Cleaned up the examples, added loop geom to velocity initializations
This commit is contained in:
Aidan Thompson
@ -1,74 +0,0 @@
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# DATE: 2013-03-21 CONTRIBUTOR: Cem Sevik CITATION: Kinaci, Haskins, Sevik and Cagin, Phys Rev B, 86, 115410 (2012)
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# Tersoff parameters for B, C, and BN-C hybrid based graphene like nano structures
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# multiple entries can be added to this file, LAMMPS reads the ones it needs
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# these entries are in LAMMPS "metal" units:
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# A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms
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# other quantities are unitless
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# Cem Sevik (csevik at anadolu.edu.tr) takes full blame for this
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# file. It specifies B-N, B-C, and N-C interaction parameters
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# generated and published by the reseacrh group of Prof. Tahir Cagin.
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# 1. Physical Review B 84, 085409 2011
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# Characterization of thermal transport in low-dimensional boron nitride nanostructures,
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#
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# 2. Physical Review B 86, 075403 2012
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# Influence of disorder on thermal transport properties of boron nitride nanostructures
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#
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# 3. Physical Review B 86, 075403 2012, Please see for further information about B-C and N-C parameters
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# Thermal conductivity of BN-C nanostructures
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#
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# The file also specifies C-C, interaction parameters
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# generated and published by the reseacrh group of Dr. D. A. Broido
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# Physical Review B 81, 205441 2010
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# Optimized Tersoff and Brenner empirical potential parameters for
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# lattice dynamics and phonon thermal transport in carbon nanotubes and graphene
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# Users in referring the full parameters can cite the full parameter paper (3) as:
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# A. Kinaci, J. B. Haskins, C. Sevik, T. Cagin, Physical Review B 86, 115410 (2012)
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# Thermal conductivity of BN-C nanostructures
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#
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# format of a single entry (one or more lines):
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# element 1, element 2, element 3,
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# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
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N B B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0
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N B N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0
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N B C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0
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B N B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0
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B N N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0
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B N C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0
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N N B 3.0 1.0 0.0 17.7959 5.9484 0.00000 0.6184432 0.019251 2.6272721 138.77866 2.0 0.1 2.8293093 128.86866
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N N N 3.0 1.0 0.0 17.7959 5.9484 0.00000 0.6184432 0.019251 2.6272721 138.77866 2.0 0.1 2.8293093 128.86866
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N N C 3.0 1.0 0.0 17.7959 5.9484 0.00000 0.6184432 0.019251 2.6272721 138.77866 2.0 0.1 2.8293093 128.86866
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B B B 3.0 1.0 0.0 0.52629 0.001587 0.5 3.9929061 1.6e-6 2.0774982 43.132016 2.0 0.1 2.2372578 40.0520156
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B B N 3.0 1.0 0.0 0.52629 0.001587 0.5 3.9929061 1.6e-6 2.0774982 43.132016 2.0 0.1 2.2372578 40.0520156
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B B C 3.0 1.0 0.0 0.52629 0.001587 0.5 3.9929061 1.6e-6 2.0774982 43.132016 2.0 0.1 2.2372578 40.0520156
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C C C 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2119 430.00 1.95 0.15 3.4879 1393.6
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C C B 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2119 430.00 1.95 0.15 3.4879 1393.6
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C C N 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2119 430.00 1.95 0.15 3.4879 1393.6
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C B B 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78
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C B N 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78
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C B C 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78
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C N B 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78
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C N N 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78
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C N C 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78
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B C C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78
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B C B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78
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B C N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78
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N C C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78
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N C B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78
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N C N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78
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1
examples/USER/misc/tersoff_shift/BNC.tersoff
Symbolic link
1
examples/USER/misc/tersoff_shift/BNC.tersoff
Symbolic link
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../../../../potentials/BNC.tersoff
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@ -1,18 +0,0 @@
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# DATE: 2007-10-25 UNITS: metal CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Tersoff, Phys Rev B, 37, 6991 (1988)
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# Tersoff parameters for various elements and mixtures
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# multiple entries can be added to this file, LAMMPS reads the ones it needs
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# these entries are in LAMMPS "metal" units:
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# A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms
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# other quantities are unitless
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# This is the Si parameterization from a particular Tersoff paper:
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# J. Tersoff, PRB, 37, 6991 (1988)
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# See the SiCGe.tersoff file for different Si variants.
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# format of a single entry (one or more lines):
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# element 1, element 2, element 3,
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# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
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Si Si Si 3.0 1.0 1.3258 4.8381 2.0417 0.0000 22.956
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0.33675 1.3258 95.373 3.0 0.2 3.2394 3264.7
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1
examples/USER/misc/tersoff_shift/Si.tersoff
Symbolic link
1
examples/USER/misc/tersoff_shift/Si.tersoff
Symbolic link
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../../../../potentials/Si.tersoff
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@ -24,7 +24,7 @@ thermo_modify line one format float %20.15g
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#### Simulation settings ####
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#### Simulation settings ####
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timestep 0.001
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timestep 0.001
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velocity all create 300.0 12345 dist gaussian mom yes rot yes
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velocity all create 300.0 12345 loop geom
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fix thermostat all nve
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fix thermostat all nve
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############# Output ###############
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############# Output ###############
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@ -24,7 +24,7 @@ neigh_modify check yes
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#### Simulation settings ####
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#### Simulation settings ####
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timestep 0.001
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timestep 0.001
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#velocity all create 300.0 12345 dist gaussian mom yes rot yes
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velocity all create 300.0 12345 loop geom
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fix thermostat all nve
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fix thermostat all nve
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############# Output ###############
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############# Output ###############
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@ -24,7 +24,7 @@ neigh_modify check yes
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#### Simulation settings ####
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#### Simulation settings ####
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timestep 0.001
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timestep 0.001
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#velocity all create 300.0 12345 dist gaussian mom yes rot yes
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velocity all create 300.0 12345 loop geom
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fix thermostat all nve
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fix thermostat all nve
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############# Output ###############
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############# Output ###############
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@ -1,111 +0,0 @@
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LAMMPS (30 Nov 2020)
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# Initialization
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units metal
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boundary p p p
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atom_style full
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processors * * 1 # domain decomposition over x and y
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# System and atom definition
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# we use different molecule ids for each layer of hBN
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# so that inter- and intra-layer
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# interactions can be specified separately
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read_data hBN-momolayer-5nm.data
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Reading data file ...
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orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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880 atoms
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.009 seconds
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mass 1 10.8110 # boron mass (g/mole) | membrane
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mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
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######################## Potential defition ########################
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pair_style tersoff/shift 0.0
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pair_coeff * * BNC.tersoff B N
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Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
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####################################################################
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# Neighbor update settings
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neighbor 2.0 bin
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neigh_modify every 1
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neigh_modify delay 0
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neigh_modify check yes
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#### Simulation settings ####
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timestep 0.001
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#velocity all create 300.0 12345 dist gaussian mom yes rot yes
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fix thermostat all nve
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############# Output ###############
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thermo 100
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thermo_style custom step etotal pe ke temp
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thermo_modify lost warn
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###### Run molecular dynamics ######
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run 1000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 4.1
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ghost atom cutoff = 4.1
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binsize = 2.05, bins = 23 24 49
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair tersoff/shift, perpetual
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attributes: full, newton on
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pair build: full/bin
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 6.651 | 6.651 | 6.651 Mbytes
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Step TotEng PotEng KinEng Temp
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0 -6551.8376 -6551.8376 0 0
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100 -6551.8404 -6552.045 0.20459665 1.8007151
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200 -6551.8415 -6552.0901 0.24854441 2.1875122
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300 -6551.8417 -6552.0785 0.23679696 2.0841195
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400 -6551.8417 -6552.0803 0.23866698 2.1005781
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500 -6551.8415 -6552.0561 0.21461008 1.8888462
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600 -6551.8414 -6552.0933 0.25192103 2.2172309
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700 -6551.8418 -6552.085 0.24321116 2.1405727
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800 -6551.8421 -6552.0818 0.23974657 2.1100799
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900 -6551.8417 -6552.0803 0.23863749 2.1003185
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1000 -6551.8407 -6552.0573 0.2165681 1.9060793
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Loop time of 2.01887 on 1 procs for 1000 steps with 880 atoms
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Performance: 42.796 ns/day, 0.561 hours/ns, 495.328 timesteps/s
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98.7% CPU use with 1 MPI tasks x no 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 | 1.9692 | 1.9692 | 1.9692 | 0.0 | 97.54
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Bond | 0.00080803 | 0.00080803 | 0.00080803 | 0.0 | 0.04
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.017753 | 0.017753 | 0.017753 | 0.0 | 0.88
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Output | 0.00098974 | 0.00098974 | 0.00098974 | 0.0 | 0.05
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Modify | 0.017247 | 0.017247 | 0.017247 | 0.0 | 0.85
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Other | | 0.01289 | | | 0.64
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Nlocal: 880.000 ave 880 max 880 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1518.00 ave 1518 max 1518 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0.00000 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 15840.0 ave 15840 max 15840 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 15840
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Ave neighs/atom = 18.000000
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Ave special neighs/atom = 0.0000000
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Neighbor list builds = 0
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:02
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File diff suppressed because it is too large
Load Diff
@ -36,7 +36,7 @@ thermo_modify line one format float %20.15g
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#### Simulation settings ####
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#### Simulation settings ####
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timestep 0.001
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timestep 0.001
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velocity all create 300.0 12345 dist gaussian mom yes rot yes
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velocity all create 300.0 12345 loop geom
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fix thermostat all nve
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fix thermostat all nve
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############# Output ###############
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############# Output ###############
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@ -62,30 +62,30 @@ Neighbor list info ...
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Per MPI rank memory allocation (min/avg/max) = 3.677 | 3.677 | 3.677 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 3.677 | 3.677 | 3.677 Mbytes
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Step TotEng PotEng KinEng Temp
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Step TotEng PotEng KinEng Temp
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0 -18183.755 -18338.829 155.0734 300
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0 -18183.755 -18338.829 155.0734 300
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100 -18183.66 -18247.917 64.256597 124.30874
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100 -18183.651 -18249.335 65.684288 127.07071
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200 -18183.654 -18242.513 58.858225 113.86523
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200 -18183.643 -18241.96 58.317656 112.81946
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300 -18183.683 -18265.139 81.456543 157.58321
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300 -18183.675 -18265.042 81.367616 157.41117
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400 -18183.671 -18258.798 75.12695 145.33818
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400 -18183.661 -18257.198 73.536882 142.26208
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500 -18183.679 -18261.264 77.585257 150.09394
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500 -18183.669 -18261.964 78.295204 151.46738
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600 -18183.673 -18258.411 74.737378 144.58453
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600 -18183.665 -18258.552 74.886287 144.8726
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700 -18183.674 -18257.786 74.11252 143.3757
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700 -18183.662 -18256.924 73.261529 141.7294
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800 -18183.679 -18263.045 79.365484 153.53791
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800 -18183.67 -18263.155 79.484227 153.76763
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900 -18183.672 -18259.796 76.123779 147.26661
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900 -18183.663 -18259.152 75.488804 146.03821
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1000 -18183.674 -18258.87 75.195714 145.47121
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1000 -18183.667 -18261.116 77.448767 149.82989
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Loop time of 8.76461 on 1 procs for 1000 steps with 4000 atoms
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Loop time of 9.3615 on 1 procs for 1000 steps with 4000 atoms
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Performance: 9.858 ns/day, 2.435 hours/ns, 114.095 timesteps/s
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Performance: 9.229 ns/day, 2.600 hours/ns, 106.820 timesteps/s
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99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
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99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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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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Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 8.7013 | 8.7013 | 8.7013 | 0.0 | 99.28
|
Pair | 9.3018 | 9.3018 | 9.3018 | 0.0 | 99.36
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Comm | 0.016631 | 0.016631 | 0.016631 | 0.0 | 0.19
|
Comm | 0.015455 | 0.015455 | 0.015455 | 0.0 | 0.17
|
||||||
Output | 0.000301 | 0.000301 | 0.000301 | 0.0 | 0.00
|
Output | 0.000312 | 0.000312 | 0.000312 | 0.0 | 0.00
|
||||||
Modify | 0.03126 | 0.03126 | 0.03126 | 0.0 | 0.36
|
Modify | 0.030194 | 0.030194 | 0.030194 | 0.0 | 0.32
|
||||||
Other | | 0.01514 | | | 0.17
|
Other | | 0.01378 | | | 0.15
|
||||||
|
|
||||||
Nlocal: 4000.00 ave 4000 max 4000 min
|
Nlocal: 4000.00 ave 4000 max 4000 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
@ -100,4 +100,4 @@ Total # of neighbors = 112000
|
|||||||
Ave neighs/atom = 28.000000
|
Ave neighs/atom = 28.000000
|
||||||
Neighbor list builds = 0
|
Neighbor list builds = 0
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
Total wall time: 0:00:08
|
Total wall time: 0:00:09
|
||||||
103
examples/USER/misc/tersoff_shift/log.31Dec20.Si_shift.g++.4
Normal file
103
examples/USER/misc/tersoff_shift/log.31Dec20.Si_shift.g++.4
Normal file
@ -0,0 +1,103 @@
|
|||||||
|
LAMMPS (30 Nov 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Generate tip
|
||||||
|
units metal
|
||||||
|
dimension 3
|
||||||
|
boundary p p p
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
variable xm equal 10
|
||||||
|
variable ym equal 10
|
||||||
|
variable zm equal 5
|
||||||
|
lattice diamond 5.481 # Si-Si
|
||||||
|
Lattice spacing in x,y,z = 5.4810000 5.4810000 5.4810000
|
||||||
|
region recbox block 0.0 ${xm} 0.0 ${ym} 0.0 ${zm}
|
||||||
|
region recbox block 0.0 10 0.0 ${ym} 0.0 ${zm}
|
||||||
|
region recbox block 0.0 10 0.0 10 0.0 ${zm}
|
||||||
|
region recbox block 0.0 10 0.0 10 0.0 5
|
||||||
|
|
||||||
|
create_box 1 recbox
|
||||||
|
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (54.810000 54.810000 27.405000)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
create_atoms 1 region recbox units box
|
||||||
|
Created 4000 atoms
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
mass * 28.0855
|
||||||
|
pair_style tersoff shift 0.05
|
||||||
|
pair_coeff * * Si.tersoff Si
|
||||||
|
Reading tersoff potential file Si.tersoff with DATE: 2007-10-25
|
||||||
|
|
||||||
|
thermo_style custom step cpu etotal pe ke temp
|
||||||
|
thermo 100
|
||||||
|
thermo_modify flush yes norm no lost warn
|
||||||
|
thermo_modify line one format float %20.15g
|
||||||
|
|
||||||
|
#### Simulation settings ####
|
||||||
|
timestep 0.001
|
||||||
|
velocity all create 300.0 12345 loop geom
|
||||||
|
fix thermostat all nve
|
||||||
|
|
||||||
|
############# Output ###############
|
||||||
|
thermo 100
|
||||||
|
thermo_style custom step etotal pe ke temp
|
||||||
|
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:693)
|
||||||
|
thermo_modify lost warn
|
||||||
|
|
||||||
|
###### Run molecular dynamics ######
|
||||||
|
run 1000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 5.2
|
||||||
|
ghost atom cutoff = 5.2
|
||||||
|
binsize = 2.6, bins = 22 22 11
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair tersoff, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.127 | 3.127 | 3.127 Mbytes
|
||||||
|
Step TotEng PotEng KinEng Temp
|
||||||
|
0 -18183.755 -18338.829 155.0734 300
|
||||||
|
100 -18183.651 -18249.335 65.684288 127.07071
|
||||||
|
200 -18183.643 -18241.96 58.317656 112.81946
|
||||||
|
300 -18183.675 -18265.042 81.367616 157.41117
|
||||||
|
400 -18183.661 -18257.198 73.536882 142.26208
|
||||||
|
500 -18183.669 -18261.964 78.295204 151.46738
|
||||||
|
600 -18183.665 -18258.552 74.886287 144.8726
|
||||||
|
700 -18183.662 -18256.924 73.261529 141.7294
|
||||||
|
800 -18183.67 -18263.155 79.484227 153.76763
|
||||||
|
900 -18183.663 -18259.152 75.488804 146.03821
|
||||||
|
1000 -18183.667 -18261.116 77.448767 149.82989
|
||||||
|
Loop time of 2.63101 on 4 procs for 1000 steps with 4000 atoms
|
||||||
|
|
||||||
|
Performance: 32.839 ns/day, 0.731 hours/ns, 380.082 timesteps/s
|
||||||
|
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 2.4651 | 2.5025 | 2.5216 | 1.4 | 95.11
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.093127 | 0.11216 | 0.14937 | 6.5 | 4.26
|
||||||
|
Output | 0.000129 | 0.00016075 | 0.000253 | 0.0 | 0.01
|
||||||
|
Modify | 0.008488 | 0.0086423 | 0.008735 | 0.1 | 0.33
|
||||||
|
Other | | 0.007586 | | | 0.29
|
||||||
|
|
||||||
|
Nlocal: 1000.00 ave 1000 max 1000 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1470.00 ave 1470 max 1470 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 28000.0 ave 28000 max 28000 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 112000
|
||||||
|
Ave neighs/atom = 28.000000
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:02
|
||||||
@ -1,8 +1,10 @@
|
|||||||
LAMMPS (30 Nov 2020)
|
LAMMPS (30 Nov 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
# Initialization
|
# Initialization
|
||||||
units metal
|
units metal
|
||||||
boundary p p p
|
boundary p p p
|
||||||
atom_style full
|
atom_style charge
|
||||||
processors * * 1 # domain decomposition over x and y
|
processors * * 1 # domain decomposition over x and y
|
||||||
|
|
||||||
# System and atom definition
|
# System and atom definition
|
||||||
@ -15,15 +17,7 @@ Reading data file ...
