From 666de878addcef838cee1cd406086c4a1deb8d20 Mon Sep 17 00:00:00 2001 From: rjones Date: Wed, 7 Aug 2013 21:29:05 +0000 Subject: [PATCH] ATC version 2.0, date: Aug7 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10558 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- .../USER/atc/cauchy_born/Ar_CauchyBorn.mat | 7 + .../atc/cauchy_born/Ar_CauchyBorn_linear.mat | 7 + .../USER/atc/cauchy_born/Au_CauchyBorn.mat | 6 + .../atc/cauchy_born/Au_CauchyBorn_linear.mat | 6 + examples/USER/atc/cauchy_born/Au_eam.mat | 5 + .../USER/atc/cauchy_born/Au_eam_linear.mat | 6 + .../USER/atc/cauchy_born/Cu_CauchyBorn.mat | 5 + .../USER/atc/cauchy_born/cb_biaxial.screen | 400 +++ examples/USER/atc/cauchy_born/cb_shear.screen | 384 +++ .../USER/atc/cauchy_born/cb_unistrain.screen | 123 + .../atc/cauchy_born/cb_unistrain_eam.screen | 145 + .../cb_unistrain_eam_linear.screen | 158 + .../cauchy_born/cb_unistrain_linear.screen | 161 + .../USER/atc/cauchy_born/cb_volumetric.screen | 389 +++ 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examples/USER/atc/molecule/in.water create mode 100644 examples/USER/atc/molecule/polarize.screen create mode 100644 examples/USER/atc/molecule/quartic_bonds.screen create mode 100644 examples/USER/atc/molecule/water.mat create mode 100644 examples/USER/atc/molecule/water.screen create mode 100644 examples/USER/atc/svn.stdout create mode 100644 examples/USER/atc/thermal/Ar_thermal.mat create mode 100644 examples/USER/atc/thermal/bar1d.screen create mode 100644 examples/USER/atc/thermal/bar1d_all_atoms.screen create mode 100644 examples/USER/atc/thermal/bar1d_combined.screen create mode 100644 examples/USER/atc/thermal/bar1d_flux.screen create mode 100644 examples/USER/atc/thermal/bar1d_frac_step.screen create mode 100644 examples/USER/atc/thermal/bar1d_hoover.screen create mode 100644 examples/USER/atc/thermal/bar1d_interpolate.screen create mode 100644 examples/USER/atc/thermal/bar1d_lumped.screen create mode 100644 examples/USER/atc/thermal/in.bar1d create mode 100644 examples/USER/atc/thermal/in.bar1d_all_atoms create mode 100644 examples/USER/atc/thermal/in.bar1d_combined create mode 100644 examples/USER/atc/thermal/in.bar1d_flux create mode 100644 examples/USER/atc/thermal/in.bar1d_frac_step create mode 100644 examples/USER/atc/thermal/in.bar1d_hoover create mode 100644 examples/USER/atc/thermal/in.bar1d_interpolate create mode 100644 examples/USER/atc/thermal/in.bar1d_lumped create mode 100644 examples/USER/atc/thermal/in.no_atoms create mode 100644 examples/USER/atc/thermal/no_atoms.screen create mode 100644 examples/USER/atc/two_temperature/Ar_ttm.mat create mode 100644 examples/USER/atc/two_temperature/Cu_ttm.mat create mode 100644 examples/USER/atc/two_temperature/bar1d_ttm.screen create mode 100644 examples/USER/atc/two_temperature/cutout.screen create mode 100644 examples/USER/atc/two_temperature/gaussianIC_ttm.screen create mode 100644 examples/USER/atc/two_temperature/in.bar1d_ttm create mode 100644 examples/USER/atc/two_temperature/in.cutout create mode 100644 examples/USER/atc/two_temperature/in.gaussianIC_ttm create mode 100644 examples/USER/atc/two_temperature/in.no_atoms create mode 100644 examples/USER/atc/two_temperature/in.restart create mode 100644 examples/USER/atc/two_temperature/in.uniform_exchange create mode 100644 examples/USER/atc/two_temperature/in.uniform_heating create mode 100644 examples/USER/atc/two_temperature/no_atoms.screen create mode 100644 examples/USER/atc/two_temperature/restart.screen create mode 100644 examples/USER/atc/two_temperature/uniform_exchange.screen create mode 100644 examples/USER/atc/two_temperature/uniform_heating.screen diff --git a/examples/USER/atc/cauchy_born/Ar_CauchyBorn.mat b/examples/USER/atc/cauchy_born/Ar_CauchyBorn.mat new file mode 100644 index 0000000000..28530f90e3 --- /dev/null +++ b/examples/USER/atc/cauchy_born/Ar_CauchyBorn.mat @@ -0,0 +1,7 @@ +material Ar real +stress cauchy-born + pair_style lj/cut 13.5 #pair_style lj/cut r_cut + pair_coeff 0.238 3.405 #pair_coeff epsilon sigma +# temperature 0 +# linear +end diff --git a/examples/USER/atc/cauchy_born/Ar_CauchyBorn_linear.mat b/examples/USER/atc/cauchy_born/Ar_CauchyBorn_linear.mat new file mode 100644 index 0000000000..76329bd5c1 --- /dev/null +++ b/examples/USER/atc/cauchy_born/Ar_CauchyBorn_linear.mat @@ -0,0 +1,7 @@ +material Ar real +stress cauchy-born + pair_style lj/cut 13.5 #pair_style lj/cut r_cut + pair_coeff 0.238 3.405 #pair_coeff epsilon sigma +# temperature 0 + linear +end diff --git a/examples/USER/atc/cauchy_born/Au_CauchyBorn.mat b/examples/USER/atc/cauchy_born/Au_CauchyBorn.mat new file mode 100644 index 0000000000..dca86b4361 --- /dev/null +++ b/examples/USER/atc/cauchy_born/Au_CauchyBorn.mat @@ -0,0 +1,6 @@ +material Au real +stress cauchy-born +pair_style lj/smooth/linear 5.456108274435118 #pair_style lj/smooth/linear r_cut +pair_coeff 0.7242785984051078 2.598146797350056 #pair_coeff epsilon sigma +#linear +end diff --git a/examples/USER/atc/cauchy_born/Au_CauchyBorn_linear.mat b/examples/USER/atc/cauchy_born/Au_CauchyBorn_linear.mat new file mode 100644 index 0000000000..c504dfb589 --- /dev/null +++ b/examples/USER/atc/cauchy_born/Au_CauchyBorn_linear.mat @@ -0,0 +1,6 @@ +material Au real +stress cauchy-born + pair_style lj/smooth/linear 5.456108274435118 #pair_style lj/smooth/linear r_cut + pair_coeff 0.7242785984051078 2.598146797350056 #pair_coeff epsilon sigma + linear +end diff --git a/examples/USER/atc/cauchy_born/Au_eam.mat b/examples/USER/atc/cauchy_born/Au_eam.mat new file mode 100644 index 0000000000..fc3d74694b --- /dev/null +++ b/examples/USER/atc/cauchy_born/Au_eam.mat @@ -0,0 +1,5 @@ +material Au metal + stress cauchy-born + pair_style eam + end +end diff --git a/examples/USER/atc/cauchy_born/Au_eam_linear.mat b/examples/USER/atc/cauchy_born/Au_eam_linear.mat new file mode 100644 index 0000000000..61a26e75fd --- /dev/null +++ b/examples/USER/atc/cauchy_born/Au_eam_linear.mat @@ -0,0 +1,6 @@ +material Au metal + stress cauchy-born + pair_style eam + linear + end +end diff --git a/examples/USER/atc/cauchy_born/Cu_CauchyBorn.mat b/examples/USER/atc/cauchy_born/Cu_CauchyBorn.mat new file mode 100644 index 0000000000..95bf483631 --- /dev/null +++ b/examples/USER/atc/cauchy_born/Cu_CauchyBorn.mat @@ -0,0 +1,5 @@ +material Cu real +stress cauchy-born +pair_style eam +#linear +end diff --git a/examples/USER/atc/cauchy_born/cb_biaxial.screen b/examples/USER/atc/cauchy_born/cb_biaxial.screen new file mode 100644 index 0000000000..4eae9d703b --- /dev/null +++ b/examples/USER/atc/cauchy_born/cb_biaxial.screen @@ -0,0 +1,400 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic +variable lattice_constant equal 5.256227487 +variable c equal 6 +variable L equal $c*${lattice_constant} +variable L equal 6*${lattice_constant} +variable L equal 6*5.2562274870000003091 +variable d equal 0.005 +variable s equal 1.005 +variable is equal 1.0/$s +variable is equal 1.0/1.0049999999999998934 +variable V0 equal $L*$L*3*${lattice_constant} +variable V0 equal 31.537364922000001854*$L*3*${lattice_constant} +variable V0 equal 31.537364922000001854*31.537364922000001854*3*${lattice_constant} +variable V0 equal 31.537364922000001854*31.537364922000001854*3*5.2562274870000003091 +# create system +lattice fcc ${lattice_constant} origin 0.25 0.25 0.25 +lattice fcc 5.2562274870000003091 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.25623 5.25623 5.25623 +region box block 0 $c 0 $c 0 3 +region box block 0 6 0 $c 0 3 +region box block 0 6 0 6 0 3 +boundary p p p +create_box 1 box +Created orthogonal box = (0 0 0) to (31.5374 31.5374 15.7687) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 432 atoms +mass 1 39.95 +group all region box +432 atoms in group all +pair_style lj/cut 13.5 +pair_coeff 1 1 0.238 3.405 +# ID group atc PhysicsType ParameterFile +fix AtC all atc field Ar_CauchyBorn.mat +ATC: constructing shape function field estimate with parameter file Ar_CauchyBorn.mat + ATC: peratom PE compute created with ID: 3 +fix_modify AtC mesh create $c $c 1 box p p p +fix_modify AtC mesh create 6 $c 1 box p p p +fix_modify AtC mesh create 6 6 1 box p p p + ATC: created uniform mesh with 98 nodes, 36 unique nodes, and 36 elements +fix_modify AtC fields none +fix_modify AtC fields add displacement +fix_modify AtC fields add internal_energy stress cauchy_born_energy cauchy_born_stress +fix_modify AtC gradients add displacement +#fix_modify AtC fields add elastic_deformation_gradient +fix_modify AtC output cb_biaxialFE 1 full_text tensor_components + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +log cb_biaxial.log +thermo 100 +variable gamma1 equal 0.0 +variable gamma2 equal 0.0 +variable dv equal 1.0 +variable step equal 0 +thermo_style custom step v_step pxx pyy pzz pxy pxz pyz v_gamma1 pe v_dv +timestep 0.0 +min_modify line quadratic +timestep 0.0 +variable i loop 4 +label loop_i + print ">>> step $i ${gamma1} ${gamma2}" +>>> step 1 0 0 + minimize 1.e-20 1.e-20 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7277 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv + 0 0 -4.8909909e-07 -4.8909886e-07 -4.8910238e-07 3.8880943e-13 -1.7762988e-12 -1.6027127e-12 0 -871.99483 1 + 1 0 -4.8909976e-07 -4.8909976e-07 -4.8910453e-07 5.2088849e-13 -1.9469417e-12 -1.714206e-12 0 -871.99483 1 +Loop time of 0.280059 on 4 procs for 1 steps with 432 atoms + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -871.994833749 -871.994833749 -871.994833749 + Force two-norm initial, final = 3.34475e-13 2.07006e-13 + Force max component initial, final = 1.93109e-14 1.59178e-14 + Final line search alpha, max atom move = 1 1.59178e-14 + Iterations, force evaluations = 1 2 + +Pair time (%) = 0.0039708 (1.41784) +Neigh time (%) = 0 (0) +Comm time (%) = 0.117534 (41.9677) +Outpt time (%) = 0 (0) +Other time (%) = 0.158554 (56.6145) + +Nlocal: 108 ave 108 max 108 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2808 ave 2808 max 2808 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 23112 ave 23112 max 23112 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 46224 ave 46224 max 46224 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 184896 +Ave neighs/atom = 428 +Neighbor list builds = 0 +Dangerous builds = 0 + run 1 +Setting up run ... + ATC: computing bond matrix ...........done +Memory usage per processor = 23.0409 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv + 1 0 -4.8909914e-07 -4.8909896e-07 -4.8910453e-07 -2.1357027e-14 -1.8692798e-12 -1.5977131e-12 0 -871.99483 1 + 2 0 -4.8909914e-07 -4.8909896e-07 -4.8910453e-07 -2.1357027e-14 -1.8692798e-12 -1.5977131e-12 0 -871.99483 1 +Loop time of 0.235875 on 4 procs for 1 steps with 432 atoms + +Pair time (%) = 0.00137603 (0.583373) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000292778 (0.124124) +Outpt time (%) = 0.0005005 (0.212189) +Other time (%) = 0.233706 (99.0803) + +Nlocal: 108 ave 108 max 108 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2808 ave 2808 max 2808 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 23112 ave 23425 max 22860 min +Histogram: 1 0 1 0 0 1 0 0 0 1 +FullNghs: 46224 ave 46224 max 46224 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 184896 +Ave neighs/atom = 428 +Neighbor list builds = 0 +Dangerous builds = 0 + variable step equal ${step}+1 + variable step equal 0+1 + change_box all x scale $s y scale ${is} remap + change_box all x scale 1.0049999999999998934 y scale ${is} remap + change_box all x scale 1.0049999999999998934 y scale 0.99502487562189068093 remap +Changing box ... + orthogonal box = (-0.0788434 0 0) to (31.6162 31.5374 15.7687) + orthogonal box = (-0.0788434 0.0784512 0) to (31.6162 31.4589 15.7687) + variable gamma1 equal lx/$L-1.0 + variable gamma1 equal lx/31.537364922000001854-1.0 + variable gamma2 equal ly/$L-1.0 + variable gamma2 equal ly/31.537364922000001854-1.0 + variable dv equal vol/${V0} + variable dv equal vol/15683.616509356999813 +next i +jump in.cb_biaxial loop_i + print ">>> step $i ${gamma1} ${gamma2}" +>>> step 2 0.0049999999999998934186 -0.0049751243781092080454 + minimize 1.e-20 1.e-20 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7277 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv + 2 1 -91.357902 91.748981 5.9495117 4.4461448e-13 -1.151199e-12 -1.6213907e-12 0.005 -871.8904 1 + 4 1 -91.357902 91.748981 5.9495117 1.1843442e-13 -1.1753736e-12 2.0631862e-13 0.005 -871.8904 1 +Loop time of 0.275171 on 4 procs for 2 steps with 432 atoms + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -871.890401015 -871.890401015 -871.890401015 + Force two-norm initial, final = 5.08157e-13 2.70169e-13 + Force max component initial, final = 5.63517e-14 1.97412e-14 + Final line search alpha, max atom move = 1 1.97412e-14 + Iterations, force evaluations = 2 4 + +Pair time (%) = 0.00895029 (3.25263) +Neigh time (%) = 0 (0) +Comm time (%) = 0.157368 (57.1892) +Outpt time (%) = 0 (0) +Other time (%) = 0.108853 (39.5582) + +Nlocal: 108 ave 108 max 108 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2808 ave 2808 max 2808 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 23112 ave 23425 max 22860 min +Histogram: 1 0 1 0 0 1 0 0 0 1 +FullNghs: 46224 ave 46224 max 46224 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 184896 +Ave neighs/atom = 428 +Neighbor list builds = 0 +Dangerous builds = 0 + run 1 +Setting up run ... + ATC: computing bond matrix ...........done +Memory usage per processor = 23.0409 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv + 4 1 -91.357902 91.748981 5.9495117 3.2472389e-13 -1.1753736e-12 2.21851e-13 0.005 -871.8904 1 + 5 1 -91.357902 91.748981 5.9495117 3.2472389e-13 -1.1753736e-12 2.21851e-13 0.005 -871.8904 1 +Loop time of 0.249931 on 4 procs for 1 steps with 432 atoms + +Pair time (%) = 0.00142711 (0.571004) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000403583 (0.161478) +Outpt time (%) = 0.00990075 (3.9614) +Other time (%) = 0.238199 (95.3061) + +Nlocal: 108 ave 108 max 108 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2808 ave 2808 max 2808 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 23112 ave 23233 max 22979 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +FullNghs: 46224 ave 46224 max 46224 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 184896 +Ave neighs/atom = 428 +Neighbor list builds = 0 +Dangerous builds = 0 + variable step equal ${step}+1 + variable step equal 1+1 + change_box all x scale $s y scale ${is} remap + change_box all x scale 1.0049999999999998934 y scale ${is} remap + change_box all x scale 1.0049999999999998934 y scale 0.99502487562189068093 remap +Changing box ... + orthogonal box = (-0.158081 0.0784512 0) to (31.6954 31.4589 15.7687) + orthogonal box = (-0.158081 0.156512 0) to (31.6954 31.3809 15.7687) + variable gamma1 equal lx/$L-1.0 + variable gamma1 equal lx/31.537364922000001854-1.0 + variable gamma2 equal ly/$L-1.0 + variable gamma2 equal ly/31.537364922000001854-1.0 + variable dv equal vol/${V0} + variable dv equal vol/15683.616509356999813 +next i +jump in.cb_biaxial loop_i + print ">>> step $i ${gamma1} ${gamma2}" +>>> step 3 0.010024999999999728573 -0.009925496893640972651 + minimize 1.e-20 1.e-20 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7277 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv + 5 2 -171.87971 184.21354 24.007425 2.4269349e-13 3.1283039e-12 2.293625e-12 0.010025 -871.15868 1 + 7 2 -171.87971 184.21354 24.007425 -1.0629975e-12 1.690591e-12 2.2967994e-12 0.010025 -871.15868 1 +Loop time of 0.510101 on 4 procs for 2 steps with 432 atoms + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -871.158684158 -871.158684158 -871.158684158 + Force two-norm initial, final = 5.1376e-13 2.56079e-13 + Force max component initial, final = 5.97855e-14 2.52853e-14 + Final line search alpha, max atom move = 1 2.52853e-14 + Iterations, force evaluations = 2 4 + +Pair time (%) = 0.0191914 (3.76227) +Neigh time (%) = 0 (0) +Comm time (%) = 0.23774 (46.6064) +Outpt time (%) = 0 (0) +Other time (%) = 0.25317 (49.6313) + +Nlocal: 108 ave 108 max 108 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2808 ave 2808 max 2808 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 23112 ave 23234 max 22979 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +FullNghs: 46224 ave 46224 max 46224 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 184896 +Ave neighs/atom = 428 +Neighbor list builds = 0 +Dangerous builds = 0 + run 1 +Setting up run ... + ATC: computing bond matrix ...........done +Memory usage per processor = 23.0409 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv + 7 2 -171.87971 184.21354 24.007425 -3.1622962e-13 1.6206953e-12 2.2890332e-12 0.010025 -871.15868 1 + 8 2 -171.87971 184.21354 24.007425 -3.1622962e-13 1.6206953e-12 2.2890332e-12 0.010025 -871.15868 1 +Loop time of 0.494811 on 4 procs for 1 steps with 432 atoms + +Pair time (%) = 0.00385392 (0.778867) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0360543 (7.28647) +Outpt time (%) = 0.0442775 (8.94838) +Other time (%) = 0.410625 (82.9863) + +Nlocal: 108 ave 108 max 108 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2808 ave 2808 max 2808 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 23112 ave 23314 max 22858 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +FullNghs: 46224 ave 46224 max 46224 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 184896 +Ave neighs/atom = 428 +Neighbor list builds = 0 +Dangerous builds = 0 + variable step equal ${step}+1 + variable step equal 2+1 + change_box all x scale $s y scale ${is} remap + change_box all x scale 1.0049999999999998934 y scale ${is} remap + change_box all x scale 1.0049999999999998934 y scale 0.99502487562189068093 remap +Changing box ... + orthogonal box = (-0.237715 0.156512 0) to (31.7751 31.3809 15.7687) + orthogonal box = (-0.237715 0.234184 0) to (31.7751 31.3032 15.7687) + variable gamma1 equal lx/$L-1.0 + variable gamma1 equal lx/31.537364922000001854-1.0 + variable gamma2 equal ly/$L-1.0 + variable gamma2 equal ly/31.537364922000001854-1.0 + variable dv equal vol/${V0} + variable dv equal vol/15683.616509356999813 +next i +jump in.cb_biaxial loop_i + print ">>> step $i ${gamma1} ${gamma2}" +>>> step 4 0.015075124999999633957 -0.014851240690189837501 + minimize 1.e-20 1.e-20 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7277 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv + 8 3 -256.21626 277.50951 57.50796 -1.4695091e-13 4.1657011e-13 7.7445306e-13 0.015075125 -870.22745 1 + 11 3 -256.21626 277.50951 57.50796 -7.7055184e-13 3.5561707e-14 -1.2297109e-12 0.015075125 -870.22745 1 +Loop time of 0.165426 on 4 procs for 3 steps with 432 atoms + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -870.227446396 -870.227446396 -870.227446396 + Force two-norm initial, final = 4.73029e-13 2.08011e-13 + Force max component initial, final = 4.59355e-14 2.3731e-14 + Final line search alpha, max atom move = 1 2.3731e-14 + Iterations, force evaluations = 3 6 + +Pair time (%) = 0.00856608 (5.17818) +Neigh time (%) = 0 (0) +Comm time (%) = 0.116189 (70.2361) +Outpt time (%) = 0 (0) +Other time (%) = 0.0406712 (24.5857) + +Nlocal: 108 ave 108 max 108 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2808 ave 2808 max 2808 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 23112 ave 23314 max 22862 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +FullNghs: 46224 ave 46224 max 46224 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 184896 +Ave neighs/atom = 428 +Neighbor list builds = 0 +Dangerous builds = 0 + run 1 +Setting up run ... + ATC: computing bond matrix ...........done +Memory usage per processor = 23.0409 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma1 PotEng dv + 11 3 -256.21626 277.50951 57.50796 -2.5822588e-13 -1.5082689e-13 -1.3384375e-12 0.015075125 -870.22745 1 + 12 3 -256.21626 277.50951 57.50796 -2.5822588e-13 -1.5082689e-13 -1.3384375e-12 0.015075125 -870.22745 1 +Loop time of 0.687404 on 4 procs for 1 steps with 432 atoms + +Pair time (%) = 0.00261223 (0.380014) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0127067 (1.8485) +Outpt time (%) = 0.0149975 (2.18176) +Other time (%) = 0.657088 (95.5897) + +Nlocal: 108 ave 108 max 108 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2808 ave 2808 max 2808 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 23112 ave 23264 max 23042 min +Histogram: 2 0 1 0 0 0 0 0 0 1 +FullNghs: 46224 ave 46224 max 46224 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 184896 +Ave neighs/atom = 428 +Neighbor list builds = 0 +Dangerous builds = 0 + variable step equal ${step}+1 + variable step equal 3+1 + change_box all x scale $s y scale ${is} remap + change_box all x scale 1.0049999999999998934 y scale ${is} remap + change_box all x scale 1.0049999999999998934 y scale 0.99502487562189068093 remap +Changing box ... + orthogonal box = (-0.317747 0.234184 0) to (31.8551 31.3032 15.7687) + orthogonal box = (-0.317747 0.311471 0) to (31.8551 31.2259 15.7687) + variable gamma1 equal lx/$L-1.0 + variable gamma1 equal lx/31.537364922000001854-1.0 + variable gamma2 equal ly/$L-1.0 + variable gamma2 equal ly/31.537364922000001854-1.0 + variable dv equal vol/${V0} + variable dv equal vol/15683.616509356999813 +next i +jump in.cb_biaxial loop_i diff --git a/examples/USER/atc/cauchy_born/cb_shear.screen b/examples/USER/atc/cauchy_born/cb_shear.screen new file mode 100644 index 0000000000..2b4145c4f2 --- /dev/null +++ b/examples/USER/atc/cauchy_born/cb_shear.screen @@ -0,0 +1,384 @@ +LAMMPS (14 Aug 2013) +units metal +atom_style atomic +variable lattice_constant equal 4.08 +variable c equal 6 # minimum size +variable Ly equal $c*${lattice_constant} +variable Ly equal 6*${lattice_constant} +variable Ly equal 6*4.0800000000000000711 +variable d equal 0.005 +variable V0 equal ($c*${lattice_constant})^3 +variable V0 equal (6*${lattice_constant})^3 +variable V0 equal (6*4.0800000000000000711)^3 +# create system +lattice fcc ${lattice_constant} origin 0.25 0.25 0.25 +lattice fcc 4.0800000000000000711 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 4.08 4.08 4.08 +# NOTE rect box + lagrangian is necessary to fool ATC's mesh +region rectbox block 0 $c 0 $c 0 3 +region rectbox block 0 6 0 $c 0 3 +region rectbox block 0 6 0 6 0 3 +region box prism 0 $c 0 $c 0 3 0 0 0 +region box prism 0 6 0 $c 0 3 0 0 0 +region box prism 0 6 0 6 0 3 0 0 0 +boundary p p p +create_box 1 box +Created triclinic box = (0 0 0) to (24.48 24.48 12.24) with tilt (0 0 0) + 2 by 2 by 1 MPI processor grid +create_atoms 1 region box +Created 432 atoms +mass 1 196.97 +group all region box +432 atoms in group all +pair_style lj/smooth/linear 5.456108274435118 +pair_coeff * * 0.7242785984051078 2.598146797350056 +neighbor 1.0 bin +#neigh_modify delay 1000000 +log cb_shear.log +thermo 100 +variable gamma equal 0.0 +variable step equal 0 +thermo_style custom step v_step pxx pyy pzz pxy pxz pyz v_gamma pe xy xz yz +timestep 1.0 +fix AtC all atc field Au_CauchyBorn.mat +ATC: constructing shape function field estimate with parameter file Au_CauchyBorn.mat + ATC: peratom PE compute created with ID: 3 +fix_modify AtC mesh create $c $c 1 rectbox p p p +fix_modify AtC mesh create 6 $c 1 rectbox p p p +fix_modify AtC mesh create 6 6 1 rectbox p p p + ATC: created uniform mesh with 98 nodes, 36 unique nodes, and 36 elements +fix_modify AtC fields add mass_density internal_energy stress +fix_modify AtC fields add displacement +fix_modify AtC fields add cauchy_born_energy cauchy_born_stress +fix_modify AtC gradients add displacement +#fix_modify AtC fields add elastic_deformation_gradient +fix_modify AtC output cb_shearFE 1 text binary tensor_components + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +min_modify line quadratic +variable dgamma equal $d/${Ly} +variable dgamma equal 0.0050000000000000001041/${Ly} +variable dgamma equal 0.0050000000000000001041/24.480000000000000426 +print "depsilon_12: ${dgamma}" +depsilon_12: 0.00020424836601307190163 +timestep 0.0 +variable i loop 4 +label loop_i + print ">>> step $i" +>>> step 1 + minimize 1.e-20 1.e-20 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: CB stiffness: 28.7742 Einstein freq: 7394.9 + ATC: computing bond matrix ...........done +Memory usage per processor = 23.608 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng Xy Xz Yz + 0 0 8.2990138e-10 8.090598e-10 1.2401824e-09 -2.047237e-10 -1.675329e-10 -2.052466e-10 0 -1697.76 0 0 0 + 2 0 1.4564068e-09 1.4626573e-09 1.5311855e-09 1.91865e-11 2.9536813e-11 -6.2429255e-12 0 -1697.76 0 0 0 +Loop time of 0.00191295 on 4 procs for 2 steps with 432 atoms + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -1697.76 -1697.76 -1697.76 + Force two-norm initial, final = 7.25089e-13 7.69958e-13 + Force max component initial, final = 6.31162e-14 5.59344e-14 + Final line search alpha, max atom move = 1 5.59344e-14 + Iterations, force evaluations = 2 4 + +Pair time (%) = 0.00124657 (65.1648) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000366986 (19.1843) +Outpt time (%) = 0 (0) +Other time (%) = 0.000299394 (15.6509) + +Nlocal: 108 ave 108 max 108 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 756 ave 756 max 756 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 4212 ave 4212 max 4212 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 8424 ave 8424 max 8424 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 33696 +Ave neighs/atom = 78 +Neighbor list builds = 0 +Dangerous builds = 0 + run 1 +Setting up run ... + ATC: computing bond matrix ...........done +Memory usage per processor = 22.9213 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng Xy Xz Yz + 2 0 1.1686684e-09 1.1704144e-09 1.1818848e-09 -7.0034742e-11 -2.0734576e-10 -2.246665e-10 0 -1697.76 0 0 0 + 3 0 1.3913827e-09 1.417767e-09 1.507396e-09 1.3580144e-11 6.6948897e-11 3.137377e-13 0 -1697.76 0 0 0 +Loop time of 0.0460081 on 4 procs for 1 steps with 432 atoms + +Pair time (%) = 0.00277305 (6.0273) +Neigh time (%) = 0 (0) +Comm time (%) = 0.012373 (26.893) +Outpt time (%) = 0.000219166 (0.476364) +Other time (%) = 0.0306429 (66.6033) + +Nlocal: 108 ave 108 max 108 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 756 ave 756 max 756 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 4212 ave 4380 max 4051 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +FullNghs: 8424 ave 8424 max 8424 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 33696 +Ave neighs/atom = 78 +Neighbor list builds = 0 +Dangerous builds = 0 + variable step equal ${step}+1 + variable step equal 0+1 + change_box all xy delta $d remap + change_box all xy delta 0.0050000000000000001041 remap +Changing box ... + triclinic box = (0 0 0) to (24.48 24.48 12.24) with tilt (0.0204 0 0) + variable gamma equal $i*${dgamma} + variable gamma equal 1*${dgamma} + variable gamma equal 1*0.00020424836601307190163 +next i +jump in.cb_shear loop_i + print ">>> step $i" +>>> step 2 + minimize 1.e-20 1.e-20 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: computing bond matrix ...........done +Memory usage per processor = 23.608 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng Xy Xz Yz + 3 1 6.886337 10.047566 -1.1516625 -2346.5185 -2.2571381e-10 -2.3527902e-10 0.00020424837 -1697.7555 0.0204 0 0 + 8 1 6.886337 10.047566 -1.1516625 -2346.5185 -2.9823269e-11 1.6162796e-11 0.00020424837 -1697.7555 0.0204 0 0 +Loop time of 0.00391698 on 4 procs for 5 steps with 432 atoms + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -1697.75552385 -1697.75552385 -1697.75552385 + Force two-norm initial, final = 1.45516e-12 6.75826e-13 + Force max component initial, final = 2.43972e-13 