5302074b3f
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10709 f3b2605a-c512-4ea7-a41b-209d697bcdaa
403 lines
16 KiB
Plaintext
403 lines
16 KiB
Plaintext
LAMMPS (30 Aug 2013)
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units real
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atom_style atomic
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variable lattice_constant equal 5.256227487
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variable c equal 6
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variable L equal $c*${lattice_constant}
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variable L equal 6*${lattice_constant}
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variable L equal 6*5.2562274870000003091
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variable d equal 0.005
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variable s equal 1.005
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variable is equal 1.0/$s
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variable is equal 1.0/1.0049999999999998934
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variable V0 equal $L*$L*3*${lattice_constant}
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variable V0 equal 31.537364922000001854*$L*3*${lattice_constant}
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variable V0 equal 31.537364922000001854*31.537364922000001854*3*${lattice_constant}
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variable V0 equal 31.537364922000001854*31.537364922000001854*3*5.2562274870000003091
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# create system
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lattice fcc ${lattice_constant} origin 0.25 0.25 0.25
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lattice fcc 5.2562274870000003091 origin 0.25 0.25 0.25
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Lattice spacing in x,y,z = 5.25623 5.25623 5.25623
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region box block 0 $c 0 $c 0 3
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region box block 0 6 0 $c 0 3
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region box block 0 6 0 6 0 3
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boundary p p p
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create_box 1 box
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Created orthogonal box = (0 0 0) to (31.5374 31.5374 15.7687)
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2 by 2 by 1 MPI processor grid
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create_atoms 1 box
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Created 432 atoms
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mass 1 39.95
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group all region box
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432 atoms in group all
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pair_style lj/cut 13.5
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pair_coeff 1 1 0.238 3.405
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# ID group atc PhysicsType ParameterFile
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fix AtC all atc field Ar_CauchyBorn.mat
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ATC: constructing shape function field estimate with parameter file Ar_CauchyBorn.mat
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ATC: version 2.0
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ATC: peratom PE compute created with ID: 3
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fix_modify AtC mesh create $c $c 1 box p p p
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fix_modify AtC mesh create 6 $c 1 box p p p
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fix_modify AtC mesh create 6 6 1 box p p p
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ATC: created uniform mesh with 98 nodes, 36 unique nodes, and 36 elements
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fix_modify AtC fields none
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fix_modify AtC fields add displacement
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fix_modify AtC fields add internal_energy stress cauchy_born_energy cauchy_born_stress
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fix_modify AtC gradients add displacement
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fix_modify AtC set reference_potential_energy 0.
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#fix_modify AtC fields add elastic_deformation_gradient
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fix_modify AtC output cb_biaxialFE 1 full_text tensor_components
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ATC: Warning : text output can create _LARGE_ files
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ATC: output custom names:
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log cb_biaxial.log
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thermo 100
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variable gamma1 equal 0.0
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variable gamma2 equal 0.0
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variable dv equal 1.0
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variable step equal 0
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thermo_style custom step v_step pxx pyy pzz pxy pxz pyz v_gamma1 pe v_dv
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timestep 0.0
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min_modify line quadratic
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timestep 0.0
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variable i loop 4
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label loop_i
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print ">>> step $i ${gamma1} ${gamma2}"
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>>> step 1 0 0
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minimize 1.e-20 1.e-20 1000 1000
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WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
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Setting up minimization ...
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ATC: CB stiffness: 7.56717 Einstein freq: 0.355649
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ATC: computing bond matrix ...........done
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Memory usage per processor = 23.7277 Mbytes
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Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv
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0 0 -4.8909909e-07 -4.8909886e-07 -4.8910238e-07 3.8880943e-13 -1.7762988e-12 -1.6027127e-12 0 -871.99483 1
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1 0 -4.8909976e-07 -4.8909976e-07 -4.8910453e-07 5.2088849e-13 -1.9469417e-12 -1.714206e-12 0 -871.99483 1
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Loop time of 0.00512052 on 4 procs for 1 steps with 432 atoms
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Minimization stats:
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Stopping criterion = energy tolerance
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Energy initial, next-to-last, final =
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-871.994833749 -871.994833749 -871.994833749
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Force two-norm initial, final = 3.34475e-13 2.07006e-13
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Force max component initial, final = 1.93109e-14 1.59178e-14
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Final line search alpha, max atom move = 1 1.59178e-14
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Iterations, force evaluations = 1 2
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Pair time (%) = 0.00403851 (78.8693)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.000856876 (16.7342)
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Outpt time (%) = 0 (0)
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Other time (%) = 0.000225127 (4.39656)
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Nlocal: 108 ave 108 max 108 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 2808 ave 2808 max 2808 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 23112 ave 23112 max 23112 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 46224 ave 46224 max 46224 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 184896
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Ave neighs/atom = 428
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Neighbor list builds = 0
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Dangerous builds = 0
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run 1
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Setting up run ...
