6284 3.177778
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350 22.523101 2270.9632 1684.9306 154.20368 586.03264 186.29543 828.98436 164.45539 0 -1016.9035 595293.56 -594870.36 2804.0926 55742.797 211.53678 1.1611927 408.91355 191.2877 1.1611927
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400 25.747934 2299.236 1742.1505 159.44041 557.0855 171.75438 844.97783 181.89643 0 -1068.3059 595296.85 -594870.09 346.86959 55742.797 219.02792 0.38093991 392.66374 201.22808 0.38093991
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450 28.921993 2335.9622 1666.2461 152.49369 669.71602 137.8956 986.46039 179.59582 0 -1060.189 595295.82 -594869.86 -125.83593 55742.797 209.50259 0.31748182 376.15783 192.41804 0.31748182
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500 32.312988 2377.923 1744.8977 159.69183 633.02533 192.86619 865.11335 173.23166 0 -1020.1061 595291.45 -594869.53 3306.7537 55742.797 219.29509 0.59010722 361.05703 204.77946 0.59010722
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550 36.691992 2428.1816 1631.766 149.33809 796.41562 183.75276 1043.9175 175.64604 0 -1030.3844 595293.08 -594869.6 1566.0362 55742.797 204.67411 1.6260367 344.40559 190.36165 1.6260367
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600 41.042781 2475.0304 1615.769 147.87406 859.26146 195.35951 1102.8743 185.82441 0 -1049.7179 595293.93 -594869 751.07631 55742.797 202.5711 1.8674049 324.5681 190.08503 1.8674049
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650 45.328915 2516.5445 1706.6033 156.18716 809.94113 177.34479 1029.3219 186.91492 0 -1005.4619 595290.9 -594869.08 2456.1336 55742.797 214.42466 0.73094758 306.66872 205.00907 0.73094758
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700 49.764606 2566.0671 1658.8261 151.81461 907.24102 186.97528 1088.6916 184.51371 0 -976.01174 595292.41 -594869.33 403.91053 55742.797 208.52534 0.43420426 292.04619 200.0061 0.43420426
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750 54.232008 2621.7889 1798.1047 164.5613 823.68424 181.39689 1029.9425 187.40871 0 -1005.4402 595300.06 -594869.68 93.345406 55742.797 226.01979 0.50741755 278.62961 220.69269 0.50741755
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800 58.691111 2682.2116 1697.0698 155.31465 985.14182 215.09199 1113.1134 201.785 0 -975.13212 595300.04 -594869.76 -978.97822 55742.797 213.08116 1.115316 269.45572 207.36081 1.115316
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850 63.191067 2745.8302 1887.0667 172.70304 858.76349 213.25376 980.55106 184.54859 0 -948.21117 595298.22 -594869.6 -1842.9661 55742.797 236.69142 1.8946563 265.28903 233.84282 1.8946563
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900 68.297608 2799.3194 1855.1338 169.78056 944.1856 201.04167 1103.4608 183.6645 0 -978.27382 595303.89 -594869.59 -1771.6573 55742.797 232.95614 1.1425454 262.10904 230.04879 1.1425454
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950 72.791466 2852.8885 1809.5899 165.61241 1043.2986 249.1926 1129.6516 191.5705 0 -961.04118 595303.8 -594869.88 -2342.8998 55742.797 227.44427 0.56184866 253.71617 224.83147 0.56184866
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1000 77.035667 2910.6565 1900.2429 173.90892 1010.4136 196.79043 1117.444 178.94619 0 -911.75161 595298.72 -594869.74 -30.451099 55742.797 238.87602 0.48940683 245.53211 238.28906 0.48940683
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1050 81.411119 2970.473 1950.8452 178.54 1019.6278 226.17987 1113.3407 186.50456 0 -935.79287 595298.24 -594868.85 -835.03656 55742.797 245.11923 0.81684119 243.27893 245.41028 0.81684119
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1100 85.352255 3032.1777 1913.2921 175.10317 1118.8856 252.39337 1183.7624 209.49478 0 -958.58165 595300.89 -594869.07 -2339.7573 55742.797 240.10633 1.5863163 244.29251 239.77436 1.5863163
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1150 88.542324 3088.7233 2015.1572 184.4258 1073.5661 215.84757 1132.2268 209.14846 0 -912.58909 595297.76 -594868.83 53.404069 55742.797 252.92982 1.5639609 247.6541 253.57807 1.5639609
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1200 92.122601 3137.9447 1895.1546 173.44324 1242.7901 238.97673 1266.308 207.46165 0 -898.18367 595297.09 -594868.86 -940.55827 55742.797 238.13441 0.75999751 245.44164 237.48006 0.75999751
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1250 95.311451 3187.5696 2117.7204 193.81231 1069.8492 181.35781 1173.5116 216.10446 0 -933.15422 595300.81 -594868.78 -1638.23 55742.797 266.21428 0.54658889 243.60628 268.65384 0.54658889
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1300 98.511654 3238.1405 2050.9414 187.70074 1187.1991 249.20898 1196.3016 223.50078 0 -909.6591 595296.3 -594868.46 -1547.4617 55742.797 257.76705 0.6695258 252.14097 258.4534 0.6695258
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1350 101.52721 3288.0387 2035.6917 186.3051 1252.347 218.31874 1254.421 222.85512 0 -868.43705 595293.49 -594868.3 390.90212 55742.797 255.64252 1.2189872 257.21253 255.58654 1.2189872
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1400 104.52829 3334.0324 2200.7086 201.40733 1133.3238 203.591 1213.1272 225.86605 0 -936.79465 595295.53 -594868 1372.2474 55742.797 276.25415 1.6144005 265.70225 277.45567 1.6144005
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1450 107.57536 3365.7397 2053.535 187.9381 1312.2047 229.27407 1349.3993 233.25524 0 -924.22271 595292.17 -594867.67 -836.52213 55742.797 257.94919 1.053914 270.4816 256.76466 1.053914
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1500 110.67807 3391.6801 2142.1349 196.04671 1249.5452 216.36803 1271.289 236.65847 0 -894.899 595287.51 -594867.38 1789.6923 55742.797 269.25236 0.63559736 274.68538 268.80398 0.63559736
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1550 113.65872 3411.9839 2115.0942 193.57196 1296.8897 192.92659 1363.4027 230.98652 0 -914.70137 595291.47 -594867.19 2191.6084 55742.797 265.85125 0.63359087 272.59399 265.26653 0.63359087
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1600 116.66477 3424.9783 2002.6546 183.28156 1422.3237 261.62038 1419.7862 242.17905 0 -928.05995 595294.38 -594867.58 -1278.1217 55742.797 251.58666 0.95135757 265.94171 250.2117 0.95135757
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1650 119.69122 3429.9661 2102.8573 192.45205 1327.1088 253.88883 1296.8164 239.01537 0 -888.25345 595293.11 -594867.47 948.16575 55742.797 263.99864 1.4686915 261.93718 264.32028 1.4686915
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1700 122.69838 3421.465 2141.4791 195.98669 1279.9859 181.31236 1326.081 226.54243 0 -878.86521 595292.19 -594867.28 241.93125 55742.797 268.9293 1.2770595 262.79349 269.67278 1.2770595
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1750 125.70436 3402.5396 2090.1999 191.29365 1312.3397 263.74025 1296.4274 228.60032 0 -905.54661 595296.37 -594867.25 -1707.3557 55742.797 262.65583 0.80319616 257.84463 263.26023 0.80319616
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1800 128.64288 3381.1607 2133.1735 195.22657 1247.9872 234.93738 1242.035 231.34689 0 -887.78079 595295.05 -594867.6 -6.7713651 55742.797 268.11425 0.66416955 258.06107 269.26102 0.66416955
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1850 131.64553 3358.3375 2097.2908 191.9426 1261.0467 207.32514 1269.9582 225.83462 0 -867.84477 595293.05 -594867.28 1032.3077 55742.797 263.55741 0.77783532 261.21918 263.90739 0.77783532
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1900 134.66459 3335.0634 2130.3209 194.96549 1204.7425 244.28549 1208.9691 209.87044 0 -885.54671 595293.8 -594866.63 -302.54262 55742.797 267.53309 1.2569444 256.95232 268.73397 1.2569444
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1950 137.77487 3309.5009 2065.148 189.00092 1244.3529 244.25407 1240.7976 222.92873 0 -891.58467 595294.86 -594866.9 -2000.0789 55742.797 259.29344 1.3652015 254.19331 259.92622 1.3652015
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2000 140.88126 3284.0767 2005.7474 183.56462 1278.3292 226.17277 1236.5565 225.16671 0 -837.57878 595295.52 -594867.51 942.09961 55742.797 251.97128 0.96329477 250.4516 252.23212 0.96329477
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Loop time of 140.882 on 1 procs for 2000 steps with 4500 atoms
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Performance: 0.613 ns/day, 39.134 hours/ns, 14.196 timesteps/s
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100.0% 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 | 90.189 | 90.189 | 90.189 | 0.0 | 64.02
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Bond | 5.0432 | 5.0432 | 5.0432 | 0.0 | 3.58
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Kspace | 39.478 | 39.478 | 39.478 | 0.0 | 28.02
|
||||
Neigh | 2.4322 | 2.4322 | 2.4322 | 0.0 | 1.73
|
||||
Comm | 0.62876 | 0.62876 | 0.62876 | 0.0 | 0.45
|
||||
Output | 0.021652 | 0.021652 | 0.021652 | 0.0 | 0.02
|
||||
Modify | 2.9918 | 2.9918 | 2.9918 | 0.0 | 2.12
|
||||
Other | | 0.09631 | | | 0.07
|
||||
|
||||
Nlocal: 4500.00 ave 4500 max 4500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 9440.00 ave 9440 max 9440 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 811251.0 ave 811251 max 811251 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 811251
|
||||
Ave neighs/atom = 180.27800
|
||||
Ave special neighs/atom = 13.333333
|
||||
Neighbor list builds = 31
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:21
|
||||
203
examples/USER/drude/butane/log.12Nov20.butane.tgnh.g++.4
Normal file
203
examples/USER/drude/butane/log.12Nov20.butane.tgnh.g++.4
Normal file
@ -0,0 +1,203 @@
|
||||
LAMMPS (29 Oct 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 250 butane system for drude polarizability example (Langevin)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
|
||||
pair_modify mix geometric tail yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
read_data data.butane
|
||||
Reading data file ...
|
||||
orthogonal box = (-19.099988 -19.099913 -19.099998) to (19.099998 19.099999 19.099987)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
4250 bonds
|
||||
reading angles ...
|
||||
6000 angles
|
||||
reading dihedrals ...
