forked from lijiext/lammps
use improper style fourier instead of non-existing style opls
This commit is contained in:
Axel Kohlmeyer
parent
8ff6122560
commit
d4d5f241eb
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@ -79,10 +79,10 @@ Dihedral Coeffs
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Improper Coeffs
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Improper Coeffs
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1 0.0000 2.1999 0.0000 0.0000 # CAO-CAO-CAT-CTT
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1 2.1999 0.0000 0.0000 -1.0000 0 # CAO-CAO-CAT-CTT
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2 0.0000 2.1999 0.0000 0.0000 # CAT-CAM-CAO-HAT
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2 2.1999 0.0000 0.0000 -1.0000 0 # CAT-CAM-CAO-HAT
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3 0.0000 2.1999 0.0000 0.0000 # CAO-CAP-CAM-HAT
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3 2.1999 0.0000 0.0000 -1.0000 0 # CAO-CAP-CAM-HAT
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4 0.0000 2.1999 0.0000 0.0000 # CAM-CAM-CAP-HAT
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4 2.1999 0.0000 0.0000 -1.0000 0 # CAM-CAM-CAP-HAT
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Atoms
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Atoms
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@ -7,7 +7,7 @@ atom_style full
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bond_style harmonic
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bond_style harmonic
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angle_style harmonic
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angle_style harmonic
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dihedral_style opls
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dihedral_style opls
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improper_style opls
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improper_style fourier
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special_bonds lj/coul 0.0 0.0 0.5
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special_bonds lj/coul 0.0 0.0 0.5
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pair_style lj/cut/thole/long 2.600 8.0 8.0
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pair_style lj/cut/thole/long 2.600 8.0 8.0
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@ -109,7 +109,7 @@ fix fNPH all nve
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compute cTEMP all temp/drude
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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]
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thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
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thermo 50
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thermo 50
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timestep 0.5
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timestep 0.5
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@ -7,7 +7,7 @@ atom_style full
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bond_style harmonic
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bond_style harmonic
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angle_style harmonic
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angle_style harmonic
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dihedral_style opls
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dihedral_style opls
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improper_style opls
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improper_style fourier
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special_bonds lj/coul 0.0 0.0 0.5
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special_bonds lj/coul 0.0 0.0 0.5
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pair_style lj/cut/thole/long 2.600 8.0 8.0
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pair_style lj/cut/thole/long 2.600 8.0 8.0
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@ -115,7 +115,7 @@ fix fINVERSE all drude/transform/inverse
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fix fMOMENTUM all momentum 100 linear 1 1 1
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fix fMOMENTUM all momentum 100 linear 1 1 1
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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]
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thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
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thermo 50
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thermo 50
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timestep 0.5
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timestep 0.5
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@ -1,14 +0,0 @@
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# 250 toluene 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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improper_style opls
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ERROR: Unknown improper style opls (src/force.cpp:634)
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Last command: improper_style opls
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@ -1,14 +0,0 @@
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# 250 toluene 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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improper_style opls
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ERROR: Unknown improper style opls (src/force.cpp:634)
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Last command: improper_style opls
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@ -1,14 +0,0 @@
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# 250 toluene system for drude polarizability example (Nose-Hoover)
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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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improper_style opls
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ERROR: Unknown improper style opls (src/force.cpp:634)
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Last command: improper_style opls
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@ -1,14 +0,0 @@
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# 250 toluene system for drude polarizability example (Nose-Hoover)
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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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improper_style opls
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ERROR: Unknown improper style opls (src/force.cpp:634)
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Last command: improper_style opls
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@ -0,0 +1,254 @@
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LAMMPS (7 Aug 2019)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
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using 1 OpenMP thread(s) per MPI task
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# 250 toluene 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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improper_style fourier
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special_bonds lj/coul 0.0 0.0 0.5
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pair_style lj/cut/thole/long 2.600 8.0 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.toluene extra/special/per/atom 1
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orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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5500 atoms
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scanning bonds ...
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4 = 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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8 = max dihedrals/atom
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scanning impropers ...
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2 = max impropers/atom
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reading bonds ...
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5500 bonds
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reading angles ...
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6000 angles
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reading dihedrals ...
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6000 dihedrals
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reading impropers ...
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1500 impropers
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5 = max # of 1-2 neighbors
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10 = max # of 1-3 neighbors
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16 = max # of 1-4 neighbors
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20 = max # of special neighbors
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special bonds CPU = 0.00199628 secs
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read_data CPU = 0.0169649 secs
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comm_modify vel yes
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group gTOLUENE molecule 1:250
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5500 atoms in group gTOLUENE
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group gCORES type 1 2 3 4 5 6 7
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3750 atoms in group gCORES
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group gDRUDES type 8 9 10 11 12
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1750 atoms in group gDRUDES
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pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
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pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
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pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
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pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
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pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
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pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
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pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
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pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
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pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
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pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
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pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
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pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
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pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
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pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
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pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
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pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
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pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
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pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
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pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
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pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
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pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
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pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
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pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
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pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
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pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
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pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
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pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
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pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
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pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
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pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
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pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
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pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
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pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
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pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
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pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
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pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
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pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
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pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
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pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
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pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
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pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
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pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