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ATC: computing bond matrix ...........done
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Memory usage per processor = 23.0409 Mbytes
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Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv
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1 0 -4.8909914e-07 -4.8909896e-07 -4.8910453e-07 -2.1357027e-14 -1.8692798e-12 -1.5977131e-12 0 -871.99483 1
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2 0 -4.8909914e-07 -4.8909896e-07 -4.8910453e-07 -2.1357027e-14 -1.8692798e-12 -1.5977131e-12 0 -871.99483 1
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Loop time of 0.112994 on 4 procs for 1 steps with 432 atoms
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Pair time (%) = 0.00135452 (1.19875)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.000260293 (0.230361)
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Outpt time (%) = 0.000591516 (0.523494)
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Other time (%) = 0.110788 (98.0474)
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Nlocal: 108 ave 108 max 108 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 2808 ave 2808 max 2808 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 23112 ave 23425 max 22860 min
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Histogram: 1 0 1 0 0 1 0 0 0 1
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FullNghs: 46224 ave 46224 max 46224 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 184896
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Ave neighs/atom = 428
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Neighbor list builds = 0
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Dangerous builds = 0
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variable step equal ${step}+1
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variable step equal 0+1
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change_box all x scale $s y scale ${is} remap
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change_box all x scale 1.0049999999999998934 y scale ${is} remap
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change_box all x scale 1.0049999999999998934 y scale 0.99502487562189068093 remap
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Changing box ...
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orthogonal box = (-0.0788434 0 0) to (31.6162 31.5374 15.7687)
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orthogonal box = (-0.0788434 0.0784512 0) to (31.6162 31.4589 15.7687)
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variable gamma1 equal lx/$L-1.0
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variable gamma1 equal lx/31.537364922000001854-1.0
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variable gamma2 equal ly/$L-1.0
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variable gamma2 equal ly/31.537364922000001854-1.0
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variable dv equal vol/${V0}
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variable dv equal vol/15683.616509356999813
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next i
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jump in.cb_biaxial loop_i
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print ">>> step $i ${gamma1} ${gamma2}"
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>>> step 2 0.0049999999999998934186 -0.0049751243781092080454
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minimize 1.e-20 1.e-20 1000 1000
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WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
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Setting up minimization ...
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ATC: computing bond matrix ...........done
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Memory usage per processor = 23.7277 Mbytes
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Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv
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2 1 -91.357902 91.748981 5.9495117 4.4461448e-13 -1.151199e-12 -1.6213907e-12 0.005 -871.8904 1
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4 1 -91.357902 91.748981 5.9495117 1.1843442e-13 -1.1753736e-12 2.0631862e-13 0.005 -871.8904 1
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Loop time of 0.00762445 on 4 procs for 2 steps with 432 atoms
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Minimization stats:
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Stopping criterion = energy tolerance
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Energy initial, next-to-last, final =
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-871.890401015 -871.890401015 -871.890401015
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Force two-norm initial, final = 5.08157e-13 2.70169e-13
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Force max component initial, final = 5.63517e-14 1.97412e-14
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Final line search alpha, max atom move = 1 1.97412e-14
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Iterations, force evaluations = 2 4
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Pair time (%) = 0.00648111 (85.0043)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.000829577 (10.8805)
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Outpt time (%) = 0 (0)
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Other time (%) = 0.000313759 (4.11517)
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Nlocal: 108 ave 108 max 108 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 2808 ave 2808 max 2808 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 23112 ave 23425 max 22860 min
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Histogram: 1 0 1 0 0 1 0 0 0 1
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FullNghs: 46224 ave 46224 max 46224 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 184896
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Ave neighs/atom = 428
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Neighbor list builds = 0
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Dangerous builds = 0
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run 1
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Setting up run ...