|
||||
6750 dihedrals
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 0.0 0.5
|
||||
special bond factors coul: 0.0 0.0 0.5
|
||||
5 = max # of 1-2 neighbors
|
||||
8 = max # of 1-3 neighbors
|
||||
12 = max # of 1-4 neighbors
|
||||
17 = max # of special neighbors
|
||||
special bonds CPU = 0.002 seconds
|
||||
read_data CPU = 0.135 seconds
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
group gBUTANE molecule 1:250
|
||||
4500 atoms in group gBUTANE
|
||||
group gCORES type 1 2 3
|
||||
3500 atoms in group gCORES
|
||||
group gDRUDES type 4 5
|
||||
1000 atoms in group gDRUDES
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 * thole 1.368000
|
||||
pair_coeff 2 * thole 1.368000
|
||||
pair_coeff 4 * thole 1.368000
|
||||
pair_coeff 5 * thole 1.368000
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 260.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gCORES create ${vTEMP} 12345
|
||||
velocity gCORES create 260 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N D D
|
||||
|
||||
fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
|
||||
0 = # of size 2 clusters
|
||||
500 = # of size 3 clusters
|
||||
500 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
find clusters CPU = 0.003 seconds
|
||||
|
||||
fix fNVT all tgnvt/drude temp ${vTEMP} ${vTEMP} 100.0 ${vTEMP_D} 20.0
|
||||
fix fNVT all tgnvt/drude temp 260 ${vTEMP} 100.0 ${vTEMP_D} 20.0
|
||||
fix fNVT all tgnvt/drude temp 260 260 100.0 ${vTEMP_D} 20.0
|
||||
fix fNVT all tgnvt/drude temp 260 260 100.0 1 20.0
|
||||
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] f_fNVT[1] f_fNVT[2] f_fNVT[3]
|
||||
thermo 50
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
|
||||
G vector (1/distance) = 0.36786669
|
||||
grid = 36 36 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.031353958
|
||||
estimated relative force accuracy = 9.4421513e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 26875 11664
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 17
|
||||
New max number of 1-2 to 1-4 neighbors: 17 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 8 8 8
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair thole, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
TGNHC thermostat for Drude model
|
||||
DOFs of molecules, atoms and dipoles: 747.0 7250.0 3000.0
|
||||
Per MPI rank memory allocation (min/avg/max) = 17.33 | 17.61 | 17.71 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] f_fNVT[1] f_fNVT[2] f_fNVT[3]
|
||||
0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 4439.7916 55742.797 334.61375 18.435655 235.53872 344.96036 18.435655
|
||||
50 1.2808116 2088.3442 1463.7416 133.96062 624.60259 190.28732 660.54143 113.40785 0 -767.95454 595300.93 -594872.61 2824.0523 55742.797 183.9497 0.52468068 309.23594 171.11764 0.52468068
|
||||
100 2.5584104 2119.7471 1619.1466 148.18318 500.60051 180.0129 696.37693 164.27736 0 -972.76956 595305.17 -594872.47 1212.1148 55742.797 203.64285 0.14251823 399.52878 183.54411 0.14251823
|
||||
150 3.8010236 2141.3696 1671.6877 152.99171 469.68182 135.1764 703.84494 168.6598 0 -966.14516 595300.44 -594872.29 4390.752 55742.797 210.26485 0.11034179 418.18146 188.92927 0.11034179
|
||||
200 5.1283429 2171.9547 1663.9057 152.2795 508.04901 189.69207 718.41361 166.26728 0 -990.56316 595295.36 -594871.12 2071.2788 55742.797 209.25133 0.20233224 435.53114 186.0233 0.20233224
|
||||
250 6.4042978 2208.7763 1678.8339 153.64571 529.94239 152.60724 831.35366 166.99449 0 -1047.7147 595297.24 -594870.54 1092.02 55742.797 210.85827 0.9252592 438.54342 187.4861 0.9252592
|
||||
300 7.6759895 2251.8197 1764.844 161.5173 486.97577 145.12518 805.82891 155.36767 0 -1045.8941 595297.22 -594870.68 2440.3181 55742.797 220.83898 3.1684561 427.70245 199.61611 3.1684561
|
||||
350 8.9352416 2270.8953 1684.8322 154.19468 586.06305 186.26267 828.9806 164.47014 0 -1016.8664 595293.58 -594870.36 2805.0915 55742.797 211.52748 1.151954 408.90784 191.27829 1.151954
|
||||
400 10.226474 2299.1993 1742.2608 159.4505 556.93851 171.73982 844.94626 181.87018 0 -1068.3641 595296.84 -594870.09 346.42411 55742.797 219.04152 0.38166821 392.61871 201.24772 0.38166821
|
||||
450 11.460384 2335.947 1666.1971 152.4892 669.74994 137.90858 986.43107 179.60302 0 -1060.1348 595295.81 -594869.87 -124.88535 55742.797 209.49545 0.32005879 376.11474 192.41461 0.32005879
|
||||
500 12.727526 2377.9345 1744.9374 159.69546 632.99715 192.8966 865.02273 173.24203 0 -1020.0569 595291.42 -594869.52 3307.6909 55742.797 219.29743 0.59718599 361.06132 204.78161 0.59718599
|
||||
550 14.002285 2428.2193 1631.8271 149.34369 796.3922 183.78402 1043.8511 175.66575 0 -1030.3885 595293.08 -594869.6 1565.6449 55742.797 204.6776 1.6372397 344.46071 190.35982 1.6372397
|
||||
600 15.309195 2474.8599 1615.6237 147.86076 859.23616 195.26628 1102.8384 185.89393 0 -1049.6659 595293.91 -594869.01 751.15809 55742.797 202.55856 1.8521167 324.58977 190.06895 1.8521167
|
||||
650 16.528946 2516.5107 1706.7483 156.20043 809.76241 177.33665 1029.1545 186.8922 0 -1005.4741 595290.93 -594869.08 2457.4736 55742.797 214.44458 0.72647262 306.69821 205.02801 0.72647262
|
||||
700 17.788857 2566.0306 1658.7538 151.808 907.27687 187.0133 1088.6084 184.61388 0 -976.00491 595292.38 -594869.33 403.14977 55742.797 208.51586 0.43547213 292.00328 200.00013 0.43547213
|
||||
750 19.056136 2621.8108 1798.0665 164.5578 823.74429 181.38067 1030.1211 187.24746 0 -1005.3911 595300.06 -594869.68 92.552993 55742.797 226.01327 0.51200863 278.52415 220.69636 0.51200863
|
||||
800 20.328816 2682.2638 1697.1503 155.32202 985.11349 215.11037 1113.1057 201.61206 0 -974.97574 595300.02 -594869.76 -976.02218 55742.797 213.08709 1.1265124 269.37146 207.37604 1.1265124
|
||||
850 21.675028 2745.7956 1887.1133 172.70731 858.68222 213.20281 980.38605 184.58101 0 -948.10772 595298.22 -594869.6 -1838.829 55742.797 236.69968 1.8882632 265.22854 233.85817 1.8882632
|
||||
900 22.973234 2799.2121 1855.3963 169.80459 943.81573 200.99559 1103.2167 183.64073 0 -978.26954 595303.83 -594869.59 -1773.6417 55742.797 232.99302 1.1323134 262.06588 230.09392 1.1323134
|
||||
950 24.248459 2852.9103 1809.6345 165.6165 1043.2758 249.23659 1129.5155 191.54177 0 -960.95833 595303.82 -594869.88 -2343.6579 55742.797 227.45041 0.56047502 253.63589 224.84652 0.56047502
|
||||
1000 25.536354 2910.7011 1900.5669 173.93856 1010.1343 196.76213 1117.2835 179.06956 0 -911.9529 595298.71 -594869.74 -33.375682 55742.797 238.91568 0.49230975 245.54917 238.33106 0.49230975
|
||||
1050 27.032801 2970.593 1950.7545 178.53171 1019.8385 226.09391 1113.2803 186.61907 0 -935.59614 595298.29 -594868.85 -832.86686 55742.797 245.10467 0.82528071 243.25364 245.39681 0.82528071
|
||||
1100 28.276849 3032.248 1914.0097 175.16884 1118.2383 252.4222 1183.4081 209.13741 0 -958.53105 595300.88 -594869.07 -2341.1239 55742.797 240.19374 1.5939531 244.2841 239.87168 1.5939531
|
||||
1150 29.492505 3088.6987 2014.6006 184.37485 1074.0982 215.76487 1132.4575 209.01044 0 -912.08646 595297.78 -594868.83 59.335425 55742.797 252.86479 1.5506297 247.67435 253.50422 1.5506297
|
||||
1200 30.792128 3137.976 1895.5574 173.4801 1242.4187 239.01663 1266.2435 206.94828 0 -898.01399 595297.09 -594868.87 -935.85119 55742.797 238.18675 0.75585601 245.80184 237.50082 0.75585601
|
||||
1250 32.351654 3187.6007 2118.7576 193.90723 1068.8431 181.27841 1173.4284 215.72666 0 -933.61935 595300.82 -594868.79 -1641.4966 55742.797 266.34429 0.54783845 244.09536 268.74691 0.54783845
|
||||
1300 34.279555 3238.1339 2050.9128 187.69812 1187.2212 249.09831 1195.8579 223.95802 0 -909.52255 595296.29 -594868.46 -1548.7665 55742.797 257.76137 0.67507496 252.48992 258.41118 0.67507496
|
||||
1350 36.142639 3287.8996 2035.6486 186.30115 1252.251 218.35091 1254.3488 223.36318 0 -868.93347 595293.43 -594868.31 385.64561 55742.797 255.63367 1.2281317 257.51447 255.54567 1.2281317
|
||||
1400 37.680265 3333.7702 2200.7264 201.40895 1133.0439 203.40304 1213.391 225.99045 0 -937.20521 595295.47 -594868.01 1368.2351 55742.797 276.25818 1.6096154 265.82263 277.44771 1.6096154
|
||||
1450 38.930719 3365.4323 2053.468 187.93197 1311.9643 229.10608 1350.1009 232.99574 0 -924.67313 595292.11 -594867.67 -844.05749 55742.797 257.94445 1.0440927 270.14303 256.79431 1.0440927
|
||||
1500 40.161434 3391.3707 2141.7727 196.01356 1249.598 216.2106 1271.1542 236.52415 0 -894.39832 595287.52 -594867.41 1800.4964 55742.797 269.20769 0.63415006 273.93125 268.83182 0.63415006
|
||||
1550 41.331434 3411.6894 2114.0335 193.47488 1297.6559 192.9656 1363.167 231.27359 0 -913.98645 595291.45 -594867.21 2209.1641 55742.797 265.71649 0.63741948 271.92193 265.18682 0.63741948
|
||||
1600 42.514856 3424.7938 2003.2634 183.33728 1421.5305 261.67378 1419.189 241.66354 0 -927.77417 595294.37 -594867.6 -1282.8296 55742.797 251.6594 0.96160577 265.79668 250.30691 0.96160577
|
||||
1650 43.712954 3429.9764 2104.4785 192.60041 1325.4979 253.75783 1296.7732 237.25083 0 -887.95744 595293.15 -594867.48 966.66903 55742.797 264.20211 1.4699573 262.83185 264.45262 1.4699573
|
||||
1700 44.988869 3421.4427 2141.3199 195.97211 1280.1228 180.56711 1326.1422 227.27194 0 -878.75929 595292.2 -594867.3 269.33339 55742.797 268.91342 1.2659937 264.28353 269.50173 1.2659937
|
||||
1750 46.32512 3402.6047 2089.4689 191.22675 1313.1357 263.71155 1295.9383 229.85515 0 -905.40883 595296.3 -594867.26 -1711.6299 55742.797 262.56648 0.79625261 258.49733 263.09439 0.79625261
|
||||
1800 47.626741 3381.3633 2132.4465 195.16003 1248.9167 234.45582 1241.8128 232.64927 0 -887.43322 595295.06 -594867.63 6.1750563 55742.797 268.02308 0.66339407 257.61935 269.20593 0.66339407
|
||||
1850 48.859097 3358.9769 2090.1997 191.29363 1268.7772 207.84877 1271.8504 229.08032 0 -865.66614 595292.95 -594867.29 1046.4693 55742.797 262.66189 0.78698303 260.47063 262.99635 0.78698303
|
||||
1900 50.086851 3336.417 2129.6659 194.90555 1206.7511 244.28118 1211.1819 208.93923 0 -884.87319 595293.88 -594866.65 -289.20276 55742.797 267.44697 1.2668343 256.868 268.64764 1.2668343
|
||||
1950 51.245913 3311.0369 2068.2384 189.28375 1242.7985 243.85893 1242.1317 220.07989 0 -891.04779 595294.68 -594866.91 -1991.6618 55742.797 259.6859 1.3553911 254.54251 260.3233 1.3553911
|
||||
2000 52.444694 3285.8337 2003.2382 183.33497 1282.5955 227.01654 1237.0479 227.77755 0 -837.34967 595295.6 -594867.49 937.91227 55742.797 251.65869 0.95505158 250.48617 251.88363 0.95505158
|
||||
Loop time of 52.4449 on 4 procs for 2000 steps with 4500 atoms
|
||||
|
||||
Performance: 1.647 ns/day, 14.568 hours/ns, 38.135 timesteps/s
|
||||
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 26.398 | 27.961 | 29.034 | 18.3 | 53.31
|
||||
Bond | 1.3959 | 1.5762 | 1.7169 | 9.5 | 3.01
|
||||
Kspace | 17.592 | 18.436 | 19.757 | 18.9 | 35.15
|
||||
Neigh | 0.8492 | 0.85015 | 0.85101 | 0.1 | 1.62
|
||||
Comm | 1.311 | 1.6626 | 2.0789 | 22.0 | 3.17
|
||||
Output | 0.010571 | 0.011494 | 0.013821 | 1.3 | 0.02
|
||||
Modify | 1.8078 | 1.8237 | 1.8372 | 0.8 | 3.48
|
||||
Other | | 0.1236 | | | 0.24
|
||||
|
||||
Nlocal: 1125.00 ave 1220 max 1043 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 5813.50 ave 5907 max 5699 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
Neighs: 202807.0 ave 217353 max 190808 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 811227
|
||||
Ave neighs/atom = 180.27267
|
||||
Ave special neighs/atom = 13.333333
|
||||
Neighbor list builds = 31
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:52
|
||||
79
examples/USER/drude/ethanol/in.ethanol.tgnh
Normal file
79
examples/USER/drude/ethanol/in.ethanol.tgnh
Normal file
@ -0,0 +1,79 @@
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
comm_modify vel yes
|
||||
read_data data.ethanol
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
|
||||
pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
|
||||
pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH
|
||||
pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH
|
||||
pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO
|
||||
pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO
|
||||
pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 1 thole 2.051000
|
||||
pair_coeff 1 2 thole 1.580265
|
||||
pair_coeff 1 4 thole 1.416087
|
||||
pair_coeff 1 6 thole 2.051000
|
||||
pair_coeff 1 7 thole 1.580265
|
||||
pair_coeff 1 8 thole 1.416087
|
||||
pair_coeff 2 2 thole 1.217570
|
||||
pair_coeff 2 4 thole 1.091074
|
||||
pair_coeff 2 6 thole 1.580265
|
||||
pair_coeff 2 7 thole 1.217570
|
||||
pair_coeff 2 8 thole 1.091074
|
||||
pair_coeff 4 4 thole 0.977720
|
||||
pair_coeff 4 6 thole 1.416087
|
||||
pair_coeff 4 7 thole 1.091074
|
||||
pair_coeff 4 8 thole 0.977720
|
||||
pair_coeff 6 6 thole 2.051000
|
||||
pair_coeff 6 7 thole 1.580265
|
||||
pair_coeff 6 8 thole 1.416087
|
||||
pair_coeff 7 7 thole 1.217570
|
||||
pair_coeff 7 8 thole 1.091074
|
||||
pair_coeff 8 8 thole 0.977720
|
||||
|
||||
group gETHANOL molecule 1:250
|
||||
group gATOMS type 1 2 3 4 5
|
||||
group gDRUDES type 6 7 8
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 300.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gATOMS create ${vTEMP} 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
|
||||
fix fDRUDE all drude C C N C N D D D
|
||||
|
||||
fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
|
||||
|
||||
fix fNPT all tgnpt/drude temp ${vTEMP} ${vTEMP} 100.0 ${vTEMP_D} 20.0 iso ${vPRESS} ${vPRESS} 1000
|
||||
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] f_fNPT[1] f_fNPT[2] f_fNPT[3]
|
||||
thermo 20
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
287
examples/USER/drude/ethanol/log.12Nov20.ethanol.tgnh.g++.1
Normal file
287
examples/USER/drude/ethanol/log.12Nov20.ethanol.tgnh.g++.1
Normal file
@ -0,0 +1,287 @@
|
||||
LAMMPS (29 Oct 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
comm_modify vel yes
|
||||
read_data data.ethanol
|
||||
Reading data file ...
|
||||
orthogonal box = (-14.013845 -14.027809 -14.018882) to (14.016930 14.017730 14.085730)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
2750 bonds
|
||||
reading angles ...
|
||||
3250 angles
|
||||
reading dihedrals ...