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pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
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pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
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pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
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pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
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pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
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pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
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pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
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pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
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pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
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pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
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pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
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pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
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pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
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pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
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pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
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pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
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pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
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pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
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pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
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pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
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pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
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pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
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pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
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pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
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pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
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pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT
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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 C C C N N D D D D D
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fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
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1250 = # of size 2 clusters
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0 = # of size 3 clusters
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250 = # of size 4 clusters
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0 = # of frozen angles
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find clusters CPU = 0.000807762 secs
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fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
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fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
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fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
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fix fNPH all nve
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compute cTEMP all temp/drude
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thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
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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:323)
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G vector (1/distance) = 0.382011
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grid = 40 40 40
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0325934
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estimated relative force accuracy = 9.8154e-05
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using double precision FFTW3
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3d grid and FFT values/proc = 103823 64000
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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: 19
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New max number of 1-2 to 1-4 neighbors: 20 (+1)
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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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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/thole/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes
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Step 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]
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0 11086.347 2910.7282 202.07402 8175.6191 6565.4851 20.333365 1.0706727e-06 -3299.85 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821
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50 4782.1702 4728.7435 328.28767 53.426722 1812.2203 685.37824 683.70917 -3277.1645 797.34329 1305983.2 -1306631.2 16874.358 48631.318 448.52419 116.25477
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100 2906.0879 3699.8031 256.85465 -793.7152 978.15364 778.36908 862.30899 -3270.1722 468.44888 1306096.8 -1306707.6 15631.384 48631.318 382.26408 35.748403
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150 2089.0918 3593.0499 249.44342 -1503.9581 751.32283 803.47802 668.4757 -3277.5983 128.17444 1306138.5 -1306716.3 15193.04 48631.318 384.75632 10.892446
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200 1547.3302 3248.639 225.53309 -1701.3089 699.65977 814.31164 692.83227 -3276.3957 -66.671816 1306160.9 -1306725.9 13787.676 48631.318 351.28242 3.8458668
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250 1177.9323 3095.949 214.93276 -1918.0167 688.87262 842.44531 615.89218 -3278.4465 -210.06178 1306154.3 -1306731 8808.5835 48631.318 335.8115 1.8330994
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||||||
|
300 895.90313 2870.3451 199.27046 -1974.442 734.95873 858.58147 624.00862 -3278.6022 -342.01951 1306163.6 -1306735 3388.4841 48631.318 311.56815 1.2987715
|
||||||
|
350 669.25785 2764.9587 191.95413 -2095.7009 662.44028 860.79714 602.69567 -3278.776 -376.37081 1306172.3 -1306738.8 8494.9184 48631.318 300.19414 1.1358594
|
||||||
|
400 531.21609 2722.6775 189.01881 -2191.4614 684.34049 868.77818 576.86096 -3280.1649 -459.66591 1306160 -1306741.6 6726.3087 48631.318 295.59622 1.1315427
|
||||||
|
450 427.05425 2611.7588 181.3184 -2184.7046 719.2042 891.88178 591.2282 -3279.339 -534.65069 1306172.2 -1306745.2 2398.5394 48631.318 283.56126 1.0726045
|
||||||
|
500 310.44891 2556.0967 177.45412 -2245.6477 720.86526 841.50195 586.3417 -3279.3029 -539.81715 1306169.5 -1306744.8 3028.595 48631.318 277.52314 1.0406334
|
||||||
|
550 207.83114 2531.3051 175.73299 -2323.4739 674.71188 855.2132 555.53227 -3280.0378 -553.93222 1306171.9 -1306746.9 4609.4408 48631.318 274.80629 1.0748601
|
||||||
|
600 88.81557 2459.9059 170.77619 -2371.0903 692.4485 834.47484 550.85905 -3280.9086 -595.31802 1306171.4 -1306744 2107.9995 48631.318 267.06312 1.0301965
|
||||||
|
650 75.616307 2416.9747 167.79573 -2341.3584 703.57186 869.98959 564.81201 -3280.7522 -619.8016 1306168 -1306747.2 1236.4829 48631.318 262.3542 1.0968447
|
||||||
|
700 49.832719 2415.7344 167.70963 -2365.9017 683.61663 882.67915 555.23571 -3280.7778 -615.06862 1306159.9 -1306751.4 2985.7048 48631.318 262.23095 1.0762424
|
||||||
|
750 41.513638 2427.218 168.50687 -2385.7044 698.87619 863.2938 564.58197 -3280.0156 -637.29964 1306160.1 -1306755.3 1653.117 48631.318 263.49803 1.0451977
|
||||||
|
800 109.53032 2481.9041 172.30339 -2372.3738 697.22709 897.36555 561.28745 -3280.6784 -651.29564 1306155 -1306751.3 1219.8761 48631.318 269.43698 1.0647792
|
||||||
|
850 98.142203 2502.3132 173.72026 -2404.171 696.5382 878.83293 566.44302 -3280.2837 -663.94587 1306155.6 -1306757.4 1122.7487 48631.318 271.67716 1.030267
|
||||||
|
900 62.992675 2409.7324 167.29295 -2346.7397 722.00541 896.64662 560.66083 -3279.4915 -644.05458 1306153.6 -1306756.1 1604.295 48631.318 261.58656 1.0609836
|
||||||
|
950 5.6677468 2403.5067 166.86073 -2397.839 725.07222 891.00249 556.81977 -3279.7848 -672.66389 1306141 -1306759.2 1019.1694 48631.318 260.91187 1.0562387
|
||||||
|
1000 38.526968 2444.97 169.73928 -2406.4431 704.72993 920.68493 534.59035 -3281.2673 -667.78091 1306141.1 -1306758.5 486.79846 48631.318 265.39928 1.098473
|
||||||
|
1050 21.698026 2388.6306 165.82798 -2366.9326 712.15539 934.39244 546.92027 -3281.1469 -654.7449 1306137.4 -1306761.9 1556.1256 48631.318 259.28203 1.0760765
|
||||||
|
1100 -26.971225 2433.8428 168.96678 -2460.814 710.11081 881.19212 524.51547 -3281.7925 -667.53202 1306137.1 -1306764.4 1203.8971 48631.318 264.20441 1.0706085
|
||||||
|
1150 -49.171269 2375.9688 164.94895 -2425.14 729.78127 918.79575 518.21967 -3281.6542 -675.7239 1306130.4 -1306765 229.44016 48631.318 257.89845 1.086519
|
||||||
|
1200 -53.421342 2422.0091 168.14524 -2475.4304 710.67274 884.2589 523.32524 -3282.2275 -674.49333 1306130.9 -1306767.9 -131.09655 48631.318 262.91124 1.0804821
|
||||||
|
1250 -58.534776 2394.4031 166.22873 -2452.9378 680.27486 909.58096 532.81959 -3281.5551 -653.13731 1306127 -1306767.9 546.96357 48631.318 259.92916 1.0424914
|
||||||
|
1300 -24.151217 2431.9902 168.83817 -2456.1414 681.27127 919.39245 536.41899 -3281.3717 -661.90875 1306121.6 -1306771.5 1455.7512 48631.318 264.00712 1.0630558
|
||||||
|
1350 -38.973062 2438.6194 169.2984 -2477.5925 707.96118 912.62518 519.44533 -3281.6739 -687.67183 1306126.1 -1306774.4 -1470.4442 48631.318 264.70225 1.1091537
|
||||||
|
1400 11.896539 2384.5407 165.54404 -2372.6442 719.03374 950.93261 550.5639 -3280.4581 -663.4921 1306122 -1306771.3 465.12854 48631.318 258.83564 1.0785364
|
||||||
|
1450 -13.118691 2436.6246 169.15991 -2449.7433 661.04397 933.07103 561.29537 -3280.6997 -672.68495 1306123.9 -1306775.7 -108.46564 48631.318 264.50636 1.0718787
|
||||||
|
1500 -38.151755 2417.4849 167.83116 -2455.6367 688.81484 892.35701 565.29013 -3279.6716 -662.1817 1306116.9 -1306777.2 517.89634 48631.318 262.44549 1.0338083
|
||||||
|
1550 -71.663334 2405.7016 167.01311 -2477.3649 681.78925 876.31247 559.003 -3280.451 -649.16641 1306112.8 -1306777.7 925.49349 48631.318 261.148 1.0609731
|
||||||
|
1600 -13.900431 2419.481 167.96973 -2433.3814 718.46559 909.67964 559.06779 -3280.8163 -667.6092 1306108 -1306780.2 13.95808 48631.318 262.63632 1.080229
|
||||||
|
1650 -16.403222 2431.075 168.77464 -2447.4783 710.99509 907.65662 551.60307 -3279.8852 -661.52624 1306104.5 -1306780.8 726.89923 48631.318 263.91553 1.0489963
|
||||||
|
1700 -18.555086 2438.2062 169.26971 -2456.7613 665.90475 943.02217 542.86579 -3280.9017 -657.99229 1306108 -1306777.7 801.41078 48631.318 264.67663 1.0750708
|
||||||
|
1750 -6.9249446 2443.9707 169.6699 -2450.8956 733.23573 890.06857 560.83229 -3280.362 -670.93883 1306098.3 -1306782.1 47.037748 48631.318 265.30892 1.0661143
|
||||||
|
1800 -21.686222 2434.3375 169.00113 -2456.0237 729.35297 899.9733 561.59516 -3280.4727 -680.98901 1306096.5 -1306782 495.63617 48631.318 264.25723 1.0723683
|
||||||
|
1850 -72.916947 2408.8254 167.22998 -2481.7423 683.24984 904.13282 549.97726 -3279.6699 -652.63212 1306099.2 -1306786 -120.61674 48631.318 261.48504 1.0659808
|
||||||
|
1900 -55.4099 2415.455 167.69023 -2470.8649 700.4473 904.72264 565.5266 -3280.4533 -673.23082 1306099.6 -1306787.4 202.15936 48631.318 262.20353 1.0709756
|
||||||
|
1950 -79.877997 2409.2307 167.25812 -2489.1087 695.9536 894.4541 564.7034 -3279.3581 -680.33472 1306100.8 -1306785.3 213.72828 48631.318 261.52921 1.0658433
|
||||||
|
2000 -102.20457 2399.4263 166.57746 -2501.6309 689.67819 894.58596 565.53233 -3280.7595 -680.39032 1306096.4 -1306786.6 1113.7499 48631.318 260.46311 1.0647045
|
||||||
|
Loop time of 68.4185 on 1 procs for 2000 steps with 5500 atoms
|
||||||
|
|
||||||
|
Performance: 1.263 ns/day, 19.005 hours/ns, 29.232 timesteps/s
|
||||||
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 48.825 | 48.825 | 48.825 | 0.0 | 71.36
|
||||||
|
Bond | 2.8852 | 2.8852 | 2.8852 | 0.0 | 4.22
|
||||||
|
Kspace | 13.795 | 13.795 | 13.795 | 0.0 | 20.16
|
||||||
|
Neigh | 1.0731 | 1.0731 | 1.0731 | 0.0 | 1.57
|
||||||
|
Comm | 0.27067 | 0.27067 | 0.27067 | 0.0 | 0.40
|
||||||
|
Output | 0.0031168 | 0.0031168 | 0.0031168 | 0.0 | 0.00
|
||||||
|
Modify | 1.5207 | 1.5207 | 1.5207 | 0.0 | 2.22
|
||||||
|
Other | | 0.04541 | | | 0.07
|
||||||
|
|
||||||
|
Nlocal: 5500 ave 5500 max 5500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 13157 ave 13157 max 13157 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 1.33822e+06 ave 1.33822e+06 max 1.33822e+06 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 1338215
|
||||||
|
Ave neighs/atom = 243.312
|
||||||
|
Ave special neighs/atom = 15.6364
|
||||||
|
Neighbor list builds = 32
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:01:08
|
||||||
|
|
@ -0,0 +1,254 @@
|
||||||
|
LAMMPS (7 Aug 2019)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# 250 toluene system for drude polarizability example (Langevin)
|
||||||
|
|
||||||
|
units real
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style full
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
dihedral_style opls
|
||||||
|
improper_style fourier
|
||||||
|
special_bonds lj/coul 0.0 0.0 0.5
|
||||||
|
|
||||||
|
pair_style lj/cut/thole/long 2.600 8.0 8.0
|
||||||
|
pair_modify mix geometric tail yes
|
||||||
|
kspace_style pppm 1.0e-4
|
||||||
|
|
||||||
|
read_data data.toluene extra/special/per/atom 1
|
||||||
|
orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
|
||||||
|
2 by 1 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
5500 atoms
|
||||||
|
scanning bonds ...