6.33382e-14 + Final line search alpha, max atom move = 1 6.33382e-14 + Iterations, force evaluations = 5 10 + +Pair time (%) = 0.00264663 (67.568) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000849068 (21.6766) +Outpt time (%) = 0 (0) +Other time (%) = 0.000421286 (10.7554) + +Nlocal: 108 ave 108 max 108 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 756 ave 756 max 756 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 4212 ave 4380 max 4051 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +FullNghs: 8424 ave 8424 max 8424 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 33696 +Ave neighs/atom = 78 +Neighbor list builds = 0 +Dangerous builds = 0 + run 1 +Setting up run ... + ATC: computing bond matrix ...........done +Memory usage per processor = 22.9213 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng Xy Xz Yz + 8 1 6.886337 10.047566 -1.1516625 -2346.5185 -1.3329305e-10 -1.817966e-10 0.00020424837 -1697.7555 0.0204 0 0 + 9 1 6.886337 10.047566 -1.1516625 -2346.5185 -1.153706e-11 6.5233191e-11 0.00020424837 -1697.7555 0.0204 0 0 +Loop time of 0.02672 on 4 procs for 1 steps with 432 atoms + +Pair time (%) = 0.000268936 (1.0065) +Neigh time (%) = 0 (0) +Comm time (%) = 9.2268e-05 (0.345314) +Outpt time (%) = 0.00226957 (8.49387) +Other time (%) = 0.0240893 (90.1543) + +Nlocal: 108 ave 108 max 108 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 756 ave 756 max 756 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 4212 ave 4312 max 4085 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +FullNghs: 8424 ave 8424 max 8424 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 33696 +Ave neighs/atom = 78 +Neighbor list builds = 0 +Dangerous builds = 0 + variable step equal ${step}+1 + variable step equal 1+1 + change_box all xy delta $d remap + change_box all xy delta 0.0050000000000000001041 remap +Changing box ... + triclinic box = (0 0 0) to (24.48 24.48 12.24) with tilt (0.0408 0 0) + variable gamma equal $i*${dgamma} + variable gamma equal 2*${dgamma} + variable gamma equal 2*0.00020424836601307190163 +next i +jump in.cb_shear loop_i + print ">>> step $i" +>>> step 3 + minimize 1.e-20 1.e-20 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: computing bond matrix ...........done +Memory usage per processor = 23.608 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng Xy Xz Yz + 9 2 27.545381 40.190743 -4.6066242 -4693.1379 -1.3165313e-10 -1.7366821e-10 0.00040849673 -1697.7421 0.0408 0 0 + 13 2 27.545381 40.190743 -4.6066242 -4693.1379 -2.0177729e-11 5.6927478e-11 0.00040849673 -1697.7421 0.0408 0 0 +Loop time of 0.00320572 on 4 procs for 4 steps with 432 atoms + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -1697.74209519 -1697.74209519 -1697.74209519 + Force two-norm initial, final = 1.45582e-12 6.63859e-13 + Force max component initial, final = 2.16244e-13 6.87297e-14 + Final line search alpha, max atom move = 1 6.87297e-14 + Iterations, force evaluations = 4 8 + +Pair time (%) = 0.00217921 (67.9787) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000676513 (21.1033) +Outpt time (%) = 0 (0) +Other time (%) = 0.000349998 (10.9179) + +Nlocal: 108 ave 108 max 108 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 756 ave 756 max 756 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 4212 ave 4312 max 4085 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +FullNghs: 8424 ave 8424 max 8424 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 33696 +Ave neighs/atom = 78 +Neighbor list builds = 0 +Dangerous builds = 0 + run 1 +Setting up run ... + ATC: computing bond matrix ...........done +Memory usage per processor = 22.9213 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng Xy Xz Yz + 13 2 27.545381 40.190743 -4.6066242 -4693.1379 -1.1765618e-10 -1.586376e-10 0.00040849673 -1697.7421 0.0408 0 0 + 14 2 27.545381 40.190743 -4.6066242 -4693.1379 -3.767429e-11 6.1228867e-11 0.00040849673 -1697.7421 0.0408 0 0 +Loop time of 0.0443209 on 4 procs for 1 steps with 432 atoms + +Pair time (%) = 0.000267744 (0.604103) +Neigh time (%) = 0 (0) +Comm time (%) = 9.21488e-05 (0.207913) +Outpt time (%) = 0.00152749 (3.44643) +Other time (%) = 0.0424336 (95.7416) + +Nlocal: 108 ave 108 max 108 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 756 ave 756 max 756 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 4212 ave 4347 max 4038 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +FullNghs: 8424 ave 8424 max 8424 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 33696 +Ave neighs/atom = 78 +Neighbor list builds = 0 +Dangerous builds = 0 + variable step equal ${step}+1 + variable step equal 2+1 + change_box all xy delta $d remap + change_box all xy delta 0.0050000000000000001041 remap +Changing box ... + triclinic box = (0 0 0) to (24.48 24.48 12.24) with tilt (0.0612 0 0) + variable gamma equal $i*${dgamma} + variable gamma equal 3*${dgamma} + variable gamma equal 3*0.00020424836601307190163 +next i +jump in.cb_shear loop_i + print ">>> step $i" +>>> step 4 + minimize 1.e-20 1.e-20 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: computing bond matrix ...........done +Memory usage per processor = 23.608 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng Xy Xz Yz + 14 3 61.977233 90.430962 -10.364808 -7039.9591 -1.4718693e-10 -1.6595966e-10 0.0006127451 -1697.7197 0.0612 0 0 + 18 3 61.977233 90.430962 -10.364808 -7039.9591 -9.9031986e-12 6.1389525e-11 0.0006127451 -1697.7197 0.0612 0 0 +Loop time of 0.083416 on 4 procs for 4 steps with 432 atoms + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -1697.71971345 -1697.71971345 -1697.71971345 + Force two-norm initial, final = 1.6934e-12 6.96493e-13 + Force max component initial, final = 2.55476e-13 6.86812e-14 + Final line search alpha, max atom move = 1 6.86812e-14 + Iterations, force evaluations = 4 8 + +Pair time (%) = 0.00221682 (2.65754) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0704444 (84.4495) +Outpt time (%) = 0 (0) +Other time (%) = 0.0107548 (12.8929) + +Nlocal: 108 ave 108 max 108 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 756 ave 756 max 756 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 4212 ave 4347 max 4038 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +FullNghs: 8424 ave 8424 max 8424 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 33696 +Ave neighs/atom = 78 +Neighbor list builds = 0 +Dangerous builds = 0 + run 1 +Setting up run ... + ATC: computing bond matrix ...........done +Memory usage per processor = 22.9213 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng Xy Xz Yz + 18 3 61.977233 90.430962 -10.364808 -7039.9591 -5.2551822e-11 -1.5970613e-10 0.0006127451 -1697.7197 0.0612 0 0 + 19 3 61.977233 90.430962 -10.364808 -7039.9591 -1.697518e-12 6.6900396e-11 0.0006127451 -1697.7197 0.0612 0 0 +Loop time of 0.178347 on 4 procs for 1 steps with 432 atoms + +Pair time (%) = 0.000270486 (0.151663) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0174391 (9.77818) +Outpt time (%) = 0.0102363 (5.73956) +Other time (%) = 0.150401 (84.3306) + +Nlocal: 108 ave 108 max 108 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 756 ave 756 max 756 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 4212 ave 4379 max 4068 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +FullNghs: 8424 ave 8424 max 8424 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 33696 +Ave neighs/atom = 78 +Neighbor list builds = 0 +Dangerous builds = 0 + variable step equal ${step}+1 + variable step equal 3+1 + change_box all xy delta $d remap + change_box all xy delta 0.0050000000000000001041 remap +Changing box ... + triclinic box = (0 0 0) to (24.48 24.48 12.24) with tilt (0.0816 0 0) + variable gamma equal $i*${dgamma} + variable gamma equal 4*${dgamma} + variable gamma equal 4*0.00020424836601307190163 +next i +jump in.cb_shear loop_i diff --git a/examples/USER/atc/cauchy_born/cb_unistrain.screen b/examples/USER/atc/cauchy_born/cb_unistrain.screen new file mode 100644 index 0000000000..86d7fe8efa --- /dev/null +++ b/examples/USER/atc/cauchy_born/cb_unistrain.screen @@ -0,0 +1,123 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic +# create domain +lattice fcc 5.256227487 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.25623 5.25623 5.25623 +region BOX block -8 8 -2 2 -2 2 +boundary f p p +create_box 1 BOX +Created orthogonal box = (-42.0498 -10.5125 -10.5125) to (42.0498 10.5125 10.5125) + 4 by 1 by 1 MPI processor grid +# create atoms +region MD block -7 7 -2 2 -2 2 +create_atoms 1 region MD +Created 896 atoms +mass 1 39.95 +# specify interal/ghost atoms +region FREE block -6 6 -2 2 -2 2 +group internal region FREE +768 atoms in group internal +# specify inter-atomic potential +pair_style lj/cut 13.5 +pair_coeff 1 1 0.238 3.405 +# specify neighbor/re-neighboring parameters +neighbor 0.3 bin +neigh_modify every 10 delay 0 check no +# setup thermal output +thermo 10 +thermo_style custom step pe ke press lx ly lz +# ID group atc PhysicsType ParameterFile +fix AtC internal atc field Ar_CauchyBorn.mat +ATC: constructing shape function field estimate with parameter file Ar_CauchyBorn.mat + ATC: peratom PE compute created with ID: 3 +fix_modify AtC mesh create 8 1 1 BOX f p p +terminate called after throwing an instance of 'terminate called after throwing an instance of 'ATC::ATC_Error' +terminate called after throwing an instance of 'ATC::ATC_Error' + ATC: P1, ERROR: elastic_deformation_gradient is not a valid field + ATC: P3, ERROR: elastic_deformation_gradient is not a valid field + ATC: created uniform mesh with 36 nodes, 9 unique nodes, and 8 elements +fix_modify AtC fields none +fix_modify AtC fields add displacement +fix_modify AtC fields add internal_energy stress cauchy_born_energy cauchy_born_stress +fix_modify AtC gradients add displacement +fix_modify AtC fields add elastic_deformation_gradient + ATC: P0, ERROR: elastic_deformation_gradient is not a valid field +[pharsalus:35580] *** Process received signal *** +[pharsalus:35580] Signal: Aborted (6) +[pharsalus:35580] Signal code: (-6) +[pharsalus:35582] *** Process received signal *** +[pharsalus:35582] Signal: Aborted (6) +[pharsalus:35582] Signal code: (-6) +ATC::ATC_Error' +[pharsalus:35579] *** Process received signal *** +[pharsalus:35579] Signal: Aborted (6) +[pharsalus:35579] Signal code: (-6) + ATC: P2, ERROR: elastic_deformation_gradient is not a valid field +terminate called after throwing an instance of 'ATC::ATC_Error' +[pharsalus:35581] *** Process received signal *** +[pharsalus:35581] Signal: Aborted (6) +[pharsalus:35581] Signal code: (-6) +[pharsalus:35582] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500] +[pharsalus:35582] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5] +[pharsalus:35582] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085] +[pharsalus:35582] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d] +[pharsalus:35582] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6] +[pharsalus:35582] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13] +[pharsalus:35582] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96] +[pharsalus:35579] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500] +[pharsalus:35579] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5] +[pharsalus:35579] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085] +[pharsalus:35579] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d] +[pharsalus:35579] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6] +[pharsalus:35579] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13] +[pharsalus:35579] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96] +[pharsalus:35579] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x68b090] +[pharsalus:35579] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x6b31d9] +[pharsalus:35579] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x792edb] +[pharsalus:35579] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7949bc] +[pharsalus:35579] [11] ../../../lmp_openmpi(main+0x49) [0x7a28f9] +[pharsalus:35579] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd] +[pharsalus:35579] [13] ../../../lmp_openmpi() [0x537209] +[pharsalus:35579] *** End of error message *** +[pharsalus:35582] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x68b090] +[pharsalus:35582] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x6b31d9] +[pharsalus:35582] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x792edb] +[pharsalus:35582] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7949bc] +[pharsalus:35582] [11] ../../../lmp_openmpi(main+0x49) [0x7a28f9] +[pharsalus:35582] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd] +[pharsalus:35582] [13] ../../../lmp_openmpi() [0x537209] +[pharsalus:35582] *** End of error message *** +[pharsalus:35581] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500] +[pharsalus:35581] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5] +[pharsalus:35581] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085] +[pharsalus:35581] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d] +[pharsalus:35581] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6] +[pharsalus:35581] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13] +[pharsalus:35581] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96] +[pharsalus:35581] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x68b090] +[pharsalus:35581] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x6b31d9] +[pharsalus:35581] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x792edb] +[pharsalus:35581] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7949bc] +[pharsalus:35581] [11] ../../../lmp_openmpi(main+0x49) [0x7a28f9] +[pharsalus:35581] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd] +[pharsalus:35581] [13] ../../../lmp_openmpi() [0x537209] +[pharsalus:35581] *** End of error message *** +-------------------------------------------------------------------------- +mpirun noticed that process rank 2 with PID 35581 on node pharsalus exited on signal 6 (Aborted). +-------------------------------------------------------------------------- +[pharsalus:35580] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500] +[pharsalus:35580] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5] +[pharsalus:35580] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085] +[pharsalus:35580] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d] +[pharsalus:35580] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6] +[pharsalus:35580] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13] +[pharsalus:35580] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96] +[pharsalus:35580] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x68b090] +[pharsalus:35580] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x6b31d9] +[pharsalus:35580] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x792edb] +[pharsalus:35580] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7949bc] +[pharsalus:35580] [11] ../../../lmp_openmpi(main+0x49) [0x7a28f9] +[pharsalus:35580] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd] +[pharsalus:35580] [13] ../../../lmp_openmpi() [0x537209] +[pharsalus:35580] *** End of error message *** diff --git a/examples/USER/atc/cauchy_born/cb_unistrain_eam.screen b/examples/USER/atc/cauchy_born/cb_unistrain_eam.screen new file mode 100644 index 0000000000..ac700f0ab3 --- /dev/null +++ b/examples/USER/atc/cauchy_born/cb_unistrain_eam.screen @@ -0,0 +1,145 @@ +LAMMPS (14 Aug 2013) +units metal +atom_style atomic +# create domain +#lattice fcc 3.615 origin 0.25 0.25 0.25 +lattice fcc 3.615 origin 0.01 0.01 0.01 +Lattice spacing in x,y,z = 3.615 3.615 3.615 +region BOX block -8 8 -2 2 -2 2 +boundary f p p +create_box 1 BOX +Created orthogonal box = (-28.92 -7.23 -7.23) to (28.92 7.23 7.23) + 4 by 1 by 1 MPI processor grid +# create atoms +region MD block -7 7 -2 2 -2 2 +create_atoms 1 region MD +Created 896 atoms +mass 1 63.55 +# specify interal/ghost atoms +region FREE block -6 6 -2 2 -2 2 +group internal region FREE +768 atoms in group internal +# specify inter-atomic potential +pair_style eam +pair_coeff * * ../../../../potentials/Cu_u3.eam +# specify neighbor/re-neighboring parameters +neighbor 0.3 bin +neigh_modify every 10 delay 0 check no +# setup thermal output +thermo 10 +thermo_style custom step pe ke press lx ly lz +# ID group atc PhysicsType ParameterFile +fix AtC internal atc field Cu_CauchyBorn.mat +ATC: constructing shape function field estimate with parameter file Cu_CauchyBorn.mat + ATC: peratom PE compute created with ID: 3 +fix_modify AtC mesh create 8 1 1 BOX f p p + ATC: created uniform mesh with 36 nodes, 9 unique nodes, and 8 elements +#fix_modify AtC kernel quartic_cylinder 10.0 +fix_modify AtC fields none +fix_modify AtC fields add displacement +fix_modify AtC fields add internal_energy stress +fix_modify AtC fields add cauchy_born_energy +fix_modify AtC fields add cauchy_born_stress +fix_modify AtC gradients add displacement +#fix_modify AtC fields add elastic_deformation_gradient +timestep 0.0 +fix_modify AtC output cb_unistrain_eamFE 1 text tensor_components binary + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +log cb_unistrain_eam.log +variable step equal 0 +thermo_style custom step v_step pe ke press lx ly lz +run 1 +Setting up run ... + ATC: CB stiffness: 12.0537 Einstein freq: 2718.63 + ATC: computing bond matrix ...........done +Memory usage per processor = 22.7644 Mbytes +Step step PotEng KinEng Press Lx Ly Lz + 0 0 -3138.143 0 -4765.0913 57.84 14.46 14.46 + 1 0 -3138.143 0 -4765.0913 57.84 14.46 14.46 +Loop time of 0.0273568 on 4 procs for 1 steps with 896 atoms + +Pair time (%) = 0.000983477 (3.595) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000149012 (0.544697) +Outpt time (%) = 0.000116587 (0.426171) +Other time (%) = 0.0261077 (95.4341) + +Nlocal: 224 ave 256 max 192 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 684.75 ave 843 max 484 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 5808 ave 6912 max 4672 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 11616 ave 13824 max 9408 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 46464 +Ave neighs/atom = 51.8571 +Neighbor list builds = 0 +Dangerous builds = 0 +variable step equal ${step}+1 +variable step equal 0+1 +displace_atoms all ramp x -0.1 0.1 x -100 100 +Displacing atoms ... +run 1 +Setting up run ... + ATC: computing bond matrix ...........done +Memory usage per processor = 22.7644 Mbytes +Step step PotEng KinEng Press Lx Ly Lz + 1 1 -3138.1235 0 -5936.0512 57.84 14.46 14.46 + 2 1 -3138.1235 0 -5936.0512 57.84 14.46 14.46 +Loop time of 0.0527597 on 4 procs for 1 steps with 896 atoms + +Pair time (%) = 0.000959635 (1.81888) +Neigh time (%) = 0 (0) +Comm time (%) = 0.00559711 (10.6087) +Outpt time (%) = 0.00891805 (16.9031) +Other time (%) = 0.0372849 (70.6693) + +Nlocal: 224 ave 256 max 192 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 684.75 ave 843 max 484 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 5808 ave 6912 max 4672 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 11616 ave 13824 max 9408 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 46464 +Ave neighs/atom = 51.8571 +Neighbor list builds = 0 +Dangerous builds = 0 +variable step equal ${step}+1 +variable step equal 1+1 +displace_atoms all ramp x -0.1 0.1 x -100 100 +Displacing atoms ... +run 1 +Setting up run ... + ATC: computing bond matrix ...........done +Memory usage per processor = 22.7644 Mbytes +Step step PotEng KinEng Press Lx Ly Lz + 2 2 -3138.0934 0 -7103.7691 57.84 14.46 14.46 + 3 2 -3138.0934 0 -7103.7691 57.84 14.46 14.46 +Loop time of 0.317459 on 4 procs for 1 steps with 896 atoms + +Pair time (%) = 0.0405899 (12.7859) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0319443 (10.0625) +Outpt time (%) = 0.0423202 (13.3309) +Other time (%) = 0.202604 (63.8207) + +Nlocal: 224 ave 256 max 192 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 684.75 ave 843 max 484 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 5808 ave 6912 max 4672 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 11616 ave 13824 max 9408 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 46464 +Ave neighs/atom = 51.8571 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/cauchy_born/cb_unistrain_eam_linear.screen b/examples/USER/atc/cauchy_born/cb_unistrain_eam_linear.screen new file mode 100644 index 0000000000..55d6ec7273 --- /dev/null +++ b/examples/USER/atc/cauchy_born/cb_unistrain_eam_linear.screen @@ -0,0 +1,158 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic +# create domain +lattice fcc 4.08 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 4.08 4.08 4.08 +region BOX block -8 8 -2 2 -2 2 +boundary f p p +create_box 1 BOX +Created orthogonal box = (-32.64 -8.16 -8.16) to (32.64 8.16 8.16) + 4 by 1 by 1 MPI processor grid +# create atoms +region MD block -7 7 -2 2 -2 2 +create_atoms 1 region MD +Created 896 atoms +pair_style eam +pair_coeff * * Au_u3.eam +mass * 196.97 +# specify interal/ghost atoms +region FREE block -6 6 -2 2 -2 2 +group internal region FREE +768 atoms in group internal +# specify inter-atomic potential +# specify neighbor/re-neighboring parameters +neighbor 0.3 bin +neigh_modify every 10 delay 0 check no +# setup thermal output +thermo 10 +thermo_style custom step pe ke press lx ly lz +# ID group atc PhysicsType ParameterFile +fix PP1 internal atc field Au_eam_linear.mat +ATC: constructing shape function field estimate with parameter file Au_eam_linear.mat + ATC: peratom PE compute created with ID: 3 +fix_modify PP1 mesh create 8 1 1 BOX f p p + ATC: created uniform mesh with 36 nodes, 9 unique nodes, and 8 elements +fix_modify PP1 fields add displacement +fix_modify PP1 fields add internal_energy stress cauchy_born_energy cauchy_born_stress +fix_modify PP1 gradients add displacement +fix_modify PP1 set reference_potential_energy 0 # correct cb and messes pe +# ID group atc PhysicsType ParameterFile +fix PP2 internal atc field Au_eam.mat +ATC: constructing shape function field estimate with parameter file Au_eam.mat + ATC: peratom PE compute created with ID: 3 +fix_modify PP2 mesh create 8 1 1 BOX f p p + ATC: created uniform mesh with 36 nodes, 9 unique nodes, and 8 elements +fix_modify PP2 fields add cauchy_born_energy cauchy_born_stress internal_energy +fix_modify PP2 set reference_potential_energy +timestep 0.0 +fix_modify PP1 output cb_unistrain_eam_linearFE 1 text tensor_components binary + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +fix_modify PP2 output cb_unistrain_eam_refFE 1 text tensor_components + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +log cb_unistrain_eam_linear.log +variable step equal 0 +thermo_style custom step v_step pe ke press lx ly lz +run 1 +Setting up run ... + ATC: created cubic stress function: + lammps ATC units + c11=1.14323 0.000478328 + c12=0.990885 0.000414586 + c44=0.279154 0.000116798 + ATC: CB stiffness: 11.5362 Einstein freq: 0.975052 + ATC: computing bond matrix ...........done + ATC: CB stiffness: 11.5362 Einstein freq: 0.975052 +Memory usage per processor = 43.4446 Mbytes +Step step PotEng KinEng Press Lx Ly Lz + 0 0 -3488.8211 0 -387.61198 65.28 16.32 16.32 + 1 0 -3488.8211 0 -387.61198 65.28 16.32 16.32 +Loop time of 0.0171664 on 4 procs for 1 steps with 896 atoms + +Pair time (%) = 0.000946522 (5.51381) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000137866 (0.803114) +Outpt time (%) = 8.52942e-05 (0.496868) +Other time (%) = 0.0159967 (93.1862) + +Nlocal: 224 ave 256 max 192 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 903 ave 1116 max 690 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 5808 ave 6912 max 4672 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 11616 ave 13824 max 9408 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 46464 +Ave neighs/atom = 51.8571 +Neighbor list builds = 0 +Dangerous builds = 0 +variable step equal ${step}+1 +variable step equal 0+1 +displace_atoms all ramp x -0.1 0.1 x -100 100 +Displacing atoms ... +run 1 +Setting up run ... + ATC: computing bond matrix ...........done +Memory usage per processor = 43.4446 Mbytes +Step step PotEng KinEng Press Lx Ly Lz + 1 1 -3488.7472 0 -447.10849 65.28 16.32 16.32 + 2 1 -3488.7472 0 -447.10849 65.28 16.32 16.32 +Loop time of 0.0233803 on 4 procs for 1 steps with 896 atoms + +Pair time (%) = 0.000981331 (4.19726) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000181496 (0.776279) +Outpt time (%) = 0.000347793 (1.48755) +Other time (%) = 0.0218697 (93.5389) + +Nlocal: 224 ave 256 max 192 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 903 ave 1116 max 690 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 5808 ave 6912 max 4672 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 11616 ave 13824 max 9408 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 46464 +Ave neighs/atom = 51.8571 +Neighbor list builds = 0 +Dangerous builds = 0 +variable step equal ${step}+1 +variable step equal 1+1 +displace_atoms all ramp x -0.1 0.1 x -100 100 +Displacing atoms ... +run 1 +Setting up run ... + ATC: computing bond matrix ...........done +Memory usage per processor = 43.4446 Mbytes +Step step PotEng KinEng Press Lx Ly Lz + 2 2 -3488.6569 0 -506.40727 65.28 16.32 16.32 + 3 2 -3488.6569 0 -506.40727 65.28 16.32 16.32 +Loop time of 0.0714502 on 4 procs for 1 steps with 896 atoms + +Pair time (%) = 0.0255377 (35.742) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0149598 (20.9374) +Outpt time (%) = 0.000393927 (0.551331) +Other time (%) = 0.0305588 (42.7693) + +Nlocal: 224 ave 256 max 192 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 903 ave 1116 max 690 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 5808 ave 6912 max 4672 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 11616 ave 13824 max 9408 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 46464 +Ave neighs/atom = 51.8571 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/cauchy_born/cb_unistrain_linear.screen b/examples/USER/atc/cauchy_born/cb_unistrain_linear.screen new file mode 100644 index 0000000000..a592b04775 --- /dev/null +++ b/examples/USER/atc/cauchy_born/cb_unistrain_linear.screen @@ -0,0 +1,161 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic +# create domain +lattice fcc 4.08 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 4.08 4.08 4.08 +region BOX block -8 8 -2 2 -2 2 +boundary f p p +create_box 1 BOX +Created orthogonal box = (-32.64 -8.16 -8.16) to (32.64 8.16 8.16) + 4 by 1 by 1 MPI processor grid +# create atoms +region MD block -7 7 -2 2 -2 2 +create_atoms 1 region MD +Created 896 atoms +#pair_style eam +#pair_coeff * * Au_u3.eam +#pair_style lj/cut/smooth 5.456108274435118 +pair_style lj/smooth/linear 5.456108274435118 +pair_coeff * * 0.7242785984051078 2.598146797350056 +mass * 196.97 +# specify interal/ghost atoms +region FREE block -6 6 -2 2 -2 2 +group internal region FREE +768 atoms in group internal +# specify inter-atomic potential +# specify neighbor/re-neighboring parameters +neighbor 0.3 bin +neigh_modify every 10 delay 0 check no +# setup thermal output +thermo 10 +thermo_style custom step pe ke press lx ly lz +# ID group atc PhysicsType ParameterFile +fix PP1 internal atc field Au_CauchyBorn_linear.mat +ATC: constructing shape function field estimate with parameter file Au_CauchyBorn_linear.mat + ATC: peratom PE compute created with ID: 3 +fix_modify PP1 mesh create 8 1 1 BOX f p p + ATC: created uniform mesh with 36 nodes, 9 unique nodes, and 8 elements +fix_modify PP1 fields add displacement +fix_modify PP1 fields add internal_energy stress cauchy_born_energy cauchy_born_stress +fix_modify PP1 