|
|||||||
1 by 1 by 1 MPI processor grid
|
1 by 1 by 1 MPI processor grid
|
||||||
reading atoms ...
|
reading atoms ...
|
||||||
880 atoms
|
880 atoms
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
read_data CPU = 0.005 seconds
|
||||||
special bond factors lj: 0 0 0
|
|
||||||
special bond factors coul: 0 0 0
|
|
||||||
0 = max # of 1-2 neighbors
|
|
||||||
0 = max # of 1-3 neighbors
|
|
||||||
0 = max # of 1-4 neighbors
|
|
||||||
1 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.001 seconds
|
|
||||||
read_data CPU = 0.096 seconds
|
|
||||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||||
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
|
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||||
|
|
||||||
@ -40,7 +34,7 @@ neigh_modify check yes
|
|||||||
|
|
||||||
#### Simulation settings ####
|
#### Simulation settings ####
|
||||||
timestep 0.001
|
timestep 0.001
|
||||||
#velocity all create 300.0 12345 dist gaussian mom yes rot yes
|
velocity all create 300.0 12345 loop geom
|
||||||
fix thermostat all nve
|
fix thermostat all nve
|
||||||
|
|
||||||
############# Output ###############
|
############# Output ###############
|
||||||
@ -59,50 +53,48 @@ Neighbor list info ...
|
|||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
(1) pair tersoff, perpetual
|
(1) pair tersoff, perpetual
|
||||||
attributes: full, newton on
|
attributes: full, newton on
|
||||||
pair build: full/bin
|
pair build: full/bin/atomonly
|
||||||
stencil: full/bin/3d
|
stencil: full/bin/3d
|
||||||
bin: standard
|
bin: standard
|
||||||
Per MPI rank memory allocation (min/avg/max) = 6.651 | 6.651 | 6.651 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 3.545 | 3.545 | 3.545 Mbytes
|
||||||
Step TotEng PotEng KinEng Temp
|
Step TotEng PotEng KinEng Temp
|
||||||
0 -6551.8376 -6551.8376 0 0
|
0 -6517.7517 -6551.8376 34.0859 300
|
||||||
100 -6551.8404 -6552.045 0.20459665 1.8007151
|
100 -6517.5918 -6540.7795 23.187734 204.08204
|
||||||
200 -6551.8415 -6552.0901 0.24854441 2.1875122
|
200 -6517.5423 -6546.3342 28.791974 253.4066
|
||||||
300 -6551.8417 -6552.0785 0.23679696 2.0841195
|
300 -6517.547 -6552.0178 34.47074 303.38708
|
||||||
400 -6551.8417 -6552.0803 0.23866698 2.1005781
|
400 -6517.5499 -6554.1682 36.618359 322.28891
|
||||||
500 -6551.8415 -6552.0561 0.21461008 1.8888462
|
500 -6517.5482 -6553.3948 35.846598 315.49641
|
||||||
600 -6551.8414 -6552.0933 0.25192103 2.2172309
|
600 -6517.5438 -6557.8044 40.260609 354.34542
|
||||||
700 -6551.8418 -6552.085 0.24321116 2.1405727
|
700 -6517.5489 -6554.8963 37.3474 328.70542
|
||||||
800 -6551.8421 -6552.0818 0.23974657 2.1100799
|
800 -6517.5426 -6557.376 39.833345 350.58494
|
||||||
900 -6551.8417 -6552.0803 0.23863749 2.1003185
|
900 -6517.5508 -6557.1115 39.560726 348.18554
|
||||||
1000 -6551.8407 -6552.0573 0.2165681 1.9060793
|
1000 -6517.5427 -6559.2989 41.756142 367.50804
|
||||||
Loop time of 1.30034 on 1 procs for 1000 steps with 880 atoms
|
Loop time of 1.03247 on 1 procs for 1000 steps with 880 atoms
|
||||||
|
|
||||||
Performance: 66.444 ns/day, 0.361 hours/ns, 769.030 timesteps/s
|
Performance: 83.682 ns/day, 0.287 hours/ns, 968.547 timesteps/s
|
||||||
99.4% CPU use with 1 MPI tasks x no OpenMP threads
|
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 1.2606 | 1.2606 | 1.2606 | 0.0 | 96.95
|
Pair | 1.0048 | 1.0048 | 1.0048 | 0.0 | 97.32
|
||||||
Bond | 0.00058399 | 0.00058399 | 0.00058399 | 0.0 | 0.04
|
Neigh | 0.010752 | 0.010752 | 0.010752 | 0.0 | 1.04
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
Comm | 0.006344 | 0.006344 | 0.006344 | 0.0 | 0.61
|
||||||
Comm | 0.014387 | 0.014387 | 0.014387 | 0.0 | 1.11
|
Output | 0.000193 | 0.000193 | 0.000193 | 0.0 | 0.02
|
||||||
Output | 0.00062956 | 0.00062956 | 0.00062956 | 0.0 | 0.05
|
Modify | 0.00687 | 0.00687 | 0.00687 | 0.0 | 0.67
|
||||||
Modify | 0.014313 | 0.014313 | 0.014313 | 0.0 | 1.10
|
Other | | 0.003494 | | | 0.34
|
||||||
Other | | 0.009804 | | | 0.75
|
|
||||||
|
|
||||||
Nlocal: 880.000 ave 880 max 880 min
|
Nlocal: 880.000 ave 880 max 880 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Nghost: 1518.00 ave 1518 max 1518 min
|
Nghost: 1538.00 ave 1538 max 1538 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Neighs: 0.00000 ave 0 max 0 min
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
FullNghs: 15840.0 ave 15840 max 15840 min
|
FullNghs: 15860.0 ave 15860 max 15860 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
Total # of neighbors = 15840
|
Total # of neighbors = 15860
|
||||||
Ave neighs/atom = 18.000000
|
Ave neighs/atom = 18.022727
|
||||||
Ave special neighs/atom = 0.0000000
|
Neighbor list builds = 15
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
Total wall time: 0:00:01
|
Total wall time: 0:00:01
|
||||||
100
examples/USER/misc/tersoff_shift/log.31Dec20.hBN_no_shift.g++.4
Normal file
100
examples/USER/misc/tersoff_shift/log.31Dec20.hBN_no_shift.g++.4
Normal file
@ -0,0 +1,100 @@
|
|||||||
|
LAMMPS (30 Nov 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Initialization
|
||||||
|
units metal
|
||||||
|
boundary p p p
|
||||||
|
atom_style charge
|
||||||
|
processors * * 1 # domain decomposition over x and y
|
||||||
|
|
||||||
|
# System and atom definition
|
||||||
|
# we use different molecule ids for each layer of hBN
|
||||||
|
# so that inter- and intra-layer
|
||||||
|
# interactions can be specified separately
|
||||||
|
read_data hBN-momolayer-5nm.data
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
880 atoms
|
||||||
|
read_data CPU = 0.006 seconds
|
||||||
|
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||||
|
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||||
|
|
||||||
|
######################## Potential defition ########################
|
||||||
|
pair_style tersoff
|
||||||
|
pair_coeff * * BNC.tersoff B N
|
||||||
|
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||||
|
####################################################################
|
||||||
|
# Neighbor update settings
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify every 1
|
||||||
|
neigh_modify delay 0
|
||||||
|
neigh_modify check yes
|
||||||
|
|
||||||
|
#### Simulation settings ####
|
||||||
|
timestep 0.001
|
||||||
|
velocity all create 300.0 12345 loop geom
|
||||||
|
fix thermostat all nve
|
||||||
|
|
||||||
|
############# Output ###############
|
||||||
|
thermo 100
|
||||||
|
thermo_style custom step etotal pe ke temp
|
||||||
|
thermo_modify lost warn
|
||||||
|
|
||||||
|
###### Run molecular dynamics ######
|
||||||
|
run 1000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 4.1
|
||||||
|
ghost atom cutoff = 4.1
|
||||||
|
binsize = 2.05, bins = 23 24 49
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair tersoff, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.297 | 3.297 | 3.297 Mbytes
|
||||||
|
Step TotEng PotEng KinEng Temp
|
||||||
|
0 -6517.7517 -6551.8376 34.0859 300
|
||||||
|
100 -6517.5918 -6540.7795 23.187734 204.08204
|
||||||
|
200 -6517.5423 -6546.3342 28.791974 253.4066
|
||||||
|
300 -6517.547 -6552.0178 34.47074 303.38708
|
||||||
|
400 -6517.5499 -6554.1682 36.618359 322.28891
|
||||||
|
500 -6517.5482 -6553.3948 35.846598 315.49641
|
||||||
|
600 -6517.5438 -6557.8044 40.260609 354.34542
|
||||||
|
700 -6517.5489 -6554.8963 37.3474 328.70542
|
||||||
|
800 -6517.5426 -6557.376 39.833345 350.58494
|
||||||
|
900 -6517.5508 -6557.1115 39.560726 348.18554
|
||||||
|
1000 -6517.5427 -6559.2989 41.756142 367.50804
|
||||||
|
Loop time of 0.305524 on 4 procs for 1000 steps with 880 atoms
|
||||||
|
|
||||||
|
Performance: 282.792 ns/day, 0.085 hours/ns, 3273.060 timesteps/s
|
||||||
|
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.25887 | 0.26645 | 0.2696 | 0.9 | 87.21
|
||||||
|
Neigh | 0.002987 | 0.0031222 | 0.003244 | 0.2 | 1.02
|
||||||
|
Comm | 0.026999 | 0.030267 | 0.037861 | 2.6 | 9.91
|
||||||
|
Output | 0.000102 | 0.0001325 | 0.000211 | 0.0 | 0.04
|
||||||
|
Modify | 0.002206 | 0.002269 | 0.002366 | 0.1 | 0.74
|
||||||
|
Other | | 0.003286 | | | 1.08
|
||||||
|
|
||||||
|
Nlocal: 220.000 ave 231 max 210 min
|
||||||
|
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||||
|
Nghost: 578.500 ave 590 max 572 min
|
||||||
|
Histogram: 1 1 1 0 0 0 0 0 0 1
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 3965.00 ave 4169 max 3784 min
|
||||||
|
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 15860
|
||||||
|
Ave neighs/atom = 18.022727
|
||||||
|
Neighbor list builds = 15
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
100
examples/USER/misc/tersoff_shift/log.31Dec20.hBN_shift.g++.1
Normal file
100
examples/USER/misc/tersoff_shift/log.31Dec20.hBN_shift.g++.1
Normal file
@ -0,0 +1,100 @@
|
|||||||
|
LAMMPS (30 Nov 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Initialization
|
||||||
|
units metal
|
||||||
|
boundary p p p
|
||||||
|
atom_style charge
|
||||||
|
processors * * 1 # domain decomposition over x and y
|
||||||
|
|
||||||
|
# System and atom definition
|
||||||
|
# we use different molecule ids for each layer of hBN
|
||||||
|
# so that inter- and intra-layer
|
||||||
|
# interactions can be specified separately
|
||||||
|
read_data hBN-momolayer-5nm.data
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
880 atoms
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||||
|
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||||
|
|
||||||
|
######################## Potential defition ########################
|
||||||
|
pair_style tersoff shift 0.0
|
||||||
|
pair_coeff * * BNC.tersoff B N
|
||||||
|
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||||
|
####################################################################
|
||||||
|
# Neighbor update settings
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify every 1
|
||||||
|
neigh_modify delay 0
|
||||||
|
neigh_modify check yes
|
||||||
|
|
||||||
|
#### Simulation settings ####
|
||||||
|
timestep 0.001
|
||||||
|
velocity all create 300.0 12345 loop geom
|
||||||
|
fix thermostat all nve
|
||||||
|
|
||||||
|
############# Output ###############
|
||||||
|
thermo 100
|
||||||
|
thermo_style custom step etotal pe ke temp
|
||||||
|
thermo_modify lost warn
|
||||||
|
|
||||||
|
###### Run molecular dynamics ######
|
||||||
|
run 1000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 4.1
|
||||||
|
ghost atom cutoff = 4.1
|
||||||
|
binsize = 2.05, bins = 23 24 49
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair tersoff, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.545 | 3.545 | 3.545 Mbytes
|
||||||
|
Step TotEng PotEng KinEng Temp
|
||||||
|
0 -6517.7517 -6551.8376 34.0859 300
|
||||||
|
100 -6517.5918 -6540.7795 23.187734 204.08204
|
||||||
|
200 -6517.5423 -6546.3342 28.791974 253.4066
|
||||||
|
300 -6517.547 -6552.0178 34.47074 303.38708
|
||||||
|
400 -6517.5499 -6554.1682 36.618359 322.28891
|
||||||
|
500 -6517.5482 -6553.3948 35.846598 315.49641
|
||||||
|
600 -6517.5438 -6557.8044 40.260609 354.34542
|
||||||
|
700 -6517.5489 -6554.8963 37.3474 328.70542
|
||||||
|
800 -6517.5426 -6557.376 39.833345 350.58494
|
||||||
|
900 -6517.5508 -6557.1115 39.560726 348.18554
|
||||||
|
1000 -6517.5427 -6559.2989 41.756142 367.50804
|
||||||
|
Loop time of 1.18721 on 1 procs for 1000 steps with 880 atoms
|
||||||
|
|
||||||
|
Performance: 72.776 ns/day, 0.330 hours/ns, 842.310 timesteps/s
|
||||||
|
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 1.1609 | 1.1609 | 1.1609 | 0.0 | 97.78
|
||||||
|
Neigh | 0.010489 | 0.010489 | 0.010489 | 0.0 | 0.88
|
||||||
|
Comm | 0.006158 | 0.006158 | 0.006158 | 0.0 | 0.52
|
||||||
|
Output | 0.000196 | 0.000196 | 0.000196 | 0.0 | 0.02
|
||||||
|
Modify | 0.00643 | 0.00643 | 0.00643 | 0.0 | 0.54
|
||||||
|
Other | | 0.003079 | | | 0.26
|
||||||
|
|
||||||
|
Nlocal: 880.000 ave 880 max 880 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1538.00 ave 1538 max 1538 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 15860.0 ave 15860 max 15860 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 15860
|
||||||
|
Ave neighs/atom = 18.022727
|
||||||
|
Neighbor list builds = 15
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:01
|
||||||
100
examples/USER/misc/tersoff_shift/log.31Dec20.hBN_shift.g++.4
Normal file
100
examples/USER/misc/tersoff_shift/log.31Dec20.hBN_shift.g++.4
Normal file
@ -0,0 +1,100 @@
|
|||||||
|
LAMMPS (30 Nov 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Initialization
|
||||||
|
units metal
|
||||||
|
boundary p p p
|
||||||
|
atom_style charge
|
||||||
|
processors * * 1 # domain decomposition over x and y
|
||||||
|
|
||||||
|
# System and atom definition
|
||||||
|
# we use different molecule ids for each layer of hBN
|
||||||
|
# so that inter- and intra-layer
|
||||||
|
# interactions can be specified separately
|
||||||
|