|
||||||
|
4 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
6 = max angles/atom
|
||||||
|
scanning dihedrals ...
|
||||||
|
8 = max dihedrals/atom
|
||||||
|
scanning impropers ...
|
||||||
|
2 = max impropers/atom
|
||||||
|
reading bonds ...
|
||||||
|
5500 bonds
|
||||||
|
reading angles ...
|
||||||
|
6000 angles
|
||||||
|
reading dihedrals ...
|
||||||
|
6000 dihedrals
|
||||||
|
reading impropers ...
|
||||||
|
1500 impropers
|
||||||
|
5 = max # of 1-2 neighbors
|
||||||
|
10 = max # of 1-3 neighbors
|
||||||
|
16 = max # of 1-4 neighbors
|
||||||
|
20 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000747919 secs
|
||||||
|
read_data CPU = 0.0168228 secs
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
group gTOLUENE molecule 1:250
|
||||||
|
5500 atoms in group gTOLUENE
|
||||||
|
group gCORES type 1 2 3 4 5 6 7
|
||||||
|
3750 atoms in group gCORES
|
||||||
|
group gDRUDES type 8 9 10 11 12
|
||||||
|
1750 atoms in group gDRUDES
|
||||||
|
|
||||||
|
pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
|
||||||
|
pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
|
||||||
|
pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
|
||||||
|
pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
|
||||||
|
pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
|
||||||
|
pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
|
||||||
|
pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
|
||||||
|
pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
|
||||||
|
pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
|
||||||
|
pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
|
||||||
|
pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
|
||||||
|
pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
|
||||||
|
pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
|
||||||
|
pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
|
||||||
|
pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
|
||||||
|
pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
|
||||||
|
pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
|
||||||
|
pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
|
||||||
|
pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
|
||||||
|
pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
|
||||||
|
pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
|
||||||
|
pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
|
||||||
|
pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
|
||||||
|
pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
|
||||||
|
pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
|
||||||
|
pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
|
||||||
|
pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
|
||||||
|
pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
|
||||||
|
pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
|
||||||
|
pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
|
||||||
|
pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
|
||||||
|
pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
|
||||||
|
pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
|
||||||
|
pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
|
||||||
|
pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
|
||||||
|
pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
|
||||||
|
pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
|
||||||
|
pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
|
||||||
|
pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
|
||||||
|
pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
|
||||||
|
pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
|
||||||
|
pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
|
||||||
|
pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
|
||||||
|
pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
|
||||||
|
pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
|
||||||
|
pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
|
||||||
|
pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
|
||||||
|
pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
|
||||||
|
pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
|
||||||
|
pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
|
||||||
|
pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
|
||||||
|
pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
|
||||||
|
pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
|
||||||
|
pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
|
||||||
|
pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
|
||||||
|
pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
|
||||||
|
pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
|
||||||
|
pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
|
||||||
|
pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
|
||||||
|
pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
|
||||||
|
pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
|
||||||
|
pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
|
||||||
|
pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
|
||||||
|
pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
|
||||||
|
pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
|
||||||
|
pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
|
||||||
|
pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
|
||||||
|
pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT
|
||||||
|
|
||||||
|
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 C C C N N D D D D D
|
||||||
|
|
||||||
|
fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
|
||||||
|
1250 = # of size 2 clusters
|
||||||
|
0 = # of size 3 clusters
|
||||||
|
250 = # of size 4 clusters
|
||||||
|
0 = # of frozen angles
|
||||||
|
find clusters CPU = 0.000355244 secs
|
||||||
|
|
||||||
|
fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||||
|
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||||
|
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
|
||||||
|
fix fNPH all nve
|
||||||
|
|
||||||
|
compute cTEMP all temp/drude
|
||||||
|
|
||||||
|
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||||
|
thermo 50
|
||||||
|
|
||||||
|
timestep 0.5
|
||||||
|
run 2000
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
|
||||||
|
G vector (1/distance) = 0.382011
|
||||||
|
grid = 40 40 40
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.0325934
|
||||||
|
estimated relative force accuracy = 9.8154e-05
|
||||||
|
using double precision FFTW3
|
||||||
|
3d grid and FFT values/proc = 34263 16000
|
||||||
|
Rebuild special list taking Drude particles into account
|
||||||
|
Old max number of 1-2 to 1-4 neighbors: 19
|
||||||
|
New max number of 1-2 to 1-4 neighbors: 20 (+1)
|
||||||
|
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
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut/thole/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes
|
||||||
|
Step 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]
|
||||||
|
0 11086.347 2910.7282 202.07402 8175.6191 6565.4851 20.333365 1.0706727e-06 -3299.85 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821
|
||||||
|
50 4712.9507 4669.1606 324.15119 43.790082 1798.561 670.61319 690.16967 -3276.9493 811.643 1305983.2 -1306633.5 17164.771 48631.318 442.24313 116.13094
|
||||||
|
100 2865.9139 3726.4166 258.70226 -860.50272 968.87546 749.70761 860.70151 -3270.7784 427.14745 1306104.7 -1306700.9 15017.273 48631.318 385.10628 35.845353
|
||||||
|
150 1982.6673 3535.974 245.481 -1553.3068 764.86116 768.15837 658.70182 -3278.7906 108.49859 1306136.5 -1306711.2 16495.352 48631.318 378.64023 10.723986
|
||||||
|
200 1440.0277 3240.5932 224.97452 -1800.5656 687.71813 791.29356 643.82915 -3276.9293 -99.549986 1306172.9 -1306719.8 13234.476 48631.318 350.46321 3.7468464
|
||||||
|