|
||||
3000 dihedrals
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 0.0 0.5
|
||||
special bond factors coul: 0.0 0.0 0.5
|
||||
5 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
10 = max # of 1-4 neighbors
|
||||
11 = max # of special neighbors
|
||||
special bonds CPU = 0.003 seconds
|
||||
read_data CPU = 0.062 seconds
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
|
||||
pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
|
||||
pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH
|
||||
pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH
|
||||
pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO
|
||||
pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO
|
||||
pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 1 thole 2.051000
|
||||
pair_coeff 1 2 thole 1.580265
|
||||
pair_coeff 1 4 thole 1.416087
|
||||
pair_coeff 1 6 thole 2.051000
|
||||
pair_coeff 1 7 thole 1.580265
|
||||
pair_coeff 1 8 thole 1.416087
|
||||
pair_coeff 2 2 thole 1.217570
|
||||
pair_coeff 2 4 thole 1.091074
|
||||
pair_coeff 2 6 thole 1.580265
|
||||
pair_coeff 2 7 thole 1.217570
|
||||
pair_coeff 2 8 thole 1.091074
|
||||
pair_coeff 4 4 thole 0.977720
|
||||
pair_coeff 4 6 thole 1.416087
|
||||
pair_coeff 4 7 thole 1.091074
|
||||
pair_coeff 4 8 thole 0.977720
|
||||
pair_coeff 6 6 thole 2.051000
|
||||
pair_coeff 6 7 thole 1.580265
|
||||
pair_coeff 6 8 thole 1.416087
|
||||
pair_coeff 7 7 thole 1.217570
|
||||
pair_coeff 7 8 thole 1.091074
|
||||
pair_coeff 8 8 thole 0.977720
|
||||
|
||||
group gETHANOL molecule 1:250
|
||||
3000 atoms in group gETHANOL
|
||||
group gATOMS type 1 2 3 4 5
|
||||
2250 atoms in group gATOMS
|
||||
group gDRUDES type 6 7 8
|
||||
750 atoms in group gDRUDES
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 300.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gATOMS create ${vTEMP} 12345
|
||||
velocity gATOMS create 300 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N C N D D D
|
||||
|
||||
fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
|
||||
250 = # of size 2 clusters
|
||||
250 = # of size 3 clusters
|
||||
250 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
|
||||
fix fNPT all tgnpt/drude temp ${vTEMP} ${vTEMP} 100.0 ${vTEMP_D} 20.0 iso ${vPRESS} ${vPRESS} 1000
|
||||
fix fNPT all tgnpt/drude temp 300 ${vTEMP} 100.0 ${vTEMP_D} 20.0 iso ${vPRESS} ${vPRESS} 1000
|
||||
fix fNPT all tgnpt/drude temp 300 300 100.0 ${vTEMP_D} 20.0 iso ${vPRESS} ${vPRESS} 1000
|
||||
fix fNPT all tgnpt/drude temp 300 300 100.0 1 20.0 iso ${vPRESS} ${vPRESS} 1000
|
||||
fix fNPT all tgnpt/drude temp 300 300 100.0 1 20.0 iso 1 ${vPRESS} 1000
|
||||
fix fNPT all tgnpt/drude temp 300 300 100.0 1 20.0 iso 1 1 1000
|
||||
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] f_fNPT[1] f_fNPT[2] f_fNPT[3]
|
||||
thermo 20
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
|
||||
G vector (1/distance) = 0.37973843
|
||||
grid = 30 30 30
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.028997858
|
||||
estimated relative force accuracy = 8.7326188e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 50653 27000
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 11
|
||||
New max number of 1-2 to 1-4 neighbors: 11 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair thole, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
TGNHC thermostat for Drude model
|
||||
DOFs of molecules, atoms and dipoles: 747.0 4500.0 2250.0
|
||||
Per MPI rank memory allocation (min/avg/max) = 22.99 | 22.99 | 22.99 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] f_fNPT[1] f_fNPT[2] f_fNPT[3]
|
||||
0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170210.19 22094.109 381.62759 10.134301 291.07893 396.91308 10.134301
|
||||
20 1.299002 9802.0013 5175.0939 694.7326 4626.9074 1138.6388 2334.7257 132.32135 0 1890.1205 514082.52 -514951.42 83148.665 22175.038 987.97886 9.5650257 2458.1912 744.58226 9.5650257
|
||||
40 2.6585262 9235.2784 5579.5869 749.03392 3655.6915 905.50827 1897.9797 277.48003 0 1696.6242 513843.84 -514965.74 60300.581 22359.787 1068.9505 1.5632512 2851.9591 773.68368 1.5632512
|
||||
60 4.0767848 8671.8892 5504.7567 738.98831 3167.1326 829.06537 2052.5827 330.50295 0 997.94126 513948.25 -514991.2 48878.532 22600.438 1054.9063 0.8609188 3046.3154 725.0357 0.8609188
|
||||
80 5.4198065 8041.4551 5718.4601 767.67701 2322.9951 733.58679 1714.9273 332.16847 0 607.45721 513906.05 -514971.19 46156.9 22855.703 1095.9536 0.67476425 2911.1504 795.36156 0.67476425
|
||||
100 6.8445274 7424.1846 5485.2445 736.36888 1938.9402 725.61122 1556.2473 334.28427 0 311.33112 513993.29 -514981.82 35649.376 23094.997 1051.3109 0.5222695 2722.3778 774.61471 0.5222695
|
||||
120 8.1987147 6864.2981 5106.0869 685.46872 1758.2112 639.80517 1608.9702 330.7119 0 225.63755 513930.12 -514977.04 28592.139 23302.575 978.67156 0.41481306 2531.1524 721.61219 0.41481306
|
||||
140 9.6125531 6355.2419 4782.2344 641.99302 1573.0074 692.8178 1572.2236 329.75157 0 62.526757 513879.29 -514963.61 24166.914 23482.684 916.61358 0.35571984 2382.5955 673.87165 0.35571984
|
||||
160 10.981043 5871.6552 4610.4861 618.9366 1261.169 680.52384 1414.3474 329.28182 0 -159.78058 513987.52 -514990.72 27542.211 23647.419 883.68752 0.35918951 2123.8994 678.40147 0.35918951
|
||||
180 12.332621 5435.5691 4279.3184 574.47885 1156.2507 684.91656 1423.9511 309.44801 0 -233.41405 513945.61 -514974.26 18688.318 23808.753 820.22155 0.31322062 1867.6728 646.89147 0.31322062
|
||||
200 13.684023 5063.6933 3974.692 533.58416 1089.0012 610.82746 1398.9423 299.55778 0 -238.71277 514006.42 -514988.03 14346.596 23962.516 761.81108 0.34323344 1649.6269 614.94153 0.34323344
|
||||
220 15.025737 4729.6345 3862.1044 518.46979 867.53006 589.15408 1361.5835 291.68077 0 -382.15023 514000.76 -514993.5 14084.228 24106.002 740.21384 0.37572015 1480.8499 617.76172 0.37572015
|
||||
240 16.361954 4425.17 3701.2817 496.88008 723.88831 584.37459 1295.507 282.13297 0 -468.19466 514014.29 -514984.22 13175.309 24240.893 709.36164 0.42725973 1335.0379 605.97228 0.42725973
|
||||
260 17.686205 4147.8236 3444.1814 462.36555 703.6422 561.69812 1304.6664 277.46507 0 -505.18688 514062.51 -514997.51 9960.5444 24367.441 660.03654 0.51674844 1202.6787 570.39815 0.51663293
|
||||
280 19.001433 3906.0499 3263.3789 438.09363 642.67099 612.03629 1258.9736 278.79088 0 -503.36734 513978.2 -514981.97 5911.2321 24482.777 625.29586 0.70431199 1076.194 550.86363 0.70431199
|
||||
300 20.239475 3688.6521 3138.7761 421.36628 549.87595 589.66541 1229.0183 274.52568 0 -529.41366 513980.02 -514993.93 8818.9035 24585 601.19081 1.2138917 967.42544 540.79666 1.2138917
|
||||
320 21.55208 3484.9768 3041.6682 408.32999 443.30859 581.36133 1221.761 276.40415 0 -581.91733 513938.29 -514992.59 9181.7725 24679.377 582.27807 1.9067083 865.20562 535.70028 1.9067083
|
||||
340 22.866527 3301.111 2892.7326 388.33607 408.3784 575.39496 1150.6761 289.75308 0 -522.13929 513897.14 -514982.44 7705.6777 24768.367 553.48144 2.4790842 782.86323 515.77305 2.4790842
|
||||
360 24.169391 3134.601 2727.1786 366.11121 407.42236 560.04836 1167.7896 290.8151 0 -534.37256 513917.26 -514994.12 5173.1603 24851.201 521.90957 2.0935593 720.9275 489.22054 2.0935593
|
||||
380 25.499891 2978.9742 2626.4574 352.58985 352.51679 565.92745 1159.8532 276.01665 0 -574.15206 513906.53 -514981.66 5406.7601 24926.52 502.85217 1.5076664 663.92569 476.44959 1.5078823
|
||||
400 26.749513 2830.4515 2571.0905 345.15709 259.36106 608.49648 1122.7921 254.35509 0 -631.46578 513898.27 -514993.09 6598.5441 24996.189 492.43661 1.0446762 619.49263 471.67242 1.0443567
|
||||
420 28.295841 2690.9016 2510.0923 336.96837 180.80925 579.44132 1054.4508 246.41333 0 -619.58628 513907.01 -514986.92 3344.148 25062.431 480.89086 0.69994647 565.8201 467.11319 0.69994647
|
||||
440 29.740652 2568.0899 2415.0979 324.2158 152.99201 549.56174 1062.4133 248.3112 0 -625.52103 513895.56 -514977.34 1508.2507 25122.432 462.77313 0.4830629 522.5615 453.15678 0.4830629
|
||||
460 31.033999 2452.8301 2374.2562 318.73299 78.573926 560.62424 1025.2699 241.11159 0 -664.87807 513904.81 -514988.36 2645.1623 25175.119 454.98091 0.39620035 489.058 449.62743 0.39620035
|
||||
480 32.287371 2343.6513 2309.9229 310.09654 33.728418 543.67605 1036.735 236.6691 0 -646.19525 513846.07 -514983.23 4840.3297 25223.454 442.64176 0.41089885 466.91678 438.90721 0.41089885
|
||||
500 33.575452 2237.0869 2186.7578 293.56219 50.329153 569.29753 1077.789 237.78011 0 -644.2024 513802.59 -514992.93 3147.641 25270.717 419.03821 0.39338041 448.26725 414.46511 0.39352695
|
||||
520 34.882586 2139.9267 2184.6613 293.28075 -44.734618 598.44589 949.76187 230.75426 0 -639.80829 513811.79 -514995.68 89.417432 25315.104 418.62009 0.43123772 424.93066 417.85161 0.43123772
|
||||
540 36.099168 2047.6906 2096.7059 281.47314 -49.015331 603.23512 994.03336 236.23878 0 -642.85411 513760.61 -515000.28 2488.0247 25353.845 401.6824 0.6095642 402.80198 401.76434 0.6095642
|
||||
560 37.392444 1959.8223 2108.0902 283.00143 -148.26783 556.77844 933.83445 228.23222 0 -640.71325 513772.73 -514999.13 3943.0471 25390.643 403.78476 0.79631768 387.29154 406.79182 0.79631768
|
||||
580 38.599277 1877.9441 2032.3004 272.827 -154.35632 567.35925 915.88654 217.432 0 -638.21268 513777.18 -514994 990.21765 25427.432 389.08915 1.184871 380.81536 390.72199 1.184871
|
||||
600 39.880662 1802.0089 2025.4302 271.90471 -223.42134 546.62696 900.79592 214.83879 0 -668.01506 513782.41 -515000.08 13.167029 25461.023 387.51997 1.7732181 375.29493 389.80736 1.773544
|
||||
620 41.151704 1729.2181 1934.4658 259.69315 -205.24769 550.82063 913.19495 217.45935 0 -675.32746 513791.35 -515002.74 241.52954 25490.189 369.99117 1.9848435 365.94576 370.90937 1.9848435
|
||||
640 42.367107 1658.2621 1869.4172 250.96067 -211.15505 560.62227 911.72129 213.95368 0 -665.21833 513766.85 -514999.08 3632.223 25516.498 357.58414 1.8379694 353.567 358.48938 1.8379694
|
||||
660 43.641386 1588.4137 1852.2333 248.65382 -263.8196 577.15612 856.06817 203.8208 0 -643.32076 513743.58 -515001.12 1748.9053 25544.141 354.40947 1.5590879 342.18406 356.67449 1.5598187
|
||||
680 44.916294 1522.8833 1803.3756 242.0949 -280.4923 569.2594 868.20962 207.92742 0 -667.28233 513741.85 -515000.45 -707.71197 25570.844 345.28497 0.99527257 329.41069 348.14899 0.99572941
|
||||
700 46.126721 1461.9096 1769.8128 237.58924 -307.90315 542.7914 861.81473 203.22264 0 -674.68634 513754.76 -514995.8 1167.0096 25593.851 338.95839 0.74443058 320.56652 342.23742 0.74427874
|
||||
720 47.342692 1403.7901 1774.9009 238.2723 -371.11079 533.63282 871.2916 186.94204 0 -661.24368 513696.56 -514998.29 1734.2343 25615.595 339.99734 0.59618884 315.31635 344.32074 0.59612251
|
||||
740 48.606886 1347.7019 1788.1767 240.05451 -440.47482 551.44173 832.07818 173.00046 0 -679.31011 513685.34 -515003.03 1108.3607 25637.321 342.57548 0.51883795 311.99896 347.87957 0.51883795
|
||||
760 49.886167 1294.2014 1732.3399 232.55868 -438.13849 563.187 825.18662 175.50788 0 -672.34818 513677.51 -515007.18 -2118.7763 25657.738 331.88911 0.47758368 305.31362 336.52173 0.47757969
|
||||
780 51.181176 1243.7936 1720.77 231.00547 -476.9764 565.28094 800.5385 187.89263 0 -663.7818 513643.08 -515009.99 142.9942 25673.523 329.66915 0.48221433 293.10673 335.95739 0.48257178
|
||||
800 52.501053 1195.7584 1713.4482 230.02255 -517.6898 575.29743 793.40588 182.96177 0 -652.3437 513594.18 -515011.19 2569.2035 25687.829 328.22734 0.57136512 282.06342 336.10937 0.57136512
|
||||
820 53.730285 1149.3704 1688.6401 226.69218 -539.26966 566.02535 783.51259 170.42752 0 -645.21365 513596.56 -515010.58 158.43243 25703.753 323.41372 0.70633792 274.90722 331.6814 0.70633792
|
||||
840 55.059346 1107.3402 1626.7277 218.38072 -519.38749 557.00463 817.13283 161.18356 0 -661.6802 513616.64 -515009.67 -859.99932 25718.477 311.42538 0.98533165 274.36623 317.78482 0.98533165
|
||||
860 56.26804 1067.0989 1619.5401 217.41582 -552.44114 567.51474 819.44456 157.01002 0 -653.65749 513563.92 -515006.67 -110.22037 25730.521 309.90587 1.3158099 279.28284 315.1959 1.3158099
|
||||
880 57.552129 1028.7737 1622.6482 217.83307 -593.87455 579.7559 769.38822 163.25737 0 -641.48094 513545.77 -515010.56 2044.3918 25741.489 310.33341 1.7085038 277.85767 315.93127 1.7085038
|
||||