read_data hBN-momolayer-5nm.data
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
880 atoms
|
||||||
|
read_data CPU = 0.007 seconds
|
||||||
|
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||||
|
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
|
||||||
|
|
||||||
|
######################## Potential defition ########################
|
||||||
|
pair_style tersoff shift 0.0
|
||||||
|
pair_coeff * * BNC.tersoff B N
|
||||||
|
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||||
|
####################################################################
|
||||||
|
# Neighbor update settings
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify every 1
|
||||||
|
neigh_modify delay 0
|
||||||
|
neigh_modify check yes
|
||||||
|
|
||||||
|
#### Simulation settings ####
|
||||||
|
timestep 0.001
|
||||||
|
velocity all create 300.0 12345 loop geom
|
||||||
|
fix thermostat all nve
|
||||||
|
|
||||||
|
############# Output ###############
|
||||||
|
thermo 100
|
||||||
|
thermo_style custom step etotal pe ke temp
|
||||||
|
thermo_modify lost warn
|
||||||
|
|
||||||
|
###### Run molecular dynamics ######
|
||||||
|
run 1000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 4.1
|
||||||
|
ghost atom cutoff = 4.1
|
||||||
|
binsize = 2.05, bins = 23 24 49
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair tersoff, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.297 | 3.297 | 3.297 Mbytes
|
||||||
|
Step TotEng PotEng KinEng Temp
|
||||||
|
0 -6517.7517 -6551.8376 34.0859 300
|
||||||
|
100 -6517.5918 -6540.7795 23.187734 204.08204
|
||||||
|
200 -6517.5423 -6546.3342 28.791974 253.4066
|
||||||
|
300 -6517.547 -6552.0178 34.47074 303.38708
|
||||||
|
400 -6517.5499 -6554.1682 36.618359 322.28891
|
||||||
|
500 -6517.5482 -6553.3948 35.846598 315.49641
|
||||||
|
600 -6517.5438 -6557.8044 40.260609 354.34542
|
||||||
|
700 -6517.5489 -6554.8963 37.3474 328.70542
|
||||||
|
800 -6517.5426 -6557.376 39.833345 350.58494
|
||||||
|
900 -6517.5508 -6557.1115 39.560726 348.18554
|
||||||
|
1000 -6517.5427 -6559.2989 41.756142 367.50804
|
||||||
|
Loop time of 0.398907 on 4 procs for 1000 steps with 880 atoms
|
||||||
|
|
||||||
|
Performance: 216.592 ns/day, 0.111 hours/ns, 2506.850 timesteps/s
|
||||||
|
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.32415 | 0.32873 | 0.33831 | 1.0 | 82.41
|
||||||
|
Neigh | 0.003216 | 0.0032905 | 0.003397 | 0.1 | 0.82
|
||||||
|
Comm | 0.050126 | 0.059974 | 0.064634 | 2.4 | 15.03
|
||||||
|
Output | 0.0001 | 0.000131 | 0.000221 | 0.0 | 0.03
|
||||||
|
Modify | 0.002423 | 0.0024955 | 0.002658 | 0.2 | 0.63
|
||||||
|
Other | | 0.004282 | | | 1.07
|
||||||
|
|
||||||
|
Nlocal: 220.000 ave 231 max 210 min
|
||||||
|
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||||
|
Nghost: 578.500 ave 590 max 572 min
|
||||||
|
Histogram: 1 1 1 0 0 0 0 0 0 1
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 3965.00 ave 4169 max 3784 min
|
||||||
|
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 15860
|
||||||
|
Ave neighs/atom = 18.022727
|
||||||
|
Neighbor list builds = 15
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
@ -46,7 +46,7 @@ create_atoms 1 region myreg &
|
|||||||
|
|
||||||
mass * 28.06
|
mass * 28.06
|
||||||
|
|
||||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
velocity all create $t 5287287 loop geom
|
||||||
|
|
||||||
# Equilibrate using Stillinger-Weber model for silicon
|
# Equilibrate using Stillinger-Weber model for silicon
|
||||||
|
|
||||||
|
|||||||
@ -1,524 +0,0 @@
|
|||||||
LAMMPS (27 Nov 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Simple regression tests for threebody potentials
|
|
||||||
|
|
||||||
# NOTE: These are not intended to represent real materials
|
|
||||||
|
|
||||||
units metal
|
|
||||||
|
|
||||||
atom_style atomic
|
|
||||||
atom_modify map array
|
|
||||||
boundary p p p
|
|
||||||
atom_modify sort 0 0.0
|
|
||||||
|
|
||||||
# temperature
|
|
||||||
|
|
||||||
variable t equal 1800.0
|
|
||||||
|
|
||||||
# cubic diamond unit cell
|
|
||||||
|
|
||||||
variable a equal 5.431
|
|
||||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
|
||||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
|
||||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
|
||||||
|
|
||||||
region myreg block 0 4 0 4 0 4
|
|
||||||
|
|
||||||
create_box 8 myreg
|
|
||||||
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
|
||||||
Created 512 atoms
|
|
||||||
Time spent = 0.000483751 secs
|
|
||||||
|
|
||||||
mass * 28.06
|
|
||||||
|
|
||||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
|
||||||
velocity all create 1800 5287287 mom yes rot yes dist gaussian
|
|
||||||
|
|
||||||
# Equilibrate using Stillinger-Weber model for silicon
|
|
||||||
|
|
||||||
pair_style sw
|
|
||||||
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
|
|
||||||
Reading potential file Si.sw with DATE: 2007-06-11
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
fix 1 all nvt temp $t $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 1800 0.1
|
|
||||||
fix_modify 1 energy yes
|
|
||||||
timestep 1.0e-3
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 10 check yes
|
|
||||||
run 100
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 4.77118
|
|
||||||
ghost atom cutoff = 4.77118
|
|
||||||
binsize = 2.38559, bins = 10 10 10
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair sw, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 2.982 | 2.982 | 2.982 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1800 -2220.3392 0 -2101.4457 12358.626
|
|
||||||
10 993.48824 -2166.8749 0 -2101.3265 14121.853
|
|
||||||
20 587.90768 -2139.6876 0 -2101.3093 11864.886
|
|
||||||
30 1030.8616 -2167.8446 0 -2101.3947 6649.2566
|
|
||||||
40 724.62874 -2145.9637 0 -2101.3436 5859.6447
|
|
||||||
50 490.9053 -2129.5491 0 -2101.3077 6326.5434
|
|
||||||
60 960.24533 -2159.427 0 -2101.3794 5733.9889
|
|
||||||
70 906.76518 -2154.3675 0 -2101.3496 8380.4834
|
|
||||||
80 800.7253 -2146.0714 0 -2101.3113 11515.737
|
|
||||||
90 1249.2719 -2173.9445 0 -2101.3818 11593.728
|
|
||||||
100 1080.3797 -2160.6174 0 -2101.3445 12414.602
|
|
||||||
Loop time of 0.129171 on 1 procs for 100 steps with 512 atoms
|
|
||||||
|
|
||||||
Performance: 66.888 ns/day, 0.359 hours/ns, 774.165 timesteps/s
|
|
||||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.12468 | 0.12468 | 0.12468 | 0.0 | 96.52
|
|
||||||
Neigh | 0.0017159 | 0.0017159 | 0.0017159 | 0.0 | 1.33
|
|
||||||
Comm | 0.00088573 | 0.00088573 | 0.00088573 | 0.0 | 0.69
|
|
||||||
Output | 0.00011206 | 0.00011206 | 0.00011206 | 0.0 | 0.09
|
|
||||||
Modify | 0.0014365 | 0.0014365 | 0.0014365 | 0.0 | 1.11
|
|
||||||
Other | | 0.0003417 | | | 0.26
|
|
||||||
|
|
||||||
Nlocal: 512 ave 512 max 512 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 1017 ave 1017 max 1017 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 14044 ave 14044 max 14044 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 14044
|
|
||||||
Ave neighs/atom = 27.4297
|
|
||||||
Neighbor list builds = 2
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
write_restart restart.equil
|
|
||||||
|
|
||||||
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
|
|
||||||
|
|
||||||
clear
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
read_restart restart.equil
|
|
||||||
restoring atom style atomic from restart
|
|
||||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
pair style sw stores no restart info
|
|
||||||
512 atoms
|
|
||||||
|
|
||||||
pair_style sw
|
|
||||||
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
|
|
||||||
Reading potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
fix 1 all nvt temp $t $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 1800 0.1
|
|
||||||
Resetting global fix info from restart file:
|
|
||||||
fix style: nvt, fix ID: 1
|
|
||||||
fix_modify 1 energy yes
|
|
||||||
timestep 1.0e-3
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 10 check yes
|
|
||||||
run 100
|
|
||||||
All restart file global fix info was re-assigned
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 5.632
|
|
||||||
ghost atom cutoff = 5.632
|
|
||||||
binsize = 2.816, bins = 8 8 8
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair sw, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 2.758 | 2.758 | 2.758 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
100 1080.3797 -621.93681 0 -562.66385 464005.01
|
|
||||||
110 1512.4547 -648.51133 0 -562.74194 463733.24
|
|
||||||
120 1959.7565 -675.18668 0 -562.8255 486580.33
|
|
||||||
130 1138.5498 -618.80419 0 -562.6427 515406.41
|
|
||||||
140 1827.3403 -662.43867 0 -562.78985 485719
|
|
||||||
150 1822.9803 -659.56725 0 -562.76627 465652.59
|
|
||||||
160 1128.3444 -611.92808 0 -562.65512 469836.33
|
|
||||||
170 1699.6402 -647.82381 0 -562.75353 467977.54
|
|
||||||
180 1840.047 -654.5552 0 -562.77005 488397.41
|
|
||||||
190 1312.0974 -617.70228 0 -562.6629 510856.48
|
|
||||||
200 1809.8409 -648.6173 0 -562.75377 490822.97
|
|
||||||
Loop time of 0.399255 on 1 procs for 100 steps with 512 atoms
|
|
||||||
|
|
||||||
Performance: 21.640 ns/day, 1.109 hours/ns, 250.467 timesteps/s
|
|
||||||
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.38979 | 0.38979 | 0.38979 | 0.0 | 97.63
|
|
||||||
Neigh | 0.0061283 | 0.0061283 | 0.0061283 | 0.0 | 1.53
|
|
||||||
Comm | 0.0013483 | 0.0013483 | 0.0013483 | 0.0 | 0.34
|
|
||||||
Output | 0.00016642 | 0.00016642 | 0.00016642 | 0.0 | 0.04
|
|
||||||
Modify | 0.0014937 | 0.0014937 | 0.0014937 | 0.0 | 0.37
|
|
||||||
Other | | 0.0003231 | | | 0.08
|
|
||||||
|
|
||||||
Nlocal: 512 ave 512 max 512 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 1386 ave 1386 max 1386 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 17388 ave 17388 max 17388 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 17388
|
|
||||||
Ave neighs/atom = 33.9609
|
|
||||||
Neighbor list builds = 5
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
# Test Vashishta model for In/P
|
|
||||||
|
|
||||||
clear
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
read_restart restart.equil
|
|
||||||
restoring atom style atomic from restart
|
|
||||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
pair style sw stores no restart info
|
|
||||||
512 atoms
|
|
||||||
|
|
||||||
pair_style vashishta
|
|
||||||
pair_coeff * * InP.vashishta In In In In P P P P
|
|
||||||
Reading potential file InP.vashishta with DATE: 2015-10-14
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
fix 1 all nvt temp $t $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 1800 0.1
|
|
||||||
Resetting global fix info from restart file:
|
|
||||||
fix style: nvt, fix ID: 1
|
|
||||||
fix_modify 1 energy yes
|
|
||||||
timestep 1.0e-3
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 10 check yes
|
|
||||||
run 100
|
|
||||||
All restart file global fix info was re-assigned
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 7
|
|
||||||
ghost atom cutoff = 7
|
|
||||||
binsize = 3.5, bins = 7 7 7
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair vashishta, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 2.783 | 2.783 | 2.783 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
100 1080.3797 -1491.8652 0 -1432.5922 358930.65
|
|
||||||
110 1299.3069 -1504.494 0 -1432.6803 347566.41
|
|
||||||
120 1396.3035 -1508.3817 0 -1432.672 336798.42
|
|
||||||
130 1055.9254 -1483.8342 0 -1432.5849 341035.18
|
|
||||||
140 1543.9033 -1513.8559 0 -1432.6931 314268.54
|
|
||||||
150 1242.5383 -1491.417 0 -1432.6036 311068.53
|
|
||||||
160 1240.1733 -1489.2495 0 -1432.6033 295776.98
|
|
||||||
170 1559.5037 -1507.824 0 -1432.6417 266170.25
|
|
||||||
180 1379.0358 -1493.4092 0 -1432.5869 251410.63
|
|
||||||
190 1465.8073 -1496.8564 0 -1432.6105 226461.31
|
|
||||||
200 1456.6383 -1493.8133 0 -1432.5852 208188.34
|
|
||||||
Loop time of 0.198058 on 1 procs for 100 steps with 512 atoms
|
|
||||||
|
|
||||||
Performance: 43.624 ns/day, 0.550 hours/ns, 504.903 timesteps/s
|
|
||||||
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.18746 | 0.18746 | 0.18746 | 0.0 | 94.65
|
|
||||||
Neigh | 0.00688 | 0.00688 | 0.00688 | 0.0 | 3.47
|
|
||||||
Comm | 0.001718 | 0.001718 | 0.001718 | 0.0 | 0.87
|
|
||||||
Output | 0.00013351 | 0.00013351 | 0.00013351 | 0.0 | 0.07
|
|
||||||
Modify | 0.0015109 | 0.0015109 | 0.0015109 | 0.0 | 0.76
|
|
||||||
Other | | 0.0003531 | | | 0.18
|
|
||||||
|
|
||||||
Nlocal: 512 ave 512 max 512 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 1810 ave 1810 max 1810 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 36480 ave 36480 max 36480 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 36480
|
|
||||||
Ave neighs/atom = 71.25
|
|
||||||
Neighbor list builds = 4
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