gradients add displacement +fix_modify PP1 set reference_potential_energy 0 # correct cb and messes pe +# ID group atc PhysicsType ParameterFile +fix PP2 internal atc field Au_CauchyBorn.mat +ATC: constructing shape function field estimate with parameter file Au_CauchyBorn.mat + ATC: peratom PE compute created with ID: 3 +fix_modify PP2 mesh create 8 1 1 BOX f p p + ATC: created uniform mesh with 36 nodes, 9 unique nodes, and 8 elements +fix_modify PP2 fields add cauchy_born_energy cauchy_born_stress internal_energy +fix_modify PP2 set reference_potential_energy +timestep 0.0 +fix_modify PP1 output cb_unistrain_linearFE 1 text tensor_components binary + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +fix_modify PP2 output cb_unistrain_refFE 1 text tensor_components + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +log cb_unistrain_linear.log +variable step equal 0 +thermo_style custom step v_step pe ke press lx ly lz +run 1 +Setting up run ... + ATC: created cubic stress function: + lammps ATC units + c11=3.10501 0.00129914 + c12=1.75749 0.000735332 + c44=1.75749 0.000735332 + ATC: CB stiffness: 28.7742 Einstein freq: 1.53992 + ATC: computing bond matrix ...........done + ATC: CB stiffness: 28.7742 Einstein freq: 1.53992 +Memory usage per processor = 43.292 Mbytes +Step step PotEng KinEng Press Lx Ly Lz + 0 0 -3435.8868 0 50.003991 65.28 16.32 16.32 + 1 0 -3435.8868 0 50.003991 65.28 16.32 16.32 +Loop time of 0.0132832 on 4 procs for 1 steps with 896 atoms + +Pair time (%) = 0.000411749 (3.09977) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000149429 (1.12495) +Outpt time (%) = 8.07047e-05 (0.60757) +Other time (%) = 0.0126413 (95.1677) + +Nlocal: 224 ave 256 max 192 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 903 ave 1116 max 690 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 4528 ave 5376 max 3648 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 9056 ave 10752 max 7360 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 36224 +Ave neighs/atom = 40.4286 +Neighbor list builds = 0 +Dangerous builds = 0 +variable step equal ${step}+1 +variable step equal 0+1 +displace_atoms all ramp x -0.1 0.1 x -100 100 +Displacing atoms ... +run 1 +Setting up run ... + ATC: computing bond matrix ...........done +Memory usage per processor = 43.292 Mbytes +Step step PotEng KinEng Press Lx Ly Lz + 1 1 -3435.904 0 -77.521908 65.28 16.32 16.32 + 2 1 -3435.904 0 -77.521908 65.28 16.32 16.32 +Loop time of 0.0176127 on 4 procs for 1 steps with 896 atoms + +Pair time (%) = 0.000424206 (2.40853) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000124991 (0.709664) +Outpt time (%) = 0.000433266 (2.45997) +Other time (%) = 0.0166302 (94.4218) + +Nlocal: 224 ave 256 max 192 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 903 ave 1116 max 690 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 4528 ave 5376 max 3648 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 9056 ave 10752 max 7360 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 36224 +Ave neighs/atom = 40.4286 +Neighbor list builds = 0 +Dangerous builds = 0 +variable step equal ${step}+1 +variable step equal 1+1 +displace_atoms all ramp x -0.1 0.1 x -100 100 +Displacing atoms ... +run 1 +Setting up run ... + ATC: computing bond matrix ...........done +Memory usage per processor = 43.292 Mbytes +Step step PotEng KinEng Press Lx Ly Lz + 2 2 -3435.8757 0 -203.99195 65.28 16.32 16.32 + 3 2 -3435.8757 0 -203.99195 65.28 16.32 16.32 +Loop time of 0.0175297 on 4 procs for 1 steps with 896 atoms + +Pair time (%) = 0.00041151 (2.3475) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000131011 (0.747365) +Outpt time (%) = 0.000337481 (1.9252) +Other time (%) = 0.0166497 (94.9799) + +Nlocal: 224 ave 256 max 192 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 903 ave 1116 max 690 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 4528 ave 5376 max 3648 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 9056 ave 10752 max 7360 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 36224 +Ave neighs/atom = 40.4286 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/cauchy_born/cb_volumetric.screen b/examples/USER/atc/cauchy_born/cb_volumetric.screen new file mode 100644 index 0000000000..3a98a5b338 --- /dev/null +++ b/examples/USER/atc/cauchy_born/cb_volumetric.screen @@ -0,0 +1,389 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic +variable lattice_constant equal 5.256227487 +variable c equal 6 +variable L equal $c*${lattice_constant} +variable L equal 6*${lattice_constant} +variable L equal 6*5.2562274870000003091 +#variable d equal 0.01 +variable d equal 0.005 +variable s equal 1.005 +variable V0 equal ($c*${lattice_constant})^3 +variable V0 equal (6*${lattice_constant})^3 +variable V0 equal (6*5.2562274870000003091)^3 +# create system +lattice fcc ${lattice_constant} origin 0.25 0.25 0.25 +lattice fcc 5.2562274870000003091 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.25623 5.25623 5.25623 +region box block 0 $c 0 $c 0 $c +region box block 0 6 0 $c 0 $c +region box block 0 6 0 6 0 $c +region box block 0 6 0 6 0 6 +boundary p p p +create_box 1 box +Created orthogonal box = (0 0 0) to (31.5374 31.5374 31.5374) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 864 atoms +mass 1 39.95 +group all region box +864 atoms in group all +pair_style lj/cut 13.5 +pair_coeff 1 1 0.238 3.405 +# ID group atc PhysicsType ParameterFile +fix AtC all atc field Ar_CauchyBorn.mat +ATC: constructing shape function field estimate with parameter file Ar_CauchyBorn.mat + ATC: peratom PE compute created with ID: 3 +fix_modify AtC mesh create $c $c $c box p p p +fix_modify AtC mesh create 6 $c $c box p p p +fix_modify AtC mesh create 6 6 $c box p p p +fix_modify AtC mesh create 6 6 6 box p p p + ATC: created uniform mesh with 343 nodes, 216 unique nodes, and 216 elements +fix_modify AtC fields none +fix_modify AtC fields add displacement +fix_modify AtC fields add internal_energy stress cauchy_born_energy cauchy_born_stress +fix_modify AtC gradients add displacement +fix_modify AtC output cb_volumetricFE 1 full_text tensor_components + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +log cb_volumetric.log +thermo 100 +variable gamma equal 0.0 +variable step equal 0 +thermo_style custom step v_step pxx pyy pzz pxy pxz pyz v_gamma pe +timestep 0.0 +min_modify line quadratic +timestep 0.0 +variable i loop 4 +label loop_i + print ">>> step $i" +>>> step 1 + minimize 1.e-20 1.e-20 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7542 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng + 0 0 -4.8909542e-07 -4.8909515e-07 -4.8909708e-07 3.5104429e-13 -1.4141608e-12 -8.6196267e-13 0 -1743.9897 + 1 0 -4.8909445e-07 -4.8909445e-07 -4.8909627e-07 2.4570879e-13 -1.3724298e-12 -8.8539776e-13 0 -1743.9897 +Loop time of 0.152578 on 4 procs for 1 steps with 864 atoms + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -1743.9896675 -1743.9896675 -1743.9896675 + Force two-norm initial, final = 4.7305e-13 3.32302e-13 + Force max component initial, final = 1.93665e-14 1.80689e-14 + Final line search alpha, max atom move = 1 1.80689e-14 + Iterations, force evaluations = 1 2 + +Pair time (%) = 0.00802612 (5.26033) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0638427 (41.8426) +Outpt time (%) = 0 (0) +Other time (%) = 0.0807094 (52.8971) + +Nlocal: 216 ave 216 max 216 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 3672 ave 3672 max 3672 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46224 ave 46224 max 46224 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 92448 ave 92448 max 92448 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 369792 +Ave neighs/atom = 428 +Neighbor list builds = 0 +Dangerous builds = 0 + run 1 +Setting up run ... + ATC: computing bond matrix ...........done +Memory usage per processor = 23.0675 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng + 1 0 -4.8909426e-07 -4.890941e-07 -4.8909627e-07 1.0203176e-13 -1.3879622e-12 -8.8539776e-13 0 -1743.9897 + 2 0 -4.8909426e-07 -4.890941e-07 -4.8909627e-07 1.0203176e-13 -1.3879622e-12 -8.8539776e-13 0 -1743.9897 +Loop time of 1.74483 on 4 procs for 1 steps with 864 atoms + +Pair time (%) = 0.00266743 (0.152876) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0846363 (4.85068) +Outpt time (%) = 0.0165098 (0.946209) +Other time (%) = 1.64102 (94.0502) + +Nlocal: 216 ave 216 max 216 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 3672 ave 3672 max 3672 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46224 ave 46289 max 46159 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +FullNghs: 92448 ave 92448 max 92448 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 369792 +Ave neighs/atom = 428 +Neighbor list builds = 0 +Dangerous builds = 0 + variable step equal ${step}+1 + variable step equal 0+1 + change_box all x scale $s y scale $s z scale $s remap + change_box all x scale 1.0049999999999998934 y scale $s z scale $s remap + change_box all x scale 1.0049999999999998934 y scale 1.0049999999999998934 z scale $s remap + change_box all x scale 1.0049999999999998934 y scale 1.0049999999999998934 z scale 1.0049999999999998934 remap +Changing box ... + orthogonal box = (-0.0788434 0 0) to (31.6162 31.5374 31.5374) + orthogonal box = (-0.0788434 -0.0788434 0) to (31.6162 31.6162 31.5374) + orthogonal box = (-0.0788434 -0.0788434 -0.0788434) to (31.6162 31.6162 31.6162) + variable gamma equal lx/$L-1.0 + variable gamma equal lx/31.537364922000001854-1.0 +next i +jump in.cb_volumetric loop_i + print ">>> step $i" +>>> step 2 + minimize 1.e-20 1.e-20 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7542 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng + 2 1 -429.84615 -429.84615 -429.84615 1.6244616e-13 -2.4910642e-13 -7.3535979e-13 0.005 -1742.4738 + 4 1 -429.84615 -429.84615 -429.84615 -1.2399576e-13 -9.5902644e-13 -1.3896357e-12 0.005 -1742.4738 +Loop time of 1.44839 on 4 procs for 2 steps with 864 atoms + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -1742.47382006 -1742.47382006 -1742.47382006 + Force two-norm initial, final = 5.8003e-13 4.02116e-13 + Force max component initial, final = 2.59532e-14 1.42178e-14 + Final line search alpha, max atom move = 1 1.42178e-14 + Iterations, force evaluations = 2 4 + +Pair time (%) = 0.0205068 (1.41584) +Neigh time (%) = 0 (0) +Comm time (%) = 1.02466 (70.7452) +Outpt time (%) = 0 (0) +Other time (%) = 0.403216 (27.8389) + +Nlocal: 216 ave 216 max 216 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 3672 ave 3672 max 3672 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46224 ave 46281 max 46167 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +FullNghs: 92448 ave 92448 max 92448 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 369792 +Ave neighs/atom = 428 +Neighbor list builds = 0 +Dangerous builds = 0 + run 1 +Setting up run ... + ATC: computing bond matrix ...........done +Memory usage per processor = 23.0675 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng + 4 1 -429.84615 -429.84615 -429.84615 -9.7213572e-14 -9.5902644e-13 -1.3896357e-12 0.005 -1742.4738 + 5 1 -429.84615 -429.84615 -429.84615 -9.7213572e-14 -9.5902644e-13 -1.3896357e-12 0.005 -1742.4738 +Loop time of 2.702 on 4 procs for 1 steps with 864 atoms + +Pair time (%) = 0.00525749 (0.194578) +Neigh time (%) = 0 (0) +Comm time (%) = 0.154782 (5.72844) +Outpt time (%) = 0.149323 (5.52637) +Other time (%) = 2.39264 (88.5506) + +Nlocal: 216 ave 216 max 216 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 3672 ave 3672 max 3672 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46224 ave 46339 max 46109 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +FullNghs: 92448 ave 92448 max 92448 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 369792 +Ave neighs/atom = 428 +Neighbor list builds = 0 +Dangerous builds = 0 + variable step equal ${step}+1 + variable step equal 1+1 + change_box all x scale $s y scale $s z scale $s remap + change_box all x scale 1.0049999999999998934 y scale $s z scale $s remap + change_box all x scale 1.0049999999999998934 y scale 1.0049999999999998934 z scale $s remap + change_box all x scale 1.0049999999999998934 y scale 1.0049999999999998934 z scale 1.0049999999999998934 remap +Changing box ... + orthogonal box = (-0.158081 -0.0788434 -0.0788434) to (31.6954 31.6162 31.6162) + orthogonal box = (-0.158081 -0.158081 -0.0788434) to (31.6954 31.6954 31.6162) + orthogonal box = (-0.158081 -0.158081 -0.158081) to (31.6954 31.6954 31.6954) + variable gamma equal lx/$L-1.0 + variable gamma equal lx/31.537364922000001854-1.0 +next i +jump in.cb_volumetric loop_i + print ">>> step $i" +>>> step 3 + minimize 1.e-20 1.e-20 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7542 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng + 5 2 -778.0092 -778.0092 -778.0092 7.4220526e-13 1.122178e-12 -9.6027588e-13 0.010025 -1730.6001 + 6 2 -778.0092 -778.0092 -778.0092 2.027045e-13 5.1825031e-13 -9.2993731e-13 0.010025 -1730.6001 +Loop time of 0.637543 on 4 procs for 1 steps with 864 atoms + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -1730.60014837 -1730.60014837 -1730.60014837 + Force two-norm initial, final = 8.6018e-13 3.15291e-13 + Force max component initial, final = 4.77673e-14 1.4759e-14 + Final line search alpha, max atom move = 1 1.4759e-14 + Iterations, force evaluations = 1 2 + +Pair time (%) = 0.00699323 (1.0969) +Neigh time (%) = 0 (0) +Comm time (%) = 0.473002 (74.1913) +Outpt time (%) = 0 (0) +Other time (%) = 0.157548 (24.7118) + +Nlocal: 216 ave 216 max 216 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 3672 ave 3672 max 3672 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46224 ave 46339 max 46109 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +FullNghs: 92448 ave 92448 max 92448 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 369792 +Ave neighs/atom = 428 +Neighbor list builds = 0 +Dangerous builds = 0 + run 1 +Setting up run ... + ATC: computing bond matrix ...........done +Memory usage per processor = 23.0675 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng + 6 2 -778.0092 -778.0092 -778.0092 2.7752314e-13 5.1825031e-13 -9.2993731e-13 0.010025 -1730.6001 + 7 2 -778.0092 -778.0092 -778.0092 2.7752314e-13 5.1825031e-13 -9.2993731e-13 0.010025 -1730.6001 +Loop time of 2.39483 on 4 procs for 1 steps with 864 atoms + +Pair time (%) = 0.00456077 (0.190443) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0782377 (3.26694) +Outpt time (%) = 0.0521472 (2.17749) +Other time (%) = 2.25988 (94.3651) + +Nlocal: 216 ave 216 max 216 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 3672 ave 3672 max 3672 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46224 ave 46348 max 46100 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +FullNghs: 92448 ave 92448 max 92448 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 369792 +Ave neighs/atom = 428 +Neighbor list builds = 0 +Dangerous builds = 0 + variable step equal ${step}+1 + variable step equal 2+1 + change_box all x scale $s y scale $s z scale $s remap + change_box all x scale 1.0049999999999998934 y scale $s z scale $s remap + change_box all x scale 1.0049999999999998934 y scale 1.0049999999999998934 z scale $s remap + change_box all x scale 1.0049999999999998934 y scale 1.0049999999999998934 z scale 1.0049999999999998934 remap +Changing box ... + orthogonal box = (-0.237715 -0.158081 -0.158081) to (31.7751 31.6954 31.6954) + orthogonal box = (-0.237715 -0.237715 -0.158081) to (31.7751 31.7751 31.6954) + orthogonal box = (-0.237715 -0.237715 -0.237715) to (31.7751 31.7751 31.7751) + variable gamma equal lx/$L-1.0 + variable gamma equal lx/31.537364922000001854-1.0 +next i +jump in.cb_volumetric loop_i + print ">>> step $i" +>>> step 4 + minimize 1.e-20 1.e-20 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: computing bond matrix ..........done +Memory usage per processor = 23.7542 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng + 7 3 -1113.9681 -1113.9681 -1113.9681 -7.697124e-13 -4.3806097e-13 1.4128091e-12 0.015075125 -1723.8495 + 8 3 -1113.9681 -1113.9681 -1113.9681 6.6266201e-13 4.7186976e-13 2.719048e-12 0.015075125 -1723.8495 +Loop time of 0.00824732 on 4 procs for 1 steps with 864 atoms + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -1723.84952404 -1723.84952404 -1723.84952404 + Force two-norm initial, final = 8.94607e-13 5.41927e-13 + Force max component initial, final = 4.1616e-14 2.31482e-14 + Final line search alpha, max atom move = 1 2.31482e-14 + Iterations, force evaluations = 1 2 + +Pair time (%) = 0.00639701 (77.5647) +Neigh time (%) = 0 (0) +Comm time (%) = 0.00148129 (17.9609) +Outpt time (%) = 0 (0) +Other time (%) = 0.000369012 (4.47433) + +Nlocal: 216 ave 216 max 216 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 3672 ave 3672 max 3672 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 41040 ave 41099 max 40981 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +FullNghs: 82080 ave 82080 max 82080 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 328320 +Ave neighs/atom = 380 +Neighbor list builds = 0 +Dangerous builds = 0 + run 1 +Setting up run ... + ATC: computing bond matrix ..........done +Memory usage per processor = 23.0675 Mbytes +Step step Pxx Pyy Pzz Pxy Pxz Pyz gamma PotEng + 8 3 -1113.9681 -1113.9681 -1113.9681 6.4417311e-13 5.3127209e-13 2.719048e-12 0.015075125 -1723.8495 + 9 3 -1113.9681 -1113.9681 -1113.9681 6.4417311e-13 5.3127209e-13 2.719048e-12 0.015075125 -1723.8495 +Loop time of 1.98395 on 4 procs for 1 steps with 864 atoms + +Pair time (%) = 0.00230694 (0.11628) +Neigh time (%) = 0 (0) +Comm time (%) = 0.00056833 (0.0286464) +Outpt time (%) = 0.050661 (2.55354) +Other time (%) = 1.93041 (97.3015) + +Nlocal: 216 ave 216 max 216 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 3672 ave 3672 max 3672 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 41040 ave 41313 max 40767 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +FullNghs: 82080 ave 82080 max 82080 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 328320 +Ave neighs/atom = 380 +Neighbor list builds = 0 +Dangerous builds = 0 + variable step equal ${step}+1 + variable step equal 3+1 + change_box all x scale $s y scale $s z scale $s remap + change_box all x scale 1.0049999999999998934 y scale $s z scale $s remap + change_box all x scale 1.0049999999999998934 y scale 1.0049999999999998934 z scale $s remap + change_box all x scale 1.0049999999999998934 y scale 1.0049999999999998934 z scale 1.0049999999999998934 remap +Changing box ... + orthogonal box = (-0.317747 -0.237715 -0.237715) to (31.8551 31.7751 31.7751) + orthogonal box = (-0.317747 -0.317747 -0.237715) to (31.8551 31.8551 31.7751) + orthogonal box = (-0.317747 -0.317747 -0.317747) to (31.8551 31.8551 31.8551) + variable gamma equal lx/$L-1.0 + variable gamma equal lx/31.537364922000001854-1.0 +next i +jump in.cb_volumetric loop_i diff --git a/examples/USER/atc/cauchy_born/flying_cube.screen b/examples/USER/atc/cauchy_born/flying_cube.screen new file mode 100644 index 0000000000..4bb47fcb27 --- /dev/null +++ b/examples/USER/atc/cauchy_born/flying_cube.screen @@ -0,0 +1,568 @@ +LAMMPS (14 Aug 2013) +log log.flying_cube +units real +atom_style atomic +variable lattice_constant equal 5.256227487 +variable c equal 6 +variable L equal (${lattice_constant}*$c) +variable L equal (5.2562274870000003091*$c) +variable L equal (5.2562274870000003091*6) +variable V equal $L*$L*$L +variable V equal 31.537364922000001854*$L*$L +variable V equal 31.537364922000001854*31.537364922000001854*$L +variable V equal 31.537364922000001854*31.537364922000001854*31.537364922000001854 +print "Volume : $V" +Volume : 31367.233018713999627 +variable s equal 10 +variable dt equal 0.1 +variable v equal 0.1 +variable m equal 39.95 +# create system +lattice fcc ${lattice_constant} origin 0.01 0.01 0.01 +lattice fcc 5.2562274870000003091 origin 0.01 0.01 0.01 +Lattice spacing in x,y,z = 5.25623 5.25623 5.25623 +region box block 0 $c 0 $c 0 $c +region box block 0 6 0 $c 0 $c +region box block 0 6 0 6 0 $c +region box block 0 6 0 6 0 6 +boundary p p p +# boundary p s s +create_box 1 box +Created orthogonal box = (0 0 0) to (31.5374 31.5374 31.5374) + 1 by 2 by 2 MPI processor grid +create_atoms 1 region box +Created 864 atoms +mass 1 $m +mass 1 39.950000000000002842 +group all region box +864 atoms in group all +pair_style lj/cut 13.5 +pair_coeff 1 1 0.238 3.405 +# define region +neighbor 1.0 bin +neigh_modify delay 0 every 200 check no +# neigh_modify delay 0 every $n +reset_timestep 0 +thermo $s +thermo 10 +compute_modify thermo_temp extra 0 +thermo_style custom step temp pxx pyy pzz etotal lx ly lz +timestep ${dt} +timestep 0.10000000000000000555 +min_modify line quadratic +minimize 0. 0. 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... +Memory usage per processor = 2.90511 Mbytes +Step Temp Pxx Pyy Pzz TotEng Lx Ly Lz + 0 0 -4.8909602e-07 -4.8909602e-07 -4.8909727e-07 -1743.9897 31.537365 31.537365 31.537365 + 10 0 -4.8910206e-07 -4.8910173e-07 -4.891027e-07 -1743.9897 31.537365 31.537365 31.537365 + 20 0 -4.8910163e-07 -4.8910171e-07 -4.8910289e-07 -1743.9897 31.537365 31.537365 31.537365 + 30 0 -4.8910045e-07 -4.8910034e-07 -4.8910129e-07 -1743.9897 31.537365 31.537365 31.537365 + 40 0 -4.8910136e-07 -4.891012e-07 -4.8910284e-07 -1743.9897 31.537365 31.537365 31.537365 + 50 0 -4.8910093e-07 -4.8910075e-07 -4.8910206e-07 -1743.9897 31.537365 31.537365 31.537365 + 60 0 -4.8910118e-07 -4.8910068e-07 -4.8910206e-07 -1743.9897 31.537365 31.537365 31.537365 + 70 0 -4.8910152e-07 -4.891015e-07 -4.8910292e-07 -1743.9897 31.537365 31.537365 31.537365 + 80 0 -4.8910039e-07 -4.891003e-07 -4.8910152e-07 -1743.9897 31.537365 31.537365 31.537365 + 90 0 -4.8910067e-07 -4.8910044e-07 -4.891015e-07 -1743.9897 31.537365 31.537365 31.537365 + 100 0 -4.8910167e-07 -4.8910159e-07 -4.8910289e-07 -1743.9897 31.537365 31.537365 31.537365 + 110 0 -4.8910086e-07 -4.8910059e-07 -4.8910202e-07 -1743.9897 31.537365 31.537365 31.537365 + 120 0 -4.8910062e-07 -4.8910061e-07 -4.8910155e-07 -1743.9897 31.537365 31.537365 31.537365 + 130 0 -4.8910107e-07 -4.8910086e-07 -4.8910219e-07 -1743.9897 31.537365 31.537365 31.537365 + 140 0 -4.8910086e-07 -4.8910076e-07 -4.8910157e-07 -1743.9897 31.537365 31.537365 31.537365 + 150 0 -4.8910119e-07 -4.8910116e-07 -4.8910235e-07 -1743.9897 31.537365 31.537365 31.537365 + 160 0 -4.8910081e-07 -4.8910037e-07 -4.8910204e-07 -1743.9897 31.537365 31.537365 31.537365 + 170 0 -4.8910074e-07 -4.8910056e-07 -4.891015e-07 -1743.9897 31.537365 31.537365 31.537365 + 180 0 -4.8910116e-07 -4.8910096e-07 -4.8910206e-07 -1743.9897 31.537365 31.537365 31.537365 + 190 0 -4.8910145e-07 -4.8910125e-07 -4.8910243e-07 -1743.9897 31.537365 31.537365 31.537365 + 200 0 -4.891014e-07 -4.8910125e-07 -4.8910228e-07 -1743.9897 31.537365 31.537365 31.537365 + 210 0 -4.8910087e-07 -4.8910055e-07 -4.8910194e-07 -1743.9897 31.537365 31.537365 31.537365 + 220 0 -4.8910114e-07 -4.8910114e-07 -4.8910217e-07 -1743.9897 31.537365 31.537365 31.537365 + 230 0 -4.8910091e-07 -4.8910061e-07 -4.8910186e-07 -1743.9897 31.537365 31.537365 31.537365 + 240 0 -4.8909998e-07 -4.8909969e-07 -4.8910083e-07 -1743.9897 31.537365 31.537365 31.537365 + 250 0 -4.8910075e-07 -4.8910067e-07 -4.8910187e-07 -1743.9897 31.537365 31.537365 31.537365 + 260 0 -4.8910094e-07 -4.8910053e-07 -4.8910199e-07 -1743.9897 31.537365 31.537365 31.537365 + 270 0 -4.8910052e-07 -4.8910007e-07 -4.8910129e-07 -1743.9897 31.537365 31.537365 31.537365 + 280 0 -4.8910008e-07 -4.8910018e-07 -4.8910121e-07 -1743.9897 31.537365 31.537365 31.537365 + 290 0 -4.8910141e-07 -4.8910101e-07 -4.8910247e-07 -1743.9897 31.537365 31.537365 31.537365 + 300 0 -4.8910129e-07 -4.8910131e-07 -4.8910231e-07 -1743.9897 31.537365 31.537365 31.537365 + 310 0 -4.8910076e-07 -4.8910049e-07 -4.8910202e-07 -1743.9897 31.537365 31.537365 31.537365 + 320 0 -4.8910069e-07 -4.8910069e-07 -4.8910182e-07 -1743.9897 31.537365 31.537365 31.537365 + 330 0 -4.8910161e-07 -4.891015e-07 -4.8910243e-07 -1743.9897 31.537365 31.537365 31.537365 + 340 0 -4.8910108e-07 -4.8910082e-07 -4.8910234e-07 -1743.9897 31.537365 31.537365 31.537365 + 350 0 -4.8910041e-07 -4.891003e-07 -4.891015e-07 -1743.9897 31.537365 31.537365 31.537365 + 360 0 -4.8910112e-07 -4.8910093e-07 -4.8910167e-07 -1743.9897 31.537365 31.537365 31.537365 + 370 0 -4.8910094e-07 -4.8910056e-07 -4.8910189e-07 -1743.9897 31.537365 31.537365 31.537365 + 380 0 -4.8910084e-07 -4.8910062e-07 -4.8910171e-07 -1743.9897 31.537365 31.537365 31.537365 + 390 0 -4.8910136e-07 -4.8910096e-07 -4.8910228e-07 -1743.9897 31.537365 31.537365 31.537365 + 400 0 -4.8910095e-07 -4.8910088e-07 -4.8910169e-07 -1743.9897 31.537365 31.537365 31.537365 + 410 0 -4.8910022e-07 -4.8910021e-07 -4.891012e-07 -1743.9897 31.537365 31.537365 31.537365 + 420 0 -4.8910064e-07 -4.8910021e-07 -4.8910148e-07 -1743.9897 31.537365 31.537365 31.537365 + 430 0 -4.8910133e-07 -4.8910124e-07 -4.8910259e-07 -1743.9897 31.537365 31.537365 31.537365 + 440 0 -4.8910157e-07 -4.8910149e-07 -4.8910257e-07 -1743.9897 31.537365 31.537365 31.537365 + 450 0 -4.8910088e-07 -4.8910081e-07 -4.8910183e-07 -1743.9897 31.537365 31.537365 31.537365 + 460 0 -4.8910078e-07 -4.8910056e-07 -4.8910168e-07 -1743.9897 31.537365 31.537365 31.537365 + 470 0 -4.8910048e-07 -4.8910015e-07 -4.8910164e-07 -1743.9897 31.537365 31.537365 31.537365 + 480 0 -4.8910054e-07 -4.8910048e-07 -4.8910165e-07 -1743.9897 31.537365 31.537365 31.537365 + 490 0 -4.8910103e-07 -4.8910094e-07 -4.8910185e-07 -1743.9897 31.537365 31.537365 31.537365 + 500 0 -4.8910081e-07 -4.8910044e-07 -4.891017e-07 -1743.9897 31.537365 31.537365 31.537365 +Loop time of 4.18888 on 4 procs for 500 steps with 864 atoms + +Minimization stats: + Stopping criterion = max force evaluations + Energy initial, next-to-last, final = + -1743.9896675 -1743.9896675 -1743.9896675 + Force two-norm initial, final = 4.69398e-13 3.47977e-13 + Force max component initial, final = 2.08236e-14 1.74791e-14 + Final line search alpha, max atom move = 1 1.74791e-14 + Iterations, force evaluations = 500 1000 + +Pair time (%) = 2.3942 (57.1561) +Neigh time (%) = 0 (0) +Comm time (%) = 1.44252 (34.4369) +Outpt time (%) = 0.00359005 (0.0857043) +Other time (%) = 0.348568 (8.32127) + +Nlocal: 216 ave 216 max 216 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 3107 ave 3107 max 3107 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 39744 ave 39744 max 39744 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 158976 +Ave neighs/atom = 184 +Neighbor list builds = 0 +Dangerous builds = 0 +reset_timestep 0 +variable xLO equal xlo +variable xHI equal xhi +variable yLO equal ylo +variable yHI equal yhi +variable zLO equal zlo +variable zHI equal zhi +# region BOX block ${xLO} ${xHI} ${yLO} ${yHI} ${zLO} ${zHI} units box +region BOX block ${xLO} ${xHI} -0.5 31.7 -0.5 31.7 units box +region BOX block 0 ${xHI} -0.5 31.7 -0.5 31.7 units box +region BOX block 0 31.537364922000001854 -0.5 31.7 -0.5 31.7 units box +fix ATC all atc field +ATC: constructing shape function field estimate + ATC: peratom PE compute created with ID: 3 +fix_modify ATC mesh create 1 1 1 box p p p + ATC: created uniform mesh with 8 nodes, 1 unique nodes, and 1 elements +fix_modify ATC fields add stress velocity displacement +fix_modify ATC fields add temperature kinetic_temperature +fix_modify ATC fields add internal_energy energy +fix_modify ATC output flying_cubeFE $s text binary tensor_components +fix_modify ATC output flying_cubeFE 10 text binary tensor_components + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +# fix_modify