250 1103.2915 3018.496 209.55567 -1915.2045 677.97905 825.32748 642.78891 -3278.0801 -226.1853 1306168.5 -1306725.5 8774.9103 48631.318 327.36313 1.8722119
|
||||||
|
300 789.07159 2827.1716 196.27319 -2038.1 735.96101 852.72545 589.14167 -3280.0357 -374.66018 1306169 -1306730.2 2259.1028 48631.318 306.85585 1.3262598
|
||||||
|
350 599.10023 2732.3739 189.69197 -2133.2737 677.67006 863.22888 565.41674 -3280.5231 -403.28794 1306177.4 -1306733.2 7989.222 48631.318 296.64126 1.1534418
|
||||||
|
400 428.26436 2591.2884 179.89727 -2163.0241 676.18745 849.24505 612.34065 -3277.4703 -457.85799 1306173.6 -1306739.1 7282.1438 48631.318 281.34719 1.0502762
|
||||||
|
450 307.26859 2534.2468 175.93722 -2226.9782 712.17636 853.98862 578.01327 -3279.7731 -533.87422 1306179.7 -1306737.2 1897.9643 48631.318 275.11317 1.0980929
|
||||||
|
500 234.60959 2495.1082 173.22007 -2260.4987 707.43541 878.25753 547.08402 -3281.2756 -549.04991 1306176.5 -1306739.5 2683.0639 48631.318 270.85452 1.0984718
|
||||||
|
550 203.34751 2445.6535 169.78673 -2242.306 669.03724 892.85034 599.20664 -3279.0757 -559.81157 1306175.9 -1306740.4 4512.9992 48631.318 265.49465 1.0628812
|
||||||
|
600 205.63573 2526.5892 175.4056 -2320.9535 685.64073 887.97693 557.42296 -3280.0332 -597.34755 1306167.8 -1306742.5 2999.5823 48631.318 274.29935 1.064682
|
||||||
|
650 176.23031 2526.3124 175.38638 -2350.0821 714.15285 895.42115 540.39191 -3280.8567 -636.27783 1306165.7 -1306748.6 871.68316 48631.318 274.2807 1.0442089
|
||||||
|
700 106.97524 2441.1059 169.47101 -2334.1306 697.16018 905.51407 564.71847 -3279.6208 -631.62324 1306159.4 -1306749.6 1953.8241 48631.318 264.98935 1.0771037
|
||||||
|
750 76.695104 2435.6635 169.09318 -2358.9684 672.01039 934.63351 545.64024 -3281.1075 -629.89722 1306152.4 -1306752.6 3044.0155 48631.318 264.39002 1.0932471
|
||||||
|
800 57.614075 2456.928 170.56945 -2399.3139 720.76364 898.68013 534.10051 -3281.5897 -659.64354 1306145.5 -1306757.1 1691.9503 48631.318 266.72089 1.0622697
|
||||||
|
850 -44.931126 2390.0608 165.92727 -2434.9919 708.70192 888.26851 537.13087 -3281.355 -665.17283 1306137.8 -1306760.3 123.07165 48631.318 259.45151 1.0516426
|
||||||
|
900 -96.878205 2358.862 163.76133 -2455.7403 672.98976 868.41571 546.69492 -3280.6939 -636.80102 1306134.5 -1306760.9 1955.7005 48631.318 256.05598 1.05337
|
||||||
|
950 -80.012575 2374.4497 164.84349 -2454.4623 679.59722 880.35157 548.35372 -3280.6061 -643.44517 1306125.8 -1306764.5 1510.9809 48631.318 257.72442 1.1017392
|
||||||
|
1000 -21.440874 2440.6729 169.44096 -2462.1138 718.56593 868.65109 555.54643 -3279.8516 -686.71673 1306126.6 -1306765 -1148.6212 48631.318 264.92977 1.1019339
|
||||||
|
1050 16.46903 2382.6961 165.41598 -2366.2271 712.51245 913.35848 579.81678 -3280.0559 -657.12122 1306129.3 -1306764 1004.5778 48631.318 258.64076 1.0684155
|
||||||
|
1100 35.847247 2483.1985 172.39325 -2447.3513 685.05704 889.42278 553.73166 -3280.0177 -663.67201 1306134.3 -1306766.2 699.1824 48631.318 269.56773 1.0838094
|
||||||
|
1150 -4.9817843 2431.4725 168.80223 -2436.4543 720.51056 868.17547 569.09902 -3280.5829 -677.99865 1306133.1 -1306768.7 435.19118 48631.318 263.96966 1.0303202
|
||||||
|
1200 -23.907197 2443.6035 169.64441 -2467.5107 684.96437 887.58483 549.43666 -3280.3144 -679.46182 1306137.2 -1306766.9 367.11148 48631.318 265.28645 1.0344036
|
||||||
|
1250 -16.904671 2389.9447 165.91921 -2406.8494 722.06959 902.90076 568.35616 -3280.6829 -683.32029 1306132.9 -1306769.1 76.759445 48631.318 259.41697 1.0908431
|
||||||
|
1300 -1.7822102 2410.2768 167.33074 -2412.0591 706.98675 904.31941 551.23506 -3280.7552 -651.51211 1306127.3 -1306769.6 1659.1113 48631.318 261.64093 1.0701648
|
||||||
|
1350 -3.569473 2446.3901 169.83786 -2449.9595 686.13971 894.85839 558.36242 -3279.9941 -664.59508 1306129 -1306773.7 783.32881 48631.318 265.5696 1.0709072
|
||||||
|
1400 -33.385576 2400.262 166.63547 -2433.6476 709.5808 890.68408 571.13105 -3280.1428 -674.51247 1306123.4 -1306773.8 -751.38571 48631.318 260.54522 1.080234
|
||||||
|
1450 -11.215152 2405.5409 167.00196 -2416.756 703.72038 913.21131 552.64196 -3280.9831 -649.19774 1306120.3 -1306776.4 1817.2174 48631.318 261.14741 1.031193
|
||||||
|
1500 -25.974102 2435.8375 169.10527 -2461.8116 689.93174 900.70619 552.63711 -3280.1497 -671.17989 1306124 -1306777.8 -98.941796 48631.318 264.45069 1.0190784
|
||||||
|
1550 -76.496407 2394.8126 166.25716 -2471.309 706.96953 886.06919 549.9101 -3280.8434 -659.57745 1306105.9 -1306779.7 -7.0989994 48631.318 259.95403 1.0772144
|
||||||
|
1600 -79.549932 2395.1114 166.2779 -2474.6614 684.11692 888.93332 562.94522 -3280.1665 -665.21744 1306114.4 -1306779.6 320.58515 48631.318 260.00641 1.0425978
|
||||||
|
1650 -99.702003 2360.5652 163.87957 -2460.2672 706.21244 900.9253 540.36599 -3280.2308 -655.96077 1306109.7 -1306781.3 307.35487 48631.318 256.23383 1.0666637
|
||||||
|
1700 -69.422658 2372.1727 164.68541 -2441.5954 676.79347 913.90473 581.60658 -3279.997 -670.33218 1306115.7 -1306779.3 -204.22848 48631.318 257.50963 1.0434075
|
||||||
|
1750 -80.889897 2425.3592 168.37782 -2506.2491 672.88937 911.52373 523.74733 -3280.4796 -673.90027 1306122 -1306782 965.12568 48631.318 263.26491 1.1001595
|
||||||
|
1800 -82.419368 2361.798 163.96515 -2444.2173 716.51571 882.9729 577.92505 -3278.9279 -671.67438 1306111.6 -1306782.6 -44.954517 48631.318 256.36957 1.0636692
|
||||||
|
1850 -93.715705 2373.3359 164.76616 -2467.0516 713.02466 907.03621 563.38626 -3280.2576 -693.30963 1306104.6 -1306781.5 -979.95945 48631.318 257.62543 1.0628288
|
||||||
|
1900 -73.60945 2449.5873 170.05983 -2523.1967 683.65116 893.94251 539.90847 -3281.4318 -680.16358 1306108 -1306787.1 598.18213 48631.318 265.91405 1.0766352
|
||||||
|
1950 -66.068291 2437.3691 169.21159 -2503.4374 672.5168 877.42934 573.56499 -3279.885 -668.54185 1306109.2 -1306787.7 733.05074 48631.318 264.61409 1.0224258
|
||||||
|
2000 -91.043979 2374.4077 164.84057 -2465.4516 692.13299 909.46192 574.60109 -3279.837 -672.33599 1306102.4 -1306791.8 -665.61581 48631.318 257.76275 1.0263294
|
||||||
|
Loop time of 23.7656 on 4 procs for 2000 steps with 5500 atoms
|
||||||
|
|
||||||
|
Performance: 3.636 ns/day, 6.602 hours/ns, 84.155 timesteps/s
|
||||||
|
94.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 11.918 | 13.096 | 14.137 | 27.0 | 55.10
|
||||||
|
Bond | 0.74012 | 0.76511 | 0.79225 | 2.9 | 3.22
|
||||||
|
Kspace | 6.7821 | 7.8285 | 9.0172 | 35.4 | 32.94
|
||||||
|
Neigh | 0.37249 | 0.37262 | 0.37278 | 0.0 | 1.57
|
||||||
|
Comm | 0.70503 | 0.7188 | 0.72807 | 1.1 | 3.02
|
||||||
|
Output | 0.0018752 | 0.0047592 | 0.013386 | 7.2 | 0.02
|
||||||
|
Modify | 0.91164 | 0.91644 | 0.92123 | 0.5 | 3.86
|
||||||
|
Other | | 0.06335 | | | 0.27
|
||||||
|
|
||||||
|
Nlocal: 1375 ave 1381 max 1368 min
|
||||||
|
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||||
|
Nghost: 7803.75 ave 7856 max 7755 min
|
||||||
|
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||||
|
Neighs: 334465 ave 349504 max 315867 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 1337859
|
||||||
|
Ave neighs/atom = 243.247
|
||||||
|
Ave special neighs/atom = 15.6364
|
||||||
|
Neighbor list builds = 32
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:23
|
||||||
|
|
@ -0,0 +1,262 @@
|
||||||
|
LAMMPS (7 Aug 2019)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# 250 toluene system for drude polarizability example (Nose-Hoover)
|
||||||
|
|
||||||
|
units real
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style full
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
dihedral_style opls
|
||||||
|
improper_style fourier
|
||||||
|
special_bonds lj/coul 0.0 0.0 0.5
|
||||||
|
|
||||||
|
pair_style lj/cut/thole/long 2.600 8.0 8.0
|
||||||
|
pair_modify mix geometric tail yes
|
||||||
|
kspace_style pppm 1.0e-4
|
||||||
|
|
||||||
|
read_data data.toluene extra/special/per/atom 1
|
||||||
|
orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
5500 atoms
|
||||||
|
scanning bonds ...