# Test Tersoff model for B/N/C
|
|
||||||
|
|
||||||
clear
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
read_restart restart.equil
|
|
||||||
restoring atom style atomic from restart
|
|
||||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
pair style sw stores no restart info
|
|
||||||
512 atoms
|
|
||||||
|
|
||||||
variable fac equal 0.6
|
|
||||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
|
||||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
|
||||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
|
||||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
|
||||||
orthogonal box = (4.3448 0 0) to (17.3792 21.724 21.724)
|
|
||||||
orthogonal box = (4.3448 4.3448 0) to (17.3792 17.3792 21.724)
|
|
||||||
orthogonal box = (4.3448 4.3448 4.3448) to (17.3792 17.3792 17.3792)
|
|
||||||
|
|
||||||
pair_style tersoff
|
|
||||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
|
||||||
Reading potential file BNC.tersoff with DATE: 2013-03-21
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
fix 1 all nvt temp $t $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 1800 0.1
|
|
||||||
Resetting global fix info from restart file:
|
|
||||||
fix style: nvt, fix ID: 1
|
|
||||||
fix_modify 1 energy yes
|
|
||||||
timestep 1.0e-3
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 10 check yes
|
|
||||||
run 100
|
|
||||||
All restart file global fix info was re-assigned
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 3.1
|
|
||||||
ghost atom cutoff = 3.1
|
|
||||||
binsize = 1.55, bins = 9 9 9
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair tersoff, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 2.74 | 2.74 | 2.74 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
100 1080.3797 -3249.8451 0 -3190.5722 1925371.8
|
|
||||||
110 1878.2843 -3300.7205 0 -3191.0964 1893058.6
|
|
||||||
120 1153.8494 -3250.2114 0 -3190.5436 1932141.4
|
|
||||||
130 1363.8664 -3261.6889 0 -3190.6116 1902268.1
|
|
||||||
140 1565.5505 -3273.0405 0 -3190.6982 1878817
|
|
||||||
150 1416.9458 -3261.1805 0 -3190.865 1916554.4
|
|
||||||
160 1288.6997 -3249.8279 0 -3190.4141 1933227.4
|
|
||||||
170 1768.3043 -3279.2164 0 -3190.4535 1898123.4
|
|
||||||
180 1375.1942 -3251.0929 0 -3190.3781 1896205.1
|
|
||||||
190 1527.0671 -3258.7679 0 -3190.4344 1900673.6
|
|
||||||
200 1586.8691 -3260.4713 0 -3190.434 1912454.8
|
|
||||||
Loop time of 0.210082 on 1 procs for 100 steps with 512 atoms
|
|
||||||
|
|
||||||
Performance: 41.127 ns/day, 0.584 hours/ns, 476.006 timesteps/s
|
|
||||||
98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.20628 | 0.20628 | 0.20628 | 0.0 | 98.19
|
|
||||||
Neigh | 0.00099182 | 0.00099182 | 0.00099182 | 0.0 | 0.47
|
|
||||||
Comm | 0.00085139 | 0.00085139 | 0.00085139 | 0.0 | 0.41
|
|
||||||
Output | 0.00013494 | 0.00013494 | 0.00013494 | 0.0 | 0.06
|
|
||||||
Modify | 0.0014665 | 0.0014665 | 0.0014665 | 0.0 | 0.70
|
|
||||||
Other | | 0.0003612 | | | 0.17
|
|
||||||
|
|
||||||
Nlocal: 512 ave 512 max 512 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 1027 ave 1027 max 1027 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 14602 ave 14602 max 14602 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 14602
|
|
||||||
Ave neighs/atom = 28.5195
|
|
||||||
Neighbor list builds = 1
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
# Test Tersoff/Mod model for Si
|
|
||||||
|
|
||||||
clear
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
read_restart restart.equil
|
|
||||||
restoring atom style atomic from restart
|
|
||||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
pair style sw stores no restart info
|
|
||||||
512 atoms
|
|
||||||
|
|
||||||
pair_style tersoff/mod
|
|
||||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
|
||||||
Reading potential file Si.tersoff.mod with DATE: 2013-07-26
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
fix 1 all nvt temp $t $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 1800 0.1
|
|
||||||
Resetting global fix info from restart file:
|
|
||||||
fix style: nvt, fix ID: 1
|
|
||||||
fix_modify 1 energy yes
|
|
||||||
timestep 1.0e-3
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 10 check yes
|
|
||||||
run 100
|
|
||||||
All restart file global fix info was re-assigned
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 4.3
|
|
||||||
ghost atom cutoff = 4.3
|
|
||||||
binsize = 2.15, bins = 11 11 11
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair tersoff/mod, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 2.744 | 2.744 | 2.744 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
100 1080.3797 -2307.5808 0 -2248.3078 18624.75
|
|
||||||
110 851.21757 -2290.7529 0 -2248.2817 21041.97
|
|
||||||
120 1074.6349 -2303.6437 0 -2248.321 15244.809
|
|
||||||
130 1006.5662 -2296.9866 0 -2248.3057 15954.09
|
|
||||||
140 855.64354 -2285.1581 0 -2248.2781 19346.662
|
|
||||||
150 1111.1546 -2300.024 0 -2248.314 14698.998
|
|
||||||
160 1114.7933 -2297.8629 0 -2248.3098 14414.14
|
|
||||||
170 853.9568 -2278.6047 0 -2248.2716 20120.632
|
|
||||||
180 1031.0925 -2288.3481 0 -2248.2949 18332.008
|
|
||||||
190 1230.3458 -2298.9946 0 -2248.3111 15520.302
|
|
||||||
200 1053.8799 -2284.8931 0 -2248.2816 20033.536
|
|
||||||
Loop time of 0.158428 on 1 procs for 100 steps with 512 atoms
|
|
||||||
|
|
||||||
Performance: 54.536 ns/day, 0.440 hours/ns, 631.200 timesteps/s
|
|
||||||
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.15318 | 0.15318 | 0.15318 | 0.0 | 96.69
|
|
||||||
Neigh | 0.0022631 | 0.0022631 | 0.0022631 | 0.0 | 1.43
|
|
||||||
Comm | 0.00093651 | 0.00093651 | 0.00093651 | 0.0 | 0.59
|
|
||||||
Output | 0.00019622 | 0.00019622 | 0.00019622 | 0.0 | 0.12
|
|
||||||
Modify | 0.0015035 | 0.0015035 | 0.0015035 | 0.0 | 0.95
|
|
||||||
Other | | 0.0003462 | | | 0.22
|
|
||||||
|
|
||||||
Nlocal: 512 ave 512 max 512 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 1001 ave 1001 max 1001 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 8872 ave 8872 max 8872 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 8872
|
|
||||||
Ave neighs/atom = 17.3281
|
|
||||||
Neighbor list builds = 3
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
# Test Tersoff/Mod/C model for Si
|
|
||||||
|
|
||||||
clear
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
read_restart restart.equil
|
|
||||||
restoring atom style atomic from restart
|
|
||||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
pair style sw stores no restart info
|
|
||||||
512 atoms
|
|
||||||
newton on on
|
|
||||||
pair_style tersoff/mod/c
|
|
||||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
|
||||||
Reading potential file Si.tersoff.modc with DATE: 2016-11-09
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
fix 1 all nvt temp $t $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 1800 0.1
|
|
||||||
Resetting global fix info from restart file:
|
|
||||||
fix style: nvt, fix ID: 1
|
|
||||||
fix_modify 1 energy yes
|
|
||||||
timestep 1.0e-3
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 10 check yes
|
|
||||||
run 100
|
|
||||||
All restart file global fix info was re-assigned
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 4.20569
|
|
||||||
ghost atom cutoff = 4.20569
|
|
||||||
binsize = 2.10285, bins = 11 11 11
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair tersoff/mod/c, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 2.739 | 2.739 | 2.739 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
100 1080.3797 -2307.5509 0 -2248.2779 21368.36
|
|
||||||
110 846.70637 -2290.4239 0 -2248.2488 22856.37
|
|
||||||
120 1083.0906 -2304.1686 0 -2248.2895 17530.457
|
|
||||||
130 1008.7015 -2297.0835 0 -2248.2781 17698.498
|
|
||||||
140 811.71413 -2282.2528 0 -2248.2417 19986.737
|
|
||||||
150 1094.4969 -2298.9718 0 -2248.2836 15822.967
|
|
||||||
160 1100.1109 -2296.9461 0 -2248.2804 15213.75
|
|
||||||
170 801.20165 -2275.2175 0 -2248.2372 20153.957
|
|
||||||
180 994.63485 -2286.1145 0 -2248.2621 19167.021
|
|
||||||
190 1215.6425 -2298.2082 0 -2248.284 15895.654
|
|
||||||
200 992.20385 -2281.0372 0 -2248.2425 19643.792
|
|
||||||
Loop time of 0.282035 on 1 procs for 100 steps with 512 atoms
|
|
||||||
|
|
||||||
Performance: 30.634 ns/day, 0.783 hours/ns, 354.565 timesteps/s
|
|
||||||
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.27701 | 0.27701 | 0.27701 | 0.0 | 98.22
|
|
||||||
Neigh | 0.0021927 | 0.0021927 | 0.0021927 | 0.0 | 0.78
|
|
||||||
Comm | 0.00089169 | 0.00089169 | 0.00089169 | 0.0 | 0.32
|
|
||||||
Output | 0.0001452 | 0.0001452 | 0.0001452 | 0.0 | 0.05
|
|
||||||
Modify | 0.0014682 | 0.0014682 | 0.0014682 | 0.0 | 0.52
|
|
||||||
Other | | 0.0003295 | | | 0.12
|
|
||||||
|
|
||||||
Nlocal: 512 ave 512 max 512 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 972 ave 972 max 972 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 8390 ave 8390 max 8390 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 8390
|
|
||||||
Ave neighs/atom = 16.3867
|
|
||||||
Neighbor list builds = 3
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
Total wall time: 0:00:01
|
|
||||||
@ -1,524 +0,0 @@
|
|||||||
LAMMPS (27 Nov 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Simple regression tests for threebody potentials
|
|
||||||
|
|
||||||
# NOTE: These are not intended to represent real materials
|
|
||||||
|
|
||||||
units metal
|
|
||||||
|
|
||||||
atom_style atomic
|
|
||||||
atom_modify map array
|
|
||||||
boundary p p p
|
|
||||||
atom_modify sort 0 0.0
|
|
||||||
|
|
||||||
# temperature
|
|
||||||
|
|
||||||
variable t equal 1800.0
|
|
||||||
|
|
||||||
# cubic diamond unit cell
|
|
||||||
|
|
||||||
variable a equal 5.431
|
|
||||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
|
||||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
|
||||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
|
||||||
|
|
||||||
region myreg block 0 4 0 4 0 4
|
|
||||||
|
|
||||||
create_box 8 myreg
|
|
||||||
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
|
||||||
Created 512 atoms
|
|
||||||
Time spent = 0.000348091 secs
|
|
||||||
|
|
||||||
mass * 28.06
|
|
||||||
|
|
||||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
|
||||||
velocity all create 1800 5287287 mom yes rot yes dist gaussian
|
|
||||||
|
|
||||||
# Equilibrate using Stillinger-Weber model for silicon
|
|
||||||
|
|
||||||
pair_style sw
|
|
||||||
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
|
|
||||||
Reading potential file Si.sw with DATE: 2007-06-11
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
fix 1 all nvt temp $t $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 1800 0.1
|
|
||||||
fix_modify 1 energy yes
|
|
||||||
timestep 1.0e-3
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 10 check yes
|
|
||||||
run 100
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 4.77118
|
|
||||||
ghost atom cutoff = 4.77118
|
|
||||||
binsize = 2.38559, bins = 10 10 10
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair sw, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 2.957 | 2.957 | 2.957 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 1800 -2220.3392 0 -2101.4457 12358.626
|
|
||||||
10 979.93888 -2165.9769 0 -2101.3242 14172.134
|
|
||||||
20 579.6159 -2139.1412 0 -2101.3085 11866.038
|
|
||||||
30 1027.5223 -2167.6187 0 -2101.3942 6885.6751
|
|
||||||
40 711.03138 -2145.0665 0 -2101.3405 6357.0866
|
|
||||||
50 497.18304 -2129.9748 0 -2101.3052 7137.6093
|
|
||||||
60 1008.411 -2162.5834 0 -2101.3804 6745.1775
|
|
||||||
70 947.58674 -2156.9872 0 -2101.3508 9678.1622
|
|
||||||
80 798.43683 -2145.8382 0 -2101.3074 12728.694
|
|
||||||
90 1259.2065 -2174.5324 0 -2101.3799 12033.395
|
|
||||||
100 1100.5203 -2161.8599 0 -2101.3468 12356.137
|
|
||||||
Loop time of 0.0414283 on 4 procs for 100 steps with 512 atoms
|
|
||||||
|
|
||||||
Performance: 208.553 ns/day, 0.115 hours/ns, 2413.811 timesteps/s
|
|
||||||
95.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.030011 | 0.032047 | 0.034036 | 0.8 | 77.36
|
|
||||||
Neigh | 0.00043392 | 0.00045151 | 0.0004642 | 0.0 | 1.09
|
|
||||||
Comm | 0.0050831 | 0.0067263 | 0.0091536 | 1.8 | 16.24
|
|
||||||
Output | 0.00018191 | 0.00018775 | 0.00020432 | 0.0 | 0.45
|
|
||||||
Modify | 0.00068116 | 0.0010136 | 0.001817 | 1.5 | 2.45
|
|
||||||
Other | | 0.001002 | | | 2.42
|
|
||||||
|
|
||||||
Nlocal: 128 ave 132 max 126 min
|
|
||||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
|
||||||
Nghost: 525 ave 527 max 521 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 2 1
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 3507 ave 3596 max 3470 min
|
|
||||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 14028
|
|
||||||
Ave neighs/atom = 27.3984
|
|
||||||
Neighbor list builds = 2
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