ATC atomic_output flying_cubeMD $m text binary tensor_components +dump dumpfc all atom $s flying_cube.dmp +dump dumpfc all atom 10 flying_cube.dmp +velocity all set $v 0.0 0.0 units box +velocity all set 0.10000000000000000555 0.0 0.0 units box +fix NVE all nve +run 3500 +Setting up run ... + ATC: computing bond matrix ...........done +Memory usage per processor = 23.3621 Mbytes +Step Temp Pxx Pyy Pzz TotEng Lx Ly Lz + 0 160162.49 1803377.9 -4.8910028e-07 -4.8910148e-07 410741.67 31.537365 31.537365 31.537365 + 10 160162.49 1803377.9 -4.891001e-07 -4.8910151e-07 410741.67 31.537365 31.537365 31.537365 + 20 160162.49 1803377.9 -4.8910035e-07 -4.8910193e-07 410741.67 31.537365 31.537365 31.537365 + 30 160162.49 1803377.9 -4.8909978e-07 -4.8910135e-07 410741.67 31.537365 31.537365 31.537365 + 40 160162.49 1803377.9 -4.8910011e-07 -4.8910149e-07 410741.67 31.537365 31.537365 31.537365 + 50 160162.49 1803377.9 -4.8910063e-07 -4.8910222e-07 410741.67 31.537365 31.537365 31.537365 + 60 160162.49 1803377.9 -4.8910116e-07 -4.8910273e-07 410741.67 31.537365 31.537365 31.537365 + 70 160162.49 1803377.9 -4.8909952e-07 -4.8910063e-07 410741.67 31.537365 31.537365 31.537365 + 80 160162.49 1803377.9 -4.8909944e-07 -4.8910079e-07 410741.67 31.537365 31.537365 31.537365 + 90 160162.49 1803377.9 -4.8909983e-07 -4.8910138e-07 410741.67 31.537365 31.537365 31.537365 + 100 160162.49 1803377.9 -4.8910034e-07 -4.8910169e-07 410741.67 31.537365 31.537365 31.537365 + 110 160162.49 1803377.9 -4.89101e-07 -4.8910251e-07 410741.67 31.537365 31.537365 31.537365 + 120 160162.49 1803377.9 -4.8910056e-07 -4.8910197e-07 410741.67 31.537365 31.537365 31.537365 + 130 160162.49 1803377.9 -4.8909949e-07 -4.8910097e-07 410741.67 31.537365 31.537365 31.537365 + 140 160162.49 1803377.9 -4.8909962e-07 -4.891013e-07 410741.67 31.537365 31.537365 31.537365 + 150 160162.49 1803377.9 -4.8910071e-07 -4.8910266e-07 410741.67 31.537365 31.537365 31.537365 + 160 160162.49 1803377.9 -4.8910088e-07 -4.8910202e-07 410741.67 31.537365 31.537365 31.537365 + 170 160162.49 1803377.9 -4.8910129e-07 -4.8910258e-07 410741.67 31.537365 31.537365 31.537365 + 180 160162.49 1803377.9 -4.890993e-07 -4.8910071e-07 410741.67 31.537365 31.537365 31.537365 + 190 160162.49 1803377.9 -4.8909971e-07 -4.8910093e-07 410741.67 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + 200 160162.49 1803377.9 -4.891008e-07 -4.8910283e-07 410741.67 31.537365 31.537365 31.537365 + 210 160162.49 1803377.9 -4.890997e-07 -4.8910144e-07 410741.67 31.537365 31.537365 31.537365 + 220 160162.49 1803377.9 -4.8910119e-07 -4.8910291e-07 410741.67 31.537365 31.537365 31.537365 + 230 160162.49 1803377.9 -4.8909943e-07 -4.8910089e-07 410741.67 31.537365 31.537365 31.537365 + 240 160162.49 1803377.9 -4.8910063e-07 -4.8910215e-07 410741.67 31.537365 31.537365 31.537365 + 250 160162.49 1803377.9 -4.8909965e-07 -4.8910022e-07 410741.67 31.537365 31.537365 31.537365 + 260 160162.49 1803377.9 -4.891006e-07 -4.891015e-07 410741.67 31.537365 31.537365 31.537365 + 270 160162.49 1803377.9 -4.8909947e-07 -4.8910024e-07 410741.67 31.537365 31.537365 31.537365 + 280 160162.49 1803377.9 -4.8910084e-07 -4.8910122e-07 410741.67 31.537365 31.537365 31.537365 + 290 160162.49 1803377.9 -4.8909975e-07 -4.8910054e-07 410741.67 31.537365 31.537365 31.537365 + 300 160162.49 1803377.9 -4.8910072e-07 -4.8910181e-07 410741.67 31.537365 31.537365 31.537365 + 310 160162.49 1803377.9 -4.8909944e-07 -4.8910007e-07 410741.67 31.537365 31.537365 31.537365 + 320 160162.49 1803377.9 -4.8910063e-07 -4.8910138e-07 410741.67 31.537365 31.537365 31.537365 + 330 160162.49 1803377.9 -4.8909953e-07 -4.8910017e-07 410741.67 31.537365 31.537365 31.537365 + 340 160162.49 1803377.9 -4.891006e-07 -4.8910125e-07 410741.67 31.537365 31.537365 31.537365 + 350 160162.49 1803377.9 -4.8909961e-07 -4.8910025e-07 410741.67 31.537365 31.537365 31.537365 + 360 160162.49 1803377.9 -4.8910103e-07 -4.8910158e-07 410741.67 31.537365 31.537365 31.537365 + 370 160162.49 1803377.9 -4.8909975e-07 -4.8910072e-07 410741.67 31.537365 31.537365 31.537365 + 380 160162.49 1803377.9 -4.8910078e-07 -4.8910186e-07 410741.67 31.537365 31.537365 31.537365 + 390 160162.49 1803377.9 -4.8909978e-07 -4.8910066e-07 410741.67 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + 400 160162.49 1803377.9 -4.8910055e-07 -4.891012e-07 410741.67 31.537365 31.537365 31.537365 + 410 160162.49 1803377.9 -4.8910124e-07 -4.8910227e-07 410741.67 31.537365 31.537365 31.537365 + 420 160162.49 1803377.9 -4.8910154e-07 -4.8910257e-07 410741.67 31.537365 31.537365 31.537365 + 430 160162.49 1803377.9 -4.8909931e-07 -4.8910036e-07 410741.67 31.537365 31.537365 31.537365 + 440 160162.49 1803377.9 -4.8909944e-07 -4.8910102e-07 410741.67 31.537365 31.537365 31.537365 + 450 160162.49 1803377.9 -4.8910046e-07 -4.8910127e-07 410741.67 31.537365 31.537365 31.537365 + 460 160162.49 1803377.9 -4.8910099e-07 -4.8910172e-07 410741.67 31.537365 31.537365 31.537365 + 470 160162.49 1803377.9 -4.890996e-07 -4.8910061e-07 410741.67 31.537365 31.537365 31.537365 + 480 160162.49 1803377.9 -4.8910115e-07 -4.8910244e-07 410741.67 31.537365 31.537365 31.537365 + 490 160162.49 1803377.9 -4.890994e-07 -4.8910022e-07 410741.67 31.537365 31.537365 31.537365 + 500 160162.49 1803377.9 -4.8910113e-07 -4.8910185e-07 410741.67 31.537365 31.537365 31.537365 + 510 160162.49 1803377.9 -4.8909993e-07 -4.8910122e-07 410741.67 31.537365 31.537365 31.537365 + 520 160162.49 1803377.9 -4.8910114e-07 -4.891021e-07 410741.67 31.537365 31.537365 31.537365 + 530 160162.49 1803377.9 -4.8909951e-07 -4.8910036e-07 410741.67 31.537365 31.537365 31.537365 + 540 160162.49 1803377.9 -4.8910118e-07 -4.891021e-07 410741.67 31.537365 31.537365 31.537365 + 550 160162.49 1803377.9 -4.8909977e-07 -4.8910067e-07 410741.67 31.537365 31.537365 31.537365 + 560 160162.49 1803377.9 -4.891014e-07 -4.8910218e-07 410741.67 31.537365 31.537365 31.537365 + 570 160162.49 1803377.9 -4.8910006e-07 -4.8910084e-07 410741.67 31.537365 31.537365 31.537365 + 580 160162.49 1803377.9 -4.8910121e-07 -4.8910187e-07 410741.67 31.537365 31.537365 31.537365 + 590 160162.49 1803377.9 -4.8910007e-07 -4.8910063e-07 410741.67 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + 600 160162.49 1803377.9 -4.8910068e-07 -4.8910167e-07 410741.67 31.537365 31.537365 31.537365 + 610 160162.49 1803377.9 -4.8910136e-07 -4.891022e-07 410741.67 31.537365 31.537365 31.537365 + 620 160162.49 1803377.9 -4.891021e-07 -4.8910323e-07 410741.67 31.537365 31.537365 31.537365 + 630 160162.49 1803377.9 -4.8910001e-07 -4.8910121e-07 410741.67 31.537365 31.537365 31.537365 + 640 160162.49 1803377.9 -4.8910029e-07 -4.8910124e-07 410741.67 31.537365 31.537365 31.537365 + 650 160162.49 1803377.9 -4.8910081e-07 -4.8910162e-07 410741.67 31.537365 31.537365 31.537365 + 660 160162.49 1803377.9 -4.8910154e-07 -4.8910247e-07 410741.67 31.537365 31.537365 31.537365 + 670 160162.49 1803377.9 -4.8910161e-07 -4.8910291e-07 410741.67 31.537365 31.537365 31.537365 + 680 160162.49 1803377.9 -4.8910203e-07 -4.8910281e-07 410741.67 31.537365 31.537365 31.537365 + 690 160162.49 1803377.9 -4.8910016e-07 -4.8910122e-07 410741.67 31.537365 31.537365 31.537365 + 700 160162.49 1803377.9 -4.8910066e-07 -4.8910144e-07 410741.67 31.537365 31.537365 31.537365 + 710 160162.49 1803377.9 -4.891009e-07 -4.8910203e-07 410741.67 31.537365 31.537365 31.537365 + 720 160162.49 1803377.9 -4.8910149e-07 -4.8910252e-07 410741.67 31.537365 31.537365 31.537365 + 730 160162.49 1803377.9 -4.8910048e-07 -4.8910151e-07 410741.67 31.537365 31.537365 31.537365 + 740 160162.49 1803377.9 -4.8910177e-07 -4.8910298e-07 410741.67 31.537365 31.537365 31.537365 + 750 160162.49 1803377.9 -4.891001e-07 -4.8910128e-07 410741.67 31.537365 31.537365 31.537365 + 760 160162.49 1803377.9 -4.8910154e-07 -4.8910271e-07 410741.67 31.537365 31.537365 31.537365 + 770 160162.49 1803377.9 -4.8910033e-07 -4.8910152e-07 410741.67 31.537365 31.537365 31.537365 + 780 160162.49 1803377.9 -4.8910155e-07 -4.8910272e-07 410741.67 31.537365 31.537365 31.537365 + 790 160162.49 1803377.9 -4.8910029e-07 -4.89101e-07 410741.67 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + 800 160162.49 1803377.9 -4.8910078e-07 -4.8910154e-07 410741.67 31.537365 31.537365 31.537365 + 810 160162.49 1803377.9 -4.891018e-07 -4.8910281e-07 410741.67 31.537365 31.537365 31.537365 + 820 160162.49 1803377.9 -4.891006e-07 -4.8910146e-07 410741.67 31.537365 31.537365 31.537365 + 830 160162.49 1803377.9 -4.8910022e-07 -4.891007e-07 410741.67 31.537365 31.537365 31.537365 + 840 160162.49 1803377.9 -4.8910043e-07 -4.891009e-07 410741.67 31.537365 31.537365 31.537365 + 850 160162.49 1803377.9 -4.8910087e-07 -4.8910142e-07 410741.67 31.537365 31.537365 31.537365 + 860 160162.49 1803377.9 -4.8910141e-07 -4.8910245e-07 410741.67 31.537365 31.537365 31.537365 + 870 160162.49 1803377.9 -4.8910209e-07 -4.8910276e-07 410741.67 31.537365 31.537365 31.537365 + 880 160162.49 1803377.9 -4.891025e-07 -4.8910339e-07 410741.67 31.537365 31.537365 31.537365 + 890 160162.49 1803377.9 -4.8910017e-07 -4.8910105e-07 410741.67 31.537365 31.537365 31.537365 + 900 160162.49 1803377.9 -4.8910109e-07 -4.8910178e-07 410741.67 31.537365 31.537365 31.537365 + 910 160162.49 1803377.9 -4.891016e-07 -4.8910262e-07 410741.67 31.537365 31.537365 31.537365 + 920 160162.49 1803377.9 -4.8910171e-07 -4.891025e-07 410741.67 31.537365 31.537365 31.537365 + 930 160162.49 1803377.9 -4.8910262e-07 -4.8910309e-07 410741.67 31.537365 31.537365 31.537365 + 940 160162.49 1803377.9 -4.8910059e-07 -4.891009e-07 410741.67 31.537365 31.537365 31.537365 + 950 160162.49 1803377.9 -4.8910111e-07 -4.8910188e-07 410741.67 31.537365 31.537365 31.537365 + 960 160162.49 1803377.9 -4.8910107e-07 -4.8910157e-07 410741.67 31.537365 31.537365 31.537365 + 970 160162.49 1803377.9 -4.891018e-07 -4.8910219e-07 410741.67 31.537365 31.537365 31.537365 + 980 160162.49 1803377.9 -4.8910204e-07 -4.8910243e-07 410741.67 31.537365 31.537365 31.537365 + 990 160162.49 1803377.9 -4.8910035e-07 -4.8910071e-07 410741.67 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + 1000 160162.49 1803377.9 -4.8910205e-07 -4.8910244e-07 410741.67 31.537365 31.537365 31.537365 + 1010 160162.49 1803377.9 -4.8910037e-07 -4.8910126e-07 410741.67 31.537365 31.537365 31.537365 + 1020 160162.49 1803377.9 -4.8910181e-07 -4.8910224e-07 410741.67 31.537365 31.537365 31.537365 + 1030 160162.49 1803377.9 -4.891006e-07 -4.8910102e-07 410741.67 31.537365 31.537365 31.537365 + 1040 160162.49 1803377.9 -4.8910185e-07 -4.8910239e-07 410741.67 31.537365 31.537365 31.537365 + 1050 160162.49 1803377.9 -4.8910046e-07 -4.8910089e-07 410741.67 31.537365 31.537365 31.537365 + 1060 160162.49 1803377.9 -4.8910166e-07 -4.8910217e-07 410741.67 31.537365 31.537365 31.537365 + 1070 160162.49 1803377.9 -4.8910042e-07 -4.8910091e-07 410741.67 31.537365 31.537365 31.537365 + 1080 160162.49 1803377.9 -4.8910181e-07 -4.8910253e-07 410741.67 31.537365 31.537365 31.537365 + 1090 160162.49 1803377.9 -4.8910038e-07 -4.8910121e-07 410741.67 31.537365 31.537365 31.537365 + 1100 160162.49 1803377.9 -4.8910188e-07 -4.8910256e-07 410741.67 31.537365 31.537365 31.537365 + 1110 160162.49 1803377.9 -4.891003e-07 -4.8910088e-07 410741.67 31.537365 31.537365 31.537365 + 1120 160162.49 1803377.9 -4.8910208e-07 -4.8910255e-07 410741.67 31.537365 31.537365 31.537365 + 1130 160162.49 1803377.9 -4.8910067e-07 -4.8910136e-07 410741.67 31.537365 31.537365 31.537365 + 1140 160162.49 1803377.9 -4.8910201e-07 -4.8910268e-07 410741.67 31.537365 31.537365 31.537365 + 1150 160162.49 1803377.9 -4.8910075e-07 -4.8910121e-07 410741.67 31.537365 31.537365 31.537365 + 1160 160162.49 1803377.9 -4.8910156e-07 -4.8910235e-07 410741.67 31.537365 31.537365 31.537365 + 1170 160162.49 1803377.9 -4.8910063e-07 -4.8910163e-07 410741.67 31.537365 31.537365 31.537365 + 1180 160162.49 1803377.9 -4.8910186e-07 -4.8910287e-07 410741.67 31.537365 31.537365 31.537365 + 1190 160162.49 1803377.9 -4.8910059e-07 -4.8910133e-07 410741.67 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + 1200 160162.49 1803377.9 -4.8910131e-07 -4.8910218e-07 410741.67 31.537365 31.537365 31.537365 + 1210 160162.49 1803377.9 -4.8910182e-07 -4.8910275e-07 410741.67 31.537365 31.537365 31.537365 + 1220 160162.49 1803377.9 -4.8910251e-07 -4.891035e-07 410741.67 31.537365 31.537365 31.537365 + 1230 160162.49 1803377.9 -4.8910028e-07 -4.8910127e-07 410741.67 31.537365 31.537365 31.537365 + 1240 160162.49 1803377.9 -4.8910048e-07 -4.8910147e-07 410741.67 31.537365 31.537365 31.537365 + 1250 160162.49 1803377.9 -4.8910121e-07 -4.8910181e-07 410741.67 31.537365 31.537365 31.537365 + 1260 160162.49 1803377.9 -4.8909966e-07 -4.8910047e-07 410741.67 31.537365 31.537365 31.537365 + 1270 160162.49 1803377.9 -4.8910146e-07 -4.8910223e-07 410741.67 31.537365 31.537365 31.537365 + 1280 160162.49 1803377.9 -4.8909992e-07 -4.8910094e-07 410741.67 31.537365 31.537365 31.537365 + 1290 160162.49 1803377.9 -4.8910138e-07 -4.891019e-07 410741.67 31.537365 31.537365 31.537365 + 1300 160162.49 1803377.9 -4.891001e-07 -4.8910051e-07 410741.67 31.537365 31.537365 31.537365 + 1310 160162.49 1803377.9 -4.8910147e-07 -4.8910247e-07 410741.67 31.537365 31.537365 31.537365 + 1320 160162.49 1803377.9 -4.8909992e-07 -4.8910037e-07 410741.67 31.537365 31.537365 31.537365 + 1330 160162.49 1803377.9 -4.891013e-07 -4.8910207e-07 410741.67 31.537365 31.537365 31.537365 + 1340 160162.49 1803377.9 -4.8910014e-07 -4.8910084e-07 410741.67 31.537365 31.537365 31.537365 + 1350 160162.49 1803377.9 -4.8910161e-07 -4.891024e-07 410741.67 31.537365 31.537365 31.537365 + 1360 160162.49 1803377.9 -4.8909974e-07 -4.8910055e-07 410741.67 31.537365 31.537365 31.537365 + 1370 160162.49 1803377.9 -4.8910123e-07 -4.8910198e-07 410741.67 31.537365 31.537365 31.537365 + 1380 160162.49 1803377.9 -4.891002e-07 -4.8910066e-07 410741.67 31.537365 31.537365 31.537365 + 1390 160162.49 1803377.9 -4.8910142e-07 -4.8910185e-07 410741.67 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + 1400 160162.49 1803377.9 -4.8910123e-07 -4.8910178e-07 410741.67 31.537365 31.537365 31.537365 + 1410 160162.49 1803377.9 -4.8910199e-07 -4.8910214e-07 410741.67 31.537365 31.537365 31.537365 + 1420 160162.49 1803377.9 -4.8910181e-07 -4.8910242e-07 410741.67 31.537365 31.537365 31.537365 + 1430 160162.49 1803377.9 -4.8909979e-07 -4.8910018e-07 410741.67 31.537365 31.537365 31.537365 + 1440 160162.49 1803377.9 -4.8910055e-07 -4.8910117e-07 410741.67 31.537365 31.537365 31.537365 + 1450 160162.49 1803377.9 -4.8910125e-07 -4.8910179e-07 410741.67 31.537365 31.537365 31.537365 + 1460 160162.49 1803377.9 -4.8910148e-07 -4.8910232e-07 410741.67 31.537365 31.537365 31.537365 + 1470 160162.49 1803377.9 -4.8910211e-07 -4.8910265e-07 410741.67 31.537365 31.537365 31.537365 + 1480 160162.49 1803377.9 -4.8910259e-07 -4.8910328e-07 410741.67 31.537365 31.537365 31.537365 + 1490 160162.49 1803377.9 -4.8910061e-07 -4.8910073e-07 410741.67 31.537365 31.537365 31.537365 + 1500 160162.49 1803377.9 -4.8910132e-07 -4.8910159e-07 410741.67 31.537365 31.537365 31.537365 + 1510 160162.49 1803377.9 -4.8910164e-07 -4.8910222e-07 410741.67 31.537365 31.537365 31.537365 + 1520 160162.49 1803377.9 -4.8910047e-07 -4.8910077e-07 410741.67 31.537365 31.537365 31.537365 + 1530 160162.49 1803377.9 -4.8910171e-07 -4.891024e-07 410741.67 31.537365 31.537365 31.537365 + 1540 160162.49 1803377.9 -4.8910063e-07 -4.8910124e-07 410741.67 31.537365 31.537365 31.537365 + 1550 160162.49 1803377.9 -4.8910194e-07 -4.8910254e-07 410741.67 31.537365 31.537365 31.537365 + 1560 160162.49 1803377.9 -4.8910033e-07 -4.891013e-07 410741.67 31.537365 31.537365 31.537365 + 1570 160162.49 1803377.9 -4.8910162e-07 -4.8910241e-07 410741.67 31.537365 31.537365 31.537365 + 1580 160162.49 1803377.9 -4.8910061e-07 -4.8910107e-07 410741.67 31.537365 31.537365 31.537365 + 1590 160162.49 1803377.9 -4.891018e-07 -4.8910259e-07 410741.67 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + 1600 160162.49 1803377.9 -4.8910144e-07 -4.8910146e-07 410741.67 31.537365 31.537365 31.537365 + 1610 160162.49 1803377.9 -4.8910161e-07 -4.8910185e-07 410741.67 31.537365 31.537365 31.537365 + 1620 160162.49 1803377.9 -4.8910094e-07 -4.8910177e-07 410741.67 31.537365 31.537365 31.537365 + 1630 160162.49 1803377.9 -4.8910123e-07 -4.8910162e-07 410741.67 31.537365 31.537365 31.537365 + 1640 160162.49 1803377.9 -4.8910206e-07 -4.8910241e-07 410741.67 31.537365 31.537365 31.537365 + 1650 160162.49 1803377.9 -4.8910246e-07 -4.8910282e-07 410741.67 31.537365 31.537365 31.537365 + 1660 160162.49 1803377.9 -4.891003e-07 -4.8910094e-07 410741.67 31.537365 31.537365 31.537365 + 1670 160162.49 1803377.9 -4.8910089e-07 -4.8910128e-07 410741.67 31.537365 31.537365 31.537365 + 1680 160162.49 1803377.9 -4.8910108e-07 -4.8910139e-07 410741.67 31.537365 31.537365 31.537365 + 1690 160162.49 1803377.9 -4.8910193e-07 -4.8910257e-07 410741.67 31.537365 31.537365 31.537365 + 1700 160162.49 1803377.9 -4.8910253e-07 -4.89103e-07 410741.67 31.537365 31.537365 31.537365 + 1710 160162.49 1803377.9 -4.8910023e-07 -4.8910072e-07 410741.67 31.537365 31.537365 31.537365 + 1720 160162.49 1803377.9 -4.8910078e-07 -4.8910154e-07 410741.67 31.537365 31.537365 31.537365 + 1730 160162.49 1803377.9 -4.8910159e-07 -4.8910181e-07 410741.67 31.537365 31.537365 31.537365 + 1740 160162.49 1803377.9 -4.8910166e-07 -4.8910204e-07 410741.67 31.537365 31.537365 31.537365 + 1750 160162.49 1803377.9 -4.8910241e-07 -4.8910257e-07 410741.67 31.537365 31.537365 31.537365 + 1760 160162.49 1803377.9 -4.8910319e-07 -4.8910314e-07 410741.67 31.537365 31.537365 31.537365 + 1770 160162.49 1803377.9 -4.8910061e-07 -4.8910065e-07 410741.67 31.537365 31.537365 31.537365 + 1780 160162.49 1803377.9 -4.8910212e-07 -4.8910225e-07 410741.67 31.537365 31.537365 31.537365 + 1790 160162.49 1803377.9 -4.8910003e-07 -4.8910077e-07 410741.67 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + 1800 160162.49 1803377.9 -4.8910129e-07 -4.8910219e-07 410741.67 31.537365 31.537365 31.537365 + 1810 160162.49 1803377.9 -4.8910037e-07 -4.8910129e-07 410741.67 31.537365 31.537365 31.537365 + 1820 160162.49 1803377.9 -4.8910138e-07 -4.8910184e-07 410741.67 31.537365 31.537365 31.537365 + 1830 160162.49 1803377.9 -4.8910012e-07 -4.8910085e-07 410741.67 31.537365 31.537365 31.537365 + 1840 160162.49 1803377.9 -4.8910138e-07 -4.8910235e-07 410741.67 31.537365 31.537365 31.537365 + 1850 160162.49 1803377.9 -4.8910015e-07 -4.8910066e-07 410741.67 31.537365 31.537365 31.537365 + 1860 160162.49 1803377.9 -4.8910204e-07 -4.8910242e-07 410741.67 31.537365 31.537365 31.537365 + 1870 160162.49 1803377.9 -4.8910022e-07 -4.8910074e-07 410741.67 31.537365 31.537365 31.537365 + 1880 160162.49 1803377.9 -4.8910147e-07 -4.8910194e-07 410741.67 31.537365 31.537365 31.537365 + 1890 160162.49 1803377.9 -4.8910029e-07 -4.8910108e-07 410741.67 31.537365 31.537365 31.537365 + 1900 160162.49 1803377.9 -4.8910167e-07 -4.8910199e-07 410741.67 31.537365 31.537365 31.537365 + 1910 160162.49 1803377.9 -4.891003e-07 -4.8910093e-07 410741.67 31.537365 31.537365 31.537365 + 1920 160162.49 1803377.9 -4.8910133e-07 -4.891017e-07 410741.67 31.537365 31.537365 31.537365 + 1930 160162.49 1803377.9 -4.8910033e-07 -4.8910102e-07 410741.67 31.537365 31.537365 31.537365 + 1940 160162.49 1803377.9 -4.8910152e-07 -4.8910179e-07 410741.67 31.537365 31.537365 31.537365 + 1950 160162.49 1803377.9 -4.8910025e-07 -4.8910087e-07 410741.67 31.537365 31.537365 31.537365 + 1960 160162.49 1803377.9 -4.8910156e-07 -4.8910235e-07 410741.67 31.537365 31.537365 31.537365 + 1970 160162.49 1803377.9 -4.8910009e-07 -4.8910059e-07 410741.67 31.537365 31.537365 31.537365 + 1980 160162.49 1803377.9 -4.8910173e-07 -4.8910251e-07 410741.67 31.537365 31.537365 31.537365 + 1990 160162.49 1803377.9 -4.8910036e-07 -4.8910106e-07 410741.67 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + 2000 160162.49 1803377.9 -4.891014e-07 -4.8910256e-07 410741.67 31.537365 31.537365 31.537365 + 2010 160162.49 1803377.9 -4.8910159e-07 -4.8910279e-07 410741.67 31.537365 31.537365 31.537365 + 2020 160162.49 1803377.9 -4.8910238e-07 -4.8910344e-07 410741.67 31.537365 31.537365 31.537365 + 2030 160162.49 1803377.9 -4.891e-07 -4.8910112e-07 410741.67 31.537365 31.537365 31.537365 + 2040 160162.49 1803377.9 -4.8910103e-07 -4.89102e-07 410741.67 31.537365 31.537365 31.537365 + 2050 160162.49 1803377.9 -4.8910276e-07 -4.8910344e-07 410741.67 31.537365 31.537365 31.537365 + 2060 160162.49 1803377.9 -4.8910112e-07 -4.8910212e-07 410741.67 31.537365 31.537365 31.537365 + 2070 160162.49 1803377.9 -4.8910247e-07 -4.8910356e-07 410741.67 31.537365 31.537365 31.537365 + 2080 160162.49 1803377.9 -4.89101e-07 -4.8910239e-07 410741.67 31.537365 31.537365 31.537365 + 2090 160162.49 1803377.9 -4.8910249e-07 -4.891037e-07 410741.67 31.537365 31.537365 31.537365 + 2100 160162.49 1803377.9 -4.8910084e-07 -4.8910161e-07 410741.67 31.537365 31.537365 31.537365 + 2110 160162.49 1803377.9 -4.8910238e-07 -4.8910322e-07 410741.67 31.537365 31.537365 31.537365 + 2120 160162.49 1803377.9 -4.8910078e-07 -4.8910089e-07 410741.67 31.537365 31.537365 31.537365 + 2130 160162.49 1803377.9 -4.8910225e-07 -4.8910277e-07 410741.67 31.537365 31.537365 31.537365 + 2140 160162.49 1803377.9 -4.8910056e-07 -4.891012e-07 410741.67 31.537365 31.537365 31.537365 + 2150 160162.49 1803377.9 -4.8910213e-07 -4.8910283e-07 410741.67 31.537365 31.537365 31.537365 + 2160 160162.49 1803377.9 -4.8910045e-07 -4.8910105e-07 410741.67 31.537365 31.537365 31.537365 + 2170 160162.49 1803377.9 -4.8910228e-07 -4.8910236e-07 410741.67 31.537365 31.537365 31.537365 + 2180 160162.49 1803377.9 -4.8910033e-07 -4.8910128e-07 410741.67 31.537365 31.537365 31.537365 + 2190 160162.49 1803377.9 -4.8910193e-07 -4.8910273e-07 410741.67 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + 2200 160162.49 1803377.9 -4.8910067e-07 -4.8910158e-07 410741.67 31.537365 31.537365 31.537365 + 2210 160162.49 1803377.9 -4.8910082e-07 -4.8910183e-07 410741.67 31.537365 31.537365 31.537365 + 2220 160162.49 1803377.9 -4.8910178e-07 -4.8910275e-07 410741.67 31.537365 31.537365 31.537365 + 2230 160162.49 1803377.9 -4.890995e-07 -4.8909947e-07 410741.67 31.537365 31.537365 31.537365 + 2240 160162.49 1803377.9 -4.8909972e-07 -4.8910015e-07 410741.67 31.537365 31.537365 31.537365 + 2250 160162.49 1803377.9 -4.8910077e-07 -4.8910141e-07 410741.67 31.537365 31.537365 31.537365 + 2260 160162.49 1803377.9 -4.8910119e-07 -4.8910189e-07 410741.67 31.537365 31.537365 31.537365 + 2270 160162.49 1803377.9 -4.8910159e-07 -4.8910229e-07 410741.67 31.537365 31.537365 31.537365 + 2280 160162.49 1803377.9 -4.8910186e-07 -4.8910267e-07 410741.67 31.537365 31.537365 31.537365 + 2290 160162.49 1803377.9 -4.8910025e-07 -4.8910102e-07 410741.67 31.537365 31.537365 31.537365 + 2300 160162.49 1803377.9 -4.8910045e-07 -4.8910163e-07 410741.67 31.537365 31.537365 31.537365 + 2310 160162.49 1803377.9 -4.8910175e-07 -4.8910306e-07 410741.67 31.537365 31.537365 31.537365 + 2320 160162.49 1803377.9 -4.8910062e-07 -4.8910178e-07 410741.67 31.537365 31.537365 31.537365 + 2330 160162.49 1803377.9 -4.8910162e-07 -4.8910281e-07 410741.67 31.537365 31.537365 31.537365 + 2340 160162.49 1803377.9 -4.891007e-07 -4.8910172e-07 410741.67 31.537365 31.537365 31.537365 + 2350 160162.49 1803377.9 -4.8910169e-07 -4.8910269e-07 410741.67 31.537365 31.537365 31.537365 + 2360 160162.49 1803377.9 -4.8910031e-07 -4.8910156e-07 410741.67 31.537365 31.537365 31.537365 + 2370 160162.49 1803377.9 -4.8910172e-07 -4.8910282e-07 410741.67 31.537365 31.537365 31.537365 + 2380 160162.49 1803377.9 -4.8910065e-07 -4.8910159e-07 410741.67 31.537365 31.537365 31.537365 + 2390 160162.49 1803377.9 -4.891016e-07 -4.8910331e-07 410741.67 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + 2400 160162.49 1803377.9 -4.8910081e-07 -4.8910169e-07 410741.67 31.537365 31.537365 31.537365 + 2410 160162.49 1803377.9 -4.8910149e-07 -4.8910258e-07 410741.67 31.537365 31.537365 31.537365 + 2420 160162.49 1803377.9 -4.8910171e-07 -4.8910257e-07 410741.67 31.537365 31.537365 31.537365 + 2430 160162.49 1803377.9 -4.8909949e-07 -4.8910035e-07 410741.67 31.537365 31.537365 31.537365 + 2440 160162.49 1803377.9 -4.8910033e-07 -4.8910099e-07 410741.67 31.537365 31.537365 31.537365 + 2450 160162.49 1803377.9 -4.891006e-07 -4.8910124e-07 410741.67 31.537365 31.537365 31.537365 + 2460 160162.49 1803377.9 -4.8910117e-07 -4.8910191e-07 410741.67 31.537365 31.537365 31.537365 + 2470 160162.49 1803377.9 -4.8910153e-07 -4.8910231e-07 410741.67 31.537365 31.537365 31.537365 + 2480 160162.49 1803377.9 -4.8910223e-07 -4.8910317e-07 410741.67 31.537365 31.537365 31.537365 + 2490 160162.49 1803377.9 -4.8909994e-07 -4.8910083e-07 410741.67 31.537365 31.537365 31.537365 + 2500 160162.49 1803377.9 -4.8910056e-07 -4.8910138e-07 410741.67 31.537365 31.537365 31.537365 + 2510 160162.49 1803377.9 -4.8910114e-07 -4.8910212e-07 410741.67 31.537365 31.537365 31.537365 + 2520 160162.49 1803377.9 -4.8910159e-07 -4.8910264e-07 410741.67 31.537365 31.537365 31.537365 + 2530 160162.49 1803377.9 -4.89102e-07 -4.8910257e-07 410741.67 31.537365 31.537365 31.537365 + 2540 160162.49 1803377.9 -4.8910012e-07 -4.8910058e-07 410741.67 31.537365 31.537365 31.537365 + 2550 160162.49 1803377.9 -4.8910014e-07 -4.8910104e-07 410741.67 31.537365 31.537365 31.537365 + 2560 160162.49 1803377.9 -4.8910087e-07 -4.8910118e-07 410741.67 31.537365 31.537365 31.537365 + 2570 160162.49 1803377.9 -4.8909951e-07 -4.8909979e-07 410741.67 31.537365 31.537365 31.537365 + 2580 160162.49 1803377.9 -4.8910101e-07 -4.8910158e-07 410741.67 31.537365 31.537365 31.537365 + 2590 160162.49 1803377.9 -4.8910231e-07 -4.8910311e-07 410741.67 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + 2600 160162.49 1803377.9 -4.8910045e-07 -4.891011e-07 410741.67 31.537365 31.537365 31.537365 + 2610 160162.49 1803377.9 -4.8909927e-07 -4.8910014e-07 410741.67 31.537365 31.537365 31.537365 + 2620 160162.49 1803377.9 -4.8910087e-07 -4.8910142e-07 410741.67 31.537365 31.537365 31.537365 + 2630 160162.49 1803377.9 -4.8910236e-07 -4.8910302e-07 410741.67 31.537365 31.537365 31.537365 + 2640 160162.49 1803377.9 -4.8910086e-07 -4.8910143e-07 410741.67 31.537365 31.537365 31.537365 + 2650 160162.49 1803377.9 -4.8909943e-07 -4.8909999e-07 410741.67 31.537365 31.537365 31.537365 + 2660 160162.49 1803377.9 -4.8910109e-07 -4.8910169e-07 410741.67 31.537365 31.537365 31.537365 + 2670 160162.49 1803377.9 -4.8910245e-07 -4.8910298e-07 410741.67 31.537365 31.537365 31.537365 + 2680 160162.49 1803377.9 -4.8910079e-07 -4.891017e-07 410741.67 31.537365 31.537365 31.537365 + 2690 160162.49 1803377.9 -4.8909909e-07 -4.8909976e-07 410741.67 31.537365 31.537365 31.537365 + 2700 160162.49 1803377.9 -4.8910075e-07 -4.8910167e-07 410741.67 31.537365 31.537365 31.537365 + 2710 160162.49 1803377.9 -4.8910231e-07 -4.8910315e-07 410741.67 31.537365 31.537365 31.537365 + 2720 160162.49 1803377.9 -4.8910065e-07 -4.8910118e-07 410741.67 31.537365 31.537365 31.537365 + 2730 160162.49 1803377.9 -4.890993e-07 -4.8910017e-07 410741.67 31.537365 31.537365 31.537365 + 2740 160162.49 1803377.9 -4.8910051e-07 -4.8910166e-07 410741.67 31.537365 31.537365 31.537365 + 2750 160162.49 1803377.9 -4.8910219e-07 -4.8910304e-07 410741.67 31.537365 31.537365 31.537365 + 2760 160162.49 1803377.9 -4.8910068e-07 -4.8910172e-07 410741.67 31.537365 31.537365 31.537365 + 2770 160162.49 1803377.9 -4.8909954e-07 -4.8910049e-07 410741.67 31.537365 31.537365 31.537365 + 2780 160162.49 1803377.9 -4.8910117e-07 -4.8910185e-07 410741.67 31.537365 31.537365 31.537365 + 2790 160162.49 1803377.9 -4.891023e-07 -4.8910319e-07 410741.67 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + 2800 160162.49 1803377.9 -4.8910068e-07 -4.8910187e-07 410741.67 31.537365 31.537365 31.537365 + 2810 160162.49 1803377.9 -4.891017e-07 -4.891029e-07 410741.67 31.537365 31.537365 31.537365 + 2820 160162.49 1803377.9 -4.8910195e-07 -4.8910323e-07 410741.67 31.537365 31.537365 31.537365 + 2830 160162.49 1803377.9 -4.8909982e-07 -4.8910124e-07 410741.67 31.537365 31.537365 31.537365 + 2840 160162.49 1803377.9 -4.8910224e-07 -4.8910355e-07 410741.67 31.537365 31.537365 31.537365 + 2850 160162.49 1803377.9 -4.8910081e-07 -4.8910218e-07 410741.67 31.537365 31.537365 31.537365 + 2860 160162.49 1803377.9 -4.8910183e-07 -4.8910321e-07 410741.67 31.537365 31.537365 31.537365 + 2870 160162.49 1803377.9 -4.8910058e-07 -4.8910172e-07 410741.67 31.537365 31.537365 31.537365 + 2880 160162.49 1803377.9 -4.8910233e-07 -4.8910328e-07 410741.67 31.537365 31.537365 31.537365 + 2890 160162.49 1803377.9 -4.891007e-07 -4.891017e-07 410741.67 31.537365 31.537365 31.537365 + 2900 160162.49 1803377.9 -4.8910183e-07 -4.8910275e-07 410741.67 31.537365 31.537365 31.537365 + 2910 160162.49 1803377.9 -4.8910014e-07 -4.8910128e-07 410741.67 31.537365 31.537365 31.537365 + 2920 160162.49 1803377.9 -4.8910169e-07 -4.8910278e-07 410741.67 31.537365 31.537365 31.537365 + 2930 160162.49 1803377.9 -4.8910007e-07 -4.8910125e-07 410741.67 31.537365 31.537365 31.537365 + 2940 160162.49 1803377.9 -4.8910148e-07 -4.8910266e-07 410741.67 31.537365 31.537365 31.537365 + 2950 160162.49 1803377.9 -4.8910016e-07 -4.8910167e-07 410741.67 31.537365 31.537365 31.537365 + 2960 160162.49 1803377.9 -4.8910147e-07 -4.8910314e-07 410741.67 31.537365 31.537365 31.537365 + 2970 160162.49 1803377.9 -4.8910006e-07 -4.8910153e-07 410741.67 31.537365 31.537365 31.537365 + 2980 160162.49 1803377.9 -4.8910123e-07 -4.8910287e-07 410741.67 31.537365 31.537365 31.537365 + 2990 160162.49 1803377.9 -4.8909973e-07 -4.8910132e-07 410741.67 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + 3000 160162.49 1803377.9 -4.8910075e-07 -4.8910221e-07 410741.67 31.537365 31.537365 31.537365 + 3010 160162.49 1803377.9 -4.8910144e-07 -4.8910237e-07 410741.67 31.537365 31.537365 31.537365 + 3020 160162.49 1803377.9 -4.8910171e-07 -4.8910255e-07 410741.67 31.537365 31.537365 31.537365 + 3030 160162.49 1803377.9 -4.8909877e-07 -4.8910042e-07 410741.67 31.537365 31.537365 31.537365 + 3040 160162.49 1803377.9 -4.8909954e-07 -4.8910108e-07 410741.67 31.537365 31.537365 31.537365 + 3050 160162.49 1803377.9 -4.8910053e-07 -4.8910155e-07 410741.67 31.537365 31.537365 31.537365 + 3060 160162.49 1803377.9 -4.8910092e-07 -4.8910213e-07 410741.67 31.537365 31.537365 31.537365 + 3070 160162.49 1803377.9 -4.8910167e-07 -4.8910266e-07 410741.67 31.537365 31.537365 31.537365 + 3080 160162.49 1803377.9 -4.8909919e-07 -4.8910041e-07 410741.67 31.537365 31.537365 31.537365 + 3090 160162.49 1803377.9 -4.8909999e-07 -4.8910152e-07 410741.67 31.537365 31.537365 31.537365 + 3100 160162.49 1803377.9 -4.8910143e-07 -4.8910247e-07 410741.67 31.537365 31.537365 31.537365 + 3110 160162.49 1803377.9 -4.8910001e-07 -4.8910126e-07 410741.67 31.537365 31.537365 31.537365 + 3120 160162.49 1803377.9 -4.8910185e-07 -4.8910299e-07 410741.67 31.537365 31.537365 31.537365 + 3130 160162.49 1803377.9 -4.8909979e-07 -4.8910147e-07 410741.67 31.537365 31.537365 31.537365 + 3140 160162.49 1803377.9 -4.8910143e-07 -4.8910276e-07 410741.67 31.537365 31.537365 31.537365 + 3150 160162.49 1803377.9 -4.8910037e-07 -4.8910137e-07 410741.67 31.537365 31.537365 31.537365 + 3160 160162.49 1803377.9 -4.8910153e-07 -4.8910266e-07 410741.67 31.537365 31.537365 31.537365 + 3170 160162.49 1803377.9 -4.8909966e-07 -4.8910099e-07 410741.67 31.537365 31.537365 31.537365 + 3180 160162.49 1803377.9 -4.8910152e-07 -4.891028e-07 410741.67 31.537365 31.537365 31.537365 + 3190 160162.49 1803377.9 -4.8909987e-07 -4.8910153e-07 410741.67 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + 3200 160162.49 1803377.9 -4.8910041e-07 -4.8910185e-07 410741.67 31.537365 31.537365 31.537365 + 3210 160162.49 1803377.9 -4.8910076e-07 -4.8910275e-07 410741.67 31.537365 31.537365 31.537365 + 3220 160162.49 1803377.9 -4.8910132e-07 -4.89103e-07 410741.67 31.537365 31.537365 31.537365 + 3230 160162.49 1803377.9 -4.8909954e-07 -4.8910119e-07 410741.67 31.537365 31.537365 31.537365 + 3240 160162.49 1803377.9 -4.8909979e-07 -4.8910156e-07 410741.67 31.537365 31.537365 31.537365 + 3250 160162.49 1803377.9 -4.8910039e-07 -4.8910223e-07 410741.67 31.537365 31.537365 31.537365 + 3260 160162.49 1803377.9 -4.8910064e-07 -4.8910239e-07 410741.67 31.537365 31.537365 31.537365 + 3270 160162.49 1803377.9 -4.8910155e-07 -4.8910333e-07 410741.67 31.537365 31.537365 31.537365 + 3280 160162.49 1803377.9 -4.8910184e-07 -4.8910355e-07 410741.67 31.537365 31.537365 31.537365 + 3290 160162.49 1803377.9 -4.8910006e-07 -4.8910145e-07 410741.67 31.537365 31.537365 31.537365 + 3300 160162.49 1803377.9 -4.8910003e-07 -4.891019e-07 410741.67 31.537365 31.537365 31.537365 + 3310 160162.49 1803377.9 -4.8910065e-07 -4.8910258e-07 410741.67 31.537365 31.537365 31.537365 + 3320 160162.49 1803377.9 -4.8910106e-07 -4.8910298e-07 410741.67 31.537365 31.537365 31.537365 + 3330 160162.49 1803377.9 -4.8910174e-07 -4.8910364e-07 410741.67 31.537365 31.537365 31.537365 + 3340 160162.49 1803377.9 -4.8909972e-07 -4.8910113e-07 410741.67 31.537365 31.537365 31.537365 + 3350 160162.49 1803377.9 -4.8910047e-07 -4.8910163e-07 410741.67 31.537365 31.537365 31.537365 + 3360 160162.49 1803377.9 -4.891017e-07 -4.8910326e-07 410741.67 31.537365 31.537365 31.537365 + 3370 160162.49 1803377.9 -4.8910039e-07 -4.8910127e-07 410741.67 31.537365 31.537365 31.537365 + 3380 160162.49 1803377.9 -4.8910152e-07 -4.8910252e-07 410741.67 31.537365 31.537365 31.537365 + 3390 160162.49 1803377.9 -4.8910045e-07 -4.8910129e-07 410741.67 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + 3400 160162.49 1803377.9 -4.89102e-07 -4.8910296e-07 410741.67 31.537365 31.537365 31.537365 + 3410 160162.49 1803377.9 -4.8910045e-07 -4.8910141e-07 410741.67 31.537365 31.537365 31.537365 + 3420 160162.49 1803377.9 -4.8910145e-07 -4.8910301e-07 410741.67 31.537365 31.537365 31.537365 + 3430 160162.49 1803377.9 -4.8910057e-07 -4.8910173e-07 410741.67 31.537365 31.537365 31.537365 + 3440 160162.49 1803377.9 -4.8910176e-07 -4.8910303e-07 410741.67 31.537365 31.537365 31.537365 + 3450 160162.49 1803377.9 -4.8910044e-07 -4.8910165e-07 410741.67 31.537365 31.537365 31.537365 + 3460 160162.49 1803377.9 -4.8910172e-07 -4.8910311e-07 410741.67 31.537365 31.537365 31.537365 + 3470 160162.49 1803377.9 -4.8910048e-07 -4.8910158e-07 410741.67 31.537365 31.537365 31.537365 + 3480 160162.49 1803377.9 -4.8910193e-07 -4.8910309e-07 410741.67 31.537365 31.537365 31.537365 + 3490 160162.49 1803377.9 -4.8910055e-07 -4.8910166e-07 410741.67 31.537365 31.537365 31.537365 + 3500 160162.49 1803377.9 -4.8910204e-07 -4.8910346e-07 410741.67 31.537365 31.537365 31.537365 +Loop time of 260.545 on 4 procs for 3500 steps with 864 atoms + +Pair time (%) = 7.82867 (3.00473) +Neigh time (%) = 0.516552 (0.198258) +Comm time (%) = 67.7833 (26.016) +Outpt time (%) = 11.4734 (4.40363) +Other time (%) = 172.943 (66.3774) + +Nlocal: 216 ave 216 max 216 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 3108 ave 3108 max 3108 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 39744 ave 39850 max 39638 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +FullNghs: 79488 ave 79488 max 79488 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 317952 +Ave neighs/atom = 368 +Neighbor list builds = 17 +Dangerous builds = 0 +variable c equal 48.88821291*48.88821291/(3.*0.0019872067) +variable T equal $m*$v*$v*$c +variable T equal 39.950000000000002842*$v*$v*$c +variable T equal 39.950000000000002842*0.10000000000000000555*$v*$c +variable T equal 39.950000000000002842*0.10000000000000000555*0.10000000000000000555*$c +variable T equal 39.950000000000002842*0.10000000000000000555*0.10000000000000000555*400907.35763815121027 +print "kinetic temperature: $T" +kinetic temperature: 160162.48937644143007 diff --git a/examples/USER/atc/cauchy_born/ftcb_constV.screen b/examples/USER/atc/cauchy_born/ftcb_constV.screen new file mode 100644 index 0000000000..bdd45bb0c2 --- /dev/null +++ b/examples/USER/atc/cauchy_born/ftcb_constV.screen @@ -0,0 +1,300 @@ +LAMMPS (14 Aug 2013) +log ftcb_constV.log +units real +atom_style atomic +variable lattice_constant equal 5.256227487 +variable c equal 6 +variable L equal (${lattice_constant}*$c) +variable L equal (5.2562274870000003091*$c) +variable L equal (5.2562274870000003091*6) +variable V equal $L*$L*$L +variable V equal 31.537364922000001854*$L*$L +variable V equal 31.537364922000001854*31.537364922000001854*$L +variable V equal 31.537364922000001854*31.537364922000001854*31.537364922000001854 +print "Volume : $V" +Volume : 31367.233018713999627 +variable Ti equal 0.0001 +variable dT equal 0.2 +variable n equal 10000 +variable m equal 200 +variable dt equal 0.1 +# create system +lattice fcc ${lattice_constant} +lattice fcc 5.2562274870000003091 +Lattice spacing in x,y,z = 5.25623 5.25623 5.25623 +region box block 0 $c 0 $c 0 $c +region box block 0 6 0 $c 0 $c +region box block 0 6 0 6 0 $c +region box block 0 6 0 6 0 6 +boundary p p p +pair_style lj/cut 13.5 +read_data ftcb_constV_setup.data +Reading data file ... + orthogonal box = (0 0 0) to (31.5374 31.5374 31.5374) + 1 by 2 by 2 MPI processor grid + 864 atoms + 864 velocities +mass 1 39.95 +pair_coeff 1 1 0.238 3.405 +# define region +neighbor 1.0 bin +neigh_modify delay 0 every 2000 check no +reset_timestep 0 +thermo $m +thermo 200 +compute_modify thermo_temp extra 0 +variable nrepeat equal $n/$m +variable nrepeat equal 10000/$m +variable nrepeat equal 10000/200 +variable sxx equal -pxx +variable intenergy equal etotal +fix TDAVE all ave/time $m ${nrepeat} $n c_thermo_temp v_sxx v_intenergy ave one file ftcb_constV.profile +fix TDAVE all ave/time 200 ${nrepeat} $n c_thermo_temp v_sxx v_intenergy ave one file ftcb_constV.profile +fix TDAVE all ave/time 200 50 $n c_thermo_temp v_sxx v_intenergy ave one file ftcb_constV.profile +fix TDAVE all ave/time 200 50 10000 c_thermo_temp v_sxx v_intenergy ave one file ftcb_constV.profile +thermo_style custom step temp press etotal lx ly lz +timestep ${dt} +timestep 0.10000000000000000555 +# filtered +fix ATCFILT all atc field Ar_CauchyBorn.mat +ATC: constructing shape function field estimate with parameter file Ar_CauchyBorn.mat + ATC: peratom PE compute created with ID: 3 +#fix_modify ATCFILT reset_atomic_reference_positions ftcb_constV_setup.data +fix_modify ATCFILT mesh create 1 1 1 box p p p + ATC: created uniform mesh with 8 nodes, 1 unique nodes, and 1 elements +fix_modify ATCFILT fields none +fix_modify ATCFILT fields add internal_energy stress cauchy_born_energy cauchy_born_stress +fix_modify ATCFILT fields add temperature displacement +fix_modify ATCFILT gradients add displacement +fix_modify ATCFILT output ftcb_constV_filteredFE $n text binary tensor_components +fix_modify ATCFILT output ftcb_constV_filteredFE 10000 text binary tensor_components + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +fix_modify ATCFILT sample_frequency $m +fix_modify ATCFILT sample_frequency 200 +variable scale equal $n*${dt} +variable scale equal 10000*${dt} +variable scale equal 10000*0.10000000000000000555 +fix_modify ATCFILT filter scale ${scale} +fix_modify ATCFILT filter scale 1000 +fix_modify ATCFILT filter on +fix_modify ATCFILT filter type step +# not filtered +fix ATC all atc field Ar_CauchyBorn.mat +ATC: constructing shape function field estimate with parameter file Ar_CauchyBorn.mat + ATC: peratom PE compute created with ID: 3 +#fix_modify ATC reset_atomic_reference_positions ftcb_constV_setup.data +fix_modify ATC mesh create 1 1 1 box p p p + ATC: created uniform mesh with 8 nodes, 1 unique nodes, and 1 elements +fix_modify ATC fields none +fix_modify ATC fields add internal_energy stress cauchy_born_energy cauchy_born_stress +fix_modify ATC fields add temperature displacement +fix_modify ATC gradients add displacement +fix_modify ATC output ftcb_constVFE $m text binary tensor_components +fix_modify ATC output ftcb_constVFE 200 text binary tensor_components + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +velocity all create ${Ti} 102486 mom yes rot yes dist gaussian +velocity all create 0.00010000000000000000479 102486 mom yes rot yes dist gaussian +# step iu T,V space +variable i loop 1 +label loop_i + print ">>> step $i, T: ${Ti}, V: $V" +>>> step 1, T: 0.00010000000000000000479, V: 31367.233018713999627 + variable Tf equal ${Ti}+${dT} + variable Tf equal 0.00010000000000000000479+${dT} + variable Tf equal 0.00010000000000000000479+0.2000000000000000111 + fix NVT all nvt temp ${Ti} ${Tf} 20 drag 0.5 tchain 1 + fix NVT all nvt temp 0.00010000000000000000479 ${Tf} 20 drag 0.5 tchain 1 + fix NVT all nvt temp 0.00010000000000000000479 0.20010000000000000009 20 drag 0.5 tchain 1 + run $n + run 10000 +Setting up run ... + ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 + ATC: computing bond matrix ...........done + ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 + ATC: computing bond matrix ...........done +Memory usage per processor = 43.8852 Mbytes +Step Temp Press TotEng Lx Ly Lz + 0 9.9884259e-05 0.00037439907 -1743.9894 31.537365 31.537365 31.537365 + 200 0.00018395916 0.0008038753 -1743.9892 31.537365 31.537365 31.537365 + 400 0.00072207452 0.0035412421 -1743.9877 31.537365 31.537365 31.537365 + 600 0.0035009087 0.01765789 -1743.9803 31.537365 31.537365 31.537365 + 800 0.013509969 0.072367846 -1743.953 31.537365 31.537365 31.537365 + 1000 0.024404761 0.16748542 -1743.9203 31.537365 31.537365 31.537365 + 1200 0.02269474 0.25683396 -1743.9165 31.537365 31.537365 31.537365 + 1400 0.020977736 0.37083837 -1743.9105 31.537365 31.537365 31.537365 + 1600 0.023822771 0.52655981 -1743.8907 31.537365 31.537365 31.537365 + 1800 0.029504552 0.724909 -1743.8607 31.537365 31.537365 31.537365 + ATC: computing bond matrix ..........done + ATC: computing bond matrix ..........done + 2000 0.034895124 0.95292512 -1743.8286 31.537365 31.537365 31.537365 + 2200 0.038474547 1.1919487 -1743.7994 31.537365 31.537365 31.537365 + 2400 0.041549289 1.4317242 -1743.7711 31.537365 31.537365 31.537365 + 2600 0.045486492 1.6680358 -1743.741 31.537365 31.537365 31.537365 + 2800 0.050155213 1.8970903 -1743.7096 31.537365 31.537365 31.537365 + 3000 0.054672553 2.1168131 -1743.6792 31.537365 31.537365 31.537365 + 3200 0.058605281 2.3306834 -1743.6507 31.537365 31.537365 31.537365 + 3400 0.062199376 2.5471875 -1743.6227 31.537365 31.537365 31.537365 + 3600 0.065809649 2.7748986 -1743.594 31.537365 31.537365 31.537365 + 3800 0.069568751 3.0179585 -1743.564 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + ATC: computing bond matrix ...........done + 4000 0.073508373 3.2739196 -1743.5326 31.537365 31.537365 31.537365 + 4200 0.077717909 3.5333376 -1743.5006 31.537365 31.537365 31.537365 + 4400 0.082309308 3.7807471 -1743.469 31.537365 31.537365 31.537365 + 4600 0.087284711 3.9974133 -1743.4392 31.537365 31.537365 31.537365 + 4800 0.092475466 4.166069 -1743.413 31.537365 31.537365 31.537365 + 5000 0.097607659 4.2765824 -1743.3918 31.537365 31.537365 31.537365 + 5200 0.10242915 4.3301667 -1743.3761 31.537365 31.537365 31.537365 + 5400 0.10679915 4.3398975 -1743.3649 31.537365 31.537365 31.537365 + 5600 0.11070065 4.3272641 -1743.3567 31.537365 31.537365 31.537365 + 5800 0.11420842 4.3165087 -1743.3493 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + ATC: computing bond matrix ...........done + 6000 0.11745522 4.3289911 -1743.3405 31.537365 31.537365 31.537365 + 6200 0.12060841 4.3789965 -1743.3288 31.537365 31.537365 31.537365 + 6400 0.1238495 4.4714313 -1743.3135 31.537365 31.537365 31.537365 + 6600 0.12734883 4.6013368 -1743.2946 31.537365 31.537365 31.537365 + 6800 0.13123277 4.7550795 -1743.2728 31.537365 31.537365 31.537365 + 7000 0.1355461 4.9131529 -1743.2497 31.537365 31.537365 31.537365 + 7200 0.14022279 5.0544601 -1743.2271 31.537365 31.537365 31.537365 + 7400 0.14508669 5.161526 -1743.2068 31.537365 31.537365 31.537365 + 7600 0.14989701 5.2254132 -1743.19 31.537365 31.537365 31.537365 + 7800 0.15442502 5.2486878 -1743.1772 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + ATC: computing bond matrix ...........done + 8000 0.1585231 5.245194 -1743.1674 31.537365 31.537365 31.537365 + 8200 0.16215368 5.2366567 -1743.159 31.537365 31.537365 31.537365 + 8400 0.16537863 5.2473985 -1743.1498 31.537365 31.537365 31.537365 + 8600 0.16833152 5.2988909 -1743.1379 31.537365 31.537365 31.537365 + 8800 0.17119053 5.4054221 -1743.1217 31.537365 31.537365 31.537365 + 9000 0.17415442 5.5714574 -1743.1004 31.537365 31.537365 31.537365 + 9200 0.17741609 5.7907947 -1743.074 31.537365 31.537365 31.537365 + 9400 0.18112875 6.0474639 -1743.0437 31.537365 31.537365 31.537365 + 9600 0.18536621 6.3183401 -1743.011 31.537365 31.537365 31.537365 + 9800 0.19008819 6.5773705 -1742.9782 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + ATC: computing bond matrix ...........done + 10000 0.19513095 6.800965 -1742.9477 31.537365 31.537365 31.537365 +Loop time of 217.59 on 4 procs for 10000 steps with 864 atoms + +Pair time (%) = 22.0583 (10.1375) +Neigh time (%) = 0.106731 (0.0490514) +Comm time (%) = 92.9321 (42.7096) +Outpt time (%) = 0.514863 (0.23662) +Other time (%) = 101.978 (46.8672) + +Nlocal: 216 ave 223 max 212 min +Histogram: 2 0 0 0 1 0 0 0 0 1 +Nghost: 3107 ave 3111 max 3100 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Neighs: 39744 ave 41133 max 38895 min +Histogram: 1 1 0 0 1 0 0 0 0 1 +FullNghs: 79488 ave 82064 max 78016 min +Histogram: 2 0 0 0 1 0 0 0 0 1 + +Total # of neighbors = 317952 +Ave neighs/atom = 368 +Neighbor list builds = 5 +Dangerous builds = 0 + unfix NVT + fix NVT all nvt temp ${Tf} ${Tf} 20 drag 0.5 tchain 1 + fix NVT all nvt temp 0.20010000000000000009 ${Tf} 20 drag 0.5 tchain 1 + fix NVT all nvt temp 0.20010000000000000009 0.20010000000000000009 20 drag 0.5 tchain 1 + run $n + run 10000 +Setting up run ... + ATC: computing bond matrix ...........done + ATC: computing bond matrix ...........done +Memory usage per processor = 44.3449 Mbytes +Step Temp Press TotEng Lx Ly Lz + 10000 0.19513095 6.800965 -1742.9477 31.537365 31.537365 31.537365 + 10200 0.1942722 6.9478502 -1742.937 31.537365 31.537365 31.537365 + 10400 0.19883577 7.0539144 -1742.9173 31.537365 31.537365 31.537365 + 10600 0.20139901 7.1014941 -1742.907 31.537365 31.537365 31.537365 + 10800 0.20081668 7.1047619 -1742.9075 31.537365 31.537365 31.537365 + 11000 0.19970238 7.094286 -1742.9103 31.537365 31.537365 31.537365 + 11200 0.1992728 7.0940423 -1742.9108 31.537365 31.537365 31.537365 + 11400 0.19903616 7.1168902 -1742.9091 31.537365 31.537365 31.537365 + 11600 0.1985796 7.1677194 -1742.9056 31.537365 31.537365 31.537365 + 11800 0.1981405 7.2439973 -1742.9 31.537365 31.537365 31.537365 + ATC: computing bond matrix ..........done + ATC: computing bond matrix ..........done + 12000 0.19807517 7.3351555 -1742.8924 31.537365 31.537365 31.537365 + 12200 0.19846191 7.4244524 -1742.884 31.537365 31.537365 31.537365 + 12400 0.19916212 7.4934365 -1742.8766 31.537365 31.537365 31.537365 + 12600 0.19999074 7.5270309 -1742.8719 31.537365 31.537365 31.537365 + 12800 0.20077516 7.5175279 -1742.8707 31.537365 31.537365 31.537365 + 13000 0.20135496 7.4665953 -1742.8734 31.537365 31.537365 31.537365 + 13200 0.20160734 7.38492 -1742.8792 31.537365 31.537365 31.537365 + 13400 0.20148742 7.2895976 -1742.887 31.537365 31.537365 31.537365 + 13600 0.2010393 7.2000327 -1742.895 31.537365 31.537365 31.537365 + 13800 0.20037365 7.1335653 -1742.9015 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + ATC: computing bond matrix ...........done + 14000 0.19963599 7.1019254 -1742.9054 31.537365 31.537365 31.537365 + 14200 0.1989806 7.1091181 -1742.9058 31.537365 31.537365 31.537365 + 14400 0.19854825 7.1508728 -1742.9031 31.537365 31.537365 31.537365 + 14600 0.1984433 7.2155437 -1742.8978 31.537365 31.537365 31.537365 + 14800 0.19871156 7.2862513 -1742.8914 31.537365 31.537365 31.537365 + 15000 0.19932573 7.3439691 -1742.8855 31.537365 31.537365 31.537365 + 15200 0.20018644 7.371098 -1742.8818 31.537365 31.537365 31.537365 + 15400 0.20114408 7.3548507 -1742.8818 31.537365 31.537365 31.537365 + 15600 0.202037 7.2896442 -1742.8862 31.537365 31.537365 31.537365 + 15800 0.2027327 7.1778389 -1742.8951 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + ATC: computing bond matrix ...........done + 16000 0.20315567 7.0286376 -1742.9079 31.537365 31.537365 31.537365 + 16200 0.20329394 6.8555641 -1742.9235 31.537365 31.537365 31.537365 + 16400 0.20318777 6.673354 -1742.9405 31.537365 31.537365 31.537365 + 16600 0.20290989 6.4951258 -1742.9576 31.537365 31.537365 31.537365 + 16800 0.20254493 6.3304266 -1742.9738 31.537365 31.537365 31.537365 + 17000 0.20217197 6.1843778 -1742.9884 31.537365 31.537365 31.537365 + 17200 0.20185124 6.0578536 -1743.0013 31.537365 31.537365 31.537365 + 17400 0.20161576 5.94845 -1743.0124 31.537365 31.537365 31.537365 + 17600 0.20146835 5.8519278 -1743.0222 31.537365 31.537365 31.537365 + 17800 0.20138485 5.7637939 -1743.0311 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + ATC: computing bond matrix ...........done + 18000 0.20132247 5.6807023 -1743.0393 31.537365 31.537365 31.537365 + 18200 0.20123183 5.6014137 -1743.047 31.537365 31.537365 31.537365 + 18400 0.20106914 5.5271637 -1743.0542 31.537365 31.537365 31.537365 + 18600 0.20080571 5.4614233 -1743.0607 31.537365 31.537365 31.537365 + 18800 0.20043268 5.4091822 -1743.0661 31.537365 31.537365 31.537365 + 19000 0.19996085 5.3759725 -1743.0697 31.537365 31.537365 31.537365 + 19200 0.1994168 5.3668762 -1743.0712 31.537365 31.537365 31.537365 + 19400 0.198837 5.3857152 -1743.0701 31.537365 31.537365 31.537365 + 19600 0.19826151 5.434538 -1743.0662 31.537365 31.537365 31.537365 + 19800 0.19772836 5.5134332 -1743.0595 31.537365 31.537365 31.537365 + ATC: computing bond matrix ...........done + ATC: computing bond matrix ...........done + 20000 0.19726939 5.6206257 -1743.0501 31.537365 31.537365 31.537365 +Loop time of 100.792 on 4 procs for 10000 steps with 864 atoms + +Pair time (%) = 15.7625 (15.6386) +Neigh time (%) = 0.0767966 (0.0761931) +Comm time (%) = 22.8833 (22.7034) +Outpt time (%) = 0.135321 (0.134258) +Other time (%) = 61.9342 (61.4475) + +Nlocal: 216 ave 231 max 208 min +Histogram: 1 1 1 0 0 0 0 0 0 1 +Nghost: 3107 ave 3115 max 3092 min +Histogram: 1 0 0 0 0 0 0 1 1 1 +Neighs: 39744 ave 42595 max 38315 min +Histogram: 1 2 0 0 0 0 0 0 0 1 +FullNghs: 79488 ave 85008 max 76544 min +Histogram: 1 1 1 0 0 0 0 0 0 1 + +Total # of neighbors = 317952 +Ave neighs/atom = 368 +Neighbor list builds = 5 +Dangerous builds = 0 + unfix NVT + variable Ti equal ${Tf} + variable Ti equal 0.20010000000000000009 +next i +jump in.ftcb_constV loop_i diff --git a/examples/USER/atc/cauchy_born/in.cb_biaxial b/examples/USER/atc/cauchy_born/in.cb_biaxial new file mode 100644 index 0000000000..c873179e91 --- /dev/null +++ b/examples/USER/atc/cauchy_born/in.cb_biaxial @@ -0,0 +1,53 @@ +# This test compares Hardy and Cauchy-Born metrics of energy density and stress +# for an Ar system subjected to biaxial deformation equivalent to shearing. +echo both +units real +atom_style atomic +variable lattice_constant equal 5.256227487 +variable c equal 6 +variable L equal $c*${lattice_constant} +variable d equal 0.005 +variable s equal 1.005 +variable is equal 1.0/$s +variable V0 equal $L*$L*3*${lattice_constant} +# create system +lattice fcc ${lattice_constant} origin 0.25 0.25 0.25 +region box block 0 $c 0 $c 0 3 +boundary p p p +create_box 1 box +create_atoms 1 box +mass 1 39.95 +group all region box +pair_style lj/cut 13.5 +pair_coeff 1 1 0.238 3.405 +# ID group atc PhysicsType ParameterFile +fix AtC all atc field Ar_CauchyBorn.mat +fix_modify AtC mesh create $c $c 1 box p p p +fix_modify AtC fields none +fix_modify AtC fields add displacement +fix_modify AtC fields add internal_energy stress cauchy_born_energy cauchy_born_stress +fix_modify AtC gradients add displacement +#fix_modify AtC fields add elastic_deformation_gradient +fix_modify AtC output cb_biaxialFE 1 full_text tensor_components +log cb_biaxial.log +thermo 100 +variable gamma1 equal 0.0 +variable gamma2 equal 0.0 +variable dv equal 1.0 +variable step equal 0 +thermo_style custom step v_step pxx pyy pzz pxy pxz pyz v_gamma1 pe v_dv +timestep 0.0 +min_modify line quadratic +timestep 0.0 +variable i loop 4 +label loop_i + print ">>> step $i ${gamma1} ${gamma2}" + minimize 1.e-20 1.e-20 1000 1000 + run 1 + variable step equal ${step}+1 + change_box all x scale $s y scale ${is} remap + variable gamma1 equal lx/$L-1.0 + variable gamma2 equal ly/$L-1.0 + variable dv equal vol/${V0} +next i +jump in.cb_biaxial loop_i diff --git a/examples/USER/atc/cauchy_born/in.cb_shear b/examples/USER/atc/cauchy_born/in.cb_shear new file mode 100644 index 0000000000..90a9b17179 --- /dev/null +++ b/examples/USER/atc/cauchy_born/in.cb_shear @@ -0,0 +1,54 @@ +# This test compares Hardy and Cauchy-Born metrics of energy density and stress +# for an Ar system subjected to shear deformation. +# +# NOTE possible problems with large shear and handling a non-ortho box +echo both +units metal +atom_style atomic +variable lattice_constant equal 4.08 +variable c equal 6 # minimum size +variable Ly equal $c*${lattice_constant} +variable d equal 0.005 +variable V0 equal ($c*${lattice_constant})^3 +# create system +lattice fcc ${lattice_constant} origin 0.25 0.25 0.25 +# NOTE rect box + lagrangian is necessary to fool ATC's mesh +region rectbox block 0 $c 0 $c 0 3 +region box prism 0 $c 0 $c 0 3 0 0 0 +boundary p p p +create_box 1 box +create_atoms 1 region box +mass 1 196.97 +group all region box +pair_style lj/smooth/linear 5.456108274435118 +pair_coeff * * 0.7242785984051078 2.598146797350056 +neighbor 1.0 bin +#neigh_modify delay 1000000 +log cb_shear.log +thermo 100 +variable gamma equal 0.0 +variable step equal 0 +thermo_style custom step v_step pxx pyy pzz pxy pxz pyz v_gamma pe xy xz yz +timestep 1.0 +fix AtC all atc field Au_CauchyBorn.mat +fix_modify AtC mesh create $c $c 1 rectbox p p p +fix_modify AtC fields add mass_density internal_energy stress +fix_modify AtC fields add displacement +fix_modify AtC fields add cauchy_born_energy cauchy_born_stress +fix_modify AtC gradients add displacement +#fix_modify AtC fields add elastic_deformation_gradient +fix_modify AtC output cb_shearFE 1 text binary tensor_components +min_modify line quadratic +variable dgamma equal $d/${Ly} +print "depsilon_12: ${dgamma}" +timestep 0.0 +variable i loop 4 +label loop_i + print ">>> step $i" + minimize 1.e-20 1.e-20 1000 1000 + run 1 + variable step equal ${step}+1 + change_box all xy delta $d remap + variable gamma equal $i*${dgamma} +next i +jump in.cb_shear loop_i diff --git a/examples/USER/atc/cauchy_born/in.cb_unistrain b/examples/USER/atc/cauchy_born/in.cb_unistrain new file mode 100644 index 0000000000..8f11dd2369 --- /dev/null +++ b/examples/USER/atc/cauchy_born/in.cb_unistrain @@ -0,0 +1,46 @@ +# This test compares Hardy and Cauchy-Born metrics of energy density and stress +# for an Ar system subjected to uniaxial strain deformation. +echo both +units real +atom_style atomic +# create domain +lattice fcc 5.256227487 origin 0.25 0.25 0.25 +region BOX block -8 8 -2 2 -2 2 +boundary f p p +create_box 1 BOX +# create atoms +region MD block -7 7 -2 2 -2 2 +create_atoms 1 region MD +mass 1 39.95 +# specify interal/ghost atoms +region FREE block -6 6 -2 2 -2 2 +group internal region FREE +# specify inter-atomic potential +pair_style lj/cut 13.5 +pair_coeff 1 1 0.238 3.405 +# specify neighbor/re-neighboring parameters +neighbor 0.3 bin +neigh_modify every 10 delay 0 check no +# setup thermal output +thermo 10 +thermo_style custom step pe ke press lx ly lz +# ID group atc PhysicsType ParameterFile +fix AtC internal atc field Ar_CauchyBorn.mat +fix_modify AtC mesh create 8 1 1 BOX f p p +fix_modify AtC fields none +fix_modify AtC fields add displacement +fix_modify AtC fields add internal_energy stress cauchy_born_energy cauchy_born_stress +fix_modify AtC gradients add displacement +fix_modify AtC fields add elastic_deformation_gradient +timestep 0.0 +fix_modify AtC output cb_unistrainFE 1 text tensor_components binary +log cb_unistrain.log +variable step equal 0 +thermo_style custom step v_step pe ke press lx ly lz +run 1 +variable step equal ${step}+1 +displace_atoms all ramp x -0.1 0.1 x -100 100 +run 1 +variable step equal ${step}+1 +displace_atoms all ramp x -0.1 0.1 x -100 100 +run 1 diff --git a/examples/USER/atc/cauchy_born/in.cb_unistrain_eam b/examples/USER/atc/cauchy_born/in.cb_unistrain_eam new file mode 100644 index 0000000000..102be6cdad --- /dev/null +++ b/examples/USER/atc/cauchy_born/in.cb_unistrain_eam @@ -0,0 +1,51 @@ +# This test compares Hardy and Cauchy-Born metrics of energy density and stress +# for an EAM system subjected to uniaxial strain deformation. +# NOTE currently the convergence is distinctly exponential, the LJ version is quadratic +echo both +units metal +atom_style atomic +# create domain +#lattice fcc 3.615 origin 0.25 0.25 0.25 +lattice fcc 3.615 origin 0.01 0.01 0.01 +region BOX block -8 8 -2 2 -2 2 +boundary f p p +create_box 1 BOX +# create atoms +region MD block -7 7 -2 2 -2 2 +create_atoms 1 region MD +mass 1 63.55 +# specify interal/ghost atoms +region FREE block -6 6 -2 2 -2 2 +group internal region FREE +# specify inter-atomic potential +pair_style eam +pair_coeff * * ../../../../potentials/Cu_u3.eam +# specify neighbor/re-neighboring parameters +neighbor 0.3 bin +neigh_modify every 10 delay 0 check no +# setup thermal output +thermo 10 +thermo_style custom step pe ke press lx ly lz +# ID group atc PhysicsType ParameterFile +fix AtC internal atc field Cu_CauchyBorn.mat +fix_modify AtC mesh create 8 1 1 BOX f p p +#fix_modify AtC kernel quartic_cylinder 10.0 +fix_modify AtC fields none +fix_modify AtC fields add displacement +fix_modify AtC fields add internal_energy stress +fix_modify AtC fields add cauchy_born_energy +fix_modify AtC fields add cauchy_born_stress +fix_modify AtC gradients add displacement +#fix_modify AtC fields add elastic_deformation_gradient +timestep 0.0 +fix_modify AtC output cb_unistrain_eamFE 1 text tensor_components binary +log cb_unistrain_eam.log +variable step equal 0 +thermo_style custom step v_step pe ke press lx ly lz +run 1 +variable step equal ${step}+1 +displace_atoms all ramp x -0.1 0.1 x -100 100 +run 1 +variable step equal ${step}+1 +displace_atoms all ramp x -0.1 0.1 x -100 100 +run 1 diff --git a/examples/USER/atc/cauchy_born/in.cb_unistrain_eam_linear b/examples/USER/atc/cauchy_born/in.cb_unistrain_eam_linear new file mode 100644 index 0000000000..cebc1b9e50 --- /dev/null +++ b/examples/USER/atc/cauchy_born/in.cb_unistrain_eam_linear @@ -0,0 +1,51 @@ +# This test compares Hardy and Cauchy-Born metrics of energy density and stress +# for an Ar system subjected to uniaxial strain deformation. +echo both +units real +atom_style atomic +# create domain +lattice fcc 4.08 origin 0.25 0.25 0.25 +region BOX block -8 8 -2 2 -2 2 +boundary f p p +create_box 1 BOX +# create atoms +region MD block -7 7 -2 2 -2 2 +create_atoms 1 region MD +pair_style eam +pair_coeff * * Au_u3.eam +mass * 196.97 +# specify interal/ghost atoms +region FREE block -6 6 -2 2 -2 2 +group internal region FREE +# specify inter-atomic potential +# specify neighbor/re-neighboring parameters +neighbor 0.3 bin +neigh_modify every 10 delay 0 check no +# setup thermal output +thermo 10 +thermo_style custom step pe ke press lx ly lz +# ID group atc PhysicsType ParameterFile +fix PP1 internal atc field Au_eam_linear.mat +fix_modify PP1 mesh create 8 1 1 BOX f p p +fix_modify PP1 fields add displacement +fix_modify PP1 fields add internal_energy stress cauchy_born_energy cauchy_born_stress +fix_modify PP1 gradients add displacement +fix_modify PP1 set reference_potential_energy 0 # correct cb and messes pe +# ID group atc PhysicsType ParameterFile +fix PP2 internal atc field Au_eam.mat +fix_modify PP2 mesh create 8 1 1 BOX f p p +fix_modify PP2 fields add cauchy_born_energy cauchy_born_stress internal_energy +fix_modify PP2 set reference_potential_energy +timestep 0.0 +fix_modify PP1 output cb_unistrain_eam_linearFE 1 text tensor_components binary +fix_modify PP2 output cb_unistrain_eam_refFE 1 text tensor_components +log cb_unistrain_eam_linear.log +variable step equal 0 +thermo_style custom step v_step pe ke press lx ly lz +run 1 +variable step equal ${step}+1 +displace_atoms all ramp x -0.1 0.1 x -100 100 +run 1 +variable step equal ${step}+1 +displace_atoms all ramp x -0.1 0.1 x -100 100 +run 1 diff --git a/examples/USER/atc/cauchy_born/in.cb_unistrain_linear b/examples/USER/atc/cauchy_born/in.cb_unistrain_linear new file mode 100644 index 0000000000..0ed6532eb2 --- /dev/null +++ b/examples/USER/atc/cauchy_born/in.cb_unistrain_linear @@ -0,0 +1,54 @@ +# This test compares Hardy and Cauchy-Born metrics of energy density and stress +# for an Ar system subjected to uniaxial strain deformation. +echo both +units real +atom_style atomic +# create domain +lattice fcc 4.08 origin 0.25 0.25 0.25 +region BOX block -8 8 -2 2 -2 2 +boundary f p p +create_box 1 BOX +# create atoms +region MD block -7 7 -2 2 -2 2 +create_atoms 1 region MD +#pair_style eam +#pair_coeff * * Au_u3.eam +#pair_style lj/cut/smooth 5.456108274435118 +pair_style lj/smooth/linear 5.456108274435118 +pair_coeff * * 0.7242785984051078 2.598146797350056 +mass * 196.97 +# specify interal/ghost atoms +region FREE block -6 6 -2 2 -2 2 +group internal region FREE +# specify inter-atomic potential +# specify neighbor/re-neighboring parameters +neighbor 0.3 bin +neigh_modify every 10 delay 0 check no +# setup thermal output +thermo 10 +thermo_style custom step pe ke press lx ly lz +# ID group atc PhysicsType ParameterFile +fix PP1 internal atc field Au_CauchyBorn_linear.mat +fix_modify PP1 mesh create 8 1 1 BOX f p p +fix_modify PP1 fields add displacement +fix_modify PP1 fields add internal_energy stress cauchy_born_energy cauchy_born_stress +fix_modify PP1 gradients add displacement +fix_modify PP1 set reference_potential_energy 0 # correct cb and messes pe +# ID group atc PhysicsType ParameterFile +fix PP2 internal atc field Au_CauchyBorn.mat +fix_modify PP2 mesh create 8 1 1 BOX f p p +fix_modify PP2 fields add cauchy_born_energy cauchy_born_stress internal_energy +fix_modify PP2 set reference_potential_energy +timestep 0.0 +fix_modify PP1 output cb_unistrain_linearFE 1 text tensor_components binary +fix_modify PP2 output cb_unistrain_refFE 1 text tensor_components +log cb_unistrain_linear.log +variable step equal 0 +thermo_style custom step v_step pe ke press lx ly lz +run 1 +variable step equal ${step}+1 +displace_atoms all ramp x -0.1 0.1 x -100 100 +run 1 +variable step equal ${step}+1 +displace_atoms all ramp x -0.1 0.1 x -100 100 +run 1 diff --git a/examples/USER/atc/cauchy_born/in.cb_volumetric b/examples/USER/atc/cauchy_born/in.cb_volumetric new file mode 100644 index 0000000000..745945c59a --- /dev/null +++ b/examples/USER/atc/cauchy_born/in.cb_volumetric @@ -0,0 +1,48 @@ +# This test compares Hardy and Cauchy-Born metrics of energy density and stress +# for an Ar system subjected to volumetric stretching. +echo both +units real +atom_style atomic +variable lattice_constant equal 5.256227487 +variable c equal 6 +variable L equal $c*${lattice_constant} +#variable d equal 0.01 +variable d equal 0.005 +variable s equal 1.005 +variable V0 equal ($c*${lattice_constant})^3 +# create system +lattice fcc ${lattice_constant} origin 0.25 0.25 0.25 +region box block 0 $c 0 $c 0 $c +boundary p p p +create_box 1 box +create_atoms 1 box +mass 1 39.95 +group all region box +pair_style lj/cut 13.5 +pair_coeff 1 1 0.238 3.405 +# ID group atc PhysicsType ParameterFile +fix AtC all atc field Ar_CauchyBorn.mat +fix_modify AtC mesh create $c $c $c box p p p +fix_modify AtC fields none +fix_modify AtC fields add displacement +fix_modify AtC fields add internal_energy stress cauchy_born_energy cauchy_born_stress +fix_modify AtC gradients add displacement +fix_modify AtC output cb_volumetricFE 1 full_text tensor_components +log cb_volumetric.log +thermo 100 +variable gamma equal 0.0 +variable step equal 0 +thermo_style custom step v_step pxx pyy pzz pxy pxz pyz v_gamma pe +timestep 0.0 +min_modify line quadratic +timestep 0.0 +variable i loop 4 +label loop_i + print ">>> step $i" + minimize 1.e-20 1.e-20 1000 1000 + run 1 + variable step equal ${step}+1 + change_box all x scale $s y scale $s z scale $s remap + variable gamma equal lx/$L-1.0 +next i +jump in.cb_volumetric loop_i diff --git a/examples/USER/atc/cauchy_born/in.flying_cube b/examples/USER/atc/cauchy_born/in.flying_cube new file mode 100644 index 0000000000..23bd7a5ae0 --- /dev/null +++ b/examples/USER/atc/cauchy_born/in.flying_cube @@ -0,0 +1,61 @@ +# This test evaluates Hardy fields for a small block of LJ material +# that's undergoing translation in the x-direction through the +# periodic boundary. +echo both +log log.flying_cube +units real +atom_style atomic +variable lattice_constant equal 5.256227487 +variable c equal 6 +variable L equal (${lattice_constant}*$c) +variable V equal $L*$L*$L +print "Volume : $V" +variable s equal 10 +variable dt equal 0.1 +variable v equal 0.1 +variable m equal 39.95 +# create system +lattice fcc ${lattice_constant} origin 0.01 0.01 0.01 +region box block 0 $c 0 $c 0 $c +boundary p p p +# boundary p s s +create_box 1 box +create_atoms 1 region box +mass 1 $m +group all region box +pair_style lj/cut 13.5 +pair_coeff 1 1 0.238 3.405 +# define region +neighbor 1.0 bin +neigh_modify delay 0 every 200 check no +# neigh_modify delay 0 every $n +reset_timestep 0 +thermo $s +compute_modify thermo_temp extra 0 +thermo_style custom step temp pxx pyy pzz etotal lx ly lz +timestep ${dt} +min_modify line quadratic +minimize 0. 0. 1000 1000 +reset_timestep 0 +variable xLO equal xlo +variable xHI equal xhi +variable yLO equal ylo +variable yHI equal yhi +variable zLO equal zlo +variable zHI equal zhi +# region BOX block ${xLO} ${xHI} ${yLO} ${yHI} ${zLO} ${zHI} units box +region BOX block ${xLO} ${xHI} -0.5 31.7 -0.5 31.7 units box +fix ATC all atc field +fix_modify ATC mesh create 1 1 1 box p p p +fix_modify ATC fields add stress velocity displacement +fix_modify ATC fields add temperature kinetic_temperature +fix_modify ATC fields add internal_energy energy +fix_modify ATC output flying_cubeFE $s text binary tensor_components +# fix_modify ATC atomic_output flying_cubeMD $m text binary tensor_components +dump dumpfc all atom $s flying_cube.dmp +velocity all set $v 0.0 0.0 units box +fix NVE all nve +run 3500 +variable c equal 48.88821291*48.88821291/(3.*0.0019872067) +variable T equal $m*$v*$v*$c +print "kinetic temperature: $T" diff --git a/examples/USER/atc/cauchy_born/in.ftcb_constV b/examples/USER/atc/cauchy_born/in.ftcb_constV new file mode 100644 index 0000000000..7178c017b0 --- /dev/null +++ b/examples/USER/atc/cauchy_born/in.ftcb_constV @@ -0,0 +1,74 @@ +# This test compares Hardy and Cauchy-Born metrics of energy density and stress +# for an Ar system undergoing dynamics at a finite temperature. +echo both +log ftcb_constV.log +units real +atom_style atomic +variable lattice_constant equal 5.256227487 +variable c equal 6 +variable L equal (${lattice_constant}*$c) +variable V equal $L*$L*$L +print "Volume : $V" +variable Ti equal 0.0001 +variable dT equal 0.2 +variable n equal 10000 +variable m equal 200 +variable dt equal 0.1 +# create system +lattice fcc ${lattice_constant} +region box block 0 $c 0 $c 0 $c +boundary p p p +pair_style lj/cut 13.5 +read_data ftcb_constV_setup.data +mass 1 39.95 +pair_coeff 1 1 0.238 3.405 +# define region +neighbor 1.0 bin +neigh_modify delay 0 every 2000 check no +reset_timestep 0 +thermo $m +compute_modify thermo_temp extra 0 +variable nrepeat equal $n/$m +variable sxx equal -pxx +variable intenergy equal etotal +fix TDAVE all ave/time $m ${nrepeat} $n c_thermo_temp v_sxx v_intenergy ave one file ftcb_constV.profile +thermo_style custom step temp press etotal lx ly lz +timestep ${dt} +# filtered +fix ATCFILT all atc field Ar_CauchyBorn.mat +#fix_modify ATCFILT reset_atomic_reference_positions ftcb_constV_setup.data +fix_modify ATCFILT mesh create 1 1 1 box p p p +fix_modify ATCFILT fields none +fix_modify ATCFILT fields add internal_energy stress cauchy_born_energy cauchy_born_stress +fix_modify ATCFILT fields add temperature displacement +fix_modify ATCFILT gradients add displacement +fix_modify ATCFILT output ftcb_constV_filteredFE $n text binary tensor_components +fix_modify ATCFILT sample_frequency $m +variable scale equal $n*${dt} +fix_modify ATCFILT filter scale ${scale} +fix_modify ATCFILT filter on +fix_modify ATCFILT filter type step +# not filtered +fix ATC all atc field Ar_CauchyBorn.mat +#fix_modify ATC reset_atomic_reference_positions ftcb_constV_setup.data +fix_modify ATC mesh create 1 1 1 box p p p +fix_modify ATC fields none +fix_modify ATC fields add internal_energy stress cauchy_born_energy cauchy_born_stress +fix_modify ATC fields add temperature displacement +fix_modify ATC gradients add displacement +fix_modify ATC output ftcb_constVFE $m text binary tensor_components +velocity all create ${Ti} 102486 mom yes rot yes dist gaussian +# step iu T,V space +variable i loop 1 +label loop_i + print ">>> step $i, T: ${Ti}, V: $V" + variable Tf equal ${Ti}+${dT} + fix NVT all nvt temp ${Ti} ${Tf} 20 drag 0.5 tchain 1 + run $n + unfix NVT + fix NVT all nvt temp ${Tf} ${Tf} 20 drag 0.5 tchain 1 + run $n + unfix NVT + variable Ti equal ${Tf} +next i +jump in.ftcb_constV loop_i diff --git a/examples/USER/atc/cauchy_born/in.read_xref b/examples/USER/atc/cauchy_born/in.read_xref new file mode 100644 index 0000000000..aab6828ef0 --- /dev/null +++ b/examples/USER/atc/cauchy_born/in.read_xref @@ -0,0 +1,37 @@ +# This is a test for reading an atomic reference configuration +echo both +units real +atom_style atomic +variable lattice_constant equal 5.256227487 +variable c equal 4 +variable L equal (${lattice_constant}*$c) +# create system +lattice fcc ${lattice_constant} +region box block 0 $c 0 $c 0 $c +boundary p p p +# the stretched configuration of the atoms +read_data read_xref_1.data +mass 1 39.95 +pair_style lj/cut 13.5 +pair_coeff 1 1 0.238 3.405 +# define region +neighbor 1.0 bin +neigh_modify delay 1000000 +thermo 1 +thermo_style custom step vol etotal +timestep 0 +fix ATC all atc field Ar_CauchyBorn.mat +# the original configuration of the atoms +fix_modify ATC reset_atomic_reference_positions read_xref_0.data +# "box" is the original box +fix_modify ATC mesh create 1 1 1 box f f f +fix_modify ATC fields none +fix_modify ATC fields add mass_density +fix_modify ATC output read_xrefFE 1 text +fix_modify ATC output index step +variable u1 atom x-f_ATC[1] +variable u2 atom y-f_ATC[2] +variable u3 atom z-f_ATC[3] +variable rho atom mass*f_ATC[4] +dump CONFIG all custom 1 read_xref.dmp id type x y z v_u1 v_u2 v_u3 v_rho +run 1 diff --git a/examples/USER/atc/cauchy_born/read_xref.screen b/examples/USER/atc/cauchy_born/read_xref.screen new file mode 100644 index 0000000000..393b8af4d1 --- /dev/null +++ b/examples/USER/atc/cauchy_born/read_xref.screen @@ -0,0 +1,83 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic +variable lattice_constant equal 5.256227487 +variable c equal 4 +variable L equal (${lattice_constant}*$c) +variable L equal (5.2562274870000003091*$c) +variable L equal (5.2562274870000003091*4) +# create system +lattice fcc ${lattice_constant} +lattice fcc 5.2562274870000003091 +Lattice spacing in x,y,z = 5.25623 5.25623 5.25623 +region box block 0 $c 0 $c 0 $c +region box block 0 4 0 $c 0 $c +region box block 0 4 0 4 0 $c +region box block 0 4 0 4 0 4 +boundary p p p +# the stretched configuration of the atoms +read_data read_xref_1.data +Reading data file ... + orthogonal box = (-1.05125 -1.05125 -1.05125) to (22.0762 22.0762 22.0762) + 1 by 2 by 2 MPI processor grid + 256 atoms + 256 velocities +mass 1 39.95 +pair_style lj/cut 13.5 +pair_coeff 1 1 0.238 3.405 +# define region +neighbor 1.0 bin +neigh_modify delay 1000000 +thermo 1 +thermo_style custom step vol etotal +timestep 0 +fix ATC all atc field Ar_CauchyBorn.mat +ATC: constructing shape function field estimate with parameter file Ar_CauchyBorn.mat + ATC: peratom PE compute created with ID: 3 +# the original configuration of the atoms +fix_modify ATC reset_atomic_reference_positions read_xref_0.data +# "box" is the original box +fix_modify ATC mesh create 1 1 1 box f f f + ATC: created uniform mesh with 8 nodes, 8 unique nodes, and 1 elements +fix_modify ATC fields none +fix_modify ATC fields add mass_density +fix_modify ATC output read_xrefFE 1 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +fix_modify ATC output index step +variable u1 atom x-f_ATC[1] +variable u2 atom y-f_ATC[2] +variable u3 atom z-f_ATC[3] +variable rho atom mass*f_ATC[4] +dump CONFIG all custom 1 read_xref.dmp id type x y z v_u1 v_u2 v_u3 v_rho +run 1 +Setting up run ... + ATC: P0, found 256 atoms in reference file + ATC: P0, read 256 reference positions + ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 +Memory usage per processor = 16.0674 Mbytes +Step Volume TotEng + 0 12370.307 -416.09102 + 1 12370.307 -416.09102 +Loop time of 0.00229579 on 4 procs for 1 steps with 256 atoms + +Pair time (%) = 0.00048399 (21.0816) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000252604 (11.0029) +Outpt time (%) = 0.00147229 (64.1301) +Other time (%) = 8.69036e-05 (3.78534) + +Nlocal: 64 ave 64 max 64 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1700 ave 1700 max 1700 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 7936 ave 7936 max 7936 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 15872 ave 15872 max 15872 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 63488 +Ave neighs/atom = 248 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/drift_diffusion/Ar_ddm.mat b/examples/USER/atc/drift_diffusion/Ar_ddm.mat new file mode 100644 index 0000000000..ac3860046c --- /dev/null +++ b/examples/USER/atc/drift_diffusion/Ar_ddm.mat @@ -0,0 +1,37 @@ +material Ar real + heat_capacity constant + capacity 1.0 + end + electron_heat_capacity constant, no density + capacity 1.0 + end + effective_mass constant + inv_effective_mass 1. + end + heat_flux linear + conductivity 1.0 + end + electron_heat_flux linear + conductivity 1.0 + end + electron_phonon_exchange linear + coefficient 1.0 + end + electron_flux linear + mobility 400.0 + diffusivity 1000.0 + end + electron_recombination linear + inv_relaxation_time 0.0 + equilibrium_carrier_density 1.0 + end + electric_field linear + permittivity 0.2 + end +end + +material Vacuum real + electric_field linear + permittivity 1.0 + end +end diff --git a/examples/USER/atc/drift_diffusion/CNT_ddm.mat b/examples/USER/atc/drift_diffusion/CNT_ddm.mat new file mode 100644 index 0000000000..b84bf3bd67 --- /dev/null +++ b/examples/USER/atc/drift_diffusion/CNT_ddm.mat @@ -0,0 +1,41 @@ +####################################################################### +material Vacuum metal +electric_field linear +permittivity 1.0 # e/V/L scales electric field vs charge +end +electron_density null +end + +####################################################################### +material C metal +#### two temperature #################### +heat_capacity constant +capacity 0.0566081301 # E / L^3 +end +electron_heat_capacity linear +capacity 9.03321225e-08 # E / L^3 +end +heat_flux linear +conductivity 602.21415 # E / t / L / T +end +electron_heat_flux linear +conductivity 0.4413627505355 # E / t / L / T +end +electron_phonon_exchange power_law +coefficient 2.247e-15 # E / t / T 2.247e-15 +exponent 4 +end +#### drift diffusion ##################### +electron_flux linear +mobility 360000.0 # L^2/t/V +diffusivity 14000000.0 # L^2/t +end +electron_recombination linear +inv_relaxation_time 0.0 # 1/t HACK +equilibrium_carrier_density 0.0 # e/L^3 HACK +end +electric_field linear +permittivity 0.06 # e/V/L scales electric field vs charge +end +end +end diff --git a/examples/USER/atc/drift_diffusion/Cu_cddm.mat b/examples/USER/atc/drift_diffusion/Cu_cddm.mat new file mode 100644 index 0000000000..7150ad505b --- /dev/null +++ b/examples/USER/atc/drift_diffusion/Cu_cddm.mat @@ -0,0 +1,45 @@ +#===================================================== +material Vacuum metal +#### two temperature #################### +#### drift diffusion ##################### +electric_field linear +#permittivity 1.0 +permittivity 1.085 # estimate based on speed of light in Cu and Cu's relative permeability of 1 +end +end +#===================================================== +material Cu metal + heat_capacity constant + capacity 0.211977459280654 + end + heat_flux linear + conductivity 67.4479848 + end + electron_heat_capacity linear no_density + #capacity 6.8439866929411762e-05 # value from TTM paper divided by bulk electron density in Cu + capacity 5.8294334393503992e-05 # source 96.8 J m^-3 K^-2 in Lin & Zhigilei 08 (ref 47), converted to AtC units and divided by bulk electron density in Cu, NOTE: should not be multiplied by electron effective mass, only electron number density + end + electron_heat_flux linear + conductivity 441.362750535 + end + electron_phonon_exchange hertel + debeye_temperature 343.5 # source wikipedia + mass_enhancement 0.08 # source Hertel 2002, ref 62 + end + electric_field linear + permittivity 1.085 # estimate based on speed of light in Cu and Cu's relative permeability of 1 + end + effective_mass constant + inv_effective_mass 0.8997 # source: Tolman & Stewart, 1916 + end + electron_drag linear + inv_momentum_relaxation_time 100. # order of magnitude estimate for metals ~ 10^-14 s + end + electron_flux convection + end + end + electron_recombination linear + inv_relaxation_time 0.0 + equilibrium_carrier_density 0.0 + end +end diff --git a/examples/USER/atc/drift_diffusion/SiGe_ddm_schrodinger.mat b/examples/USER/atc/drift_diffusion/SiGe_ddm_schrodinger.mat new file mode 100644 index 0000000000..dc41b1156f --- /dev/null +++ b/examples/USER/atc/drift_diffusion/SiGe_ddm_schrodinger.mat @@ -0,0 +1,86 @@ +# barrier +material Si metal +#### two temperature #################### +heat_capacity constant + capacity 0.124578126430817 # E / L^3 +end +electron_heat_capacity constant, no density #power_law +#capacity 3.53391324615404e-11 + capacity 3.53391324615404e-8 # E / L^3 +end +heat_flux linear + conductivity 722.65698 # E / t / L / T +end +electron_heat_flux linear + conductivity 0.0441362750535 # E / t / L / T +end +electron_phonon_exchange linear + coefficient 6.0221415e-09 # E / t / T +end +#### drift diffusion ##################### +electron_flux linear + mobility 360000.0 # L^2/t/V + diffusivity 14000000.0 # L^2/t +end +electron_recombination linear +# inv_relaxation_time 0.0 # 1/t HACK +# equilibrium_carrier_density 1.0 # e/L^3 HACK +end +electric_field linear + permittivity 11.68 # e/V/L scales electric field vs charge +end +effective_mass constant + inv_effective_mass 1.0 # unit-less +end +electron_density fermi_dirac + fermi_energy 0.0 + band_edge 0.5 +# reference_temperature 300.0 # HACK + donor_concentration 0.001 +# donor_ionization_energy 0.1 # relative to band edge HACK +end +end + +# well +material Ge metal +#### two temperature #################### +heat_capacity constant + capacity 0.124578126430817 # E / L^3 +end +electron_heat_capacity constant #power_law +#capacity 3.53391324615404e-11 + capacity 3.53391324615404e-8 # E / L^3 +end +heat_flux linear + conductivity 722.65698 # E / t / L / T +end +electron_heat_flux linear + conductivity 0.0441362750535 # E / t / L / T +end +electron_phonon_exchange linear + coefficient 6.0221415e-09 # E / t / T +end +#### drift diffusion ##################### +electron_flux linear + mobility 360000.0 # L^2/t/V + diffusivity 14000000.0 # L^2/t +end +electron_recombination linear + inv_relaxation_time 0.0 # 1/t HACK + equilibrium_carrier_density 1.0 # e/L^3 HACK +end +electric_field linear + permittivity 11.68 # (SAME AS Si) e/V/L scales electric field vs charge +end +effective_mass constant + inv_effective_mass 1.0 # unit-less (SAME AS Si) +end +electron_density fermi_dirac + fermi_energy 0.0 + band_edge -0.5 +# reference_temperature 0.0 # HACK +# reference_temperature 300.0 # HACK +# donor_concentration 0.001 # HACK +# donor_ionization_energy 0.1 # relative to band edge HACK +end +end diff --git a/examples/USER/atc/drift_diffusion/SiVacuum_cddm_schrodinger.mat b/examples/USER/atc/drift_diffusion/SiVacuum_cddm_schrodinger.mat new file mode 100644 index 0000000000..2ba1d53a11 --- /dev/null +++ b/examples/USER/atc/drift_diffusion/SiVacuum_cddm_schrodinger.mat @@ -0,0 +1,64 @@ +#===================================================== +material Vacuum metal +#### two temperature #################### +#### drift diffusion ##################### +electric_field linear +permittivity 1.0 +end +end + +#===================================================== +material Si metal +#### two temperature #################### +heat_capacity constant + capacity 0.124578126430817 # E / L^3 +end +electron_heat_capacity constant, no density #power_law +#capacity 3.53391324615404e-11 + capacity 3.53391324615404e-8 # E / L^3 +end +heat_flux linear + conductivity 722.65698 # E / t / L / T +end +electron_heat_flux linear + conductivity 0.0441362750535 # E / t / L / T +end +electron_phonon_exchange linear + coefficient 6.0221415e-09 # E / t / T +end +#### drift diffusion ##################### +electron_flux linear + mobility 360000.0 # L^2/t/V + #diffusivity 14000000.0 # L^2/t + diffusivity 1400.0 # L^2/t + mask_y 1 + mask_z 1 +end +electron_recombination linear +# inv_relaxation_time 0.0 # 1/t HACK +# equilibrium_carrier_density 1.0 # e/L^3 HACK +end +electric_field linear + permittivity 11.68 # e/V/L http://en.wikipedia.org/wiki/Relative_permittivity +end +effective_mass constant + inv_effective_mass 1.0 # unit-less +end +electron_density fermi_dirac + fermi_energy 0.0 # HACK + band_edge -1.0 # -1.0 +# reference_temperature 0.0 # HACK +# donor_concentration 0.001 # HACK +# donor_ionization_energy 0.1 # relative to band edge HACK +end + +### convective functions +electron_drag linear + inv_momentum_relaxation_time 100. +end +electron_flux convection +end + +end + + diff --git a/examples/USER/atc/drift_diffusion/SiVacuum_ddm_schrodinger.mat b/examples/USER/atc/drift_diffusion/SiVacuum_ddm_schrodinger.mat new file mode 100644 index 0000000000..e564b8e320 --- /dev/null +++ b/examples/USER/atc/drift_diffusion/SiVacuum_ddm_schrodinger.mat @@ -0,0 +1,52 @@ +material Vacuum metal +electric_field linear +permittivity 1.0 +end +end + +material Si metal +#### two temperature #################### +heat_capacity constant + capacity 0.124578126430817 # E / L^3 +end +electron_heat_capacity constant, no density #power_law +#capacity 3.53391324615404e-11 + capacity 3.53391324615404e-8 # E / L^3 +end +heat_flux linear + conductivity 722.65698 # E / t / L / T +end +electron_heat_flux linear + conductivity 0.0441362750535 # E / t / L / T +end +electron_phonon_exchange linear + coefficient 6.0221415e-09 # E / t / T +end +#### drift diffusion ##################### +electron_flux linear + mobility 360000.0 # L^2/t/V + #diffusivity 14000000.0 # L^2/t + diffusivity 1400.0 # L^2/t + mask_y 1 + mask_z 1 +end +electron_recombination linear +# inv_relaxation_time 0.0 # 1/t HACK +# equilibrium_carrier_density 1.0 # e/L^3 HACK +end +electric_field linear + permittivity 11.68 # e/V/L http://en.wikipedia.org/wiki/Relative_permittivity +end +effective_mass constant + inv_effective_mass 1.0 # unit-less +end +electron_density fermi_dirac + fermi_energy 0.0 # HACK + band_edge -1.0 # -1.0 +# reference_temperature 0.0 # HACK +# donor_concentration 0.001 # HACK +# donor_ionization_energy 0.1 # relative to band edge HACK +end +end + + diff --git a/examples/USER/atc/drift_diffusion/Si_ddm.mat b/examples/USER/atc/drift_diffusion/Si_ddm.mat new file mode 100644 index 0000000000..3cb461785b --- /dev/null +++ b/examples/USER/atc/drift_diffusion/Si_ddm.mat @@ -0,0 +1,35 @@ +material Si metal +#### two temperature #################### +heat_capacity constant +capacity 0.124578126430817 # E / L^3 +end +electron_heat_capacity constant, no density #power_law +#capacity 3.53391324615404e-11 +capacity 3.53391324615404e-8 # E / L^3 +end +effective_mass constant +inv_effective_mass 1. +end +heat_flux linear +conductivity 722.65698 # E / t / L / T +end +electron_heat_flux linear +conductivity 0.0441362750535 # E / t / L / T +end +electron_phonon_exchange linear +coefficient 6.0221415e-09 # E / t / T +end +#### drift diffusion ##################### +electron_flux linear +mobility 360000.0 # L^2/t/V +diffusivity 14000000.0 # L^2/t +end +electron_recombination linear +inv_relaxation_time 0.0 # 1/t HACK +equilibrium_carrier_density 1.0 # e/L^3 HACK +end +electric_field linear +permittivity 0.06 # e/V/L scales electric field vs charge +end +#donor_concentration 1.0e-4 # e/L^3 HACK must be consistent w/ n0 ? +end diff --git a/examples/USER/atc/drift_diffusion/Si_ddm_eq.mat b/examples/USER/atc/drift_diffusion/Si_ddm_eq.mat new file mode 100644 index 0000000000..f9d6da7fed --- /dev/null +++ b/examples/USER/atc/drift_diffusion/Si_ddm_eq.mat @@ -0,0 +1,44 @@ +material Si metal +#### two temperature #################### +heat_capacity constant + capacity 0.124578126430817 # E / L^3 +end +electron_heat_capacity constant, no density #power_law +#capacity 3.53391324615404e-11 + capacity 3.53391324615404e-8 # E / L^3 +end +heat_flux linear + conductivity 722.65698 # E / t / L / T +end +electron_heat_flux linear + conductivity 0.0441362750535 # E / t / L / T +end +electron_phonon_exchange linear + coefficient 6.0221415e-09 # E / t / T +end +#### drift diffusion ##################### +electron_flux linear + mobility 360000.0 # L^2/t/V + diffusivity 14000000.0 # L^2/t +end +electron_recombination linear + inv_relaxation_time 0.0 # 1/t HACK + equilibrium_carrier_density 1.0 # e/L^3 HACK +end +electric_field linear +#permittivity 0.06 # e/V/L scales electric field vs charge + permittivity 1.0 # e/V/L scales electric field vs charge +end +effective_mass constant + #inv_effective_mass 2308171.85625180610344519705 # rescale by 1/hbar^2 old bug? + inv_effective_mass 1.0 +end +band_edge_potential constant + band_edge 0.0 +end +electron_density exponential + intrinsic_energy 0.0 # 1.0 e/L^3 HACK must be consistent w/ n0 ? + intrinsic_concentration 0.0 # 1.0 e/L^3 HACK must be consistent w/ n0 ? + reference_temperature 300.0 # HACK +end +end diff --git a/examples/USER/atc/drift_diffusion/Si_ddm_schrodinger.mat b/examples/USER/atc/drift_diffusion/Si_ddm_schrodinger.mat new file mode 100644 index 0000000000..851ad27acc --- /dev/null +++ b/examples/USER/atc/drift_diffusion/Si_ddm_schrodinger.mat @@ -0,0 +1,41 @@ +material Si metal +#### two temperature #################### +heat_capacity constant + capacity 0.124578126430817 # E / L^3 +end +electron_heat_capacity constant, no density #power_law +#capacity 3.53391324615404e-11 + capacity 3.53391324615404e-8 # E / L^3 +end +heat_flux linear + conductivity 722.65698 # E / t / L / T +end +electron_heat_flux linear + conductivity 0.0441362750535 # E / t / L / T +end +electron_phonon_exchange linear + coefficient 6.0221415e-09 # E / t / T +end +#### drift diffusion ##################### +electron_flux linear + mobility 360000.0 # L^2/t/V + diffusivity 14000000.0 # L^2/t +end +electron_recombination linear +# inv_relaxation_time 0.0 # 1/t HACK +# equilibrium_carrier_density 1.0 # e/L^3 HACK +end +electric_field linear + permittivity 11.68 # e/V/L http://en.wikipedia.org/wiki/Relative_permittivity +end +effective_mass constant + inv_effective_mass 1.0 # 0.13123421851033382246725208450724 # unit-less +end +electron_density fermi_dirac + fermi_energy 0.5 # HACK + band_edge 0.0 # -1.0 +# reference_temperature 0.0 # HACK + donor_concentration 0.0001 # HACK +# donor_ionization_energy 0.1 # relative to band edge HACK +end +end diff --git a/examples/USER/atc/drift_diffusion/Si_ddm_thermopower.mat b/examples/USER/atc/drift_diffusion/Si_ddm_thermopower.mat new file mode 100644 index 0000000000..297f960072 --- /dev/null +++ b/examples/USER/atc/drift_diffusion/Si_ddm_thermopower.mat @@ -0,0 +1,36 @@ +material Si metal +#### drift diffusion ##################### +electron_flux thermopower +mobility 360000.0 # L^2/t/V , diffusivity from Einstein rel. +Seebeck 1.0e-9 # HACK order kB +end +end +electron_recombination linear +inv_relaxation_time 0.0 # 1/t HACK +equilibrium_carrier_density 1.0 # e/L^3 HACK +end +electric_field linear +permittivity 0.06 # e/V/L scales electric field vs charge +end +#donor_concentration 1.0 # e/L^3 HACK must be consistent w/ n0 ? +#### two temperature #################### +heat_capacity constant +capacity 0.124578126430817 # E / L^3 +end +electron_heat_capacity constant, no density #power_law +#capacity 3.53391324615404e-11 +capacity 3.53391324615404e-8 # E / L^3 +end +effective_mass constant +inv_effective_mass 1. +end +heat_flux linear +conductivity 722.65698 # E / t / L / T +end +electron_heat_flux thermopower # links to electron_flux +conductivity 0.0441362750535 # E / t / L / T +end +electron_phonon_exchange linear +coefficient 6.0221415e-09 # E / t / T +end +end diff --git a/examples/USER/atc/drift_diffusion/convective_pulse.screen b/examples/USER/atc/drift_diffusion/convective_pulse.screen new file mode 100644 index 0000000000..4bf03d346e --- /dev/null +++ b/examples/USER/atc/drift_diffusion/convective_pulse.screen @@ -0,0 +1,144 @@ +LAMMPS (14 Aug 2013) +units metal + +variable V equal 5000.0 +variable n0 equal 0.085 +variable dn equal 2.0*${n0} +variable dn equal 2.0*0.085000000000000006106 +variable dt equal 0.0005 +variable s equal 10 + +timestep ${dt} +timestep 0.00050000000000000001041 + +atom_style atomic +lattice fcc 1.0 +Lattice spacing in x,y,z = 1 1 1 +region simRegion block -50 50 0 1 0 1 +boundary f p p +create_box 1 simRegion +Created orthogonal box = (-50 0 0) to (50 1 1) + 4 by 1 by 1 MPI processor grid +mass 1 1.0 # need to keep this +atom_modify sort 0 1 + +# ID group atc PhysicsType ParameterFile +fix AtC all atc convective_drift_diffusion Cu_cddm.mat +ATC: constructing convective_drift_diffusion coupling with parameter file Cu_cddm.mat + ATC: peratom PE compute created with ID: 3 + ATC: 2 materials defined from Cu_cddm.mat + ATC: creating convective_drift_diffusion extrinsic model + ATC: 2 materials defined from Cu_cddm.mat + ATC: 2 materials defined from Cu_cddm.mat + ATC: 2 materials defined from Cu_cddm.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 100 1 1 simRegion f p p + ATC: created uniform mesh with 404 nodes, 101 unique nodes, and 100 elements + +fix_modify AtC material all Cu + +fix_modify AtC mesh create_nodeset lbc -50.0 -50.0 -INF INF -INF INF + ATC: created nodeset lbc with 1 nodes +fix_modify AtC mesh create_nodeset rbc 50.0 50.0 -INF INF -INF INF + ATC: created nodeset rbc with 1 nodes + +# fix a temperature +fix_modify AtC initial temperature all 300.0 +#fix_modify AtC initial electron_temperature all 300.0 +fix_modify AtC fix electron_temperature all 300. +#fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5.0 300. 300. +fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 ${dn} ${n0} +fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 0.17000000000000001221 ${n0} +fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 0.17000000000000001221 0.085000000000000006106 +#fix_modify AtC fix electron_density all ${n0} +# isolate system: +# diffusion: dn/dx = 0 +# drift : n = 0 +fix_modify AtC fix electron_density lbc ${n0} +fix_modify AtC fix electron_density lbc 0.085000000000000006106 +fix_modify AtC fix electron_density rbc ${n0} +fix_modify AtC fix electron_density rbc 0.085000000000000006106 +fix_modify AtC fix temperature lbc 300.0 +fix_modify AtC fix temperature rbc 300.0 +fix_modify AtC fix electron_temperature lbc 300.0 +fix_modify AtC fix electron_temperature rbc 300.0 +fix_modify AtC fix electric_potential all 0. +fix_modify AtC extrinsic electron_integration implicit + +# electron velocity +fix_modify AtC initial electron_velocity x all 0. +#fix_modify AtC fix electron_velocity x all 0. +fix_modify AtC initial electron_velocity y all 0. +fix_modify AtC fix electron_velocity y all 0 +fix_modify AtC initial electron_velocity z all 0. +fix_modify AtC fix electron_velocity z all 0. + +# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5] +thermo_modify format 1 %5i format 2 %7.2g +fix_modify AtC output convective_pulseFE $s text binary +fix_modify AtC output convective_pulseFE 10 text binary + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +thermo $s +thermo 10 +#run 100 + +# free electric field and allow shielding +fix_modify AtC unfix electric_potential all +fix_modify AtC fix electric_potential lbc -$V +fix_modify AtC fix electric_potential lbc -5000 +fix_modify AtC fix electric_potential rbc 0 +fix_modify AtC source electric_potential all ${n0} +fix_modify AtC source electric_potential all 0.085000000000000006106 +fix_modify AtC extrinsic electron_integration implicit 10 +run 100 +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: all initial conditions for electric_potential have not been defined and the undefined are assumed zero + ATC: WARNING: material: [vacuum] cannot find electron_phonon_exchange + ATC: WARNING: physics model: [convection drift-diffusion], material: [vacuum] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [vacuum] cannot find electron_flux + ATC: WARNING: physics model: [convection drift-diffusion], material: [vacuum] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [cu] cannot find electron_recombination + ATC: WARNING: physics model: [convection drift-diffusion], material: [cu] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [vacuum] cannot find electron_drag_coefficient + ATC: WARNING: physics model: [convection drift-diffusion], material: [vacuum] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [vacuum] cannot find electron_drag_power + ATC: WARNING: physics model: [convection drift-diffusion], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 0.432198 Mbytes +Step CPU AtC[1] AtC[2] AtC[3] AtC[4] AtC[5] + 0 0 0.65909742 300 0.0054411845 300 10.091586 + 10 3 0.65909742 300 0.0054411845 300 10.091586 + 20 6 0.65909742 300 0.0054411845 300 10.091586 + 30 10 0.65909742 300 0.0054411845 300 10.091586 + 40 14 0.65909742 300 0.0054411845 300 10.091586 + 50 17 0.65909742 300 0.0054411845 300 10.091586 + 60 20 0.65909742 300 0.0054411845 300 10.091586 + 70 23 0.65909742 300 0.0054411845 300 10.091586 + 80 33 0.65909742 300 0.0054411845 300 10.091586 + 90 37 0.65909742 300 0.0054411845 300 10.091586 + 100 40 0.65909742 300 0.0054411845 300 10.091586 +Loop time of 39.7392 on 4 procs for 100 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000300825 (0.000756998) +Outpt time (%) = 0.125219 (0.315103) +Other time (%) = 39.6136 (99.6841) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/drift_diffusion/ddm_schrodinger.screen b/examples/USER/atc/drift_diffusion/ddm_schrodinger.screen new file mode 100644 index 0000000000..5ef5fc8cf8 --- /dev/null +++ b/examples/USER/atc/drift_diffusion/ddm_schrodinger.screen @@ -0,0 +1,78 @@ +LAMMPS (14 Aug 2013) +units metal + +variable dt equal 0.0000001 +variable s equal 1 +variable L equal 10.0 +variable N equal 40 +variable T equal 30000.0 +variable E equal 0.5 + +timestep ${dt} +timestep 9.9999999999999995475e-08 + +atom_style atomic +lattice fcc 1.0 +Lattice spacing in x,y,z = 1 1 1 +region simRegion block 0 $L 0 1 0 1 +region simRegion block 0 10 0 1 0 1 +boundary f p p +create_box 1 simRegion +Created orthogonal box = (0 0 0) to (10 1 1) + 4 by 1 by 1 MPI processor grid +mass 1 1.0 # need to keep this +atom_modify sort 0 1 + +# ID group atc PhysicsType ParameterFile +fix AtC all atc drift_diffusion-schrodinger Si_ddm_schrodinger.mat +ATC: constructing drift_diffusion-schrodinger coupling with parameter file Si_ddm_schrodinger.mat + ATC: peratom PE compute created with ID: 3 + ATC: 1 materials defined from Si_ddm_schrodinger.mat + ATC: creating drift_diffusion extrinsic model + ATC: 1 materials defined from Si_ddm_schrodinger.mat + ATC: 1 materials defined from Si_ddm_schrodinger.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create $N 1 1 simRegion f p p +fix_modify AtC mesh create 40 1 1 simRegion f p p + ATC: created uniform mesh with 164 nodes, 41 unique nodes, and 40 elements + +variable a equal $L-0.1 +variable a equal 10-0.1 +variable b equal $L+0.1 +variable b equal 10+0.1 +fix_modify AtC mesh create_nodeset lbc -0.1 0.1 -INF INF -INF INF + ATC: created nodeset lbc with 1 nodes +fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 9.9000000000000003553 $b -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 9.9000000000000003553 10.099999999999999645 -INF INF -INF INF + ATC: created nodeset rbc with 1 nodes + +# ics/bcs : density consistent with wave function +fix_modify AtC initial temperature all 300.0 +fix_modify AtC fix temperature all 300.0 +fix_modify AtC initial electron_temperature all $T +fix_modify AtC initial electron_temperature all 30000 +fix_modify AtC fix electron_temperature all $T +fix_modify AtC fix electron_temperature all 30000 +fix_modify AtC initial electron_density all 0.0 +#fix_modify AtC fix electron_density lbc 0 +#fix_modify AtC fix electron_density rbc 0 +fix_modify AtC initial electric_potential all 0.0 +fix_modify AtC initial electron_wavefunction all 0.0 +fix_modify AtC fix electron_wavefunction lbc 0 +fix_modify AtC fix electron_wavefunction rbc 0 + +thermo $s +thermo 1 +# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5] +thermo_modify format 1 %5i format 2 %7.2g +fix_modify AtC output ddm_schrodingerFE $s text +fix_modify AtC output ddm_schrodingerFE 1 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +fix_modify AtC extrinsic electron_integration implicit 1 +fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 1 # 100 +ERROR: Illegal fix_modify command (../fix.cpp:104) diff --git a/examples/USER/atc/drift_diffusion/finite_well.screen b/examples/USER/atc/drift_diffusion/finite_well.screen new file mode 100644 index 0000000000..a59a2ad60f --- /dev/null +++ b/examples/USER/atc/drift_diffusion/finite_well.screen @@ -0,0 +1,105 @@ +LAMMPS (14 Aug 2013) +units metal + +variable E equal 0.1 +variable L equal 10.0 +#variable N equal 100 +variable N equal 80 +variable T equal 1000 +variable n0 equal 0.0001 +variable dn equal 2.0*${n0} +variable dn equal 2.0*0.00010000000000000000479 +variable dt equal 0.0000001 +variable s equal 1 + +timestep ${dt} +timestep 9.9999999999999995475e-08 + +atom_style atomic +lattice fcc 1.0 +Lattice spacing in x,y,z = 1 1 1 +variable a equal 0.5*$L +variable a equal 0.5*10 +region simRegion block -$a $a 0 1 0 1 +region simRegion block -5 $a 0 1 0 1 +region simRegion block -5 5 0 1 0 1 +boundary f p p +create_box 1 simRegion +Created orthogonal box = (-5 0 0) to (5 1 1) + 4 by 1 by 1 MPI processor grid +mass 1 1.0 # need to keep this +atom_modify sort 0 1 + +# ID group atc PhysicsType ParameterFile +fix AtC all atc drift_diffusion-schrodinger SiGe_ddm_schrodinger.mat +ATC: constructing drift_diffusion-schrodinger coupling with parameter file SiGe_ddm_schrodinger.mat + ATC: peratom PE compute created with ID: 3 + ATC: 2 materials defined from SiGe_ddm_schrodinger.mat + ATC: creating drift_diffusion extrinsic model + ATC: 2 materials defined from SiGe_ddm_schrodinger.mat + ATC: 2 materials defined from SiGe_ddm_schrodinger.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create $N 1 1 simRegion f p p +fix_modify AtC mesh create 80 1 1 simRegion f p p + ATC: created uniform mesh with 324 nodes, 81 unique nodes, and 80 elements +variable a equal 0.2*$L+0.001 +variable a equal 0.2*10+0.001 +fix_modify AtC mesh create_elementset well -$a $a -INF INF -INF INF +fix_modify AtC mesh create_elementset well -2.0009999999999998899 $a -INF INF -INF INF +fix_modify AtC mesh create_elementset well -2.0009999999999998899 2.0009999999999998899 -INF INF -INF INF + ATC: created elementset well with 32 elements +fix_modify AtC mesh create_nodeset well -$a $a -INF INF -INF INF +fix_modify AtC mesh create_nodeset well -2.0009999999999998899 $a -INF INF -INF INF +fix_modify AtC mesh create_nodeset well -2.0009999999999998899 2.0009999999999998899 -INF INF -INF INF + ATC: created nodeset well with 33 nodes +fix_modify AtC material well Ge + +variable b equal $a-0.002 +variable b equal 2.0009999999999998899-0.002 +fix_modify AtC mesh create_nodeset lbc -$a -$b -INF INF -INF INF +fix_modify AtC mesh create_nodeset lbc -2.0009999999999998899 -$b -INF INF -INF INF +fix_modify AtC mesh create_nodeset lbc -2.0009999999999998899 -1.9989999999999998881 -INF INF -INF INF + ATC: created nodeset lbc with 1 nodes +fix_modify AtC mesh create_nodeset rbc $b $a -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 1.9989999999999998881 $a -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 1.9989999999999998881 2.0009999999999998899 -INF INF -INF INF + ATC: created nodeset rbc with 1 nodes + +# ics/bcs +fix_modify AtC initial temperature all 300.0 +fix_modify AtC fix temperature all 300.0 +# +fix_modify AtC initial electron_temperature all $T +fix_modify AtC initial electron_temperature all 1000 +fix_modify AtC fix electron_temperature all $T +fix_modify AtC fix electron_temperature all 1000 +# +fix_modify AtC initial electron_density all 0.0 +#fix_modify AtC fix electron_density all -0.001 +#fix_modify AtC fix electron_density well 0.002 +# +fix_modify AtC initial electric_potential all 0.0 +#fix_modify AtC fix electric_potential lbc 0.5 +#fix_modify AtC fix electric_potential rbc 0.5 +fix_modify AtC fix electric_potential lbc 0.0 +fix_modify AtC fix electric_potential rbc 0.0 +# +fix_modify AtC initial electron_wavefunction all 0.0 +fix_modify AtC fix electron_wavefunction lbc 0.0 +fix_modify AtC fix electron_wavefunction rbc 0.0 + + +thermo $s +thermo 1 +# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5] +thermo_modify format 1 %5i format 2 %7.2g +fix_modify AtC output finite_wellFE $s text +fix_modify AtC output finite_wellFE 1 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +fix_modify AtC extrinsic electron_integration implicit 3 +fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 3 # 30 +ERROR: Illegal fix_modify command (../fix.cpp:104) diff --git a/examples/USER/atc/drift_diffusion/in.convective_pulse b/examples/USER/atc/drift_diffusion/in.convective_pulse new file mode 100644 index 0000000000..c45ea874e9 --- /dev/null +++ b/examples/USER/atc/drift_diffusion/in.convective_pulse @@ -0,0 +1,72 @@ +# DESCRIPTION: haynes-schockley +echo both +units metal + +variable V equal 5000.0 +variable n0 equal 0.085 +variable dn equal 2.0*${n0} +variable dt equal 0.0005 +variable s equal 10 + +timestep ${dt} + +atom_style atomic +lattice fcc 1.0 +region simRegion block -50 50 0 1 0 1 +boundary f p p +create_box 1 simRegion +mass 1 1.0 # need to keep this +atom_modify sort 0 1 + +# ID group atc PhysicsType ParameterFile +fix AtC all atc convective_drift_diffusion Cu_cddm.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 100 1 1 simRegion f p p + +fix_modify AtC material all Cu + +fix_modify AtC mesh create_nodeset lbc -50.0 -50.0 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 50.0 50.0 -INF INF -INF INF + +# fix a temperature +fix_modify AtC initial temperature all 300.0 +#fix_modify AtC initial electron_temperature all 300.0 +fix_modify AtC fix electron_temperature all 300. +#fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5.0 300. 300. +fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 ${dn} ${n0} +#fix_modify AtC fix electron_density all ${n0} +# isolate system: +# diffusion: dn/dx = 0 +# drift : n = 0 +fix_modify AtC fix electron_density lbc ${n0} +fix_modify AtC fix electron_density rbc ${n0} +fix_modify AtC fix temperature lbc 300.0 +fix_modify AtC fix temperature rbc 300.0 +fix_modify AtC fix electron_temperature lbc 300.0 +fix_modify AtC fix electron_temperature rbc 300.0 +fix_modify AtC fix electric_potential all 0. +fix_modify AtC extrinsic electron_integration implicit + +# electron velocity +fix_modify AtC initial electron_velocity x all 0. +#fix_modify AtC fix electron_velocity x all 0. +fix_modify AtC initial electron_velocity y all 0. +fix_modify AtC fix electron_velocity y all 0 +fix_modify AtC initial electron_velocity z all 0. +fix_modify AtC fix electron_velocity z all 0. + +# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5] +thermo_modify format 1 %5i format 2 %7.2g +fix_modify AtC output convective_pulseFE $s text binary +thermo $s +#run 100 + +# free electric field and allow shielding +fix_modify AtC unfix electric_potential all +fix_modify AtC fix electric_potential lbc -$V +fix_modify AtC fix electric_potential rbc 0 +fix_modify AtC source electric_potential all ${n0} +fix_modify AtC extrinsic electron_integration implicit 10 +run 100 diff --git a/examples/USER/atc/drift_diffusion/in.ddm_schrodinger b/examples/USER/atc/drift_diffusion/in.ddm_schrodinger new file mode 100644 index 0000000000..8cbe4f9627 --- /dev/null +++ b/examples/USER/atc/drift_diffusion/in.ddm_schrodinger @@ -0,0 +1,66 @@ +# needs description +# DESCRIPTION: haynes-schockley +# poisson eqn for E-field: epsilon phi,xx = -e (n - p + N_D - N_A) +# w/ E = phi,x + +echo both +units metal + +variable dt equal 0.0000001 +variable s equal 1 +variable L equal 10.0 +variable N equal 40 +variable T equal 30000.0 +variable E equal 0.5 + +timestep ${dt} + +atom_style atomic +lattice fcc 1.0 +region simRegion block 0 $L 0 1 0 1 +boundary f p p +create_box 1 simRegion +mass 1 1.0 # need to keep this +atom_modify sort 0 1 + +# ID group atc PhysicsType ParameterFile +fix AtC all atc drift_diffusion-schrodinger Si_ddm_schrodinger.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create $N 1 1 simRegion f p p + +variable a equal $L-0.1 +variable b equal $L+0.1 +fix_modify AtC mesh create_nodeset lbc -0.1 0.1 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF + +# ics/bcs : density consistent with wave function +fix_modify AtC initial temperature all 300.0 +fix_modify AtC fix temperature all 300.0 +fix_modify AtC initial electron_temperature all $T +fix_modify AtC fix electron_temperature all $T +fix_modify AtC initial electron_density all 0.0 +#fix_modify AtC fix electron_density lbc 0 +#fix_modify AtC fix electron_density rbc 0 +fix_modify AtC initial electric_potential all 0.0 +fix_modify AtC initial electron_wavefunction all 0.0 +fix_modify AtC fix electron_wavefunction lbc 0 +fix_modify AtC fix electron_wavefunction rbc 0 + +thermo $s +# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5] +thermo_modify format 1 %5i format 2 %7.2g +fix_modify AtC output ddm_schrodingerFE $s text +fix_modify AtC extrinsic electron_integration implicit 1 +fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 1 # 100 +fix_modify AtC unfix electric_potential all +# ends zero +fix_modify AtC fix electric_potential lbc 0 +fix_modify AtC fix electric_potential rbc 0 +run 1 +# ends from gradient +fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 0 +fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 0 +run 1 + diff --git a/examples/USER/atc/drift_diffusion/in.finite_well b/examples/USER/atc/drift_diffusion/in.finite_well new file mode 100644 index 0000000000..6abe0c88e6 --- /dev/null +++ b/examples/USER/atc/drift_diffusion/in.finite_well @@ -0,0 +1,75 @@ +#needs description +echo both +units metal + +variable E equal 0.1 +variable L equal 10.0 +#variable N equal 100 +variable N equal 80 +variable T equal 1000 +variable n0 equal 0.0001 +variable dn equal 2.0*${n0} +variable dt equal 0.0000001 +variable s equal 1 + +timestep ${dt} + +atom_style atomic +lattice fcc 1.0 +variable a equal 0.5*$L +region simRegion block -$a $a 0 1 0 1 +boundary f p p +create_box 1 simRegion +mass 1 1.0 # need to keep this +atom_modify sort 0 1 + +# ID group atc PhysicsType ParameterFile +fix AtC all atc drift_diffusion-schrodinger SiGe_ddm_schrodinger.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create $N 1 1 simRegion f p p +variable a equal 0.2*$L+0.001 +fix_modify AtC mesh create_elementset well -$a $a -INF INF -INF INF +fix_modify AtC mesh create_nodeset well -$a $a -INF INF -INF INF +fix_modify AtC material well Ge + +variable b equal $a-0.002 +fix_modify AtC mesh create_nodeset lbc -$a -$b -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc $b $a -INF INF -INF INF + +# ics/bcs +fix_modify AtC initial temperature all 300.0 +fix_modify AtC fix temperature all 300.0 +# +fix_modify AtC initial electron_temperature all $T +fix_modify AtC fix electron_temperature all $T +# +fix_modify AtC initial electron_density all 0.0 +#fix_modify AtC fix electron_density all -0.001 +#fix_modify AtC fix electron_density well 0.002 +# +fix_modify AtC initial electric_potential all 0.0 +#fix_modify AtC fix electric_potential lbc 0.5 +#fix_modify AtC fix electric_potential rbc 0.5 +fix_modify AtC fix electric_potential lbc 0.0 +fix_modify AtC fix electric_potential rbc 0.0 +# +fix_modify AtC initial electron_wavefunction all 0.0 +fix_modify AtC fix electron_wavefunction lbc 0.0 +fix_modify AtC fix electron_wavefunction rbc 0.0 + + +thermo $s +# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5] +thermo_modify format 1 %5i format 2 %7.2g +fix_modify AtC output finite_wellFE $s text +fix_modify AtC extrinsic electron_integration implicit 3 +fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 3 # 30 +variable m equal 1*$s +# (A) no field +run $m +# (B) fixed boundary field +fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 1 +fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 1 +run $m diff --git a/examples/USER/atc/drift_diffusion/in.no_atoms_ddm b/examples/USER/atc/drift_diffusion/in.no_atoms_ddm new file mode 100644 index 0000000000..89dd9acca1 --- /dev/null +++ b/examples/USER/atc/drift_diffusion/in.no_atoms_ddm @@ -0,0 +1,65 @@ +# needs description +# DESCRIPTION: haynes-schockley +# continuity eqn: n,t = J,x + (G-R) = D n,xx + mu (n E),x + G - 1/tau (n - n_0) +# w/ J = D n,x + mu n phi,x +# poisson eqn for E-field: epsilon phi,xx = -e (n - p + N_D - N_A) +# w/ E = phi,x +# NOTE: does not conserve electrons even with fixed E field and zero mobility +# if J=0 --> n,x = mu/D n phi,x + +echo both +units metal + +variable E equal 10.0 +variable n0 equal 0.0001 +variable dn equal 2.0*${n0} +variable dt equal 0.0000001 + +timestep ${dt} + +atom_style atomic +lattice fcc 1.0 +region simRegion block -50 50 0 1 0 1 +boundary f p p +create_box 1 simRegion +mass 1 1.0 # need to keep this +atom_modify sort 0 1 + +# ID group atc PhysicsType ParameterFile +fix AtC all atc drift_diffusion Si_ddm.