900 58.752011 990.85148 1635.8709 219.60816 -645.01941 590.07687 741.99946 160.20976 0 -648.65733 513521.95 -515010.6 -616.21441 25753.742 312.82551 1.8081896 279.97773 318.48679 1.8081896
|
||||
920 60.02342 953.65737 1657.228 222.47525 -703.57061 574.2732 734.42873 151.5283 0 -657.51865 513506.29 -515012.57 -2391.2196 25763.907 316.97803 1.6721323 286.84832 322.1911 1.6717714
|
||||
940 61.246864 917.3708 1532.2653 205.69958 -614.89448 576.8991 775.3663 162.78532 0 -639.35069 513524.45 -515015.04 564.89367 25770.107 293.21271 1.2280076 293.75433 293.31884 1.2282942
|
||||
960 62.520232 883.18364 1537.9463 206.46223 -654.76268 563.51425 761.32405 161.47799 0 -631.38061 513503.44 -515013.14 1374.3226 25776.278 294.40866 0.9786147 300.31219 293.62423 0.97818807
|
||||
980 63.72859 851.43088 1538.0246 206.47273 -686.59368 565.62724 756.61795 152.08723 0 -645.22417 513500.66 -515016.36 -203.76984 25783.711 294.53876 0.71003563 300.78246 293.69924 0.71029723
|
||||
1000 65.325249 822.29342 1546.1186 207.55932 -723.82514 573.24707 705.27714 145.40402 0 -627.3824 513491.87 -515012.24 -1482.5195 25790.098 296.12917 0.61958842 301.40343 295.45106 0.61958842
|
||||
1020 67.066265 795.41337 1551.6368 208.30012 -756.22343 597.40466 700.03219 143.14559 0 -631.02663 513445.32 -515011.1 748.62224 25794.159 297.21498 0.5543604 297.93873 297.29299 0.5543604
|
||||
1040 68.784411 769.92029 1548.9081 207.9338 -778.9878 581.53993 723.87795 137.61133 0 -624.63041 513420.31 -515017.7 1356.2174 25798.811 296.7141 0.50251818 294.64447 297.25547 0.50251818
|
||||
1060 70.531164 745.98628 1514.0024 203.24787 -768.0161 590.02417 718.13714 148.25485 0 -620.67061 513412.77 -515016.53 -984.90789 25804.672 289.98962 0.57944566 296.06714 289.17408 0.57944566
|
||||
1080 72.339286 724.41988 1468.7378 197.17131 -744.31795 587.12574 750.82761 166.43289 0 -611.54088 513376.94 -515014.1 -1369.9774 25808.741 281.26901 0.68044534 297.86474 278.70146 0.68043227
|
||||
1100 74.081078 705.1492 1475.7507 198.11275 -770.60147 596.03939 703.74275 166.87407 0 -604.94878 513382.71 -515015.02 322.11458 25810.632 282.54351 0.84350846 304.3263 279.11613 0.84359917
|
||||
1120 75.92559 688.04772 1517.3948 203.70329 -829.34708 589.83314 688.24666 158.8665 0 -610.41803 513358.01 -515013.88 1171.4548 25812.799 290.41298 1.1090646 307.74167 287.73002 1.1090646
|
||||
1140 77.724149 672.36504 1512.4831 203.04391 -840.11804 611.8019 686.11567 154.1589 0 -600.4798 513325.18 -515016.9 -1129.2791 25816.098 289.32063 1.4608372 307.70226 286.46216 1.4608372
|
||||
1160 79.533442 657.64948 1524.9394 204.71611 -867.2899 614.09367 686.86805 145.77079 0 -587.50349 513287.47 -515013.99 -1405.9783 25817.666 291.61223 1.6855491 302.37391 290.02089 1.6855106
|
||||
1180 81.243201 643.07936 1483.2148 199.11478 -840.13545 607.70554 729.46823 145.73396 0 -581.12793 513268.2 -515010.11 951.82863 25817.313 283.62844 1.6507547 296.31179 281.7127 1.6507678
|
||||
1200 83.124235 628.84892 1508.103 202.45591 -879.25413 610.27958 699.47204 146.65751 0 -581.22705 513258.98 -515013.42 845.8635 25818.085 288.47775 1.4683346 288.26595 288.70552 1.4687429
|
||||
1220 84.861868 615.48595 1506.3938 202.22645 -890.90781 640.61601 705.74981 149.24915 0 -568.44006 513197.45 -515015.53 -989.87699 25819.897 288.2897 1.1425522 284.47457 289.11499 1.1433225
|
||||
1240 86.657973 603.46611 1521.8 204.29466 -918.3339 627.93094 681.9999 147.50604 0 -563.03024 513206.69 -515019.43 -1294.0886 25820.275 291.33208 0.93495852 284.52005 292.65658 0.93566845
|
||||
1260 88.527368 592.83025 1550.0222 208.08336 -957.19193 638.74876 684.27892 144.10419 0 -567.28292 513161.98 -515019.02 366.82518 25818.88 296.84123 0.70423253 289.40784 298.27306 0.70423253
|
||||
1280 90.26083 583.62238 1500.3203 201.41111 -916.69791 658.39007 717.40575 149.49357 0 -560.74831 513138.12 -515019.36 468.99306 25817.909 287.36089 0.59306602 294.54267 286.36029 0.59306602
|
||||
1300 92.13165 575.42151 1519.3082 203.96014 -943.88664 655.72041 704.25181 141.32573 0 -550.47558 513125.5 -515020.21 -1022.3924 25817.559 291.00356 0.58689962 300.73954 289.58167 0.58691655
|
||||
1320 93.894194 568.3477 1518.4074 203.83922 -950.05966 670.96379 726.82052 139.93925 0 -527.97883 513058.34 -515018.15 -972.06273 25815.822 290.83615 0.57457637 307.54777 288.256 0.57459152
|
||||
1340 95.719114 562.07892 1523.1375 204.47422 -961.05857 677.25051 688.02873 138.64793 0 -528.35304 513081.3 -515017.94 1058.9949 25813.039 291.70253 0.66885112 312.02785 288.52311 0.66873042
|
||||
1360 97.524416 556.93389 1560.3959 209.47598 -1003.462 665.73523 686.80959 139.77318 0 -523.04289 513045.29 -515018.03 937.16072 25811.796 298.7948 0.7861094 312.82634 296.66456 0.78666076
|
||||
1380 99.357452 553.33396 1516.3062 203.55714 -962.97224 678.04454 713.74957 137.42774 0 -517.91272 513044.03 -515018.31 -292.99291 25811.915 290.25807 0.98357958 308.02329 287.50255 0.98357958
|
||||
1400 101.09848 550.59887 1532.5676 205.74016 -981.9687 668.87709 700.85053 135.12927 0 -539.20798 513074.89 -515022.51 -1158.8487 25811.561 293.25245 1.2705054 302.5546 291.90379 1.2705054
|
||||
1420 102.92972 548.73321 1476.7658 198.24903 -928.03261 677.96546 739.35433 145.56163 0 -552.34431 513084.77 -515023.34 9.5625031 25809.75 282.48418 1.436009 300.29464 279.71597 1.436009
|
||||
1440 104.66752 547.12666 1527.8761 205.11036 -980.74947 650.61377 711.8671 147.59824 0 -556.66671 513090.53 -515024.69 1019.1836 25808.157 292.23402 1.5483375 300.12772 291.11848 1.5483375
|
||||
1460 106.50314 545.65053 1490.3999 200.07935 -944.74941 670.75445 719.7737 150.18449 0 -549.39105 513087.25 -515023.32 -1319.4425 25807.672 285.07809 1.4821899 301.34029 282.56847 1.4823299
|
||||
1480 108.28741 544.77516 1526.097 204.87152 -981.32183 652.3433 696.79415 149.20209 0 -556.6563 513098.18 -515021.18 -742.16174 25805.656 292.01497 1.2636175 302.51451 290.4664 1.2639932
|
||||
1500 110.12511 545.19541 1545.583 207.48742 -1000.3876 645.73389 715.44716 136.9985 0 -567.26011 513090.87 -515022.18 -400.28471 25802.486 295.86865 0.987897 302.34922 294.99013 0.987897
|
||||
1520 111.89057 546.1418 1523.2045 204.48322 -977.06274 643.78664 737.65713 128.87884 0 -556.6123 513087.83 -515018.61 382.6378 25799.004 291.65193 0.81691637 299.79434 290.49472 0.81691637
|
||||
1540 113.68915 548.12322 1532.5317 205.73534 -984.40845 662.00085 713.14115 141.83628 0 -546.54637 513065.85 -515020.69 -558.02865 25796.128 293.49257 0.69415483 292.07299 293.92389 0.69415483
|
||||
1560 115.74426 551.58749 1524.0291 204.59391 -972.44159 662.89347 709.62799 163.91089 0 -538.91833 513050.59 -515020.55 -1648.6737 25792.534 291.9015 0.60340834 283.91962 293.42109 0.60340834
|
||||
1580 118.02455 556.31359 1557.1932 209.04604 -1000.8797 650.22504 703.18471 164.34921 0 -547.76291 513048.79 -515019.67 218.40066 25787.071 298.26162 0.59762744 279.75915 301.53187 0.59762744
|
||||
1600 119.98362 561.8489 1536.2864 206.2394 -974.4375 650.4012 725.52549 152.37926 0 -524.6233 513039.24 -515017.36 724.91327 25782.038 294.23674 0.63726972 276.89513 297.31161 0.63726972
|
||||
1620 121.24569 568.29298 1516.8518 203.6304 -948.55886 669.43634 758.17152 141.59579 0 -508.64869 513005.84 -515014.95 305.45057 25778.393 290.46698 0.74019001 276.01771 293.0592 0.74019001
|
||||
1640 122.52086 575.42679 1531.3719 205.57965 -955.94515 683.26836 731.47049 143.09022 0 -504.62735 513005.89 -515015.04 -1258.1839 25775.243 293.18351 0.89655264 276.95868 296.07228 0.89655264
|
||||
1660 123.85319 583.33428 1520.971 204.18338 -937.63676 670.138 752.36615 158.20486 0 -497.10065 512993.63 -515014.87 990.4476 25771.018 291.11283 1.0757415 276.8874 293.66833 1.0757415
|
||||
1680 125.13263 591.99646 1532.4661 205.72654 -940.46967 689.25478 743.16987 168.03522 0 -502.0189 512975.1 -515014.01 1349.4251 25768.301 293.2049 1.3360644 279.26444 295.71449 1.3360644
|
||||
1700 126.41729 600.72595 1576.928 211.69534 -976.20204 698.82384 728.20266 164.32429 0 -509.63109 512960.78 -515018.71 -714.74537 25767.499 301.65964 1.4963853 288.03969 304.12166 1.4963853
|
||||
1720 127.8002 608.72776 1572.2293 211.06457 -963.50155 686.50487 751.5254 162.66596 0 -520.30848 512974.4 -515018.29 -1233.7505 25765.895 300.75432 1.507047 296.46478 301.66689 1.507047
|
||||
1740 129.05369 615.86972 1571.5987 210.97992 -955.72903 672.03255 760.03518 170.57691 0 -531.78859 512987.74 -515014.32 -5.6954413 25762.646 300.66959 1.422713 303.78613 300.35269 1.422713
|
||||
1760 130.46587 622.55796 1579.5377 212.04568 -956.97974 706.80226 734.80437 178.63803 0 -529.02192 512966.71 -515014.91 1439.5408 25759.728 302.30266 1.1633531 310.55359 301.13515 1.1641118
|
||||
1780 131.77476 628.52662 1584.4407 212.70388 -955.91404 676.79766 773.29727 172.22703 0 -534.56221 512976.35 -515020.03 -1144.3707 25758.632 303.36936 0.86750014 314.93649 301.6529 0.86760316
|
||||
1800 133.12003 634.21603 1614.4896 216.73781 -980.27353 677.17437 758.17735 157.86038 0 -522.96761 512972.14 -515022.66 -952.36111 25756.246 309.15671 0.80472277 318.00054 307.89448 0.80488217
|
||||
1820 134.41588 639.49479 1633.2745 219.2596 -993.77971 706.25176 736.76382 153.75695 0 -523.32693 512955.21 -515022.44 534.27821 25752.618 312.8094 0.68438418 326.33448 310.77281 0.68437053
|
||||
1840 135.69809 643.87101 1634.8429 219.47015 -990.97185 701.84421 766.76216 151.35177 0 -502.94871 512911.91 -515019.89 654.67154 25749.912 313.13395 0.62866073 330.35595 310.48258 0.62856511
|
||||
1860 137.01849 646.9769 1624.5262 218.08519 -977.54933 717.81093 788.02881 151.94179 0 -495.90915 512881.92 -515021.34 -1064.2782 25748.146 311.14125 0.66359764 330.55161 308.12656 0.66359764
|
||||
1880 138.29577 648.32991 1639.5616 220.10361 -991.23166 726.93665 759.79041 159.81907 0 -493.81895 512873.87 -515017.83 -1411.6366 25744.916 313.99078 0.74007658 329.3198 311.65549 0.74007658
|
||||
1900 139.67366 648.89417 1644.4291 220.75706 -995.53493 724.72865 762.39029 163.96612 0 -495.61342 512866.53 -515017.54 1351.1833 25740.228 314.85836 0.89300573 324.54001 313.46241 0.89316115
|
||||
1920 140.93714 648.51479 1660.4204 222.90381 -1011.9056 683.6849 759.17365 164.85228 0 -494.26512 512891.03 -515016.38 401.57284 25737.361 317.86954 1.0199045 319.35529 317.83552 1.0202343
|
||||
1940 142.29997 646.69169 1612.2108 216.43189 -965.51908 714.97385 778.57354 175.15205 0 -508.7717 512893.53 -515018.97 -1076.6986 25735.181 308.53939 1.2258299 312.47436 308.09188 1.2258299
|
||||
1960 143.5485 643.66804 1612.4723 216.467 -968.80423 729.94319 778.86473 177.62474 0 -483.88964 512849.44 -515020.79 -696.10678 25731.708 308.50602 1.4206534 300.71602 310.00483 1.4206534
|
||||
1980 144.89715 639.49991 1600.0251 214.79602 -960.52514 725.68053 773.8468 176.16615 0 -469.86188 512851.09 -515017.45 822.18174 25727.586 306.08335 1.5058554 291.63271 308.68799 1.505066
|
||||
2000 146.15013 633.86554 1648.9263 221.36078 -1015.0607 703.29388 761.03433 170.08933 0 -468.34451 512835.81 -515016.94 763.74636 25724.778 315.51687 1.3681009 284.57812 320.86295 1.3683497
|
||||
Loop time of 146.15 on 1 procs for 2000 steps with 3000 atoms
|
||||
|
||||
Performance: 0.591 ns/day, 40.597 hours/ns, 13.685 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 | 92.462 | 92.462 | 92.462 | 0.0 | 63.26
|
||||
Bond | 2.9377 | 2.9377 | 2.9377 | 0.0 | 2.01
|
||||
Kspace | 28.493 | 28.493 | 28.493 | 0.0 | 19.50
|
||||
Neigh | 4.3811 | 4.3811 | 4.3811 | 0.0 | 3.00
|
||||
Comm | 0.86167 | 0.86167 | 0.86167 | 0.0 | 0.59
|
||||
Output | 0.040132 | 0.040132 | 0.040132 | 0.0 | 0.03
|
||||
Modify | 16.886 | 16.886 | 16.886 | 0.0 | 11.55
|
||||
Other | | 0.08886 | | | 0.06
|
||||
|
||||
Nlocal: 3000.00 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 10696.0 ave 10696 max 10696 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 737603.0 ave 737603 max 737603 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 737603
|
||||
Ave neighs/atom = 245.86767
|
||||
Ave special neighs/atom = 10.500000
|
||||
Neighbor list builds = 59
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:26
|
||||
287
examples/USER/drude/ethanol/log.12Nov20.ethanol.tgnh.g++.4
Normal file
287
examples/USER/drude/ethanol/log.12Nov20.ethanol.tgnh.g++.4
Normal file
@ -0,0 +1,287 @@
|
||||
LAMMPS (29 Oct 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
comm_modify vel yes
|
||||
read_data data.ethanol
|
||||
Reading data file ...