write_restart restart.equil
|
|
||||||
|
|
||||||
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
|
|
||||||
|
|
||||||
clear
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
read_restart restart.equil
|
|
||||||
restoring atom style atomic from restart
|
|
||||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
pair style sw stores no restart info
|
|
||||||
512 atoms
|
|
||||||
|
|
||||||
pair_style sw
|
|
||||||
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
|
|
||||||
Reading potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
fix 1 all nvt temp $t $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 1800 0.1
|
|
||||||
Resetting global fix info from restart file:
|
|
||||||
fix style: nvt, fix ID: 1
|
|
||||||
fix_modify 1 energy yes
|
|
||||||
timestep 1.0e-3
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 10 check yes
|
|
||||||
run 100
|
|
||||||
All restart file global fix info was re-assigned
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 5.632
|
|
||||||
ghost atom cutoff = 5.632
|
|
||||||
binsize = 2.816, bins = 8 8 8
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair sw, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 2.717 | 2.718 | 2.718 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
100 1100.5203 -621.61663 0 -561.10352 462716.2
|
|
||||||
110 1478.2708 -644.61282 0 -561.16927 464567.29
|
|
||||||
120 1989.4577 -675.5312 0 -561.25985 486476.63
|
|
||||||
130 1185.4652 -620.23829 0 -561.09359 514103.86
|
|
||||||
140 1726.9774 -654.21952 0 -561.20676 488915.22
|
|
||||||
150 1863.2061 -660.66167 0 -561.21416 466985.15
|
|
||||||
160 1119.0313 -609.68409 0 -561.08624 471511.61
|
|
||||||
170 1708.2653 -646.79823 0 -561.18829 468697.42
|
|
||||||
180 1891.8451 -656.32585 0 -561.2042 489912.65
|
|
||||||
190 1345.7703 -618.29258 0 -561.09909 512364.68
|
|
||||||
200 1865.9507 -650.72167 0 -561.19281 491531.23
|
|
||||||
Loop time of 0.117532 on 4 procs for 100 steps with 512 atoms
|
|
||||||
|
|
||||||
Performance: 73.512 ns/day, 0.326 hours/ns, 850.834 timesteps/s
|
|
||||||
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.096347 | 0.10005 | 0.10244 | 0.8 | 85.13
|
|
||||||
Neigh | 0.000947 | 0.0010053 | 0.0011535 | 0.3 | 0.86
|
|
||||||
Comm | 0.0098422 | 0.012949 | 0.016335 | 2.2 | 11.02
|
|
||||||
Output | 0.00017452 | 0.00022596 | 0.00037885 | 0.0 | 0.19
|
|
||||||
Modify | 0.00078702 | 0.0013881 | 0.0021975 | 1.6 | 1.18
|
|
||||||
Other | | 0.001909 | | | 1.62
|
|
||||||
|
|
||||||
Nlocal: 128 ave 133 max 125 min
|
|
||||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
|
||||||
Nghost: 754.5 ave 759 max 748 min
|
|
||||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 4353 ave 4512 max 4252 min
|
|
||||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 17412
|
|
||||||
Ave neighs/atom = 34.0078
|
|
||||||
Neighbor list builds = 3
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
# Test Vashishta model for In/P
|
|
||||||
|
|
||||||
clear
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
read_restart restart.equil
|
|
||||||
restoring atom style atomic from restart
|
|
||||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
pair style sw stores no restart info
|
|
||||||
512 atoms
|
|
||||||
|
|
||||||
pair_style vashishta
|
|
||||||
pair_coeff * * InP.vashishta In In In In P P P P
|
|
||||||
Reading potential file InP.vashishta with DATE: 2015-10-14
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
fix 1 all nvt temp $t $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 1800 0.1
|
|
||||||
Resetting global fix info from restart file:
|
|
||||||
fix style: nvt, fix ID: 1
|
|
||||||
fix_modify 1 energy yes
|
|
||||||
timestep 1.0e-3
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 10 check yes
|
|
||||||
run 100
|
|
||||||
All restart file global fix info was re-assigned
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 7
|
|
||||||
ghost atom cutoff = 7
|
|
||||||
binsize = 3.5, bins = 7 7 7
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair vashishta, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 2.739 | 2.739 | 2.739 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
100 1100.5203 -1495.2135 0 -1434.7004 357102.51
|
|
||||||
110 1238.7371 -1502.5372 0 -1434.7528 348870.19
|
|
||||||
120 1409.575 -1511.3137 0 -1434.7612 336831.6
|
|
||||||
130 1081.541 -1487.5554 0 -1434.6881 339244.71
|
|
||||||
140 1484.7455 -1512.0076 0 -1434.7646 313026.51
|
|
||||||
150 1263.0321 -1494.834 0 -1434.7018 306496.02
|
|
||||||
160 1253.4363 -1492.1804 0 -1434.7025 290683.01
|
|
||||||
170 1536.7348 -1508.3735 0 -1434.7312 261755.69
|
|
||||||
180 1342.0478 -1493.0615 0 -1434.6754 248519.54
|
|
||||||
190 1457.921 -1498.4355 0 -1434.6991 223607.39
|
|
||||||
200 1499.5384 -1498.7005 0 -1434.6898 204647.17
|
|
||||||
Loop time of 0.060006 on 4 procs for 100 steps with 512 atoms
|
|
||||||
|
|
||||||
Performance: 143.986 ns/day, 0.167 hours/ns, 1666.501 timesteps/s
|
|
||||||
95.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.043862 | 0.047754 | 0.04964 | 1.0 | 79.58
|
|
||||||
Neigh | 0.0018079 | 0.0018883 | 0.0019724 | 0.1 | 3.15
|
|
||||||
Comm | 0.0067413 | 0.0083464 | 0.011978 | 2.3 | 13.91
|
|
||||||
Output | 0.00018859 | 0.00029892 | 0.00062919 | 0.0 | 0.50
|
|
||||||
Modify | 0.00088429 | 0.0011829 | 0.0014911 | 0.8 | 1.97
|
|
||||||
Other | | 0.0005357 | | | 0.89
|
|
||||||
|
|
||||||
Nlocal: 128 ave 129 max 127 min
|
|
||||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
|
||||||
Nghost: 992.75 ave 1001 max 987 min
|
|
||||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 9116 ave 9213 max 9051 min
|
|
||||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 36464
|
|
||||||
Ave neighs/atom = 71.2188
|
|
||||||
Neighbor list builds = 4
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
# Test Tersoff model for B/N/C
|
|
||||||
|
|
||||||
clear
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
read_restart restart.equil
|
|
||||||
restoring atom style atomic from restart
|
|
||||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
pair style sw stores no restart info
|
|
||||||
512 atoms
|
|
||||||
|
|
||||||
variable fac equal 0.6
|
|
||||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
|
||||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
|
||||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
|
||||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
|
||||||
orthogonal box = (4.3448 0 0) to (17.3792 21.724 21.724)
|
|
||||||
orthogonal box = (4.3448 4.3448 0) to (17.3792 17.3792 21.724)
|
|
||||||
orthogonal box = (4.3448 4.3448 4.3448) to (17.3792 17.3792 17.3792)
|
|
||||||
|
|
||||||
pair_style tersoff
|
|
||||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
|
||||||
Reading potential file BNC.tersoff with DATE: 2013-03-21
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
fix 1 all nvt temp $t $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 1800 0.1
|
|
||||||
Resetting global fix info from restart file:
|
|
||||||
fix style: nvt, fix ID: 1
|
|
||||||
fix_modify 1 energy yes
|
|
||||||
timestep 1.0e-3
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 10 check yes
|
|
||||||
run 100
|
|
||||||
All restart file global fix info was re-assigned
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 3.1
|
|
||||||
ghost atom cutoff = 3.1
|
|
||||||
binsize = 1.55, bins = 9 9 9
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair tersoff, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 2.699 | 2.699 | 2.699 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
100 1100.5203 -3252.8699 0 -3192.3567 1930742.5
|
|
||||||
110 1858.7735 -3301.1227 0 -3192.8403 1901753.1
|
|
||||||
120 1107.7693 -3248.8236 0 -3192.2522 1953649.4
|
|
||||||
130 1315.4397 -3260.1471 0 -3192.2616 1898713.9
|
|
||||||
140 1541.4371 -3273.1832 0 -3192.41 1887352.3
|
|
||||||
150 1424.7104 -3262.9648 0 -3192.216 1960688.1
|
|
||||||
160 1291.2932 -3251.5548 0 -3192.0201 1914541.2
|
|
||||||
170 1719.1133 -3277.7936 0 -3192.33 1893926
|
|
||||||
180 1312.8066 -3248.6914 0 -3192.1477 1921417.4
|
|
||||||
190 1481.3472 -3257.1585 0 -3191.8991 1927045.6
|
|
||||||
200 1615.282 -3263.8377 0 -3192.055 1920616.3
|
|
||||||
Loop time of 0.0635643 on 4 procs for 100 steps with 512 atoms
|
|
||||||
|
|
||||||
Performance: 135.925 ns/day, 0.177 hours/ns, 1573.210 timesteps/s
|
|
||||||
97.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.051391 | 0.053262 | 0.05459 | 0.6 | 83.79
|
|
||||||
Neigh | 0.00052404 | 0.00052798 | 0.00053144 | 0.0 | 0.83
|
|
||||||
Comm | 0.0063059 | 0.0079132 | 0.0095143 | 1.5 | 12.45
|
|
||||||
Output | 0.00017905 | 0.00029147 | 0.00062609 | 0.0 | 0.46
|
|
||||||
Modify | 0.00064421 | 0.00096625 | 0.0012674 | 0.0 | 1.52
|
|
||||||
Other | | 0.0006039 | | | 0.95
|
|
||||||
|
|
||||||
Nlocal: 128 ave 131 max 125 min
|
|
||||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
|
||||||
Nghost: 526.75 ave 532 max 523 min
|
|
||||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 3646.5 ave 3722 max 3567 min
|
|
||||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 14586
|
|
||||||
Ave neighs/atom = 28.4883
|
|
||||||
Neighbor list builds = 2
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
# Test Tersoff/Mod model for Si
|
|
||||||
|
|
||||||
clear
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
read_restart restart.equil
|
|
||||||
restoring atom style atomic from restart
|
|
||||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
pair style sw stores no restart info
|
|
||||||
512 atoms
|
|
||||||
|
|
||||||
pair_style tersoff/mod
|
|
||||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
|
||||||
Reading potential file Si.tersoff.mod with DATE: 2013-07-26
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
fix 1 all nvt temp $t $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 1800 0.1
|
|
||||||
Resetting global fix info from restart file:
|
|
||||||
fix style: nvt, fix ID: 1
|
|
||||||
fix_modify 1 energy yes
|
|
||||||
timestep 1.0e-3
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 10 check yes
|
|
||||||
run 100
|
|
||||||
All restart file global fix info was re-assigned
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 4.3
|
|
||||||
ghost atom cutoff = 4.3
|
|
||||||
binsize = 2.15, bins = 11 11 11
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair tersoff/mod, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 2.701 | 2.701 | 2.701 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
100 1100.5203 -2308.936 0 -2248.4229 18087.231
|
|
||||||
110 821.82813 -2288.8477 0 -2248.3856 21245.995
|
|
||||||
120 1082.3774 -2304.2287 0 -2248.4366 15467.483
|
|
||||||
130 995.26561 -2296.2957 0 -2248.4145 16341.517
|
|
||||||
140 826.97009 -2283.3692 0 -2248.3897 19123.5
|
|
||||||
150 1048.4178 -2296.0496 0 -2248.4172 15060.312
|
|
||||||
160 1101.7884 -2297.2417 0 -2248.426 15070.879
|
|
||||||
170 859.48562 -2279.1747 0 -2248.383 21416.479
|
|
||||||
180 1041.679 -2289.2303 0 -2248.4038 19572.707
|
|
||||||
190 1278.0514 -2302.2822 0 -2248.4257 16006.173
|
|
||||||
200 1097.0682 -2287.8121 0 -2248.3929 20906.774
|
|
||||||
Loop time of 0.046846 on 4 procs for 100 steps with 512 atoms
|
|
||||||
|
|
||||||
Performance: 184.434 ns/day, 0.130 hours/ns, 2134.653 timesteps/s
|
|
||||||
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.037434 | 0.039142 | 0.041109 | 0.7 | 83.55
|
|
||||||
Neigh | 0.0005877 | 0.00059921 | 0.00061464 | 0.0 | 1.28
|
|
||||||
Comm | 0.0036416 | 0.0055436 | 0.0073476 | 1.8 | 11.83
|
|
||||||
Output | 0.00016212 | 0.00027066 | 0.00059533 | 0.0 | 0.58
|
|
||||||
Modify | 0.00063038 | 0.00065678 | 0.00067234 | 0.0 | 1.40
|
|
||||||
Other | | 0.0006335 | | | 1.35
|
|
||||||
|
|
||||||
Nlocal: 128 ave 131 max 126 min
|
|
||||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
|
||||||
Nghost: 518 ave 525 max 513 min
|
|
||||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 2202 ave 2257 max 2175 min
|
|
||||||
Histogram: 1 1 1 0 0 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 8808
|
|
||||||
Ave neighs/atom = 17.2031
|
|
||||||
Neighbor list builds = 3
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
# Test Tersoff/Mod/C model for Si
|
|
||||||
|
|
||||||
clear
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
read_restart restart.equil
|
|
||||||
restoring atom style atomic from restart
|
|
||||||
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
pair style sw stores no restart info
|
|
||||||
512 atoms
|
|
||||||
newton on on
|
|
||||||
pair_style tersoff/mod/c
|
|
||||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
|
||||||
Reading potential file Si.tersoff.modc with DATE: 2016-11-09
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
fix 1 all nvt temp $t $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 $t 0.1