|
||||||
|
4 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
6 = max angles/atom
|
||||||
|
scanning dihedrals ...
|
||||||
|
8 = max dihedrals/atom
|
||||||
|
scanning impropers ...
|
||||||
|
2 = max impropers/atom
|
||||||
|
reading bonds ...
|
||||||
|
5500 bonds
|
||||||
|
reading angles ...
|
||||||
|
6000 angles
|
||||||
|
reading dihedrals ...
|
||||||
|
6000 dihedrals
|
||||||
|
reading impropers ...
|
||||||
|
1500 impropers
|
||||||
|
5 = max # of 1-2 neighbors
|
||||||
|
10 = max # of 1-3 neighbors
|
||||||
|
16 = max # of 1-4 neighbors
|
||||||
|
20 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.0019815 secs
|
||||||
|
read_data CPU = 0.0168803 secs
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
group gTOLUENE molecule 1:250
|
||||||
|
5500 atoms in group gTOLUENE
|
||||||
|
group gCORES type 1 2 3 4 5 6 7
|
||||||
|
3750 atoms in group gCORES
|
||||||
|
group gDRUDES type 8 9 10 11 12
|
||||||
|
1750 atoms in group gDRUDES
|
||||||
|
|
||||||
|
pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
|
||||||
|
pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
|
||||||
|
pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
|
||||||
|
pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
|
||||||
|
pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
|
||||||
|
pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
|
||||||
|
pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
|
||||||
|
pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
|
||||||
|
pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
|
||||||
|
pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
|
||||||
|
pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
|
||||||
|
pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
|
||||||
|
pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
|
||||||
|
pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
|
||||||
|
pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
|
||||||
|
pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
|
||||||
|
pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
|
||||||
|
pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
|
||||||
|
pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
|
||||||
|
pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
|
||||||
|
pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
|
||||||
|
pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
|
||||||
|
pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
|
||||||
|
pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
|
||||||
|
pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
|
||||||
|
pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
|
||||||
|
pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
|
||||||
|
pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
|
||||||
|
pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
|
||||||
|
pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
|
||||||
|
pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
|
||||||
|
pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
|
||||||
|
pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
|
||||||
|
pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
|
||||||
|
pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
|
||||||
|
pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
|
||||||
|
pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
|
||||||
|
pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
|
||||||
|
pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
|
||||||
|
pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
|
||||||
|
pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
|
||||||
|
pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
|
||||||
|
pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
|
||||||
|
pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
|
||||||
|
pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
|
||||||
|
pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
|
||||||
|
pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
|
||||||
|
pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
|
||||||
|
pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
|
||||||
|
pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
|
||||||
|
pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
|
||||||
|
pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
|
||||||
|
pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
|
||||||
|
pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
|
||||||
|
pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
|
||||||
|
pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
|
||||||
|
pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
|
||||||
|
pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
|
||||||
|
pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
|
||||||
|
pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
|
||||||
|
pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
|
||||||
|
pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
|
||||||
|
pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
|
||||||
|
pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
|
||||||
|
pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
|
||||||
|
pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
|
||||||
|
pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
|
||||||
|
pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT
|
||||||
|
|
||||||
|
|
||||||
|
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 C C C N N D D D D D
|
||||||
|
|
||||||
|
fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
|
||||||
|
1250 = # of size 2 clusters
|
||||||
|
0 = # of size 3 clusters
|
||||||
|
250 = # of size 4 clusters
|
||||||
|
0 = # of frozen angles
|
||||||
|
find clusters CPU = 0.000715256 secs
|
||||||
|
|
||||||
|
compute cTEMP_CORE gCORES temp/com
|
||||||
|
compute cTEMP all temp/drude
|
||||||
|
|
||||||
|
fix fDIRECT all drude/transform/direct
|
||||||
|
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
|
||||||
|
fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
|
||||||
|
fix fNVT1 gCORES nvt temp 260 260 100.0
|
||||||
|
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
|
||||||
|
fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
|
||||||
|
fix fNVT2 gDRUDES nvt temp 1 1 20.0
|
||||||
|
fix fINVERSE all drude/transform/inverse
|
||||||
|
|
||||||
|
fix fMOMENTUM all momentum 100 linear 1 1 1
|
||||||
|
|
||||||
|
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||||
|
thermo 50
|
||||||
|
|
||||||
|
timestep 0.5
|
||||||
|
run 2000
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
|
||||||
|
G vector (1/distance) = 0.382011
|
||||||
|
grid = 40 40 40
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.0325934
|
||||||
|
estimated relative force accuracy = 9.8154e-05
|
||||||
|
using double precision FFTW3
|
||||||
|
3d grid and FFT values/proc = 103823 64000
|
||||||
|
Rebuild special list taking Drude particles into account
|
||||||
|
Old max number of 1-2 to 1-4 neighbors: 19
|
||||||
|
New max number of 1-2 to 1-4 neighbors: 20 (+1)
|
||||||
|
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
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut/thole/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes
|
||||||
|
Step 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]
|
||||||
|
0 11086.347 2910.7282 202.07402 8175.6191 6565.4851 20.333365 1.0706727e-06 -3299.85 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821
|
||||||
|
50 3563.3755 4630.6343 321.47655 -1067.2588 735.72049 604.78665 689.14827 -3277.411 815.58183 1306088.7 -1306723.8 17813.424 48631.318 503.827 0.0087118192
|
||||||
|
100 3327.4724 4395.1107 305.12559 -1067.6382 597.93176 651.62645 945.4151 -3267.2851 584.58833 1306135.9 -1306715.8 17407.337 48631.318 478.20171 0.0075985539
|
||||||
|
150 3036.9065 4740.2304 329.08513 -1703.3239 558.64983 619.91284 658.80687 -3278.7837 285.12462 1306173 -1306720 18448.248 48631.318 515.75286 0.0063215188
|
||||||
|
200 2697.958 4559.3445 316.52733 -1861.3864 522.09334 593.89129 754.61446 -3273.49 87.660461 1306183.9 -1306730 17888.936 48631.318 496.07143 0.0068706164