|
||||
orthogonal box = (-14.013845 -14.027809 -14.018882) to (14.016930 14.017730 14.085730)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
2750 bonds
|
||||
reading angles ...
|
||||
3250 angles
|
||||
reading dihedrals ...
|
||||
3000 dihedrals
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 0.0 0.5
|
||||
special bond factors coul: 0.0 0.0 0.5
|
||||
5 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
10 = max # of 1-4 neighbors
|
||||
11 = max # of special neighbors
|
||||
special bonds CPU = 0.003 seconds
|
||||
read_data CPU = 0.115 seconds
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
|
||||
pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
|
||||
pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH
|
||||
pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH
|
||||
pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO
|
||||
pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO
|
||||
pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 1 thole 2.051000
|
||||
pair_coeff 1 2 thole 1.580265
|
||||
pair_coeff 1 4 thole 1.416087
|
||||
pair_coeff 1 6 thole 2.051000
|
||||
pair_coeff 1 7 thole 1.580265
|
||||
pair_coeff 1 8 thole 1.416087
|
||||
pair_coeff 2 2 thole 1.217570
|
||||
pair_coeff 2 4 thole 1.091074
|
||||
pair_coeff 2 6 thole 1.580265
|
||||
pair_coeff 2 7 thole 1.217570
|
||||
pair_coeff 2 8 thole 1.091074
|
||||
pair_coeff 4 4 thole 0.977720
|
||||
pair_coeff 4 6 thole 1.416087
|
||||
pair_coeff 4 7 thole 1.091074
|
||||
pair_coeff 4 8 thole 0.977720
|
||||
pair_coeff 6 6 thole 2.051000
|
||||
pair_coeff 6 7 thole 1.580265
|
||||
pair_coeff 6 8 thole 1.416087
|
||||
pair_coeff 7 7 thole 1.217570
|
||||
pair_coeff 7 8 thole 1.091074
|
||||
pair_coeff 8 8 thole 0.977720
|
||||
|
||||
group gETHANOL molecule 1:250
|
||||
3000 atoms in group gETHANOL
|
||||
group gATOMS type 1 2 3 4 5
|
||||
2250 atoms in group gATOMS
|
||||
group gDRUDES type 6 7 8
|
||||
750 atoms in group gDRUDES
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 300.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gATOMS create ${vTEMP} 12345
|
||||
velocity gATOMS create 300 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N C N D D D
|
||||
|
||||
fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
|
||||
250 = # of size 2 clusters
|
||||
250 = # of size 3 clusters
|
||||
250 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
|
||||
fix fNPT all tgnpt/drude temp ${vTEMP} ${vTEMP} 100.0 ${vTEMP_D} 20.0 iso ${vPRESS} ${vPRESS} 1000
|
||||
fix fNPT all tgnpt/drude temp 300 ${vTEMP} 100.0 ${vTEMP_D} 20.0 iso ${vPRESS} ${vPRESS} 1000
|
||||
fix fNPT all tgnpt/drude temp 300 300 100.0 ${vTEMP_D} 20.0 iso ${vPRESS} ${vPRESS} 1000
|
||||
fix fNPT all tgnpt/drude temp 300 300 100.0 1 20.0 iso ${vPRESS} ${vPRESS} 1000
|
||||
fix fNPT all tgnpt/drude temp 300 300 100.0 1 20.0 iso 1 ${vPRESS} 1000
|
||||
fix fNPT all tgnpt/drude temp 300 300 100.0 1 20.0 iso 1 1 1000
|
||||
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] f_fNPT[1] f_fNPT[2] f_fNPT[3]
|
||||
thermo 20
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
|
||||
G vector (1/distance) = 0.37973843
|
||||
grid = 30 30 30
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.028997858
|
||||
estimated relative force accuracy = 8.7326188e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 17908 7200
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 11
|
||||
New max number of 1-2 to 1-4 neighbors: 11 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair thole, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
TGNHC thermostat for Drude model
|
||||
DOFs of molecules, atoms and dipoles: 747.0 4500.0 2250.0
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.30 | 16.32 | 16.34 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] f_fNPT[1] f_fNPT[2] f_fNPT[3]
|
||||
0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170210.19 22094.109 381.62759 10.134301 291.07893 396.91308 10.134301
|
||||
20 0.5489804 9803.4819 5175.7976 694.82706 4627.6843 1139.1179 2334.7381 132.32214 0 1890.1377 514082.74 -514951.37 83147.098 22175.037 987.97841 9.8830686 2458.1459 744.58371 9.8830686
|
||||
40 1.1305859 9235.5604 5579.723 749.0522 3655.8374 905.64066 1897.9743 277.47993 0 1696.6152 513843.93 -514965.8 60300.791 22359.784 1068.9531 1.6180875 2851.9045 773.69577 1.6180875
|
||||
60 1.7763265 8672.0018 5504.7529 738.98781 3167.2488 829.16747 2052.5807 330.50296 0 997.97233 513948.23 -514991.2 48877.822 22600.434 1054.8974 0.8814188 3046.2785 725.0302 0.8814188
|
||||
80 2.3974232 8041.5241 5718.5668 767.69134 2322.9573 733.63486 1714.8909 332.16188 0 607.44872 513906.01 -514971.19 46157.199 22855.699 1095.9682 0.68487797 2911.1669 795.37545 0.68487797
|
||||
100 3.0302813 7424.2386 5485.3388 736.38155 1938.8999 725.65842 1556.2309 334.30067 0 311.29882 513993.24 -514981.83 35648.625 23094.994 1051.3251 0.52778467 2722.3899 774.63067 0.52778467
|
||||
120 3.6273007 6864.3426 5106.0771 685.46741 1758.2655 639.83956 1608.9962 330.73079 0 225.62345 513930.12 -514977.04 28591.458 23302.572 978.66797 0.41866327 2531.1648 721.6052 0.41866327
|
||||
140 4.196656 6355.3019 4782.0272 641.9652 1573.2747 692.74007 1572.242 329.76251 0 62.485696 513879.64 -514963.6 24167.635 23482.68 916.57384 0.35834425 2382.631 673.81858 0.35834425
|
||||
160 4.779717 5871.7118 4610.7111 618.9668 1261.0006 680.57069 1414.3177 329.24321 0 -159.81123 513987.38 -514990.7 27541.231 23647.415 883.72945 0.36200572 2123.9268 678.44584 0.36200572
|
||||
180 5.338641 5435.6217 4279.7314 574.5343 1155.8903 684.86021 1423.9782 309.42239 0 -233.49805 513945.42 -514974.29 18687.102 23808.747 820.29876 0.31648848 1867.6601 646.98347 0.31648848
|
||||
200 5.9102262 5063.7313 3974.8766 533.60893 1088.8548 610.8373 1399.1355 299.45065 0 -238.66713 514006.14 -514988.04 14346.964 23962.508 761.84531 0.34591369 1649.624 614.98194 0.34591369
|
||||
220 6.4670983 4729.6679 3862.1203 518.47192 867.54758 589.19356 1361.7383 291.57325 0 -382.16606 514000.72 -514993.51 14083.524 24105.992 740.21525 0.37963928 1480.8429 617.76448 0.37963928
|
||||
240 7.0337756 4425.2126 3701.4126 496.89765 723.79998 584.3439 1295.3888 282.13205 0 -468.28082 514014.44 -514984.22 13173.086 24240.879 709.38377 0.43418988 1335.0115 606.00249 0.43418988
|
||||
260 7.6151553 4147.9089 3443.8677 462.32342 704.04123 561.65864 1304.8745 277.43914 0 -505.26328 514062.78 -514997.45 9958.5179 24367.421 659.97189 0.52765671 1202.5793 570.33937 0.52753359
|
||||
280 8.1803862 3906.1678 3262.9801 438.0401 643.18765 611.98615 1259.2636 278.89902 0 -503.31011 513978.3 -514981.95 5914.4091 24482.749 625.21285 0.7191852 1076.0582 550.78956 0.7191852
|
||||
300 8.7043311 3688.7789 3139.2097 421.42449 549.56918 589.70836 1228.8579 274.66549 0 -529.44562 513979.71 -514993.93 8820.6294 24584.968 601.2678 1.2327257 967.30569 540.9051 1.2327257
|
||||
320 9.2828722 3485.0301 3041.6251 408.32421 443.40492 581.268 1221.8962 276.57911 0 -581.90861 513938.2 -514992.63 9180.621 24679.345 582.26671 1.9139563 865.07721 535.70848 1.9139563
|
||||
340 9.8440863 3301.0782 2892.3054 388.27872 408.77286 575.63973 1150.7154 289.94072 0 -522.07034 513896.97 -514982.42 7703.8271 24768.334 553.40856 2.4558958 782.77492 515.70254 2.4558958
|
||||
360 10.398275 3134.468 2727.432 366.14522 407.03603 560.03929 1167.6565 290.68699 0 -534.30813 513917.05 -514994.09 5177.6501 24851.165 521.97249 2.0603668 720.8089 489.31359 2.0603668
|
||||
380 10.971208 2978.8927 2626.9512 352.65614 351.94143 566.26677 1159.7933 275.53948 0 -574.10697 513905.99 -514981.54 5406.9463 24926.487 502.95796 1.4831172 663.80755 476.59194 1.4833313
|
||||
400 11.487591 2830.3779 2572.5528 345.3534 257.82518 609.13682 1122.447 253.59547 0 -631.51589 513897.17 -514993.01 6594.5632 24996.158 492.72116 1.0347263 619.38728 472.02151 1.0352452
|
||||
420 12.147771 2690.8114 2511.4485 337.15043 179.36289 580.62912 1054.4972 245.98614 0 -619.15187 513904.39 -514986.98 3340.3887 25062.398 481.15102 0.69884987 565.60536 467.45245 0.69884987
|
||||
440 12.683915 2567.8386 2417.1223 324.48758 150.71626 550.84021 1061.6154 248.79898 0 -625.11745 513892.15 -514977.57 1516.8529 25122.396 463.15967 0.48668891 522.23117 453.66261 0.48668891
|
||||
460 13.219765 2452.4983 2377.8819 319.21973 74.616329 562.85065 1024.1437 240.77499 0 -664.71238 513899.97 -514988.41 2625.4899 25175.085 455.6735 0.40127583 488.72927 450.48999 0.40127583
|
||||
480 13.734817 2343.3317 2306.9816 309.70169 36.35008 544.98865 1036.7003 239.14437 0 -646.5969 513844.75 -514982.63 4826.9949 25223.402 442.07562 0.41558073 466.54905 438.30802 0.41558073
|
||||
500 14.2704 2236.968 2183.0006 293.0578 53.967445 569.68824 1077.5153 241.06612 0 -644.36418 513802.58 -514992.52 3137.1149 25270.633 418.31485 0.39923526 447.67208 413.72065 0.39935381
|
||||
520 14.830149 2139.9757 2184.3136 293.23408 -44.337922 598.68848 949.68592 231.65813 0 -640.55841 513811.34 -514995.15 74.532539 25314.977 418.54937 0.44074429 424.27621 417.87775 0.44074429
|
||||
540 15.342945 2047.7713 2097.3453 281.55898 -49.574068 603.65225 992.19405 234.95516 0 -644.08949 513763.2 -514999.49 2503.1827 25353.667 401.80131 0.61813129 402.19428 402.00395 0.61813129
|
||||
560 15.876281 1959.9733 2106.7002 282.81483 -146.72689 554.39132 933.09924 226.68229 0 -642.41154 513779.76 -514998.25 3929.9055 25390.434 403.5098 0.81842484 386.57171 406.59055 0.81842484
|
||||
580 16.38257 1878.3658 2030.0966 272.53115 -151.7308 563.56362 914.74758 216.22925 0 -639.68928 513785.76 -514992.34 1013.3048 25427.188 388.65548 1.2108332 381.10541 390.16777 1.2108332
|
||||
600 16.920685 1802.551 2017.1476 270.7928 -214.59656 542.55586 900.05624 215.01335 0 -670.18556 513796.03 -514998.07 18.493782 25460.775 385.93337 1.7700661 377.13463 387.65116 1.7700661
|
||||
620 17.474131 1730.0309 1927.5545 258.76534 -197.52353 548.09305 912.68313 219.66229 0 -677.86412 513801.32 -515001.42 211.58879 25489.947 368.6727 1.9725715 368.40356 368.96285 1.9725715
|
||||
640 17.983631 1659.1463 1874.5489 251.64958 -215.40256 560.91381 910.47755 215.67628 0 -668.88025 513765.74 -514999.33 3576.6139 25516.217 358.58525 1.8035012 356.22593 359.21531 1.8035012
|
||||
660 18.557287 1589.2837 1850.4075 248.40872 -261.12386 578.2925 854.48492 205.27001 0 -645.94735 513747.59 -515000.82 1704.7835 25543.749 354.0776 1.5147284 344.22319 355.94967 1.5157289
|
||||
680 19.099188 1523.7572 1809.2809 242.88766 -285.52371 571.10597 870.42753 209.32749 0 -670.04285 513734.83 -515001.17 -730.02178 25570.285 346.40935 1.010892 331.62309 349.09523 1.010892
|
||||
700 19.606934 1462.426 1781.0971 239.10411 -318.67111 547.9598 858.22372 204.5839 0 -674.26004 513742.06 -514997.24 1193.1019 25593.123 341.12225 0.74301975 322.22823 344.48583 0.74301975
|
||||
720 20.138988 1403.965 1772.7176 237.9792 -368.75257 537.38813 872.15383 187.31368 0 -658.83726 513691.57 -514998.34 1717.9835 25614.736 339.57934 0.59520661 315.58412 343.78893 0.59520661
|
||||