|
|
||||||
fix 1 all nvt temp 1800 1800 0.1
|
|
||||||
Resetting global fix info from restart file:
|
|
||||||
fix style: nvt, fix ID: 1
|
|
||||||
fix_modify 1 energy yes
|
|
||||||
timestep 1.0e-3
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 10 check yes
|
|
||||||
run 100
|
|
||||||
All restart file global fix info was re-assigned
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 4.20569
|
|
||||||
ghost atom cutoff = 4.20569
|
|
||||||
binsize = 2.10285, bins = 11 11 11
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair tersoff/mod/c, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 2.701 | 2.701 | 2.701 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
100 1100.5203 -2308.5955 0 -2248.0824 20775.991
|
|
||||||
110 813.33618 -2287.9469 0 -2248.04 22564.16
|
|
||||||
120 1100.0902 -2305.051 0 -2248.092 17540.971
|
|
||||||
130 1022.9471 -2297.7384 0 -2248.0801 17985.336
|
|
||||||
140 761.99242 -2278.7251 0 -2248.0345 20462.975
|
|
||||||
150 1053.3973 -2296.1039 0 -2248.081 16130.559
|
|
||||||
160 1089.2622 -2296.1059 0 -2248.0833 15434.234
|
|
||||||
170 776.25788 -2273.4496 0 -2248.0321 20642.702
|
|
||||||
180 1016.1885 -2287.4305 0 -2248.0641 19276.936
|
|
||||||
190 1266.3943 -2301.3675 0 -2248.0865 16199.281
|
|
||||||
200 1012.4185 -2282.134 0 -2248.0423 20795.113
|
|
||||||
Loop time of 0.0840016 on 4 procs for 100 steps with 512 atoms
|
|
||||||
|
|
||||||
Performance: 102.855 ns/day, 0.233 hours/ns, 1190.454 timesteps/s
|
|
||||||
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.068133 | 0.071658 | 0.075315 | 1.0 | 85.31
|
|
||||||
Neigh | 0.00057864 | 0.00058872 | 0.00060058 | 0.0 | 0.70
|
|
||||||
Comm | 0.0049844 | 0.008617 | 0.012086 | 2.8 | 10.26
|
|
||||||
Output | 0.0001626 | 0.00027418 | 0.00060463 | 0.0 | 0.33
|
|
||||||
Modify | 0.00070477 | 0.0011689 | 0.0022428 | 1.8 | 1.39
|
|
||||||
Other | | 0.001694 | | | 2.02
|
|
||||||
|
|
||||||
Nlocal: 128 ave 129 max 127 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
||||||
Nghost: 489.75 ave 501 max 481 min
|
|
||||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 2094.5 ave 2121 max 2060 min
|
|
||||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
|
||||||
|
|
||||||
Total # of neighbors = 8378
|
|
||||||
Ave neighs/atom = 16.3633
|
|
||||||
Neighbor list builds = 3
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
547
examples/threebody/log.31Dec20.threebody.g++.1
Normal file
547
examples/threebody/log.31Dec20.threebody.g++.1
Normal file
@ -0,0 +1,547 @@
|
|||||||
|
LAMMPS (30 Nov 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Simple regression tests for threebody potentials
|
||||||
|
|
||||||
|
# NOTE: These are not intended to represent real materials
|
||||||
|
|
||||||
|
units metal
|
||||||
|
|
||||||
|
atom_style atomic
|
||||||
|
atom_modify map array
|
||||||
|
boundary p p p
|
||||||
|
atom_modify sort 0 0.0
|
||||||
|
|
||||||
|
# temperature
|
||||||
|
|
||||||
|
variable t equal 1800.0
|
||||||
|
|
||||||
|
# cubic diamond unit cell
|
||||||
|
|
||||||
|
variable a equal 5.431
|
||||||
|
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||||
|
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||||
|
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
|
||||||
|
|
||||||
|
region myreg block 0 4 0 4 0 4
|
||||||
|
|
||||||
|
create_box 8 myreg
|
||||||
|
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
||||||
|
Created 512 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass * 28.06
|
||||||
|
|
||||||
|
velocity all create $t 5287287 loop geom
|
||||||
|
velocity all create 1800 5287287 loop geom
|
||||||
|
|
||||||
|
# Equilibrate using Stillinger-Weber model for silicon
|
||||||
|
|
||||||
|
pair_style sw
|
||||||
|
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
|
||||||
|
Reading sw potential file Si.sw with DATE: 2007-06-11
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
fix 1 all nvt temp $t $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 1800 0.1
|
||||||
|
fix_modify 1 energy yes
|
||||||
|
timestep 1.0e-3
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 10 check yes
|
||||||
|
run 100
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 4.77118
|
||||||
|
ghost atom cutoff = 4.77118
|
||||||
|
binsize = 2.38559, bins = 10 10 10
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair sw, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.983 | 2.983 | 2.983 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1800 -2220.3392 0 -2101.4457 12358.626
|
||||||
|
10 1006.0192 -2167.7053 0 -2101.3286 13892.426
|
||||||
|
20 588.26396 -2139.7132 0 -2101.3117 11295.566
|
||||||
|
30 990.55956 -2165.2164 0 -2101.3931 6279.0239
|
||||||
|
40 700.12917 -2144.4279 0 -2101.3427 5594.2388
|
||||||
|
50 523.64239 -2131.7796 0 -2101.3122 6013.0994
|
||||||
|
60 989.47092 -2161.3716 0 -2101.3839 5819.2688
|
||||||
|
70 877.27433 -2152.4432 0 -2101.3461 9116.6569
|
||||||
|
80 800.80221 -2146.1371 0 -2101.313 11995.66
|
||||||
|
90 1293.9689 -2176.9021 0 -2101.3848 11692.45
|
||||||
|
100 1112.9699 -2162.7259 0 -2101.3478 12263.758
|
||||||
|
Loop time of 0.092666 on 1 procs for 100 steps with 512 atoms
|
||||||
|
|
||||||
|
Performance: 93.238 ns/day, 0.257 hours/ns, 1079.144 timesteps/s
|
||||||
|
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.089633 | 0.089633 | 0.089633 | 0.0 | 96.73
|
||||||
|
Neigh | 0.001474 | 0.001474 | 0.001474 | 0.0 | 1.59
|
||||||
|
Comm | 0.00041 | 0.00041 | 0.00041 | 0.0 | 0.44
|
||||||
|
Output | 0.000153 | 0.000153 | 0.000153 | 0.0 | 0.17
|
||||||
|
Modify | 0.000782 | 0.000782 | 0.000782 | 0.0 | 0.84
|
||||||
|
Other | | 0.000214 | | | 0.23
|
||||||
|
|
||||||
|
Nlocal: 512.000 ave 512 max 512 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1017.00 ave 1017 max 1017 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 13988.0 ave 13988 max 13988 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 13988
|
||||||
|
Ave neighs/atom = 27.320312
|
||||||
|
Neighbor list builds = 2
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_restart restart.equil
|
||||||
|
System init for write_restart ...
|
||||||
|
|
||||||
|
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
|
||||||
|
|
||||||
|
clear
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
read_restart restart.equil
|
||||||
|
Reading restart file ...
|
||||||
|
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||||
|
restoring atom style atomic from restart
|
||||||
|
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
pair style sw stores no restart info
|
||||||
|
512 atoms
|
||||||
|
read_restart CPU = 0.002 seconds
|
||||||
|
|
||||||
|
pair_style sw
|
||||||
|
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
|
||||||
|
Reading sw potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
fix 1 all nvt temp $t $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 1800 0.1
|
||||||
|
Resetting global fix info from restart file:
|
||||||
|
fix style: nvt, fix ID: 1
|
||||||
|
fix_modify 1 energy yes
|
||||||
|
timestep 1.0e-3
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 10 check yes
|
||||||
|
run 100
|
||||||
|
All restart file global fix info was re-assigned
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 5.6320004
|
||||||
|
ghost atom cutoff = 5.6320004
|
||||||
|
binsize = 2.8160002, bins = 8 8 8
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair sw, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.001 | 3.001 | 3.001 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
100 1112.9699 -625.76163 0 -564.38354 462129.66
|
||||||
|
110 1502.8461 -649.55768 0 -564.45814 463413.45
|
||||||
|
120 1926.4523 -674.71265 0 -564.53612 486338.88
|
||||||
|
130 1152.6663 -621.47264 0 -564.37203 514892.2
|
||||||
|
140 1762.244 -659.86941 0 -564.4985 488159.88
|
||||||
|
150 1767.8665 -657.67178 0 -564.48386 466721.31
|
||||||
|
160 1075.2874 -610.12809 0 -564.36709 470151.9
|
||||||
|
170 1697.9313 -649.3684 0 -564.47207 467953.71
|
||||||
|
180 1856.1197 -657.14338 0 -564.48754 488372.27
|
||||||
|
190 1346.1107 -621.42431 0 -564.38065 511750.04
|
||||||
|
200 1919.5266 -657.26587 0 -564.47797 488684.56
|
||||||
|
Loop time of 0.289193 on 1 procs for 100 steps with 512 atoms
|
||||||
|
|
||||||
|
Performance: 29.876 ns/day, 0.803 hours/ns, 345.790 timesteps/s
|
||||||
|
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.28463 | 0.28463 | 0.28463 | 0.0 | 98.42
|
||||||
|
Neigh | 0.002821 | 0.002821 | 0.002821 | 0.0 | 0.98
|
||||||
|
Comm | 0.000605 | 0.000605 | 0.000605 | 0.0 | 0.21
|
||||||
|
Output | 0.000176 | 0.000176 | 0.000176 | 0.0 | 0.06
|
||||||
|
Modify | 0.000769 | 0.000769 | 0.000769 | 0.0 | 0.27
|
||||||
|
Other | | 0.000188 | | | 0.07
|
||||||
|
|
||||||
|
Nlocal: 512.000 ave 512 max 512 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1428.00 ave 1428 max 1428 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 17344.0 ave 17344 max 17344 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 17344
|
||||||
|
Ave neighs/atom = 33.875000
|
||||||
|
Neighbor list builds = 3
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
# Test Vashishta model for In/P
|
||||||
|
|
||||||
|
clear
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
read_restart restart.equil
|
||||||
|
Reading restart file ...
|
||||||
|
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||||
|
restoring atom style atomic from restart
|
||||||
|
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
pair style sw stores no restart info
|
||||||
|
512 atoms
|
||||||
|
read_restart CPU = 0.001 seconds
|
||||||
|
|
||||||
|
pair_style vashishta
|
||||||
|
pair_coeff * * InP.vashishta In In In In P P P P
|
||||||
|
Reading vashishta potential file InP.vashishta with DATE: 2015-10-14
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
fix 1 all nvt temp $t $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 1800 0.1
|
||||||
|
Resetting global fix info from restart file:
|
||||||
|
fix style: nvt, fix ID: 1
|
||||||
|
fix_modify 1 energy yes
|
||||||
|
timestep 1.0e-3
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 10 check yes
|
||||||
|
run 100
|
||||||
|
All restart file global fix info was re-assigned
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 7
|
||||||
|
ghost atom cutoff = 7
|
||||||
|
binsize = 3.5, bins = 7 7 7
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair vashishta, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
100 1112.9699 -1497.2988 0 -1435.9207 355619.19
|
||||||
|
110 1250.545 -1504.5795 0 -1435.9786 345188.52
|
||||||
|
120 1360.2275 -1509.3443 0 -1435.9801 333306.3
|
||||||
|
130 1066.4516 -1487.9076 0 -1435.9076 334465.11
|
||||||
|
140 1481.0477 -1513.0511 0 -1435.988 308725.1
|
||||||
|
150 1216.1167 -1493.0774 0 -1435.9217 304249.09
|
||||||
|
160 1211.4398 -1490.7459 0 -1435.9164 288897.09
|
||||||
|
170 1542.2025 -1510.0774 0 -1435.9608 260104.14
|
||||||
|
180 1302.9041 -1491.7765 0 -1435.8971 249514.04
|
||||||
|
190 1332.3326 -1491.5271 0 -1435.9213 227537.99
|
||||||
|
200 1352.1813 -1490.4513 0 -1435.9049 207626.42
|
||||||
|
Loop time of 0.126684 on 1 procs for 100 steps with 512 atoms
|
||||||
|
|
||||||
|
Performance: 68.201 ns/day, 0.352 hours/ns, 789.366 timesteps/s
|
||||||
|
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.11981 | 0.11981 | 0.11981 | 0.0 | 94.57
|
||||||
|
Neigh | 0.004903 | 0.004903 | 0.004903 | 0.0 | 3.87
|
||||||
|
Comm | 0.000846 | 0.000846 | 0.000846 | 0.0 | 0.67
|
||||||
|
Output | 0.000145 | 0.000145 | 0.000145 | 0.0 | 0.11
|
||||||
|
Modify | 0.000772 | 0.000772 | 0.000772 | 0.0 | 0.61
|
||||||
|
Other | | 0.000207 | | | 0.16
|
||||||
|
|
||||||
|
Nlocal: 512.000 ave 512 max 512 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1838.00 ave 1838 max 1838 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 36482.0 ave 36482 max 36482 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 36482
|
||||||
|
Ave neighs/atom = 71.253906
|
||||||
|
Neighbor list builds = 4
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
# Test Tersoff model for B/N/C
|
||||||
|
|
||||||
|
clear
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
read_restart restart.equil
|
||||||
|
Reading restart file ...
|
||||||
|
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||||
|
restoring atom style atomic from restart
|
||||||
|
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
pair style sw stores no restart info
|
||||||
|
512 atoms
|
||||||
|
read_restart CPU = 0.001 seconds
|
||||||
|
|
||||||
|
variable fac equal 0.6
|
||||||
|
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||||
|
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||||
|
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||||
|
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||||
|
Changing box ...