|
||||||
|
250 2348.7568 4410.585 306.19988 -2061.8283 506.05007 575.35171 715.55054 -3276.3261 -18.364473 1306177.3 -1306741.4 11592.05 48631.318 479.88562 0.0071741032
|
||||||
|
300 2019.8258 4040.1415 280.48226 -2020.3157 604.3077 641.66689 693.93801 -3278.5312 -115.73641 1306183.2 -1306749.1 3631.3628 48631.318 439.57995 0.0069886387
|
||||||
|
350 1699.5166 3944.9851 273.87613 -2245.4685 452.07416 638.0653 658.79117 -3279.6053 -157.07584 1306196.9 -1306754.6 13544.368 48631.318 429.22694 0.0062868111
|
||||||
|
400 1399.2929 3726.098 258.68014 -2326.8051 457.91943 621.44726 639.39903 -3279.2395 -188.85914 1306185.4 -1306762.8 10792.274 48631.318 405.41134 0.0059340078
|
||||||
|
450 1120.5249 3518.345 244.25712 -2397.8201 519.48856 584.65789 646.36689 -3278.6685 -289.59913 1306184.1 -1306764.2 2755.5598 48631.318 382.80716 0.0055707485
|
||||||
|
500 868.0166 3359.8794 233.25583 -2491.8628 460.7393 581.49563 581.01731 -3281.5544 -252.20169 1306184.3 -1306765.7 6120.3639 48631.318 365.56528 0.0058756154
|
||||||
|
550 637.01567 3214.9521 223.19441 -2577.9364 431.81483 578.87411 540.94047 -3281.5337 -266.36075 1306182.8 -1306764.5 8622.4334 48631.318 349.79661 0.0058589653
|
||||||
|
600 418.04086 3113.4064 216.14472 -2695.3655 430.45935 538.68157 522.24598 -3283.456 -311.87901 1306174.3 -1306765.8 7068.9273 48631.318 338.74797 0.0059567598
|
||||||
|
650 218.5966 2930.8439 203.47052 -2712.2473 514.47294 514.28379 551.52551 -3282.0904 -405.37401 1306164.5 -1306769.5 -13.553736 48631.318 318.88482 0.0052667842
|
||||||
|
700 45.22721 2830.1443 196.47956 -2784.917 451.11156 498.26423 541.18835 -3282.1427 -375.95313 1306157.1 -1306774.4 3947.6276 48631.318 307.92741 0.0068019029
|
||||||
|
750 -114.28621 2798.3153 194.26988 -2912.6016 412.753 503.2878 481.32173 -3284.3411 -393.53984 1306147 -1306779.1 7143.3414 48631.318 304.46466 0.0061596717
|
||||||
|
800 -263.63817 2694.8084 187.08403 -2958.4466 455.67914 487.49754 476.8659 -3284.3133 -451.9578 1306145 -1306787.2 1185.9502 48631.318 293.20288 0.0058203332
|
||||||
|
850 -397.71592 2559.1921 177.66902 -2956.9081 458.83317 481.2262 478.31241 -3284.068 -437.26503 1306138.6 -1306792.6 346.80209 48631.318 278.44745 0.0054921692
|
||||||
|
900 -515.1823 2544.8753 176.67509 -3060.0576 395.00163 457.58988 446.68352 -3285.485 -423.56221 1306145 -1306795.3 3712.8598 48631.318 276.88864 0.0074054008
|
||||||
|
950 -617.28259 2451.1723 170.16987 -3068.4549 383.64277 446.59877 434.4624 -3285.1348 -391.59344 1306142.3 -1306798.7 5429.2488 48631.318 266.69431 0.0057487316
|
||||||
|
1000 -703.15534 2334.837 162.09342 -3037.9923 424.34948 462.21112 451.80809 -3284.3803 -426.53369 1306133.9 -1306799.3 1137.6145 48631.318 254.03675 0.0053914731
|
||||||
|
1050 -771.1763 2303.837 159.94128 -3075.0133 426.21409 436.50718 435.09987 -3285.1939 -411.14054 1306125.6 -1306802.1 1636.9383 48631.318 250.66295 0.0069342505
|
||||||
|
1100 -822.72236 2283.4196 158.52382 -3106.142 376.67684 447.77729 418.45768 -3286.5919 -377.48204 1306118.9 -1306803.8 4760.5163 48631.318 248.44119 0.0074025012
|
||||||
|
1150 -857.06075 2259.0717 156.8335 -3116.1324 400.31523 431.65981 457.68066 -3285.1977 -430.47723 1306115.8 -1306805.9 3194.5161 48631.318 245.79223 0.007063589
|
||||||
|
1200 -875.50848 2238.2637 155.38893 -3113.7722 445.38524 460.97125 432.10511 -3285.4238 -472.46606 1306114.7 -1306809 -653.49784 48631.318 243.52819 0.0071448738
|
||||||
|
1250 -880.37572 2294.6889 159.30618 -3175.0646 411.35427 444.73793 420.06468 -3286.0366 -458.05371 1306104.4 -1306811.5 945.80793 48631.318 249.66481 0.011853487
|
||||||
|
1300 -871.31064 2284.2298 158.58007 -3155.5405 404.97412 441.75285 426.34477 -3285.4859 -424.79609 1306094.9 -1306813.2 4406.6196 48631.318 248.48563 0.084424118
|
||||||
|
1350 -816.70005 2325.9264 161.47481 -3142.6265 696.80296 442.50053 431.19923 -3285.7859 -450.2699 1305836.2 -1306813.3 593.8098 48631.318 251.40749 2.9297319
|
||||||
|
1400 -794.25335 2263.5101 157.14163 -3057.7635 645.65165 466.22086 446.22268 -3285.1821 -420.65317 1305903.7 -1306813.8 1386.3633 48631.318 245.20554 1.8916154
|
||||||
|
1450 -776.10866 2287.6575 158.81803 -3063.7661 427.03477 479.10627 439.67495 -3285.9537 -395.13186 1306087.6 -1306816.1 2936.7806 48631.318 248.87167 0.061343245
|
||||||
|
1500 -725.48181 2371.413 164.63266 -3096.8948 390.03204 464.30903 446.91959 -3284.7809 -393.16613 1306095.4 -1306815.6 3544.25 48631.318 258.01286 0.011586563
|
||||||
|
1550 -671.4904 2315.9297 160.7808 -2987.4201 457.04935 500.25282 464.76203 -3284.9311 -400.98103 1306091.7 -1306815.3 2052.6339 48631.318 251.97726 0.0094517862
|
||||||
|
1600 -618.83633 2449.0918 170.02543 -3067.9281 425.47487 474.65876 471.99171 -3284.3677 -430.32107 1306091.3 -1306816.6 441.15682 48631.318 266.46311 0.014260935
|
||||||
|
1650 -567.82245 2425.2238 168.36842 -2993.0462 421.01953 511.27133 463.22065 -3285.038 -377.24066 1306088.4 -1306814.7 5198.8565 48631.318 263.83185 0.074738268
|
||||||
|
1700 -502.4486 2441.8554 169.52305 -2944.304 642.39962 512.90234 490.38297 -3283.9751 -417.39288 1305929.1 -1306817.7 1141.4411 48631.318 264.52393 2.043674
|
||||||
|
1750 -459.52196 2499.0746 173.49543 -2958.5966 679.38259 505.31787 484.77659 -3284.6272 -384.27736 1305861.6 -1306820.8 1527.2046 48631.318 270.10074 3.1869342
|
||||||
|
1800 -471.14403 2476.2266 171.90923 -2947.3706 442.47741 530.45656 474.03057 -3284.0954 -371.95117 1306084.3 -1306822.6 3392.2533 48631.318 269.36446 0.10416401
|
||||||
|
1850 -462.80763 2536.7112 176.10831 -2999.5188 437.08241 525.07462 474.0838 -3283.7906 -422.23719 1306091.6 -1306821.3 1629.8629 48631.318 275.99502 0.016806806
|
||||||
|
1900 -469.89289 2468.9765 171.4059 -2938.8694 446.77624 531.61059 496.01046 -3284.2338 -395.15325 1306085.7 -1306819.6 3119.5402 48631.318 268.62645 0.014601992
|
||||||
|
1950 -491.08007 2445.5966 169.78278 -2936.6767 457.80452 527.23373 470.18125 -3283.9608 -391.86377 1306101.9 -1306818 1122.5275 48631.318 266.08018 0.018911601
|
||||||
|
2000 -518.40811 2418.7208 167.91696 -2937.1289 415.93135 536.5973 480.44651 -3283.7881 -363.72783 1306096.2 -1306818.7 4475.7317 48631.318 263.09007 0.13504326
|
||||||
|
Loop time of 70.696 on 1 procs for 2000 steps with 5500 atoms
|
||||||
|
|
||||||
|
Performance: 1.222 ns/day, 19.638 hours/ns, 28.290 timesteps/s
|
||||||
|
97.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 48.367 | 48.367 | 48.367 | 0.0 | 68.42
|
||||||
|
Bond | 2.9191 | 2.9191 | 2.9191 | 0.0 | 4.13
|
||||||
|
Kspace | 14.266 | 14.266 | 14.266 | 0.0 | 20.18
|
||||||
|
Neigh | 1.5262 | 1.5262 | 1.5262 | 0.0 | 2.16
|
||||||
|
Comm | 0.27841 | 0.27841 | 0.27841 | 0.0 | 0.39
|
||||||
|
Output | 0.0035572 | 0.0035572 | 0.0035572 | 0.0 | 0.01
|
||||||
|
Modify | 3.2856 | 3.2856 | 3.2856 | 0.0 | 4.65
|
||||||
|
Other | | 0.05018 | | | 0.07
|
||||||
|
|
||||||
|
Nlocal: 5500 ave 5500 max 5500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 15317 ave 15317 max 15317 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 1.30285e+06 ave 1.30285e+06 max 1.30285e+06 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 1302849
|
||||||
|
Ave neighs/atom = 236.882
|
||||||
|
Ave special neighs/atom = 15.6364
|
||||||
|
Neighbor list builds = 44
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:01:10
|
||||||
|
|
@ -0,0 +1,262 @@
|
||||||
|
LAMMPS (7 Aug 2019)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# 250 toluene system for drude polarizability example (Nose-Hoover)
|
||||||
|
|
||||||
|
units real
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style full
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
dihedral_style opls
|
||||||
|
improper_style fourier
|
||||||
|
special_bonds lj/coul 0.0 0.0 0.5
|
||||||
|
|
||||||
|
pair_style lj/cut/thole/long 2.600 8.0 8.0
|
||||||
|
pair_modify mix geometric tail yes
|
||||||
|
kspace_style pppm 1.0e-4
|
||||||
|
|
||||||
|
read_data data.toluene extra/special/per/atom 1
|
||||||
|
orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
|
||||||
|
2 by 1 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
5500 atoms
|
||||||
|
scanning bonds ...