740 20.654731 1347.9142 1778.2063 238.71603 -430.29207 554.12065 833.24568 175.13397 0 -676.57227 513685.79 -515002.01 1164.2855 25636.35 340.66194 0.52336173 311.70411 345.69611 0.52336173
|
||||
760 21.20085 1294.8201 1727.5363 231.91382 -432.71627 562.83637 826.41881 177.39944 0 -670.89859 513677.68 -515006.15 -2179.3296 25656.719 330.96325 0.48927201 305.61756 335.39128 0.48927201
|
||||
780 21.736798 1244.1479 1729.459 232.17193 -485.31103 563.29093 800.45744 179.65918 0 -660.60078 513641.9 -515010.01 140.35372 25672.399 331.32725 0.49993893 293.14787 337.88591 0.49993893
|
||||
800 22.313875 1195.9276 1716.8118 230.47411 -520.8842 572.20526 790.59915 174.22123 0 -646.04585 513597.21 -515009.08 2706.2932 25686.61 328.8596 0.60065349 282.54175 336.7676 0.60065349
|
||||
820 22.880819 1149.3267 1681.646 225.75325 -532.31925 564.24784 783.06404 168.40012 0 -638.53799 513598.2 -515007.69 291.5994 25702.646 322.07401 0.70343079 279.53588 329.34955 0.70332477
|
||||
840 23.400356 1107.2877 1640.6002 220.24304 -533.31252 558.56409 815.12167 157.71519 0 -653.87313 513597.92 -515008.76 -762.24777 25717.669 314.07832 1.0007715 278.89623 320.12842 1.0010942
|
||||
860 23.930137 1066.5896 1621.3757 217.66224 -554.78609 569.30332 821.05893 152.83409 0 -645.45431 513552.23 -515004.75 100.50325 25730.157 310.25167 1.3271389 283.08497 314.96823 1.3271389
|
||||
880 24.425549 1027.6567 1624.8454 218.12803 -597.18868 587.96681 765.45362 159.91238 0 -628.42404 513525.88 -515007.98 2270.6911 25741.827 310.74777 1.7225758 280.31191 316.00736 1.7225758
|
||||
900 24.945527 989.67183 1619.7368 217.44223 -630.06494 605.34666 753.15286 166.12808 0 -637.67643 513491.85 -515008.87 -504.34781 25755.03 309.75098 1.7673447 280.95321 314.73839 1.7673447
|
||||
920 25.481976 952.75609 1646.0573 220.97563 -693.30118 586.10824 737.80362 161.44982 0 -645.91448 513480.65 -515013.4 -2245.0436 25766.26 314.83888 1.6620102 286.24272 319.79545 1.6618169
|
||||
940 26.009417 916.27341 1558.2262 209.18472 -641.95282 584.88671 784.61327 161.29551 0 -636.55462 513482.98 -515019.17 351.20595 25773.56 298.17626 1.2572795 293.25423 299.19214 1.2573671
|
||||
960 26.54868 881.26579 1570.5631 210.84088 -689.29727 567.48803 757.85558 154.89763 0 -628.37927 513476.62 -515017.78 1224.7198 25780.472 300.67272 0.95167357 297.40913 301.41483 0.95167357
|
||||
980 27.082306 848.00567 1563.3504 209.87262 -715.34478 576.51161 766.15302 148.2325 0 -637.27495 513450.83 -515019.79 -304.57224 25788.336 299.38564 0.72910884 295.89994 300.16415 0.72910884
|
||||
1000 27.619404 817.47747 1553.8221 208.59349 -736.34466 586.86696 709.60783 150.55877 0 -608.57994 513440.8 -515015.6 -1422.5332 25794.968 297.60262 0.62762006 294.24682 298.35812 0.62773318
|
||||
1020 28.12313 789.1786 1563.9655 209.95519 -774.78691 608.04057 694.03517 152.80101 0 -605.61567 513386.72 -515010.76 1005.4938 25799.349 299.58342 0.54306229 290.32557 301.31971 0.54293571
|
||||
1040 28.647646 762.65087 1534.0005 205.93252 -771.3496 587.61838 735.74998 150.09823 0 -603.04152 513371.63 -515013.4 1470.8094 25804.634 293.84005 0.54036941 291.28531 294.46003 0.54036941
|
||||
1060 29.166844 737.77923 1518.4576 203.84597 -780.67842 594.18573 720.72071 149.63679 0 -601.17736 513365.82 -515009.86 -729.10372 25811.329 290.84548 0.57532052 295.86391 290.20631 0.57532052
|
||||
1080 29.694185 715.33941 1497.4861 201.03063 -782.14665 601.83156 732.61956 157.72044 0 -593.12281 513331.09 -515012.29 -1329.475 25816.507 286.76945 0.70534246 298.86373 284.95298 0.70534246
|
||||
1100 30.187888 694.69953 1511.5454 202.91803 -816.84589 616.66719 703.13897 158.99611 0 -577.76244 513295.95 -515013.83 324.57282 25819.509 289.39998 0.85625823 302.74025 287.37843 0.85625823
|
||||
1120 30.72232 675.80012 1511.985 202.97705 -836.18488 604.64779 695.06693 153.9432 0 -584.60486 513304.31 -515009.54 1125.7488 25822.677 289.3669 1.1300709 304.44007 287.0563 1.1300629
|
||||
1140 31.225571 658.36551 1521.8389 204.29988 -863.47335 629.12728 674.88861 150.24405 0 -590.89933 513286.66 -515013.49 -980.39731 25826.849 291.15043 1.376207 307.33908 288.65717 1.3761333
|
||||
1160 31.744542 641.31431 1531.9582 205.65836 -890.64389 626.42495 680.62653 148.56061 0 -577.09298 513242.55 -515011.72 -1275.5851 25829.398 292.96469 1.6693561 303.6583 291.38487 1.6693561
|
||||
1180 32.314241 624.85166 1471.4431 197.53448 -846.59145 617.3346 711.86666 153.07391 0 -572.06725 513251.25 -515008.05 1129.9547 25830.175 281.38976 1.6087801 294.57721 279.38824 1.6087801
|
||||
1200 32.836834 609.19491 1498.3739 201.14982 -889.17902 629.25511 684.67985 160.94667 0 -569.8543 513217.89 -515012.1 714.83828 25832.193 286.64705 1.3880783 283.02115 287.44058 1.3888122
|
||||
1220 33.330996 594.74278 1478.8355 198.52688 -884.09277 636.92004 698.39685 160.32561 0 -562.35565 513195.99 -515013.37 -758.81758 25835.054 283.01514 1.1229017 278.46407 283.95841 1.1229296
|
||||
1240 33.860993 582.31866 1493.1918 200.45414 -910.87313 618.74977 681.25809 152.31533 0 -562.54483 513217.1 -515017.75 -1008.5931 25836.703 285.8671 0.88995954 281.0699 286.85402 0.88995954
|
||||
1260 34.359886 571.65412 1485.3064 199.39557 -913.6523 627.02685 698.36302 149.47819 0 -579.83549 513207.17 -515015.85 -191.59975 25836.765 284.43438 0.70581205 287.41841 284.12865 0.70581205
|
||||
1280 34.886036 563.01807 1489.0976 199.90452 -926.07957 639.7656 697.32018 156.99221 0 -585.76217 513181.62 -515016.02 169.07813 25836.47 285.20229 0.61087596 293.46017 284.02179 0.61087596
|
||||
1300 35.37543 555.84411 1527.2006 205.01966 -971.35646 641.09274 662.1865 159.13537 0 -579.97157 513161.92 -515015.72 -1463.4981 25836.182 292.51734 0.58590366 295.34409 292.24276 0.58590366
|
||||
1320 35.905183 550.05933 1490.5448 200.09879 -940.48543 625.52991 696.21744 165.64927 0 -566.29494 513152.4 -515013.99 -1001.3282 25833.961 285.49188 0.58134778 295.28397 284.05681 0.58136859
|
||||
1340 36.400304 545.82552 1477.3653 198.3295 -931.53974 649.76738 698.13673 166.18782 0 -561.79356 513131.65 -515015.49 256.39573 25830.414 282.92884 0.6685389 293.55866 281.35291 0.66910289
|
||||
1360 36.922034 543.45958 1491.565 200.23575 -948.10541 625.58496 716.94864 163.71131 0 -571.55519 513134.22 -515017.02 297.35038 25827.363 285.59777 0.79202277 296.88495 283.9144 0.79202277
|
||||
1380 37.451357 542.88076 1508.4282 202.49956 -965.54741 646.84583 717.12486 157.01613 0 -570.9963 513101.79 -515017.33 -727.70264 25824.817 288.73715 1.0078391 299.43294 287.15417 1.0078391
|
||||
1400 37.973437 543.25917 1541.9768 207.00331 -998.71768 642.88473 676.64442 147.18972 0 -575.45961 513127.78 -515017.75 -1351.9224 25821.311 295.05395 1.2758201 298.33888 294.70535 1.2758201
|
||||
1420 38.477087 544.25328 1494.226 200.59298 -949.97275 637.44698 691.08413 146.44269 0 -570.05548 513163.4 -515018.29 -270.25101 25816.213 285.82275 1.45608 293.72434 284.70163 1.45608
|
||||
1440 39.004978 546.23983 1496.1396 200.84988 -949.89981 631.74619 738.457 152.80933 0 -573.9543 513118.44 -515017.39 211.73327 25811.001 286.12443 1.60978 287.34634 286.11175 1.60978
|
||||
1460 39.506582 548.84457 1466.6766 196.8946 -917.83206 633.37692 721.14643 162.99807 0 -556.88904 513139.89 -515018.35 -423.45238 25806.343 280.53109 1.4808771 287.46457 279.56727 1.4808771
|
||||
1480 40.013021 551.95616 1529.776 205.3654 -977.81982 643.3714 687.91646 168.45052 0 -559.19128 513096.53 -515014.9 -1060.0608 25801.347 292.71931 1.2657554 295.62549 292.43217 1.2657554
|
||||
1500 40.538129 555.97974 1537.2966 206.37501 -981.31688 625.22061 717.66026 158.35427 0 -572.42591 513106.71 -515016.83 -521.38973 25795.193 294.26369 1.0278009 305.22402 292.64051 1.0278009
|
||||
1520 41.025889 561.04463 1546.2574 207.57796 -985.21278 635.77714 721.02166 143.98506 0 -562.3667 513090.07 -515013.7 480.66458 25788.679 296.07983 0.80049966 308.03207 294.29295 0.80049966
|
||||
1540 41.55805 566.68767 1533.2704 205.83452 -966.58278 654.42171 733.05018 143.06827 0 -536.78594 513051.91 -515012.25 -13.266306 25783.154 293.62787 0.70845158 300.7356 292.64315 0.70845158
|
||||
1560 42.081834 573.47741 1545.9514 207.53687 -972.47397 667.35837 705.11749 148.50883 0 -511.03863 513035.3 -515017.72 -1128.9314 25777.865 296.082 0.65411382 299.13367 295.77283 0.65411382
|
||||
1580 42.665773 580.84578 1594.8648 214.10328 -1014.0191 665.14281 711.19644 150.09976 0 -528.59268 513008.73 -515020.6 202.40236 25771.588 305.48503 0.59346496 305.13087 305.74762 0.59346496
|
||||
1600 43.198806 587.93053 1593.0533 213.8601 -1005.1228 667.00914 717.18229 154.08514 0 -518.43498 512998.02 -515022.99 1129.067 25765.95 305.11474 0.64754135 305.66863 305.22598 0.64754135
|
||||
1620 43.714818 594.73059 1540.0228 206.74099 -945.29217 676.98346 739.79112 155.99494 0 -494.24155 512994.51 -515018.33 526.11962 25762.249 294.90314 0.75499506 297.8325 294.6134 0.75499506
|
||||
1640 44.259458 602.01816 1574.0462 211.30848 -972.02805 663.3896 727.17417 151.24073 0 -494.0956 513000.57 -515020.3 -575.47503 25759.514 301.37613 0.86690808 296.74738 302.34638 0.86686227
|
||||
1660 44.764134 609.8688 1585.4465 212.83891 -975.57766 664.90151 754.20462 143.39975 0 -512.60013 512995.21 -515020.69 120.01767 25756.288 303.44799 1.1375937 302.29356 303.8427 1.1375483
|
||||
1680 45.295079 617.0121 1599.4294 214.71606 -982.41735 673.71348 740.31978 139.29744 0 -523.39592 513004.17 -515016.52 1018.995 25753.537 306.06349 1.2857605 306.24911 306.23701 1.2851446
|
||||
1700 45.797194 622.7816 1587.5062 213.11542 -964.72461 681.14985 737.5354 142.64373 0 -527.89471 513016.69 -515014.85 -762.54382 25752.152 303.67113 1.5346092 313.56414 302.2316 1.5344941
|
||||
1720 46.320299 627.3514 1607.6889 215.82486 -980.33755 664.85413 752.47086 151.63477 0 -558.53514 513025.83 -515016.59 -1533.2781 25749.855 307.5455 1.5204255 324.85436 304.8785 1.5204255
|
||||
1740 46.830115 630.51695 1598.6908 214.6169 -968.17382 653.58364 747.05167 160.79211 0 -580.54509 513063.86 -515012.91 -682.94257 25745.444 305.87278 1.3989272 333.2609 301.5297 1.3989272
|
||||
1760 47.394788 632.38111 1593.237 213.88475 -960.85589 650.78705 764.11644 167.2889 0 -573.51639 513045.53 -515015.07 563.26755 25740.336 304.94629 1.1225547 334.94227 300.17035 1.1225547
|
||||
1780 47.922889 633.30997 1598.6499 214.61141 -965.33996 653.54119 765.83593 164.00427 0 -562.23222 513033.51 -515020 -1327.8381 25735.912 306.08499 0.88668411 334.15679 301.62884 0.88668411
|
||||
1800 48.463113 633.70382 1649.9701 221.50091 -1016.2663 659.96781 745.28779 159.23213 0 -549.62971 512990.43 -515021.55 -1220.9829 25730.022 315.99137 0.72802345 326.79654 314.40852 0.72802345
|
||||
1820 48.984029 633.58292 1659.156 222.73407 -1025.573 665.57877 731.85128 149.46328 0 -533.84488 512983.77 -515022.39 259.29033 25722.788 317.77089 0.68459607 313.70692 318.65732 0.68459607
|
||||
1840 49.535432 632.84896 1602.3796 215.1121 -969.53059 677.68273 790.85762 153.52845 0 -510.95603 512938.27 -515018.91 271.83168 25716.16 306.91304 0.62307528 301.73642 307.97704 0.62193772