|
||||||
|
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||||
|
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||||
|
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||||
|
|
||||||
|
pair_style tersoff
|
||||||
|
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||||
|
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
fix 1 all nvt temp $t $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 1800 0.1
|
||||||
|
Resetting global fix info from restart file:
|
||||||
|
fix style: nvt, fix ID: 1
|
||||||
|
fix_modify 1 energy yes
|
||||||
|
timestep 1.0e-3
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 10 check yes
|
||||||
|
run 100
|
||||||
|
All restart file global fix info was re-assigned
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 3.1
|
||||||
|
ghost atom cutoff = 3.1
|
||||||
|
binsize = 1.55, bins = 9 9 9
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair tersoff, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.982 | 2.982 | 2.982 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
100 1112.9699 -3259.7676 0 -3198.3895 1912461.3
|
||||||
|
110 1772.8268 -3301.5479 0 -3198.8218 1885295.6
|
||||||
|
120 1169.7287 -3258.74 0 -3197.9294 1898705.2
|
||||||
|
130 1308.5623 -3265.1338 0 -3197.5922 1894187.5
|
||||||
|
140 1486.0361 -3274.951 0 -3197.776 1871927.6
|
||||||
|
150 1419.0362 -3267.7302 0 -3197.2296 1925234.6
|
||||||
|
160 1196.6689 -3250.1492 0 -3196.7078 1902235.1
|
||||||
|
170 1707.5846 -3281.7658 0 -3196.9721 1863047.3
|
||||||
|
180 1337.4358 -3254.9844 0 -3196.8222 1880420.9
|
||||||
|
190 1441.8052 -3259.0364 0 -3196.3556 1904512.1
|
||||||
|
200 1569.0317 -3265.0089 0 -3196.3328 1899462.7
|
||||||
|
Loop time of 0.114312 on 1 procs for 100 steps with 512 atoms
|
||||||
|
|
||||||
|
Performance: 75.583 ns/day, 0.318 hours/ns, 874.799 timesteps/s
|
||||||
|
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.1121 | 0.1121 | 0.1121 | 0.0 | 98.06
|
||||||
|
Neigh | 0.000773 | 0.000773 | 0.000773 | 0.0 | 0.68
|
||||||
|
Comm | 0.000415 | 0.000415 | 0.000415 | 0.0 | 0.36
|
||||||
|
Output | 0.000136 | 0.000136 | 0.000136 | 0.0 | 0.12
|
||||||
|
Modify | 0.000703 | 0.000703 | 0.000703 | 0.0 | 0.61
|
||||||
|
Other | | 0.000186 | | | 0.16
|
||||||
|
|
||||||
|
Nlocal: 512.000 ave 512 max 512 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1028.00 ave 1028 max 1028 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 14604.0 ave 14604 max 14604 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 14604
|
||||||
|
Ave neighs/atom = 28.523438
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
# Test Tersoff/Mod model for Si
|
||||||
|
|
||||||
|
clear
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
read_restart restart.equil
|
||||||
|
Reading restart file ...
|
||||||
|
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||||
|
restoring atom style atomic from restart
|
||||||
|
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
pair style sw stores no restart info
|
||||||
|
512 atoms
|
||||||
|
read_restart CPU = 0.001 seconds
|
||||||
|
|
||||||
|
pair_style tersoff/mod
|
||||||
|
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||||
|
Reading tersoff/mod potential file Si.tersoff.mod with DATE: 2013-07-26
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
fix 1 all nvt temp $t $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 1800 0.1
|
||||||
|
Resetting global fix info from restart file:
|
||||||
|
fix style: nvt, fix ID: 1
|
||||||
|
fix_modify 1 energy yes
|
||||||
|
timestep 1.0e-3
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 10 check yes
|
||||||
|
run 100
|
||||||
|
All restart file global fix info was re-assigned
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 4.3
|
||||||
|
ghost atom cutoff = 4.3
|
||||||
|
binsize = 2.15, bins = 11 11 11
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair tersoff/mod, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.986 | 2.986 | 2.986 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
100 1112.9699 -2309.6047 0 -2248.2266 17662.891
|
||||||
|
110 835.77436 -2289.6119 0 -2248.1918 19964.211
|
||||||
|
120 1067.0735 -2303.0587 0 -2248.2414 13767.101
|
||||||
|
130 957.60664 -2293.7047 0 -2248.2139 14850.338
|
||||||
|
140 865.12471 -2285.7774 0 -2248.1971 17101.553
|
||||||
|
150 1104.7368 -2299.5468 0 -2248.2286 13031.988
|
||||||
|
160 1077.1682 -2295.3841 0 -2248.2227 13615.019
|
||||||
|
170 843.8591 -2277.9713 0 -2248.1911 18966.532
|
||||||
|
180 1008.7412 -2286.922 0 -2248.2075 17275.649
|
||||||
|
190 1237.9346 -2299.5487 0 -2248.2305 14334.006
|
||||||
|
200 1060.2161 -2285.3352 0 -2248.1952 18999.834
|
||||||
|
Loop time of 0.12412 on 1 procs for 100 steps with 512 atoms
|
||||||
|
|
||||||
|
Performance: 69.610 ns/day, 0.345 hours/ns, 805.672 timesteps/s
|
||||||
|
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.12079 | 0.12079 | 0.12079 | 0.0 | 97.32
|
||||||
|
Neigh | 0.001821 | 0.001821 | 0.001821 | 0.0 | 1.47
|
||||||
|
Comm | 0.000407 | 0.000407 | 0.000407 | 0.0 | 0.33
|
||||||
|
Output | 0.000159 | 0.000159 | 0.000159 | 0.0 | 0.13
|
||||||
|
Modify | 0.000736 | 0.000736 | 0.000736 | 0.0 | 0.59
|
||||||
|
Other | | 0.000203 | | | 0.16
|
||||||
|
|
||||||
|
Nlocal: 512.000 ave 512 max 512 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1007.00 ave 1007 max 1007 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 8884.00 ave 8884 max 8884 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 8884
|
||||||
|
Ave neighs/atom = 17.351562
|
||||||
|
Neighbor list builds = 3
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
# Test Tersoff/Mod/C model for Si
|
||||||
|
|
||||||
|
clear
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
read_restart restart.equil
|
||||||
|
Reading restart file ...
|
||||||
|
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||||
|
restoring atom style atomic from restart
|
||||||
|
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
pair style sw stores no restart info
|
||||||
|
512 atoms
|
||||||
|
read_restart CPU = 0.001 seconds
|
||||||
|
newton on on
|
||||||
|
pair_style tersoff/mod/c
|
||||||
|
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||||
|
Reading tersoff/mod/c potential file Si.tersoff.modc with DATE: 2016-11-09
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
fix 1 all nvt temp $t $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 1800 0.1
|
||||||
|
Resetting global fix info from restart file:
|
||||||
|
fix style: nvt, fix ID: 1
|
||||||
|
fix_modify 1 energy yes
|
||||||
|
timestep 1.0e-3
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 10 check yes
|
||||||
|
run 100
|
||||||
|
All restart file global fix info was re-assigned
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 4.205694
|
||||||
|
ghost atom cutoff = 4.205694
|
||||||
|
binsize = 2.102847, bins = 11 11 11
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair tersoff/mod/c, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.980 | 2.980 | 2.980 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
100 1112.9699 -2309.1331 0 -2247.755 20346.718
|
||||||
|
110 831.93715 -2288.8853 0 -2247.7187 21758.195
|
||||||
|
120 1077.6698 -2303.2846 0 -2247.7693 16036.053
|
||||||
|
130 972.43247 -2294.1847 0 -2247.7467 16614.835
|
||||||
|
140 815.76148 -2282.0495 0 -2247.7194 18310.116
|
||||||
|
150 1072.7096 -2297.0491 0 -2247.7574 13896.767
|
||||||
|
160 1061.8824 -2294.0028 0 -2247.7522 13663.179
|
||||||
|
170 787.17244 -2273.8946 0 -2247.7175 18586.606
|
||||||
|
180 932.5662 -2281.6828 0 -2247.7315 18154.167
|
||||||
|
190 1205.7299 -2297.2769 0 -2247.7608 14504.136
|
||||||
|
200 1022.5285 -2282.7039 0 -2247.7245 18710.495
|
||||||
|
Loop time of 0.12973 on 1 procs for 100 steps with 512 atoms
|
||||||
|
|
||||||
|
Performance: 66.600 ns/day, 0.360 hours/ns, 770.832 timesteps/s
|
||||||
|
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.12643 | 0.12643 | 0.12643 | 0.0 | 97.45
|
||||||
|
Neigh | 0.001798 | 0.001798 | 0.001798 | 0.0 | 1.39
|
||||||
|
Comm | 0.000421 | 0.000421 | 0.000421 | 0.0 | 0.32
|
||||||
|
Output | 0.00016 | 0.00016 | 0.00016 | 0.0 | 0.12
|
||||||
|
Modify | 0.000733 | 0.000733 | 0.000733 | 0.0 | 0.57
|
||||||
|
Other | | 0.000192 | | | 0.15
|
||||||
|
|
||||||
|
Nlocal: 512.000 ave 512 max 512 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 958.000 ave 958 max 958 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 8416.00 ave 8416 max 8416 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 8416
|
||||||
|
Ave neighs/atom = 16.437500
|
||||||
|
Neighbor list builds = 3
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
547
examples/threebody/log.31Dec20.threebody.g++.4
Normal file
547
examples/threebody/log.31Dec20.threebody.g++.4
Normal file
@ -0,0 +1,547 @@
|
|||||||
|
LAMMPS (30 Nov 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Simple regression tests for threebody potentials
|
||||||
|
|
||||||
|
# NOTE: These are not intended to represent real materials
|
||||||
|
|
||||||
|
units metal
|
||||||
|
|
||||||
|
atom_style atomic
|
||||||
|
atom_modify map array
|
||||||
|
boundary p p p
|
||||||
|
atom_modify sort 0 0.0
|
||||||
|
|
||||||
|
# temperature
|
||||||
|
|
||||||
|
variable t equal 1800.0
|
||||||
|
|
||||||
|
# cubic diamond unit cell
|
||||||
|
|
||||||
|
variable a equal 5.431
|
||||||
|
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||||
|
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||||
|
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
|
||||||
|
|
||||||
|
region myreg block 0 4 0 4 0 4
|
||||||
|
|
||||||
|
create_box 8 myreg
|
||||||
|
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
||||||
|
Created 512 atoms
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
mass * 28.06
|
||||||
|
|
||||||
|
velocity all create $t 5287287 loop geom
|
||||||
|
velocity all create 1800 5287287 loop geom
|
||||||
|
|
||||||
|
# Equilibrate using Stillinger-Weber model for silicon
|
||||||
|
|
||||||
|
pair_style sw
|
||||||
|
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
|
||||||
|
Reading sw potential file Si.sw with DATE: 2007-06-11
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
fix 1 all nvt temp $t $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 1800 0.1
|
||||||
|
fix_modify 1 energy yes
|
||||||
|
timestep 1.0e-3
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 10 check yes
|
||||||
|
run 100
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 4.77118
|
||||||
|
ghost atom cutoff = 4.77118
|
||||||
|
binsize = 2.38559, bins = 10 10 10
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair sw, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.958 | 2.958 | 2.958 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1800 -2220.3392 0 -2101.4457 12358.626
|
||||||
|
10 1006.0192 -2167.7053 0 -2101.3286 13892.426
|
||||||
|
20 588.26396 -2139.7132 0 -2101.3117 11295.566
|
||||||
|
30 990.55956 -2165.2164 0 -2101.3931 6279.0239
|
||||||
|
40 700.12917 -2144.4279 0 -2101.3427 5594.2388
|
||||||
|
50 523.64239 -2131.7796 0 -2101.3122 6013.0994
|
||||||
|
60 989.47092 -2161.3716 0 -2101.3839 5819.2688
|
||||||
|
70 877.27433 -2152.4432 0 -2101.3461 9116.6569
|
||||||
|
80 800.80221 -2146.1371 0 -2101.313 11995.66
|
||||||
|
90 1293.9689 -2176.9021 0 -2101.3848 11692.45
|
||||||
|
100 1112.9699 -2162.7259 0 -2101.3478 12263.758
|
||||||
|
Loop time of 0.0284905 on 4 procs for 100 steps with 512 atoms
|
||||||
|
|
||||||
|
Performance: 303.259 ns/day, 0.079 hours/ns, 3509.942 timesteps/s
|
||||||
|
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.022257 | 0.023383 | 0.025192 | 0.7 | 82.07
|
||||||
|
Neigh | 0.00036 | 0.00037475 | 0.000387 | 0.0 | 1.32
|
||||||
|
Comm | 0.002084 | 0.0039075 | 0.005034 | 1.8 | 13.72
|
||||||
|
Output | 9.9e-05 | 0.00011525 | 0.00016 | 0.0 | 0.40
|
||||||
|
Modify | 0.000428 | 0.00043675 | 0.000443 | 0.0 | 1.53
|
||||||
|
Other | | 0.0002728 | | | 0.96
|
||||||
|
|
||||||
|
Nlocal: 128.000 ave 132 max 125 min
|
||||||
|
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||||
|
Nghost: 525.000 ave 528 max 521 min
|
||||||
|
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 3497.00 ave 3619 max 3397 min
|
||||||
|
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 13988
|
||||||
|
Ave neighs/atom = 27.320312
|
||||||
|
Neighbor list builds = 2
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_restart restart.equil
|
||||||
|
System init for write_restart ...
|
||||||
|
|
||||||
|
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
|
||||||
|
|
||||||
|
clear
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
read_restart restart.equil
|
||||||
|
Reading restart file ...
|
||||||
|
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||||
|
restoring atom style atomic from restart
|
||||||
|
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
pair style sw stores no restart info
|
||||||
|
512 atoms
|
||||||
|
read_restart CPU = 0.000 seconds
|
||||||
|
|
||||||
|
pair_style sw
|
||||||
|
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
|
||||||
|
Reading sw potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
fix 1 all nvt temp $t $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 1800 0.1
|
||||||
|
Resetting global fix info from restart file:
|
||||||
|
fix style: nvt, fix ID: 1
|
||||||
|
fix_modify 1 energy yes
|
||||||
|
timestep 1.0e-3
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 10 check yes
|
||||||
|
run 100
|
||||||
|
All restart file global fix info was re-assigned
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 5.6320004
|
||||||
|
ghost atom cutoff = 5.6320004
|
||||||
|
binsize = 2.8160002, bins = 8 8 8
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair sw, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.967 | 2.967 | 2.968 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
100 1112.9699 -625.76163 0 -564.38354 462129.66
|
||||||
|
110 1502.8461 -649.55768 0 -564.45814 463413.45
|
||||||
|
120 1926.4523 -674.71265 0 -564.53613 486338.88
|
||||||
|
130 1152.6663 -621.47265 0 -564.37203 514892.19
|
||||||
|
140 1762.244 -659.86941 0 -564.4985 488159.88
|
||||||
|
150 1767.8665 -657.67179 0 -564.48386 466721.31
|
||||||
|
160 1075.2874 -610.1281 0 -564.36709 470151.9
|
||||||
|
170 1697.9313 -649.3684 0 -564.47208 467953.7
|
||||||
|
180 1856.1197 -657.14338 0 -564.48754 488372.26
|
||||||
|
190 1346.1107 -621.42432 0 -564.38065 511750.03
|
||||||
|
200 1919.5266 -657.26587 0 -564.47797 488684.56
|
||||||
|
Loop time of 0.084576 on 4 procs for 100 steps with 512 atoms
|
||||||
|
|
||||||
|
Performance: 102.157 ns/day, 0.235 hours/ns, 1182.369 timesteps/s
|
||||||
|
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.072089 | 0.074912 | 0.076672 | 0.7 | 88.57
|
||||||
|
Neigh | 0.000745 | 0.0008125 | 0.000883 | 0.0 | 0.96
|
||||||
|
Comm | 0.006054 | 0.0077975 | 0.010598 | 2.1 | 9.22
|
||||||
|
Output | 0.000129 | 0.00015525 | 0.000219 | 0.0 | 0.18
|
||||||
|
Modify | 0.000523 | 0.000578 | 0.000641 | 0.0 | 0.68
|
||||||
|
Other | | 0.0003213 | | | 0.38
|
||||||
|
|
||||||
|
Nlocal: 128.000 ave 135 max 122 min
|
||||||
|
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||||
|
Nghost: 759.750 ave 770 max 751 min
|
||||||
|
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 4336.00 ave 4563 max 4128 min
|
||||||
|
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 17344
|
||||||
|
Ave neighs/atom = 33.875000
|
||||||
|
Neighbor list builds = 3
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
# Test Vashishta model for In/P
|
||||||
|
|
||||||
|
clear
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
read_restart restart.equil
|
||||||
|
Reading restart file ...