|
||||||
|
4 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
6 = max angles/atom
|
||||||
|
scanning dihedrals ...
|
||||||
|
8 = max dihedrals/atom
|
||||||
|
scanning impropers ...
|
||||||
|
2 = max impropers/atom
|
||||||
|
reading bonds ...
|
||||||
|
5500 bonds
|
||||||
|
reading angles ...
|
||||||
|
6000 angles
|
||||||
|
reading dihedrals ...
|
||||||
|
6000 dihedrals
|
||||||
|
reading impropers ...
|
||||||
|
1500 impropers
|
||||||
|
5 = max # of 1-2 neighbors
|
||||||
|
10 = max # of 1-3 neighbors
|
||||||
|
16 = max # of 1-4 neighbors
|
||||||
|
20 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000718355 secs
|
||||||
|
read_data CPU = 0.0167146 secs
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
group gTOLUENE molecule 1:250
|
||||||
|
5500 atoms in group gTOLUENE
|
||||||
|
group gCORES type 1 2 3 4 5 6 7
|
||||||
|
3750 atoms in group gCORES
|
||||||
|
group gDRUDES type 8 9 10 11 12
|
||||||
|
1750 atoms in group gDRUDES
|
||||||
|
|
||||||
|
pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
|
||||||
|
pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
|
||||||
|
pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
|
||||||
|
pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
|
||||||
|
pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
|
||||||
|
pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
|
||||||
|
pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
|
||||||
|
pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
|
||||||
|
pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
|
||||||
|
pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
|
||||||
|
pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
|
||||||
|
pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
|
||||||
|
pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
|
||||||
|
pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
|
||||||
|
pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
|
||||||
|
pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
|
||||||
|
pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
|
||||||
|
pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
|
||||||
|
pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
|
||||||
|
pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
|
||||||
|
pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
|
||||||
|
pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
|
||||||
|
pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
|
||||||
|
pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
|
||||||
|
pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
|
||||||
|
pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
|
||||||
|
pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
|
||||||
|
pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
|
||||||
|
pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
|
||||||
|
pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
|
||||||
|
pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
|
||||||
|
pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
|
||||||
|
pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
|
||||||
|
pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
|
||||||
|
pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
|
||||||
|
pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
|
||||||
|
pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
|
||||||
|
pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
|
||||||
|
pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
|
||||||
|
pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
|
||||||
|
pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
|
||||||
|
pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
|
||||||
|
pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
|
||||||
|
pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
|
||||||
|
pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
|
||||||
|
pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
|
||||||
|
pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
|
||||||
|
pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
|
||||||
|
pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
|
||||||
|
pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
|
||||||
|
pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
|
||||||
|
pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
|
||||||
|
pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
|
||||||
|
pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
|
||||||
|
pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
|
||||||
|
pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
|
||||||
|
pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
|
||||||
|
pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
|
||||||
|
pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
|
||||||
|
pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
|
||||||
|
pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
|
||||||
|
pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
|
||||||
|
pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
|
||||||
|
pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
|
||||||
|
pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
|
||||||
|
pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
|
||||||
|
pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
|
||||||
|
pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT
|
||||||
|
|
||||||
|
|
||||||
|
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 C C C N N D D D D D
|
||||||
|
|
||||||
|
fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
|
||||||
|
1250 = # of size 2 clusters
|
||||||
|
0 = # of size 3 clusters
|
||||||
|
250 = # of size 4 clusters
|
||||||
|
0 = # of frozen angles
|
||||||
|
find clusters CPU = 0.000344038 secs
|
||||||
|
|
||||||
|
compute cTEMP_CORE gCORES temp/com
|
||||||
|
compute cTEMP all temp/drude
|
||||||
|
|
||||||
|
fix fDIRECT all drude/transform/direct
|
||||||
|
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
|
||||||
|
fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
|
||||||
|
fix fNVT1 gCORES nvt temp 260 260 100.0
|
||||||
|
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
|
||||||
|
fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
|
||||||
|
fix fNVT2 gDRUDES nvt temp 1 1 20.0
|
||||||
|
fix fINVERSE all drude/transform/inverse
|
||||||
|
|
||||||
|
fix fMOMENTUM all momentum 100 linear 1 1 1
|
||||||
|
|
||||||
|
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||||
|
thermo 50
|
||||||
|
|
||||||
|
timestep 0.5
|
||||||
|
run 2000
|
||||||
|
PPPM initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
|
||||||
|
G vector (1/distance) = 0.382011
|
||||||
|
grid = 40 40 40
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.0325934
|
||||||
|
estimated relative force accuracy = 9.8154e-05
|
||||||
|
using double precision FFTW3
|
||||||
|
3d grid and FFT values/proc = 34263 16000
|
||||||
|
Rebuild special list taking Drude particles into account
|
||||||
|
Old max number of 1-2 to 1-4 neighbors: 19
|
||||||
|
New max number of 1-2 to 1-4 neighbors: 20 (+1)
|
||||||
|
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
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut/thole/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes
|
||||||
|
Step 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]
|
||||||
|
0 11086.347 2910.7282 202.07402 8175.6191 6565.4851 20.333365 1.0706727e-06 -3299.85 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821
|
||||||
|
50 3563.376 4630.6343 321.47655 -1067.2583 735.72048 604.78665 689.14826 -3277.411 815.58183 1306088.7 -1306723.8 17813.425 48631.318 503.827 0.0087118179
|
||||||
|