|
||||
1860 50.131212 631.44034 1614.3342 216.71695 -982.89384 704.07775 755.95641 164.4832 0 -496.35082 512910.85 -515021.91 193.91175 25710.384 309.1988 0.63700741 295.94067 311.60525 0.63654587
|
||||
1880 50.855644 629.18958 1597.9323 214.51508 -968.74275 705.91154 777.10222 163.27419 0 -490.72673 512895.73 -515020.04 -974.53867 25705.004 306.00767 0.74633313 296.65573 307.7641 0.74633313
|
||||
1900 51.442767 625.97644 1641.4591 220.35835 -1015.4827 686.52567 770.03702 156.74058 0 -497.98541 512884.62 -515015.42 634.14021 25698.897 314.30703 0.85093529 303.58173 316.29697 0.85093529
|
||||
1920 52.143124 621.81199 1629.0055 218.68651 -1007.1935 697.66793 744.88149 154.37261 0 -496.80305 512905.46 -515012.77 706.77423 25693.859 311.83949 1.0371868 309.16955 312.48998 1.0372355
|
||||
1940 52.903306 616.46004 1627.6423 218.50351 -1011.1823 701.93564 779.10792 151.5545 0 -486.4562 512854.72 -515012.04 -356.74685 25690.093 311.50393 1.2116518 310.99764 311.79486 1.2113866
|
||||
1960 53.626542 609.78344 1638.9504 220.02157 -1029.167 696.4213 776.28011 154.35764 0 -474.71134 512832.29 -515013.81 -303.73538 25686.165 313.59711 1.3852662 315.5116 313.48837 1.3852662
|
||||
1980 54.31028 600.96661 1637.173 219.78295 -1036.2064 718.42192 759.0789 153.6092 0 -472.50282 512815.84 -515010.66 -151.6766 25681.92 313.21609 1.4792586 321.24113 312.09275 1.4792586
|
||||
2000 54.986641 589.81965 1648.0734 221.24629 -1058.2538 690.75922 747.98481 160.84305 0 -487.54224 512840.7 -515011 980.73982 25677.907 315.36457 1.3399431 321.77651 314.51049 1.3399431
|
||||
Loop time of 54.9868 on 4 procs for 2000 steps with 3000 atoms
|
||||
|
||||
Performance: 1.571 ns/day, 15.274 hours/ns, 36.372 timesteps/s
|
||||
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 27.901 | 28.34 | 29.027 | 7.9 | 51.54
|
||||
Bond | 0.92918 | 0.94546 | 0.97217 | 1.7 | 1.72
|
||||
Kspace | 14.647 | 15.356 | 15.836 | 11.2 | 27.93
|
||||
Neigh | 1.6543 | 1.6584 | 1.6622 | 0.2 | 3.02
|
||||
Comm | 1.5279 | 1.6227 | 1.7184 | 5.6 | 2.95
|
||||
Output | 0.022354 | 0.027337 | 0.040941 | 4.8 | 0.05
|
||||
Modify | 5.7813 | 6.226 | 6.5243 | 12.2 | 11.32
|
||||
Other | | 0.8108 | | | 1.47
|
||||
|
||||
Nlocal: 750.000 ave 763 max 736 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Nghost: 6184.00 ave 6204 max 6165 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 185088.0 ave 189615 max 180533 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 740354
|
||||
Ave neighs/atom = 246.78467
|
||||
Ave special neighs/atom = 10.500000
|
||||
Neighbor list builds = 63
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:55
|
||||
@ -1,6 +1,6 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -11,9 +11,9 @@
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
/* -------------------------------------------------------------------------------------
|
||||
Contributing authors: Mark Stevens (SNL), Aidan Thompson (SNL), Zheng Gong (ENS Lyon)
|
||||
------------------------------------------------------------------------- */
|
||||
---------------------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_tgnh_drude.h"
|
||||
#include <cstring>
|
||||
@ -50,7 +50,7 @@ enum{ISO,ANISO,TRICLINIC};
|
||||
|
||||
FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg),
|
||||
rfix(NULL), irregular(NULL), id_temp(NULL), id_press(NULL)
|
||||
rfix(nullptr), irregular(nullptr), id_temp(nullptr), id_press(nullptr)
|
||||
{
|
||||
if (narg < 4) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
|
||||
@ -75,8 +75,8 @@ FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
tcomputeflag = 0;
|
||||
pcomputeflag = 0;
|
||||
id_temp = NULL;
|
||||
id_press = NULL;
|
||||
id_temp = nullptr;
|
||||
id_press = nullptr;
|
||||
|
||||
// turn on tilt factor scaling, whenever applicable
|
||||
|
||||
@ -112,24 +112,23 @@ FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) :
|
||||
if (strcmp(arg[iarg],"temp") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
tstat_flag = 1;
|
||||
t_start = force->numeric(FLERR,arg[iarg+1]);
|
||||
t_start = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
||||
t_target = t_start;
|
||||
t_stop = force->numeric(FLERR,arg[iarg+2]);
|
||||
t_period = force->numeric(FLERR,arg[iarg+3]);
|
||||
t_stop = utils::numeric(FLERR,arg[iarg+2],false,lmp);
|
||||
t_period = utils::numeric(FLERR,arg[iarg+3],false,lmp);
|
||||
if (t_start <= 0.0 || t_stop <= 0.0)
|
||||
error->all(FLERR,
|
||||
"Target temperature for fix nvt/npt/nph cannot be 0.0");
|
||||
tdrude_target = force->numeric(FLERR,arg[iarg+4]);
|
||||
tdrude_period = force->numeric(FLERR,arg[iarg+5]);
|
||||
tdrude_target = utils::numeric(FLERR,arg[iarg+4],false,lmp);
|
||||
tdrude_period = utils::numeric(FLERR,arg[iarg+5],false,lmp);
|
||||
iarg += 6;
|
||||
|
||||
} else if (strcmp(arg[iarg],"iso") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
pcouple = XYZ;
|
||||
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
|
||||
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
|
||||
p_period[0] = p_period[1] = p_period[2] =
|
||||
force->numeric(FLERR,arg[iarg+3]);
|
||||
p_start[0] = p_start[1] = p_start[2] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
||||
p_stop[0] = p_stop[1] = p_stop[2] = utils::numeric(FLERR,arg[iarg+2],false,lmp);
|
||||
p_period[0] = p_period[1] = p_period[2] = utils::numeric(FLERR,arg[iarg+3],false,lmp);
|
||||
p_flag[0] = p_flag[1] = p_flag[2] = 1;
|
||||
if (dimension == 2) {
|
||||
p_start[2] = p_stop[2] = p_period[2] = 0.0;
|
||||
@ -139,10 +138,9 @@ FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) :
|
||||
} else if (strcmp(arg[iarg],"aniso") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
pcouple = NONE;
|
||||
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
|
||||
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
|
||||
p_period[0] = p_period[1] = p_period[2] =
|
||||
force->numeric(FLERR,arg[iarg+3]);
|
||||
p_start[0] = p_start[1] = p_start[2] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
||||
p_stop[0] = p_stop[1] = p_stop[2] = utils::numeric(FLERR,arg[iarg+2],false,lmp);
|
||||
p_period[0] = p_period[1] = p_period[2] = utils::numeric(FLERR,arg[iarg+3],false,lmp);
|
||||
p_flag[0] = p_flag[1] = p_flag[2] = 1;
|
||||
if (dimension == 2) {
|
||||
p_start[2] = p_stop[2] = p_period[2] = 0.0;
|
||||
@ -153,15 +151,13 @@ FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) :
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
pcouple = NONE;
|
||||
scalexy = scalexz = scaleyz = 0;
|
||||
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
|
||||
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
|
||||
p_period[0] = p_period[1] = p_period[2] =
|
||||
force->numeric(FLERR,arg[iarg+3]);
|
||||
p_start[0] = p_start[1] = p_start[2] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
||||
p_stop[0] = p_stop[1] = p_stop[2] = utils::numeric(FLERR,arg[iarg+2],false,lmp);
|
||||
p_period[0] = p_period[1] = p_period[2] = utils::numeric(FLERR,arg[iarg+3],false,lmp);
|
||||
p_flag[0] = p_flag[1] = p_flag[2] = 1;
|
||||
p_start[3] = p_start[4] = p_start[5] = 0.0;
|
||||
p_stop[3] = p_stop[4] = p_stop[5] = 0.0;
|
||||
p_period[3] = p_period[4] = p_period[5] =
|
||||
force->numeric(FLERR,arg[iarg+3]);
|
||||
p_period[3] = p_period[4] = p_period[5] = utils::numeric(FLERR,arg[iarg+3],false,lmp);
|
||||
p_flag[3] = p_flag[4] = p_flag[5] = 1;
|
||||
if (dimension == 2) {
|
||||
p_start[2] = p_stop[2] = p_period[2] = 0.0;
|
||||
@ -174,25 +170,25 @@ FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) :
|
||||
iarg += 4;
|
||||
} else if (strcmp(arg[iarg],"x") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
p_start[0] = force->numeric(FLERR,arg[iarg+1]);
|
||||
p_stop[0] = force->numeric(FLERR,arg[iarg+2]);
|
||||
p_period[0] = force->numeric(FLERR,arg[iarg+3]);
|
||||
p_start[0] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
||||
p_stop[0] = utils::numeric(FLERR,arg[iarg+2],false,lmp);
|
||||
p_period[0] = utils::numeric(FLERR,arg[iarg+3],false,lmp);
|
||||
p_flag[0] = 1;
|
||||
deviatoric_flag = 1;
|
||||
iarg += 4;
|
||||
} else if (strcmp(arg[iarg],"y") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
p_start[1] = force->numeric(FLERR,arg[iarg+1]);
|
||||
p_stop[1] = force->numeric(FLERR,arg[iarg+2]);
|
||||
p_period[1] = force->numeric(FLERR,arg[iarg+3]);
|
||||
p_start[1] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
||||
p_stop[1] = utils::numeric(FLERR,arg[iarg+2],false,lmp);
|
||||
p_period[1] = utils::numeric(FLERR,arg[iarg+3],false,lmp);
|
||||
p_flag[1] = 1;
|
||||
deviatoric_flag = 1;
|
||||
iarg += 4;
|
||||
} else if (strcmp(arg[iarg],"z") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
p_start[2] = force->numeric(FLERR,arg[iarg+1]);
|
||||
p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
|
||||
p_period[2] = force->numeric(FLERR,arg[iarg+3]);
|
||||
p_start[2] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
||||
p_stop[2] = utils::numeric(FLERR,arg[iarg+2],false,lmp);
|
||||
p_period[2] = utils::numeric(FLERR,arg[iarg+3],false,lmp);
|
||||
p_flag[2] = 1;
|
||||
deviatoric_flag = 1;
|
||||
iarg += 4;
|
||||
@ -201,9 +197,9 @@ FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
} else if (strcmp(arg[iarg],"yz") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
p_start[3] = force->numeric(FLERR,arg[iarg+1]);
|
||||
p_stop[3] = force->numeric(FLERR,arg[iarg+2]);
|
||||
p_period[3] = force->numeric(FLERR,arg[iarg+3]);
|
||||
p_start[3] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
||||
p_stop[3] = utils::numeric(FLERR,arg[iarg+2],false,lmp);
|
||||
p_period[3] = utils::numeric(FLERR,arg[iarg+3],false,lmp);
|
||||
p_flag[3] = 1;
|
||||
deviatoric_flag = 1;
|
||||
scaleyz = 0;
|
||||
@ -212,9 +208,9 @@ FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) :
|
||||
error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
|
||||
} else if (strcmp(arg[iarg],"xz") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
p_start[4] = force->numeric(FLERR,arg[iarg+1]);
|
||||
p_stop[4] = force->numeric(FLERR,arg[iarg+2]);
|
||||
p_period[4] = force->numeric(FLERR,arg[iarg+3]);
|
||||
p_start[4] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
||||
p_stop[4] = utils::numeric(FLERR,arg[iarg+2],false,lmp);
|
||||
p_period[4] = utils::numeric(FLERR,arg[iarg+3],false,lmp);
|
||||
p_flag[4] = 1;
|
||||
deviatoric_flag = 1;
|
||||
scalexz = 0;
|
||||
@ -223,9 +219,9 @@ FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) :
|
||||
error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
|
||||
} else if (strcmp(arg[iarg],"xy") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
p_start[5] = force->numeric(FLERR,arg[iarg+1]);
|
||||
p_stop[5] = force->numeric(FLERR,arg[iarg+2]);
|
||||
p_period[5] = force->numeric(FLERR,arg[iarg+3]);
|
||||
p_start[5] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
||||
p_stop[5] = utils::numeric(FLERR,arg[iarg+2],false,lmp);
|
||||
p_period[5] = utils::numeric(FLERR,arg[iarg+3],false,lmp);