|
||||||
|
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||||
|
restoring atom style atomic from restart
|
||||||
|
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
pair style sw stores no restart info
|
||||||
|
512 atoms
|
||||||
|
read_restart CPU = 0.001 seconds
|
||||||
|
|
||||||
|
pair_style vashishta
|
||||||
|
pair_coeff * * InP.vashishta In In In In P P P P
|
||||||
|
Reading vashishta potential file InP.vashishta with DATE: 2015-10-14
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
fix 1 all nvt temp $t $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 1800 0.1
|
||||||
|
Resetting global fix info from restart file:
|
||||||
|
fix style: nvt, fix ID: 1
|
||||||
|
fix_modify 1 energy yes
|
||||||
|
timestep 1.0e-3
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 10 check yes
|
||||||
|
run 100
|
||||||
|
All restart file global fix info was re-assigned
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 7
|
||||||
|
ghost atom cutoff = 7
|
||||||
|
binsize = 3.5, bins = 7 7 7
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair vashishta, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.988 | 2.988 | 2.988 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
100 1112.9699 -1497.2988 0 -1435.9207 355619.19
|
||||||
|
110 1250.545 -1504.5795 0 -1435.9786 345188.52
|
||||||
|
120 1360.2275 -1509.3443 0 -1435.9801 333306.3
|
||||||
|
130 1066.4516 -1487.9076 0 -1435.9076 334465.11
|
||||||
|
140 1481.0477 -1513.0511 0 -1435.988 308725.1
|
||||||
|
150 1216.1167 -1493.0774 0 -1435.9217 304249.09
|
||||||
|
160 1211.4398 -1490.7459 0 -1435.9164 288897.09
|
||||||
|
170 1542.2025 -1510.0774 0 -1435.9608 260104.14
|
||||||
|
180 1302.9041 -1491.7765 0 -1435.8971 249514.04
|
||||||
|
190 1332.3326 -1491.5271 0 -1435.9213 227537.99
|
||||||
|
200 1352.1813 -1490.4513 0 -1435.9049 207626.42
|
||||||
|
Loop time of 0.0404882 on 4 procs for 100 steps with 512 atoms
|
||||||
|
|
||||||
|
Performance: 213.395 ns/day, 0.112 hours/ns, 2469.852 timesteps/s
|
||||||
|
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.032713 | 0.033094 | 0.033544 | 0.2 | 81.74
|
||||||
|
Neigh | 0.001251 | 0.0012875 | 0.001308 | 0.1 | 3.18
|
||||||
|
Comm | 0.004788 | 0.005204 | 0.00557 | 0.4 | 12.85
|
||||||
|
Output | 0.000123 | 0.0001385 | 0.000182 | 0.0 | 0.34
|
||||||
|
Modify | 0.000492 | 0.00050725 | 0.000533 | 0.0 | 1.25
|
||||||
|
Other | | 0.0002565 | | | 0.63
|
||||||
|
|
||||||
|
Nlocal: 128.000 ave 131 max 124 min
|
||||||
|
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||||
|
Nghost: 1013.25 ave 1025 max 1002 min
|
||||||
|
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 9120.50 ave 9356 max 8868 min
|
||||||
|
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 36482
|
||||||
|
Ave neighs/atom = 71.253906
|
||||||
|
Neighbor list builds = 4
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
# Test Tersoff model for B/N/C
|
||||||
|
|
||||||
|
clear
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
read_restart restart.equil
|
||||||
|
Reading restart file ...
|
||||||
|
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||||
|
restoring atom style atomic from restart
|
||||||
|
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
pair style sw stores no restart info
|
||||||
|
512 atoms
|
||||||
|
read_restart CPU = 0.001 seconds
|
||||||
|
|
||||||
|
variable fac equal 0.6
|
||||||
|
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||||
|
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||||
|
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||||
|
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||||
|
Changing box ...
|
||||||
|
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||||
|
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||||
|
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||||
|
|
||||||
|
pair_style tersoff
|
||||||
|
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||||
|
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
fix 1 all nvt temp $t $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 1800 0.1
|
||||||
|
Resetting global fix info from restart file:
|
||||||
|
fix style: nvt, fix ID: 1
|
||||||
|
fix_modify 1 energy yes
|
||||||
|
timestep 1.0e-3
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 10 check yes
|
||||||
|
run 100
|
||||||
|
All restart file global fix info was re-assigned
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 3.1
|
||||||
|
ghost atom cutoff = 3.1
|
||||||
|
binsize = 1.55, bins = 9 9 9
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair tersoff, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.948 | 2.948 | 2.948 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
100 1112.9699 -3259.7676 0 -3198.3895 1912461.3
|
||||||
|
110 1772.8268 -3301.5479 0 -3198.8218 1885295.6
|
||||||
|
120 1169.7287 -3258.74 0 -3197.9294 1898705.2
|
||||||
|
130 1308.5623 -3265.1338 0 -3197.5922 1894187.5
|
||||||
|
140 1486.0361 -3274.951 0 -3197.776 1871927.6
|
||||||
|
150 1419.0362 -3267.7302 0 -3197.2296 1925234.6
|
||||||
|
160 1196.6689 -3250.1492 0 -3196.7078 1902235.1
|
||||||
|
170 1707.5846 -3281.7658 0 -3196.9721 1863047.3
|
||||||
|
180 1337.4358 -3254.9844 0 -3196.8222 1880420.9
|
||||||
|
190 1441.8052 -3259.0364 0 -3196.3556 1904512.1
|
||||||
|
200 1569.0317 -3265.0089 0 -3196.3328 1899462.7
|
||||||
|
Loop time of 0.03452 on 4 procs for 100 steps with 512 atoms
|
||||||
|
|
||||||
|
Performance: 250.290 ns/day, 0.096 hours/ns, 2896.871 timesteps/s
|
||||||
|
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.029269 | 0.029729 | 0.030688 | 0.3 | 86.12
|
||||||
|
Neigh | 0.000203 | 0.00023375 | 0.000271 | 0.0 | 0.68
|
||||||
|
Comm | 0.00275 | 0.0036492 | 0.004132 | 0.9 | 10.57
|
||||||
|
Output | 0.000104 | 0.000121 | 0.000165 | 0.0 | 0.35
|
||||||
|
Modify | 0.000456 | 0.0004605 | 0.000463 | 0.0 | 1.33
|
||||||
|
Other | | 0.000326 | | | 0.94
|
||||||
|
|
||||||
|
Nlocal: 128.000 ave 132 max 123 min
|
||||||
|
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||||
|
Nghost: 529.500 ave 533 max 524 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 3651.00 ave 3783 max 3494 min
|
||||||
|
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 14604
|
||||||
|
Ave neighs/atom = 28.523438
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
# Test Tersoff/Mod model for Si
|
||||||
|
|
||||||
|
clear
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
read_restart restart.equil
|
||||||
|
Reading restart file ...
|
||||||
|
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||||
|
restoring atom style atomic from restart
|
||||||
|
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
pair style sw stores no restart info
|
||||||
|
512 atoms
|
||||||
|
read_restart CPU = 0.001 seconds
|
||||||
|
|
||||||
|
pair_style tersoff/mod
|
||||||
|
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||||
|
Reading tersoff/mod potential file Si.tersoff.mod with DATE: 2013-07-26
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
fix 1 all nvt temp $t $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 1800 0.1
|
||||||
|
Resetting global fix info from restart file:
|
||||||
|
fix style: nvt, fix ID: 1
|
||||||
|
fix_modify 1 energy yes
|
||||||
|
timestep 1.0e-3
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 10 check yes
|
||||||
|
run 100
|
||||||
|
All restart file global fix info was re-assigned
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 4.3
|
||||||
|
ghost atom cutoff = 4.3
|
||||||
|
binsize = 2.15, bins = 11 11 11
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair tersoff/mod, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.950 | 2.950 | 2.950 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
100 1112.9699 -2309.6047 0 -2248.2266 17662.891
|
||||||
|
110 835.77436 -2289.6119 0 -2248.1918 19964.211
|
||||||
|
120 1067.0735 -2303.0587 0 -2248.2414 13767.101
|
||||||
|
130 957.60664 -2293.7047 0 -2248.2139 14850.338
|
||||||
|
140 865.12471 -2285.7774 0 -2248.1971 17101.553
|
||||||
|
150 1104.7368 -2299.5468 0 -2248.2286 13031.988
|
||||||
|
160 1077.1682 -2295.3841 0 -2248.2227 13615.019
|
||||||
|
170 843.8591 -2277.9713 0 -2248.1911 18966.532
|
||||||
|
180 1008.7412 -2286.922 0 -2248.2075 17275.649
|
||||||
|
190 1237.9346 -2299.5487 0 -2248.2305 14334.006
|
||||||
|
200 1060.2161 -2285.3352 0 -2248.1952 18999.834
|
||||||
|
Loop time of 0.043388 on 4 procs for 100 steps with 512 atoms
|
||||||
|
|
||||||
|
Performance: 199.133 ns/day, 0.121 hours/ns, 2304.785 timesteps/s
|
||||||
|
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.033874 | 0.036197 | 0.037433 | 0.7 | 83.43
|
||||||
|
Neigh | 0.000538 | 0.00055575 | 0.000575 | 0.0 | 1.28
|
||||||
|
Comm | 0.004381 | 0.0055505 | 0.007783 | 1.8 | 12.79
|
||||||
|
Output | 0.000141 | 0.0001635 | 0.000228 | 0.0 | 0.38
|
||||||
|
Modify | 0.000532 | 0.000615 | 0.000692 | 0.0 | 1.42
|
||||||
|
Other | | 0.000306 | | | 0.71
|
||||||
|
|
||||||
|
Nlocal: 128.000 ave 135 max 121 min
|
||||||
|
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||||
|
Nghost: 515.000 ave 518 max 508 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 1 2
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 2221.00 ave 2328 max 2103 min
|
||||||
|
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 8884
|
||||||
|
Ave neighs/atom = 17.351562
|
||||||
|
Neighbor list builds = 3
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
# Test Tersoff/Mod/C model for Si
|
||||||
|
|
||||||
|
clear
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
read_restart restart.equil
|
||||||
|
Reading restart file ...
|
||||||
|
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||||
|
restoring atom style atomic from restart
|
||||||
|
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
pair style sw stores no restart info
|
||||||
|
512 atoms
|
||||||
|
read_restart CPU = 0.001 seconds
|
||||||
|
newton on on
|
||||||
|
pair_style tersoff/mod/c
|
||||||
|
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||||
|
Reading tersoff/mod/c potential file Si.tersoff.modc with DATE: 2016-11-09
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
fix 1 all nvt temp $t $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 $t 0.1
|
||||||
|
fix 1 all nvt temp 1800 1800 0.1
|
||||||
|
Resetting global fix info from restart file:
|
||||||
|
fix style: nvt, fix ID: 1
|
||||||
|
fix_modify 1 energy yes
|
||||||
|
timestep 1.0e-3
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 10 check yes
|
||||||
|
run 100
|
||||||
|
All restart file global fix info was re-assigned
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 4.205694
|
||||||
|
ghost atom cutoff = 4.205694
|
||||||
|
binsize = 2.102847, bins = 11 11 11
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair tersoff/mod/c, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.950 | 2.950 | 2.950 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
100 1112.9699 -2309.1331 0 -2247.755 20346.718
|
||||||
|
110 831.93715 -2288.8853 0 -2247.7187 21758.195
|
||||||
|
120 1077.6698 -2303.2846 0 -2247.7693 16036.053
|
||||||
|
130 972.43247 -2294.1847 0 -2247.7467 16614.835
|
||||||
|
140 815.76148 -2282.0495 0 -2247.7194 18310.116
|
||||||
|
150 1072.7096 -2297.0491 0 -2247.7574 13896.767
|
||||||
|
160 1061.8824 -2294.0028 0 -2247.7522 13663.179
|
||||||
|
170 787.17244 -2273.8946 0 -2247.7175 18586.606
|
||||||
|
180 932.5662 -2281.6828 0 -2247.7315 18154.167
|
||||||
|
190 1205.7299 -2297.2769 0 -2247.7608 14504.136
|
||||||
|
200 1022.5285 -2282.7039 0 -2247.7245 18710.495
|
||||||
|
Loop time of 0.0526065 on 4 procs for 100 steps with 512 atoms
|
||||||
|
|
||||||
|
Performance: 164.238 ns/day, 0.146 hours/ns, 1900.906 timesteps/s
|
||||||
|
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.044962 | 0.045875 | 0.046737 | 0.3 | 87.20
|
||||||
|
Neigh | 0.000603 | 0.00062075 | 0.000646 | 0.0 | 1.18
|
||||||
|
Comm | 0.003882 | 0.0047085 | 0.005598 | 1.0 | 8.95
|
||||||
|
Output | 0.000159 | 0.0001995 | 0.000321 | 0.0 | 0.38
|
||||||
|
Modify | 0.000767 | 0.0007775 | 0.000792 | 0.0 | 1.48
|
||||||
|
Other | | 0.0004255 | | | 0.81
|
||||||
|
|
||||||
|
Nlocal: 128.000 ave 131 max 122 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||||
|
Nghost: 483.000 ave 485 max 479 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 2104.00 ave 2169 max 2008 min
|
||||||
|
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 8416
|
||||||
|
Ave neighs/atom = 16.437500
|
||||||
|
Neighbor list builds = 3
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
Reference in New Issue
Block a user