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ATC: computing bond matrix ...........done
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Memory usage per processor = 23.0409 Mbytes
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Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv
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4 1 -91.357902 91.748981 5.9495117 3.2472389e-13 -1.1753736e-12 2.21851e-13 0.005 -871.8904 1
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5 1 -91.357902 91.748981 5.9495117 3.2472389e-13 -1.1753736e-12 2.21851e-13 0.005 -871.8904 1
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Loop time of 0.117523 on 4 procs for 1 steps with 432 atoms
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Pair time (%) = 0.00136477 (1.16128)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.000315309 (0.268296)
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Outpt time (%) = 0.00367075 (3.12344)
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Other time (%) = 0.112172 (95.447)
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Nlocal: 108 ave 108 max 108 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 2808 ave 2808 max 2808 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 23112 ave 23233 max 22979 min
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Histogram: 1 0 0 1 0 0 0 1 0 1
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FullNghs: 46224 ave 46224 max 46224 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 184896
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Ave neighs/atom = 428
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Neighbor list builds = 0
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Dangerous builds = 0
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variable step equal ${step}+1
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variable step equal 1+1
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change_box all x scale $s y scale ${is} remap
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change_box all x scale 1.0049999999999998934 y scale ${is} remap
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change_box all x scale 1.0049999999999998934 y scale 0.99502487562189068093 remap
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Changing box ...
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orthogonal box = (-0.158081 0.0784512 0) to (31.6954 31.4589 15.7687)
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orthogonal box = (-0.158081 0.156512 0) to (31.6954 31.3809 15.7687)
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variable gamma1 equal lx/$L-1.0
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variable gamma1 equal lx/31.537364922000001854-1.0
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variable gamma2 equal ly/$L-1.0
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variable gamma2 equal ly/31.537364922000001854-1.0
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variable dv equal vol/${V0}
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variable dv equal vol/15683.616509356999813
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next i
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jump in.cb_biaxial loop_i
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print ">>> step $i ${gamma1} ${gamma2}"
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>>> step 3 0.010024999999999728573 -0.009925496893640972651
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minimize 1.e-20 1.e-20 1000 1000
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WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
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Setting up minimization ...
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ATC: computing bond matrix ...........done
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Memory usage per processor = 23.7277 Mbytes
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Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv
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5 2 -171.87971 184.21354 24.007425 2.4269349e-13 3.1283039e-12 2.293625e-12 0.010025 -871.15868 1
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7 2 -171.87971 184.21354 24.007425 -1.0629975e-12 1.690591e-12 2.2967994e-12 0.010025 -871.15868 1
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Loop time of 0.00757968 on 4 procs for 2 steps with 432 atoms
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Minimization stats:
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Stopping criterion = energy tolerance
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Energy initial, next-to-last, final =
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-871.158684158 -871.158684158 -871.158684158
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Force two-norm initial, final = 5.1376e-13 2.56079e-13
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Force max component initial, final = 5.97855e-14 2.52853e-14
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Final line search alpha, max atom move = 1 2.52853e-14
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Iterations, force evaluations = 2 4
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Pair time (%) = 0.00633496 (83.5782)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.00088197 (11.636)
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Outpt time (%) = 0 (0)
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Other time (%) = 0.000362754 (4.78587)
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Nlocal: 108 ave 108 max 108 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 2808 ave 2808 max 2808 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 23112 ave 23234 max 22979 min
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Histogram: 1 0 0 1 0 0 0 1 0 1
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FullNghs: 46224 ave 46224 max 46224 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 184896
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Ave neighs/atom = 428
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Neighbor list builds = 0
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Dangerous builds = 0
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run 1
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Setting up run ...
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ATC: computing bond matrix ...........done
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Memory usage per processor = 23.0409 Mbytes
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Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv
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7 2 -171.87971 184.21354 24.007425 -3.1622962e-13 1.6206953e-12 2.2890332e-12 0.010025 -871.15868 1
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8 2 -171.87971 184.21354 24.007425 -3.1622962e-13 1.6206953e-12 2.2890332e-12 0.010025 -871.15868 1
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Loop time of 0.114526 on 4 procs for 1 steps with 432 atoms
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Pair time (%) = 0.00134146 (1.17132)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.000257552 (0.224885)
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Outpt time (%) = 0.00364625 (3.18378)
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Other time (%) = 0.109281 (95.42)
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Nlocal: 108 ave 108 max 108 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 2808 ave 2808 max 2808 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 23112 ave 23314 max 22858 min
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Histogram: 1 0 0 0 0 1 0 1 0 1
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FullNghs: 46224 ave 46224 max 46224 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 184896
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Ave neighs/atom = 428
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Neighbor list builds = 0
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Dangerous builds = 0
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variable step equal ${step}+1
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variable step equal 2+1
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change_box all x scale $s y scale ${is} remap
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change_box all x scale 1.0049999999999998934 y scale ${is} remap
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change_box all x scale 1.0049999999999998934 y scale 0.99502487562189068093 remap
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Changing box ...