100 3327.4722 4395.1107 305.12559 -1067.6385 597.93175 651.62645 945.4151 -3267.2851 584.58833 1306135.9 -1306715.8 17407.335 48631.318 478.2017 0.0075985638
|
||||||
|
150 3036.9065 4740.2304 329.08513 -1703.3238 558.64983 619.91284 658.80686 -3278.7837 285.12462 1306173 -1306720 18448.248 48631.318 515.75286 0.0063215227
|
||||||
|
200 2697.9581 4559.3445 316.52734 -1861.3864 522.09335 593.8913 754.61446 -3273.49 87.660464 1306183.9 -1306730 17888.937 48631.318 496.07143 0.006870622
|
||||||
|
250 2348.7563 4410.585 306.19988 -2061.8288 506.05006 575.35172 715.55055 -3276.3261 -18.364482 1306177.3 -1306741.4 11592.049 48631.318 479.88562 0.0071741023
|
||||||
|
300 2019.8256 4040.1415 280.48225 -2020.3159 604.30771 641.66688 693.93802 -3278.5312 -115.73639 1306183.2 -1306749.1 3631.3625 48631.318 439.57995 0.0069886424
|
||||||
|
350 1699.5169 3944.9851 273.87613 -2245.4682 452.07416 638.06529 658.79116 -3279.6053 -157.07584 1306196.9 -1306754.6 13544.368 48631.318 429.22695 0.0062868216
|
||||||
|
400 1399.2927 3726.098 258.68014 -2326.8053 457.91943 621.44727 639.39905 -3279.2395 -188.85912 1306185.4 -1306762.8 10792.273 48631.318 405.41133 0.0059340084
|
||||||
|
450 1120.5246 3518.345 244.25712 -2397.8204 519.48859 584.6579 646.36688 -3278.6685 -289.59912 1306184.1 -1306764.2 2755.5597 48631.318 382.80717 0.005570751
|
||||||
|
500 868.01643 3359.8794 233.25583 -2491.863 460.73928 581.49568 581.01732 -3281.5544 -252.20168 1306184.3 -1306765.7 6120.364 48631.318 365.56528 0.0058756204
|
||||||
|
550 637.01646 3214.9521 223.19441 -2577.9356 431.81484 578.87415 540.94046 -3281.5337 -266.36074 1306182.8 -1306764.5 8622.4353 48631.318 349.79661 0.0058589476
|
||||||
|
600 418.04028 3113.4063 216.14471 -2695.3661 430.45936 538.68158 522.24597 -3283.456 -311.87897 1306174.3 -1306765.8 7068.9275 48631.318 338.74796 0.0059567639
|
||||||
|
650 218.59562 2930.8439 203.47052 -2712.2482 514.47296 514.2838 551.52551 -3282.0904 -405.37401 1306164.5 -1306769.5 -13.554086 48631.318 318.88481 0.0052667849
|
||||||
|
700 45.227739 2830.1443 196.47957 -2784.9165 451.11157 498.26426 541.18833 -3282.1427 -375.95321 1306157.1 -1306774.4 3947.6268 48631.318 307.92741 0.0068018884
|
||||||
|
750 -114.28676 2798.3154 194.26988 -2912.6022 412.75298 503.28782 481.32167 -3284.3411 -393.53987 1306147 -1306779.1 7143.3424 48631.318 304.46466 0.0061596613
|
||||||
|
800 -263.63827 2694.8085 187.08403 -2958.4468 455.67916 487.49754 476.86576 -3284.3133 -451.95784 1306145 -1306787.2 1185.9474 48631.318 293.20289 0.0058203323
|
||||||
|
850 -397.71592 2559.1922 177.66903 -2956.9082 458.83313 481.22619 478.31233 -3284.068 -437.26509 1306138.6 -1306792.6 346.80221 48631.318 278.44747 0.0054921238
|
||||||
|
900 -515.18134 2544.8753 176.67509 -3060.0567 395.0016 457.5898 446.68361 -3285.485 -423.56234 1306145.1 -1306795.3 3712.8594 48631.318 276.88864 0.0074054726
|
||||||
|
950 -617.28607 2451.1721 170.16985 -3068.4582 383.6428 446.59872 434.46241 -3285.1348 -391.59326 1306142.3 -1306798.7 5429.2191 48631.318 266.69429 0.0057487961
|
||||||
|
1000 -703.15541 2334.8366 162.09339 -3037.992 424.34957 462.21115 451.80811 -3284.3803 -426.53346 1306133.9 -1306799.3 1137.6144 48631.318 254.03671 0.0053915025
|
||||||
|
1050 -771.17572 2303.8364 159.94123 -3075.0121 426.21406 436.50744 435.10013 -3285.1938 -411.13999 1306125.6 -1306802.1 1636.9467 48631.318 250.66288 0.0069341736
|
||||||
|
1100 -822.72317 2283.421 158.52392 -3106.1442 376.67703 447.77728 418.45763 -3286.5919 -377.48075 1306118.9 -1306803.8 4760.4718 48631.318 248.44134 0.0074024122
|
||||||
|
1150 -857.06061 2259.0725 156.83355 -3116.1331 400.31517 431.65949 457.68078 -3285.1977 -430.47775 1306115.8 -1306805.9 3194.5159 48631.318 245.79231 0.007063706
|
||||||
|
1200 -875.50971 2238.2632 155.38889 -3113.7729 445.38534 460.97161 432.10511 -3285.4238 -472.46582 1306114.7 -1306809 -653.49627 48631.318 243.52813 0.0071446561
|
||||||
|
1250 -880.37609 2294.689 159.30619 -3175.0651 411.35498 444.73774 420.06429 -3286.0366 -458.05353 1306104.4 -1306811.5 945.79687 48631.318 249.66483 0.011854196
|
||||||
|
1300 -871.31122 2284.2295 158.58005 -3155.5407 404.97869 441.75305 426.34479 -3285.4859 -424.79602 1306094.8 -1306813.2 4406.6128 48631.318 248.4856 0.084411062
|
||||||
|
1350 -816.69657 2325.9211 161.47444 -3142.6176 696.85542 442.50059 431.19981 -3285.7859 -450.27129 1305836.1 -1306813.3 593.86622 48631.318 251.40736 2.9289249
|
||||||
|
1400 -794.25213 2263.5122 157.14177 -3057.7643 645.6531 466.2204 446.22253 -3285.1821 -420.65316 1305903.7 -1306813.8 1386.3481 48631.318 245.20568 1.8917548
|
||||||
|
1450 -776.1076 2287.6591 158.81814 -3063.7667 427.0331 479.10417 439.67675 -3285.9536 -395.13308 1306087.6 -1306816.1 2936.7117 48631.318 248.87185 0.061341392
|
||||||
|
1500 -725.48032 2371.4108 164.63251 -3096.8911 390.03135 464.30817 446.91941 -3284.7808 -393.16302 1306095.4 -1306815.6 3544.3635 48631.318 258.01262 0.011585228
|
||||||
|
1550 -671.48696 2315.9233 160.78035 -2987.4102 457.04771 500.26018 464.7623 -3284.931 -400.98142 1306091.7 -1306815.3 2052.6204 48631.318 251.97656 0.0094518433
|
||||||
|
1600 -618.82679 2449.0893 170.02525 -3067.9161 425.47171 474.66369 471.99137 -3284.3677 -430.3224 1306091.3 -1306816.6 441.31257 48631.318 266.46283 0.014263201
|
||||||
|
1650 -567.82233 2425.2281 168.36872 -2993.0504 421.02008 511.26686 463.22202 -3285.0378 -377.24205 1306088.4 -1306814.7 5198.6214 48631.318 263.83232 0.074728934
|
||||||
|
1700 -502.46013 2441.8437 169.52224 -2944.3039 642.39863 512.90005 490.39655 -3283.975 -417.39351 1305929.1 -1306817.7 1141.2401 48631.318 264.52268 2.0436397
|
||||||
|
1750 -459.52135 2499.0847 173.49613 -2958.606 679.34078 505.30943 484.78276 -3284.6269 -384.28217 1305861.7 -1306820.8 1527.0852 48631.318 270.10144 3.1876179
|
||||||
|
1800 -471.14322 2476.2445 171.91047 -2947.3877 442.48278 530.4566 474.0343 -3284.0957 -371.97492 1306084.3 -1306822.6 3392.0306 48631.318 269.36641 0.1041603
|
||||||
|
1850 -462.80151 2536.7173 176.10873 -2999.5188 437.07855 525.05914 474.07725 -3283.7908 -422.22641 1306091.6 -1306821.3 1630.1204 48631.318 275.99568 0.016808725
|
||||||
|
1900 -469.8785 2468.9596 171.40473 -2938.8381 446.7879 531.6128 496.02681 -3284.2335 -395.17163 1306085.7 -1306819.6 3119.2384 48631.318 268.62462 0.014603394
|
||||||
|
1950 -491.07182 2445.6794 169.78853 -2936.7512 457.80204 527.21208 470.1608 -3283.9622 -391.90163 1306101.9 -1306818 1122.0978 48631.318 266.08919 0.018903661
|
||||||
|
2000 -518.41243 2418.604 167.90885 -2937.0165 415.92605 536.62844 480.48912 -3283.7876 -363.72641 1306096.2 -1306818.7 4474.8778 48631.318 263.07743 0.13492637
|
||||||
|
Loop time of 22.3198 on 4 procs for 2000 steps with 5500 atoms
|
||||||
|
|
||||||
|
Performance: 3.871 ns/day, 6.200 hours/ns, 89.606 timesteps/s
|
||||||
|
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 11.452 | 12.249 | 12.556 | 13.2 | 54.88
|
||||||
|
Bond | 0.71352 | 0.72923 | 0.74557 | 1.3 | 3.27
|
||||||
|
Kspace | 5.7189 | 6.0293 | 6.8195 | 18.6 | 27.01
|
||||||
|
Neigh | 0.44028 | 0.44044 | 0.44065 | 0.0 | 1.97
|
||||||
|
Comm | 0.39667 | 0.40817 | 0.41558 | 1.1 | 1.83
|
||||||
|
Output | 0.0019479 | 0.0032187 | 0.0068657 | 3.7 | 0.01
|
||||||
|
Modify | 2.413 | 2.4256 | 2.4347 | 0.5 | 10.87
|
||||||
|
Other | | 0.0349 | | | 0.16
|
||||||
|
|
||||||
|
Nlocal: 1375 ave 1407 max 1349 min
|
||||||
|
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||||
|
Nghost: 8082.5 ave 8114 max 8047 min
|
||||||
|
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||||
|
Neighs: 325715 ave 343636 max 314954 min
|
||||||
|
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 1302860
|
||||||
|
Ave neighs/atom = 236.884
|
||||||
|
Ave special neighs/atom = 15.6364
|
||||||
|
Neighbor list builds = 44
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:22
|
||||||
Loading…
Reference in New Issue