|
||||
p_flag[5] = 1;
|
||||
deviatoric_flag = 1;
|
||||
scalexy = 0;
|
||||
@ -242,12 +238,12 @@ FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) :
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"tchain") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
mtchain = force->inumeric(FLERR,arg[iarg+1]);
|
||||
mtchain = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
|
||||
if (mtchain < 1) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"pchain") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
mpchain = force->inumeric(FLERR,arg[iarg+1]);
|
||||
mpchain = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
|
||||
if (mpchain < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"mtk") == 0) {
|
||||
@ -258,17 +254,17 @@ FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) :
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"tloop") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
nc_tchain = force->inumeric(FLERR,arg[iarg+1]);
|
||||
nc_tchain = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
|
||||
if (nc_tchain < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"ploop") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
nc_pchain = force->inumeric(FLERR,arg[iarg+1]);
|
||||
nc_pchain = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
|
||||
if (nc_pchain < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"nreset") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
nreset_h0 = force->inumeric(FLERR,arg[iarg+1]);
|
||||
nreset_h0 = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
|
||||
if (nreset_h0 < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"scalexy") == 0) {
|
||||
@ -297,9 +293,9 @@ FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) :
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"fixedpoint") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
fixedpoint[0] = force->numeric(FLERR,arg[iarg+1]);
|
||||
fixedpoint[1] = force->numeric(FLERR,arg[iarg+2]);
|
||||
fixedpoint[2] = force->numeric(FLERR,arg[iarg+3]);
|
||||
fixedpoint[0] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
||||
fixedpoint[1] = utils::numeric(FLERR,arg[iarg+2],false,lmp);
|
||||
fixedpoint[2] = utils::numeric(FLERR,arg[iarg+3],false,lmp);
|
||||
iarg += 4;
|
||||
} else error->all(FLERR,"Illegal fix nvt/npt/nph command");
|
||||
}
|
||||
@ -410,8 +406,12 @@ FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) :
|
||||
if (p_flag[i]) pstat_flag = 1;
|
||||
|
||||
if (pstat_flag) {
|
||||
if (p_flag[0] || p_flag[1] || p_flag[2]) box_change_size = 1;
|
||||
if (p_flag[3] || p_flag[4] || p_flag[5]) box_change_shape = 1;
|
||||
if (p_flag[0]) box_change |= BOX_CHANGE_X;
|
||||
if (p_flag[1]) box_change |= BOX_CHANGE_Y;
|
||||
if (p_flag[2]) box_change |= BOX_CHANGE_Z;
|
||||
if (p_flag[3]) box_change |= BOX_CHANGE_YZ;
|
||||
if (p_flag[4]) box_change |= BOX_CHANGE_XZ;
|
||||
if (p_flag[5]) box_change |= BOX_CHANGE_XY;
|
||||
no_change_box = 1;
|
||||
|
||||
// pstyle = TRICLINIC if any off-diagonal term is controlled -> 6 dof
|
||||
@ -425,10 +425,9 @@ FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) :
|
||||
// pre_exchange only required if flips can occur due to shape changes
|
||||
|
||||
if (flipflag && (p_flag[3] || p_flag[4] || p_flag[5]))
|
||||
pre_exchange_flag = 1;
|
||||
if (flipflag && (domain->yz != 0.0 || domain->xz != 0.0 ||
|
||||
domain->xy != 0.0))
|
||||
pre_exchange_flag = 1;
|
||||
pre_exchange_flag = pre_exchange_migrate = 1;
|
||||
if (flipflag && (domain->yz != 0.0 || domain->xz != 0.0 || domain->xy != 0.0))
|
||||
pre_exchange_flag = pre_exchange_migrate = 1;
|
||||
}
|
||||
|
||||
// convert input periods to frequencies
|
||||
@ -511,10 +510,10 @@ FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) :
|
||||
}
|
||||
|
||||
nrigid = 0;
|
||||
rfix = NULL;
|
||||
rfix = nullptr;
|
||||
|
||||
if (pre_exchange_flag) irregular = new Irregular(lmp);
|
||||
else irregular = NULL;
|
||||
else irregular = nullptr;
|
||||
|
||||
// initialize vol0,t0 to zero to signal uninitialized
|
||||
// values then assigned in init(), if necessary
|
||||
@ -677,7 +676,7 @@ void FixTGNHDrude::init()
|
||||
|
||||
delete [] rfix;
|
||||
nrigid = 0;
|
||||
rfix = NULL;
|
||||
rfix = nullptr;
|
||||
|
||||
for (int i = 0; i < modify->nfix; i++)
|
||||
if (modify->fix[i]->rigid_flag) nrigid++;
|
||||
@ -743,13 +742,13 @@ void FixTGNHDrude::setup_mol_mass_dof() {
|
||||
|
||||
// DOFs
|
||||
t_current = temperature->compute_scalar();
|
||||
_tdof = temperature->dof;
|
||||
tdof = temperature->dof;
|
||||
dof_mol = 3 * n_mol_in_group;
|
||||
// remove DOFs of COM motion based on the number of atoms in the group
|
||||
if (n_mol_in_group > 1)
|
||||
dof_mol -= ((double) 3) * group->count(igroup) / atom->natoms;
|
||||
dof_drude = 3 * n_drude;
|
||||
dof_int = _tdof - dof_mol - dof_drude;
|
||||
dof_int = tdof - dof_mol - dof_drude;
|
||||
|
||||
if (comm->me == 0) {
|
||||
if (screen) {
|
||||
@ -774,7 +773,7 @@ void FixTGNHDrude::setup(int /*vflag*/)
|
||||
// If no thermostat or using fix nphug,
|
||||
// t_target must be defined by other means.
|
||||
|
||||
if (tstat_flag && strstr(style,"nphug") == NULL) {
|
||||
if (tstat_flag && strstr(style,"nphug") == nullptr) {
|
||||
compute_temp_target();
|
||||
} else if (pstat_flag) {
|
||||
|
||||
@ -931,7 +930,7 @@ void FixTGNHDrude::final_integrate()
|
||||
// compute appropriately coupled elements of mvv_current
|
||||
|
||||
t_current = temperature->compute_scalar();
|
||||
_tdof = temperature->dof;
|
||||
tdof = temperature->dof;
|
||||
|
||||
// need to recompute pressure to account for change in KE
|
||||
// t_current is up-to-date, but compute_temperature is not
|
||||
@ -1559,6 +1558,8 @@ double FixTGNHDrude::compute_scalar()
|
||||
|
||||
double FixTGNHDrude::compute_vector(int n)
|
||||
{
|
||||
if (!temp_computed_end_of_step)
|
||||
compute_temp_mol_int_drude(true);
|
||||
switch (n){
|
||||
case 0:
|
||||
return t_mol;
|
||||
@ -1595,7 +1596,7 @@ void FixTGNHDrude::reset_dt()
|
||||
dto = 0.5*step_respa[0];
|
||||
}
|
||||
|
||||
void FixTGNHDrude::compute_temp_mol_int_drude() {
|
||||
void FixTGNHDrude::compute_temp_mol_int_drude(bool end_of_step) {
|
||||
double **v = atom->v;
|
||||
double *mass = atom->mass;
|
||||
int *molecule = atom->molecule;
|
||||
@ -1690,6 +1691,8 @@ void FixTGNHDrude::compute_temp_mol_int_drude() {
|
||||
ke2drude = ke2_int_drude[1] * force->mvv2e;
|
||||
t_int = ke2int / dof_int / boltz;
|
||||
t_drude = ke2drude / dof_drude / boltz;
|
||||
|
||||
temp_computed_end_of_step = end_of_step;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -1698,7 +1701,7 @@ void FixTGNHDrude::compute_temp_mol_int_drude() {
|
||||
|
||||
void FixTGNHDrude::nhc_temp_integrate()
|
||||
{
|
||||
compute_temp_mol_int_drude();
|
||||
compute_temp_mol_int_drude(false);
|
||||
|
||||
// update masses of thermostat in case target temperature changes
|
||||
etamol_mass[0] = ke2mol_target / (t_freq*t_freq);
|
||||
@ -2225,7 +2228,7 @@ void FixTGNHDrude::nh_omega_dot()
|
||||
mtk_term1 = 0.0;
|
||||
if (mtk_flag) {
|
||||
if (pstyle == ISO) {
|
||||
mtk_term1 = _tdof * boltz * t_current;
|
||||
mtk_term1 = tdof * boltz * t_current;
|
||||
mtk_term1 /= pdim * atom->natoms;
|
||||
} else {
|
||||
double *mvv_current = temperature->vector;
|
||||
|
||||
@ -44,7 +44,7 @@ class FixTGNHDrude : public Fix {
|
||||
protected:
|
||||
int dimension,which;
|
||||
double dtv,dtf,dthalf,dt4,dt8,dto;
|
||||
double boltz,nktv2p,_tdof;
|
||||
double boltz,nktv2p,tdof;
|
||||
double vol0; // reference volume
|
||||
double t0; // reference temperature
|
||||
// used for barostat mass
|
||||
@ -147,7 +147,8 @@ class FixTGNHDrude : public Fix {
|
||||
double dof_mol, dof_int, dof_drude; // DOFs of different modes in the fix group
|
||||
void setup_mol_mass_dof();
|
||||
double **v_mol, **v_mol_tmp;
|
||||
void compute_temp_mol_int_drude();
|
||||
void compute_temp_mol_int_drude(bool); // calculate the temperatures of three sets of DOFs
|
||||
bool temp_computed_end_of_step = false;
|
||||
double tdrude_target, tdrude_freq;
|
||||
double t_mol, t_int, t_drude;
|
||||
double ke2mol, ke2int, ke2drude;
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -13,6 +13,7 @@
|
||||
|
||||
#include "fix_tgnpt_drude.h"
|
||||
#include <cstring>
|
||||
|
||||
#include "modify.h"
|
||||
#include "error.h"
|
||||
|
||||
@ -34,35 +35,23 @@ FixTGNPTDrude::FixTGNPTDrude(LAMMPS *lmp, int narg, char **arg) :
|
||||
// compute group = all since pressure is always global (group all)
|
||||
// and thus its KE/temperature contribution should use group all
|
||||
|
||||
int n = strlen(id) + 6;
|
||||
id_temp = new char[n];
|
||||
strcpy(id_temp,id);
|
||||
strcat(id_temp,"_temp");
|
||||
std::string tcmd = id + std::string("_temp");
|
||||
id_temp = new char[tcmd.size()+1];
|
||||
strcpy(id_temp, tcmd.c_str());
|
||||
|
||||
char **newarg = new char*[3];
|
||||
newarg[0] = id_temp;
|
||||
newarg[1] = (char *) "all";
|
||||
newarg[2] = (char *) "temp";
|
||||
|
||||
modify->add_compute(3,newarg);
|
||||
delete [] newarg;
|
||||
tcmd += " all temp";
|
||||
modify->add_compute(tcmd);
|
||||
tcomputeflag = 1;
|
||||
|
||||
// create a new compute pressure style
|
||||
// id = fix-ID + press, compute group = all
|
||||
// pass id_temp as 4th arg to pressure constructor
|
||||
|
||||
n = strlen(id) + 7;
|
||||
id_press = new char[n];
|
||||
strcpy(id_press,id);
|
||||
strcat(id_press,"_press");
|
||||
std::string pcmd = id + std::string("_press");
|
||||
id_press = new char[pcmd.size()+1];
|
||||
strcpy(id_press, pcmd.c_str());
|
||||
|
||||
newarg = new char*[4];
|
||||
newarg[0] = id_press;
|
||||
newarg[1] = (char *) "all";
|
||||
newarg[2] = (char *) "pressure";
|
||||
newarg[3] = id_temp;
|
||||
modify->add_compute(4,newarg);
|
||||
delete [] newarg;
|
||||
pcmd += " all pressure " + std::string(id_temp);
|
||||
modify->add_compute(pcmd);
|
||||
pcomputeflag = 1;
|
||||
}
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -13,6 +13,7 @@
|
||||
|
||||
#include "fix_tgnvt_drude.h"
|
||||
#include <cstring>
|
||||
|
||||
#include "group.h"
|
||||
#include "modify.h"
|
||||
#include "error.h"
|
||||
@ -33,17 +34,11 @@ FixTGNVTDrude::FixTGNVTDrude(LAMMPS *lmp, int narg, char **arg) :
|
||||
// create a new compute temp style
|
||||
// id = fix-ID + temp
|
||||
|
||||
int n = strlen(id) + 6;
|
||||
id_temp = new char[n];
|
||||
strcpy(id_temp,id);
|
||||
strcat(id_temp,"_temp");
|
||||
std::string tcmd = id + std::string("_temp");
|
||||
id_temp = new char[tcmd.size()+1];
|
||||
strcpy(id_temp, tcmd.c_str());
|
||||
|
||||
char **newarg = new char*[3];
|
||||
newarg[0] = id_temp;
|
||||
newarg[1] = group->names[igroup];
|
||||
newarg[2] = (char *) "temp";
|
||||
|
||||
modify->add_compute(3,newarg);
|
||||
delete [] newarg;
|
||||
tcmd += fmt::format(" {} temp", group->names[igroup]);
|
||||
modify->add_compute(tcmd);
|
||||
tcomputeflag = 1;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user