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orthogonal box = (-0.237715 0.156512 0) to (31.7751 31.3809 15.7687)
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orthogonal box = (-0.237715 0.234184 0) to (31.7751 31.3032 15.7687)
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variable gamma1 equal lx/$L-1.0
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variable gamma1 equal lx/31.537364922000001854-1.0
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variable gamma2 equal ly/$L-1.0
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variable gamma2 equal ly/31.537364922000001854-1.0
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variable dv equal vol/${V0}
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variable dv equal vol/15683.616509356999813
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next i
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jump in.cb_biaxial loop_i
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print ">>> step $i ${gamma1} ${gamma2}"
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>>> step 4 0.015075124999999633957 -0.014851240690189837501
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minimize 1.e-20 1.e-20 1000 1000
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WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
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Setting up minimization ...
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ATC: computing bond matrix ...........done
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Memory usage per processor = 23.7277 Mbytes
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Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv
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8 3 -256.21626 277.50951 57.50796 -1.4695091e-13 4.1657011e-13 7.7445306e-13 0.015075125 -870.22745 1
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11 3 -256.21626 277.50951 57.50796 -7.7055184e-13 3.5561707e-14 -1.2297109e-12 0.015075125 -870.22745 1
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Loop time of 0.0105235 on 4 procs for 3 steps with 432 atoms
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Minimization stats:
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Stopping criterion = energy tolerance
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Energy initial, next-to-last, final =
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-870.227446396 -870.227446396 -870.227446396
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Force two-norm initial, final = 4.73029e-13 2.08011e-13
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Force max component initial, final = 4.59355e-14 2.3731e-14
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Final line search alpha, max atom move = 1 2.3731e-14
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Iterations, force evaluations = 3 6
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Pair time (%) = 0.00857157 (81.4517)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.00147575 (14.0234)
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Outpt time (%) = 0 (0)
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Other time (%) = 0.000476182 (4.52494)
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Nlocal: 108 ave 108 max 108 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 2808 ave 2808 max 2808 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 23112 ave 23314 max 22862 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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FullNghs: 46224 ave 46224 max 46224 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 184896
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Ave neighs/atom = 428
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Neighbor list builds = 0
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Dangerous builds = 0
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run 1
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Setting up run ...
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ATC: computing bond matrix ...........done
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Memory usage per processor = 23.0409 Mbytes
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Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv
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11 3 -256.21626 277.50951 57.50796 -2.5822588e-13 -1.5082689e-13 -1.3384375e-12 0.015075125 -870.22745 1
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12 3 -256.21626 277.50951 57.50796 -2.5822588e-13 -1.5082689e-13 -1.3384375e-12 0.015075125 -870.22745 1
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Loop time of 0.115736 on 4 procs for 1 steps with 432 atoms
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Pair time (%) = 0.00132596 (1.14568)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.00026691 (0.230619)
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Outpt time (%) = 0.00371403 (3.20905)
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Other time (%) = 0.110429 (95.4147)
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Nlocal: 108 ave 108 max 108 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 2808 ave 2808 max 2808 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 23112 ave 23264 max 23042 min
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Histogram: 2 0 1 0 0 0 0 0 0 1
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FullNghs: 46224 ave 46224 max 46224 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 184896
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Ave neighs/atom = 428
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Neighbor list builds = 0
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Dangerous builds = 0
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variable step equal ${step}+1
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|
variable step equal 3+1
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|
change_box all x scale $s y scale ${is} remap
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|
change_box all x scale 1.0049999999999998934 y scale ${is} remap
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change_box all x scale 1.0049999999999998934 y scale 0.99502487562189068093 remap
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|
Changing box ...
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orthogonal box = (-0.317747 0.234184 0) to (31.8551 31.3032 15.7687)
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orthogonal box = (-0.317747 0.311471 0) to (31.8551 31.2259 15.7687)
|
|
variable gamma1 equal lx/$L-1.0
|
|
variable gamma1 equal lx/31.537364922000001854-1.0
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variable gamma2 equal ly/$L-1.0
|
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variable gamma2 equal ly/31.537364922000001854-1.0
|
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variable dv equal vol/${V0}
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variable dv equal vol/15683.616509356999813
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|
next i
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jump in.cb_biaxial loop_i
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