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 100 1 1 simRegion f p p + +fix_modify AtC mesh create_nodeset lbc -50.1 -49.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 49.9 50.1 -INF INF -INF INF + +# fix a temperature +fix_modify AtC initial temperature all 300.0 +fix_modify AtC initial electron_temperature all 300.0 +fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 ${dn} ${n0} +# isolate system: +# diffusion: dn/dx = 0 +# drift : n = 0 +fix_modify AtC fix electron_density lbc ${n0} +fix_modify AtC fix electron_density rbc ${n0} +fix_modify AtC fix electric_potential all linear 0 0 0 $E 0 0 1 +variable perm equal 0.06 +variable nD equal 1.0e-4 +fix_modify AtC source electric_potential all ${nD} + +variable s equal 10 +thermo $s +# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5] +thermo_modify format 1 %5i format 2 %7.2g +fix_modify AtC output no_atoms_ddmFE $s text +fix_modify AtC extrinsic electron_integration implicit +run 40 + +# free electric field and allow shielding +fix_modify AtC unfix electric_potential all +fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 1 +fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 1 +fix_modify AtC extrinsic electron_integration implicit 10 +run 40 diff --git a/examples/USER/atc/drift_diffusion/in.null_material_ddm b/examples/USER/atc/drift_diffusion/in.null_material_ddm new file mode 100644 index 0000000000..623b171880 --- /dev/null +++ b/examples/USER/atc/drift_diffusion/in.null_material_ddm @@ -0,0 +1,79 @@ +# needs description +#AtC drift diffusion Coupling +# DESCRIPTION: +# electric potential solved over whole domain +# all others only over the lower half +# temperature is fixed over whole domain + +# NOTE the vacuum can fully masked out by making the material +# have null electron_density in Ar_ddm.mat + +echo both +units metal + +variable s equal 100 +variable T equal 20 +variable n equal 0.000004 +variable tol equal 0.1 +variable W equal 1000 + +atom_style atomic + +lattice fcc 5.405 origin 0.25 0.25 0.25 +region FE block -8 8 -6 6 0 3 +region MD block -7 7 -6 0 0 3 +region FREE block -4 4 -6 0 0 3 + +boundary f f p + +# create atoms +create_box 1 FE +mass 1 39.95 +atom_modify sort 0 1 + +timestep 0.002 +thermo $s + +# ID group atc PhysicsType ParameterFile +fix AtC all atc drift_diffusion Ar_ddm.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 4 4 1 FE f f p + +variable a equal $W+${tol} +fix_modify AtC mesh create_elementset wire -$a $a -INF ${tol} -INF INF +fix_modify AtC mesh create_elementset gap -$a $a -${tol} INF -INF INF +# void is the complement of the wire nodeset +variable a equal $W-${tol} +fix_modify AtC mesh create_nodeset void -$a $a ${tol} INF -INF INF +fix_modify AtC mesh output null_material_ddmMESH binary + +fix_modify AtC control thermal none + +# fix a temperature +fix_modify AtC initial temperature all $T +fix_modify AtC initial electron_temperature all $T +fix_modify AtC initial electron_density all $n +fix_modify AtC initial electric_potential all 0.0 +fix_modify AtC initial temperature void 0.0 +fix_modify AtC initial electron_density void 0.0 +fix_modify AtC initial electric_potential void 0.0 + +# create vacuum +fix_modify AtC material gap Vacuum + +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] +fix_modify AtC output null_material_ddmFE $s full_text binary +fix_modify AtC extrinsic electron_integration implicit + +# +fix_modify AtC mesh create_nodeset lbc -8.1 -7.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 7.9 8.1 -INF INF -INF INF +fix_modify AtC fix electron_temperature lbc $T +fix_modify AtC fix electron_temperature rbc $T +fix_modify AtC fix electron_density lbc $n +fix_modify AtC fix electric_potential lbc 0.0 + +variable m equal $s*10 +run $m + diff --git a/examples/USER/atc/drift_diffusion/in.poisson1d_noatoms b/examples/USER/atc/drift_diffusion/in.poisson1d_noatoms new file mode 100644 index 0000000000..7882d5487f --- /dev/null +++ b/examples/USER/atc/drift_diffusion/in.poisson1d_noatoms @@ -0,0 +1,41 @@ +# needs description +# note the units +units metal +variable nx equal 40 +variable h equal 0.25 +variable L equal $h*${nx} +variable T equal 300 +variable n0 equal 0.000025 +variable V equal 5. +variable E equal -0.0001 +variable s equal 0.0001 +atom_style atomic +timestep 0.0 +boundary f f f +lattice fcc 1.0 +region BOX block 0 $L 0 1 0 1 +create_box 1 BOX +mass * 1.0 +atom_modify sort 0 1 +fix AtC all atc drift_diffusion Si_ddm.mat +fix_modify AtC mesh create ${nx} 1 1 BOX f p p +# boundary conditions +fix_modify AtC mesh create_nodeset lbc -0.1 0.1 -INF INF -INF INF +fix_modify AtC mesh create_faceset rbc -INF $L -INF INF -INF INF +fix_modify AtC internal_quadrature off +fix_modify AtC control thermal none +fix_modify AtC extrinsic electron_integration explicit 1 +# fix temperature +fix_modify AtC fix temperature all $T +fix_modify AtC fix electron_temperature all $T +# fix electron density +fix_modify AtC fix electron_density all ${n0} +# bcs for electric potential +fix_modify AtC initial electric_potential all 0 +fix_modify AtC fix electric_potential lbc $V +fix_modify AtC fix_flux electric_potential rbc $E +fix_modify AtC source electric_potential all $s +thermo 1 +thermo_style custom step cpu +fix_modify AtC output poisson1d_noatomsFE 1 text +run 1 diff --git a/examples/USER/atc/drift_diffusion/in.poisson2d_noatoms b/examples/USER/atc/drift_diffusion/in.poisson2d_noatoms new file mode 100644 index 0000000000..097344a59c --- /dev/null +++ b/examples/USER/atc/drift_diffusion/in.poisson2d_noatoms @@ -0,0 +1,73 @@ +# needs description +echo both +variable nx equal 80 # 80 # 40 +variable ny equal ${nx} +variable nz equal 1 +variable h equal 1.0 +variable l equal -$h +variable u equal $h +#variable l equal -$h*${nx} +#variable u equal $h*${nx} +variable T equal 300 +variable n0 equal 0.005 +variable S equal 1 +variable V equal 5. +# STEP THE GATE VOLTAGE UP +atom_style atomic +timestep 0.0 +boundary f f f +lattice fcc 1.0 +region BOX block $l $u $l $u 0 1 +create_box 1 BOX +mass * 12.01 +atom_modify sort 0 1 +# ID group atc PhysicsType ParameterFile +fix AtC all atc drift_diffusion CNT_ddm.mat +# ID part keywords nx ny nz region +fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p +#fix_modify AtC extrinsic poisson_solver iterative +# boundary conditions +variable a equal $l-0.1 +variable b equal $l+0.1 +fix_modify AtC mesh create_nodeset bot -INF INF $a $b -INF INF +fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF +variable a equal $u-0.1 +variable b equal $u+0.1 +fix_modify AtC mesh create_nodeset top -INF INF $a $b -INF INF +fix_modify AtC mesh create_nodeset lbc $a $b -INF INF -INF INF +variable a equal -0.1 +variable b equal 0.1 +fix_modify AtC mesh create_nodeset origin -INF INF $a $b -INF INF +variable a equal -2*$h +variable b equal 2*$h +variable a equal -8*$h +variable b equal 8*$h +fix_modify AtC mesh create_elementset wire -INF INF $a $b -INF INF +fix_modify AtC material wire C +# simplify +fix_modify AtC internal_quadrature off +fix_modify AtC control thermal none +fix_modify AtC extrinsic electron_integration explicit 1 +fix_modify AtC extrinsic poisson_solver iterative +# isolate system: +# diffusion: dn/dx = 0 +# drift : n = 0 +# fix temperature +fix_modify AtC fix temperature all $T +fix_modify AtC fix electron_temperature all $T +# fix electron density +fix_modify AtC fix electron_density all 0 +# NEED TO BE ABLE TO TURN OFF electron integration and just do Poisson solve +fix_modify AtC fix electron_density origin ${n0} +# bcs for electric potential +fix_modify AtC unfix electric_potential all +fix_modify AtC initial electric_potential all 0 +fix_modify AtC fix electric_potential lbc 0 +fix_modify AtC fix electric_potential rbc $V +thermo 1 +# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5] +thermo_modify format 1 %5i format 2 %7.2g +fix_modify AtC output poisson2d_noatomsFE 1 full_text +#fix_modify AtC mesh output poisson2dMESH +run 1 diff --git a/examples/USER/atc/drift_diffusion/in.schrodinger-poisson2d_Jconstraint b/examples/USER/atc/drift_diffusion/in.schrodinger-poisson2d_Jconstraint new file mode 100644 index 0000000000..aecab24e9a --- /dev/null +++ b/examples/USER/atc/drift_diffusion/in.schrodinger-poisson2d_Jconstraint @@ -0,0 +1,138 @@ +# needs description +# STEP THE GATE VOLTAGE UP +# NEED TO TURN OFF T EQNS FOR VACUUM +# HACK need to define well and open bcs +echo both +#variable iter equal 2 # need two for potential to affect density +variable iter1 equal 4 # NOTE <<<< +variable iter2 equal 25 # NOTE <<<< +variable r equal 1 +variable nx equal 12 # 30 40 10 +variable mx equal 4 # 4 2 +#variable ny equal ${nx} +variable ny equal 12 # 30 40 +variable my equal 8 # 12 6 +variable nz equal 1 +variable hx equal 1.0 +variable hy equal ${hx}*${nx}/${ny} +variable l equal -${hx}*${nx} +variable u equal ${hx}*${nx} +variable w equal ${hy}*${my} +variable q equal ${hx}*${mx} +variable y equal ${nx}+1-${mx} +variable T equal 300 +variable S equal 1 +variable n0 equal 0.00007 +variable J0 equal 40.0 # 100.0 40.0 +variable Vs equal 1.0 +#variable Vg equal 1.0 # 10.0 0.0 +variable tol equal 0.01 +################################################# +atom_style atomic +timestep 0.001 +boundary f f f +lattice fcc 1.0 +region BOX block ${l} ${u} ${l} ${u} 0 1 +create_box 1 BOX +mass * 12.01 +atom_modify sort 0 1 +# ID group atc PhysicsType ParameterFile +fix AtC all atc drift_diffusion-schrodinger-slice SiVacuum_ddm_schrodinger.mat +# ID part keywords nx ny nz region +fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p +# surfaces & regions +variable a equal $l-${tol} +variable b equal $l+$q+${tol} +variable c equal -$w-${tol} +variable d equal $w+${tol} +variable e equal $l+$q-${tol} +fix_modify AtC mesh create_nodeset bot -INF INF $a $b -INF INF +fix_modify AtC mesh create_nodeset lbc $a $b -INF INF -INF INF +variable a equal $u-$q-${tol} +variable b equal $u+${tol} +variable e equal $u-$q+${tol} +fix_modify AtC mesh create_nodeset top -INF INF $a $b -INF INF +fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF +variable a equal -$w-${tol} +variable b equal $w+${tol} +variable c equal $l+$q-${tol} +variable d equal $u-$q+${tol} +fix_modify AtC mesh create_elementset wire $c $d $a $b -INF INF +fix_modify AtC mesh create_nodeset wire $c $d $a $b -INF INF +variable e equal $c+2*${tol} +variable f equal $c+${tol} +fix_modify AtC mesh create_nodeset lwire $c $e $a $b -INF INF +fix_modify AtC mesh create_faceset lwire $f INF $a $b -INF INF +variable e equal $d-2*${tol} +variable f equal $d-${tol} +fix_modify AtC mesh create_nodeset rwire $e $d $a $b -INF INF +fix_modify AtC mesh create_faceset rwire -INF $f $a $b -INF INF +variable e equal $a+2*${tol} +fix_modify AtC mesh create_nodeset bwire $c $d $a $e -INF INF +variable e equal $b-2*${tol} +fix_modify AtC mesh create_nodeset twire $c $d $e $b -INF INF +# new material +fix_modify AtC material wire Si +# simplify +fix_modify AtC extrinsic one_dimensional x wire $y +#fix_modify AtC extrinsic poisson_solver iterative +fix_modify AtC internal_quadrature off +fix_modify AtC control thermal none +fix_modify AtC extrinsic electron_integration implicit 1 +fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency ${iter1} +#fix_modify AtC extrinsic conserve density 10 +fix_modify AtC extrinsic schrodinger_poisson_solver conserve flux ${iter2} +fix_modify AtC extrinsic schrodinger_poisson_solver initial_fermi_level 0.1 +fix_modify AtC extrinsic schrodinger_poisson_solver safe_fermi_increment 0.1 +#fix_modify AtC extrinsic initial_fermi_level 0.5 +# isolate system: +# diffusion: dn/dx = 0 +# drift : n = 0 +# fix temperature +fix_modify AtC fix temperature all $T +fix_modify AtC initial electron_temperature all $T +fix_modify AtC fix electron_temperature all $T # <<< +#fix_modify AtC unfix electron_temperature wire +fix_modify AtC fix electron_temperature lbc $T +fix_modify AtC fix electron_temperature rbc $T +### NOTE there seems to be leakage into the vacuum +# electric potential ic +fix_modify AtC initial electric_potential all 0.0 +fix_modify AtC fix electric_potential lbc 0 +fix_modify AtC fix electric_potential rbc ${Vs} +#fix_modify AtC fix electric_potential bot ${Vg} # remove this if Vg=0 +# electron density ic +fix_modify AtC initial electron_density all 0 +fix_modify AtC fix electron_density all 0 +fix_modify AtC unfix electron_density wire +fix_modify AtC initial electron_density wire ${n0} +fix_modify AtC fix electron_density twire 0.0 +fix_modify AtC fix electron_density bwire 0.0 +fix_modify AtC fix electron_density lwire ${n0} +fix_modify AtC fix electron_density rwire ${n0} +#fix_modify AtC fix electron_density lbc ${n0} +#fix_modify AtC fix electron_density rbc ${n0} +fix_modify AtC unfix electron_density lwire +fix_modify AtC unfix electron_density rwire +fix_modify AtC fix_flux electron_density lwire -${J0} # <<<< +fix_modify AtC fix_flux electron_density rwire ${J0} # <<<< +# HACK +#fix_modify AtC fix electron_density all 0 +# electron wavefunction ic/bcs +fix_modify AtC initial electron_wavefunction all 0.0 +fix_modify AtC fix electron_wavefunction top 0.0 +fix_modify AtC fix electron_wavefunction bot 0.0 +fix_modify AtC fix electron_wavefunction all 0 +fix_modify AtC unfix electron_wavefunction wire +#fix_modify AtC fix electron_wavefunction lwire 0.0 # <<<< bit of hack +#fix_modify AtC fix electron_wavefunction rwire 0.0 # <<<< bit of hack +fix_modify AtC fix electron_wavefunction twire 0.0 +fix_modify AtC fix electron_wavefunction bwire 0.0 +thermo 1 +# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5] +thermo_modify format 1 %5i format 2 %7.2g +fix_modify AtC output schrodinger-poisson2d_JconstraintFE $r full_text binary tensor_components +fix_modify AtC mesh output schrodinger-poisson2dMESH +run $r +# NOW BIAS diff --git a/examples/USER/atc/drift_diffusion/in.schrodinger-poisson2d_convective b/examples/USER/atc/drift_diffusion/in.schrodinger-poisson2d_convective new file mode 100644 index 0000000000..2de28a55fa --- /dev/null +++ b/examples/USER/atc/drift_diffusion/in.schrodinger-poisson2d_convective @@ -0,0 +1,150 @@ +# needs description +# STEP THE GATE VOLTAGE UP +# NEED TO TURN OFF T EQNS FOR VACUUM +# HACK need to define well and open bcs +echo both +#variable iter equal 2 # need two for potential to affect density +variable iter1 equal 4 # NOTE <<<< +variable iter2 equal 25 # NOTE <<<< +variable r equal 1 +variable nx equal 12 # 30 40 10 +variable mx equal 4 # 4 2 +#variable ny equal ${nx} +variable ny equal 12 # 30 40 +variable my equal 8 # 12 6 +variable nz equal 1 +variable hx equal 1.0 +variable hy equal ${hx}*${nx}/${ny} +variable l equal -${hx}*${nx} +variable u equal ${hx}*${nx} +variable w equal ${hy}*${my} +variable q equal ${hx}*${mx} +variable y equal ${nx}+1-${mx} +variable T equal 300 +variable S equal 1 +variable n0 equal 0.00007 +variable v0 equal 1000.0 +variable J0 equal ${n0}*${v0} +print "prescribed flux: ${J0}" +variable Vs equal 1.0 +#variable Vg equal 1.0 # 10.0 0.0 +variable tol equal 0.01 +################################################# +atom_style atomic +timestep 0.001 +boundary f f f +lattice fcc 1.0 +region BOX block ${l} ${u} ${l} ${u} 0 1 +create_box 1 BOX +mass * 12.01 +atom_modify sort 0 1 +# ID group atc PhysicsType ParameterFile +fix AtC all atc convective_drift_diffusion-schrodinger SiVacuum_cddm_schrodinger.mat +# ID part keywords nx ny nz region +fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p +# surfaces & regions +variable a equal $l-${tol} +variable b equal $l+$q+${tol} +variable c equal -$w-${tol} +variable d equal $w+${tol} +variable e equal $l+$q-${tol} +fix_modify AtC mesh create_nodeset bot -INF INF $a $b -INF INF +fix_modify AtC mesh create_nodeset lbc $a $b -INF INF -INF INF +variable a equal $u-$q-${tol} +variable b equal $u+${tol} +variable e equal $u-$q+${tol} +fix_modify AtC mesh create_nodeset top -INF INF $a $b -INF INF +fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF +variable a equal -$w-${tol} +variable b equal $w+${tol} +variable c equal $l+$q-${tol} +variable d equal $u-$q+${tol} +fix_modify AtC mesh create_elementset wire $c $d $a $b -INF INF +fix_modify AtC mesh create_nodeset wire $c $d $a $b -INF INF +variable e equal $c+2*${tol} +variable f equal $c+${tol} +fix_modify AtC mesh create_nodeset lwire $c $e $a $b -INF INF +fix_modify AtC mesh create_faceset lwire $f INF $a $b -INF INF +variable e equal $d-2*${tol} +variable f equal $d-${tol} +fix_modify AtC mesh create_nodeset rwire $e $d $a $b -INF INF +fix_modify AtC mesh create_faceset rwire -INF $f $a $b -INF INF +variable e equal $a+2*${tol} +fix_modify AtC mesh create_nodeset bwire $c $d $a $e -INF INF +variable e equal $b-2*${tol} +fix_modify AtC mesh create_nodeset twire $c $d $e $b -INF INF +# new material +fix_modify AtC material wire Si +# simplify +fix_modify AtC extrinsic one_dimensional x wire $y +#fix_modify AtC extrinsic poisson_solver iterative +fix_modify AtC internal_quadrature off +fix_modify AtC control thermal none +fix_modify AtC extrinsic electron_integration implicit 1 +fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency ${iter1} +#fix_modify AtC extrinsic conserve density 10 +fix_modify AtC extrinsic schrodinger_poisson_solver conserve flux ${iter2} +fix_modify AtC extrinsic schrodinger_poisson_solver initial_fermi_level 0.1 +fix_modify AtC extrinsic schrodinger_poisson_solver safe_fermi_increment 0.1 +#fix_modify AtC extrinsic initial_fermi_level 0.5 +# isolate system: +# diffusion: dn/dx = 0 +# drift : n = 0 +# fix temperature +fix_modify AtC fix temperature all $T +fix_modify AtC initial electron_temperature all $T +fix_modify AtC fix electron_temperature all $T # <<< +#fix_modify AtC unfix electron_temperature wire +fix_modify AtC fix electron_temperature lbc $T +fix_modify AtC fix electron_temperature rbc $T +### NOTE there seems to be leakage into the vacuum +# electric potential ic +fix_modify AtC initial electric_potential all 0.0 +fix_modify AtC fix electric_potential lbc 0 +fix_modify AtC fix electric_potential rbc ${Vs} +#fix_modify AtC fix electric_potential bot ${Vg} # remove this if Vg=0 +# electron density ic +fix_modify AtC initial electron_density all 0 +fix_modify AtC fix electron_density all 0 +fix_modify AtC unfix electron_density wire +fix_modify AtC initial electron_density wire ${n0} +fix_modify AtC fix electron_density twire 0.0 +fix_modify AtC fix electron_density bwire 0.0 +fix_modify AtC fix electron_density lwire ${n0} +fix_modify AtC fix electron_density rwire ${n0} +#fix_modify AtC fix electron_density lbc ${n0} +#fix_modify AtC fix electron_density rbc ${n0} +fix_modify AtC unfix electron_density lwire +fix_modify AtC unfix electron_density rwire +fix_modify AtC fix_flux electron_density lwire ${J0} # <<<< +fix_modify AtC fix_flux electron_density rwire -${J0} # <<<< +# HACK +#fix_modify AtC fix electron_density all 0 +# electron wavefunction ic/bcs +fix_modify AtC initial electron_wavefunction all 0.0 +fix_modify AtC fix electron_wavefunction top 0.0 +fix_modify AtC fix electron_wavefunction bot 0.0 +fix_modify AtC fix electron_wavefunction all 0 +fix_modify AtC unfix electron_wavefunction wire +#fix_modify AtC fix electron_wavefunction lwire 0.0 # <<<< bit of hack +#fix_modify AtC fix electron_wavefunction rwire 0.0 # <<<< bit of hack +fix_modify AtC fix electron_wavefunction twire 0.0 +fix_modify AtC fix electron_wavefunction bwire 0.0 + +fix_modify AtC initial electron_velocity x all 0.0 +fix_modify AtC initial electron_velocity y all 0.0 +fix_modify AtC initial electron_velocity z all 0.0 +fix_modify AtC fix electron_velocity x all ${v0} +fix_modify AtC fix electron_velocity y all 0.0 +fix_modify AtC fix electron_velocity z all 0.0 +fix_modify AtC initial electron_velocity x wire ${v0} +fix_modify AtC fix electron_velocity x wire ${v0} + +thermo 1 +# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5] +thermo_modify format 1 %5i format 2 %7.2g +fix_modify AtC output schrodinger-poisson2d_convectiveFE $r full_text binary tensor_components +fix_modify AtC mesh output schrodinger-poisson2dMESH +run $r +# NOW BIAS diff --git a/examples/USER/atc/drift_diffusion/in.schrodinger-poisson2d_noatoms b/examples/USER/atc/drift_diffusion/in.schrodinger-poisson2d_noatoms new file mode 100644 index 0000000000..fd5902ee6a --- /dev/null +++ b/examples/USER/atc/drift_diffusion/in.schrodinger-poisson2d_noatoms @@ -0,0 +1,124 @@ +# needs description +# MOVE/COPY this to .._noatoms for bmark +# STEP THE GATE VOLTAGE UP +# NEED TO TURN OFF T EQNS FOR VACUUM +# HACK need to define well and open bcs +echo both +#variable iter equal 2 # need two for potential to affect density +variable iter equal 1 # NOTE <<<< +variable r equal 1 +variable nx equal 30 # 30 # 40 10 +variable mx equal 4 # 4 2 +#variable ny equal ${nx} +variable ny equal 30 # 40 +variable my equal 12 # 6 +variable nz equal 1 +variable hx equal 1.0 +variable hy equal ${hx}*${nx}/${ny} +variable l equal -${hx}*${nx} +variable u equal ${hx}*${nx} +variable w equal ${hy}*${my} +variable q equal ${hx}*${mx} +variable y equal ${nx}+1-${mx} +variable T equal 300 +variable E equal 0.1 +variable S equal 1 +variable n0 equal 0.01 +variable V equal 5. +variable tol equal 0.01 +################################################# +atom_style atomic +timestep 0.001 +boundary f f f +lattice fcc 1.0 +region BOX block ${l} ${u} ${l} ${u} 0 1 +create_box 1 BOX +mass * 12.01 +atom_modify sort 0 1 +# ID group atc PhysicsType ParameterFile +fix AtC all atc drift_diffusion-schrodinger-slice SiVacuum_ddm_schrodinger.mat +# ID part keywords nx ny nz region +fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p +# surfaces & regions +variable a equal $l-${tol} +variable b equal $l+$q+${tol} +variable c equal -$w-${tol} +variable d equal $w+${tol} +variable e equal $l+$q-${tol} +fix_modify AtC mesh create_nodeset bot -INF INF $a $b -INF INF +fix_modify AtC mesh create_nodeset lbc $a $b -INF INF -INF INF +variable a equal $u-$q-${tol} +variable b equal $u+${tol} +variable e equal $u-$q+${tol} +fix_modify AtC mesh create_nodeset top -INF INF $a $b -INF INF +fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF +variable a equal -$w-${tol} +variable b equal $w+${tol} +variable c equal $l+$q-${tol} +variable d equal $u-$q+${tol} +fix_modify AtC mesh create_elementset wire $c $d $a $b -INF INF +fix_modify AtC mesh create_nodeset wire $c $d $a $b -INF INF +variable e equal $c+2*${tol} +fix_modify AtC mesh create_nodeset lwire $c $e $a $b -INF INF +variable e equal $d-2*${tol} +fix_modify AtC mesh create_nodeset rwire $e $d $a $b -INF INF +variable e equal $a+2*${tol} +fix_modify AtC mesh create_nodeset bwire $c $d $a $e -INF INF +variable e equal $b-2*${tol} +fix_modify AtC mesh create_nodeset twire $c $d $e $b -INF INF +# new material +fix_modify AtC material wire Si +# simplify +fix_modify AtC extrinsic one_dimensional x wire $y +#fix_modify AtC extrinsic poisson_solver iterative +fix_modify AtC internal_quadrature off +fix_modify AtC control thermal none +fix_modify AtC extrinsic electron_integration implicit 1 +fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency ${iter} +fix_modify AtC extrinsic schrodinger_poisson_solver conserve density 10 +fix_modify AtC extrinsic schrodinger_poisson_solver initial_fermi_level 0.1 +fix_modify AtC extrinsic schrodinger_poisson_solver safe_fermi_increment 0.1 +# isolate system: +# diffusion: dn/dx = 0 +# drift : n = 0 +# fix temperature +fix_modify AtC fix temperature all $T +fix_modify AtC initial electron_temperature all $T +#fix_modify AtC fix electron_temperature all $T +#fix_modify AtC unfix electron_temperature wire +fix_modify AtC fix electron_temperature lbc $T +fix_modify AtC fix electron_temperature rbc $T +### NOTE there seems to be leakage into the vacuum +# electric potential ic +fix_modify AtC initial electric_potential all 0.0 +fix_modify AtC fix electric_potential lbc 0 +fix_modify AtC fix electric_potential rbc 1 +# electron density ic +fix_modify AtC initial electron_density all 0 +fix_modify AtC fix electron_density all 0 +fix_modify AtC unfix electron_density wire +fix_modify AtC initial electron_density wire ${n0} +fix_modify AtC fix electron_density lwire ${n0} +fix_modify AtC fix electron_density rwire ${n0} +fix_modify AtC fix electron_density twire 0.0 +fix_modify AtC fix electron_density bwire 0.0 +# HACK +#fix_modify AtC fix electron_density all 0 +# electron wavefunction ic/bcs +fix_modify AtC initial electron_wavefunction all 0.0 +fix_modify AtC fix electron_wavefunction top 0.0 +fix_modify AtC fix electron_wavefunction bot 0.0 +fix_modify AtC fix electron_wavefunction all 0 +fix_modify AtC unfix electron_wavefunction wire +fix_modify AtC fix electron_wavefunction lwire 0.0 # dummy value +fix_modify AtC fix electron_wavefunction rwire 0.0 # dummy value +fix_modify AtC fix electron_wavefunction twire 0.0 +fix_modify AtC fix electron_wavefunction bwire 0.0 +thermo 1 +# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5] +thermo_modify format 1 %5i format 2 %7.2g +fix_modify AtC output schrodinger-poisson2d_noatomsFE $r full_text binary tensor_components +fix_modify AtC mesh output schrodinger-poisson2dMESH +run $r +# NOW BIAS diff --git a/examples/USER/atc/drift_diffusion/no_atoms_ddm.screen b/examples/USER/atc/drift_diffusion/no_atoms_ddm.screen new file mode 100644 index 0000000000..fc9561628c --- /dev/null +++ b/examples/USER/atc/drift_diffusion/no_atoms_ddm.screen @@ -0,0 +1,142 @@ +LAMMPS (14 Aug 2013) +units metal + +variable E equal 10.0 +variable n0 equal 0.0001 +variable dn equal 2.0*${n0} +variable dn equal 2.0*0.00010000000000000000479 +variable dt equal 0.0000001 + +timestep ${dt} +timestep 9.9999999999999995475e-08 + +atom_style atomic +lattice fcc 1.0 +Lattice spacing in x,y,z = 1 1 1 +region simRegion block -50 50 0 1 0 1 +boundary f p p +create_box 1 simRegion +Created orthogonal box = (-50 0 0) to (50 1 1) + 4 by 1 by 1 MPI processor grid +mass 1 1.0 # need to keep this +atom_modify sort 0 1 + +# ID group atc PhysicsType ParameterFile +fix AtC all atc drift_diffusion Si_ddm.mat +ATC: constructing drift_diffusion coupling with parameter file Si_ddm.mat + ATC: peratom PE compute created with ID: 3 + ATC: 1 materials defined from Si_ddm.mat + ATC: creating drift_diffusion extrinsic model + ATC: 1 materials defined from Si_ddm.mat + ATC: 1 materials defined from Si_ddm.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 100 1 1 simRegion f p p + ATC: created uniform mesh with 404 nodes, 101 unique nodes, and 100 elements + +fix_modify AtC mesh create_nodeset lbc -50.1 -49.9 -INF INF -INF INF + ATC: created nodeset lbc with 1 nodes +fix_modify AtC mesh create_nodeset rbc 49.9 50.1 -INF INF -INF INF + ATC: created nodeset rbc with 1 nodes + +# fix a temperature +fix_modify AtC initial temperature all 300.0 +fix_modify AtC initial electron_temperature all 300.0 +fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 ${dn} ${n0} +fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 0.00020000000000000000958 ${n0} +fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 0.00020000000000000000958 0.00010000000000000000479 +# isolate system: +# diffusion: dn/dx = 0 +# drift : n = 0 +fix_modify AtC fix electron_density lbc ${n0} +fix_modify AtC fix electron_density lbc 0.00010000000000000000479 +fix_modify AtC fix electron_density rbc ${n0} +fix_modify AtC fix electron_density rbc 0.00010000000000000000479 +fix_modify AtC fix electric_potential all linear 0 0 0 $E 0 0 1 +fix_modify AtC fix electric_potential all linear 0 0 0 10 0 0 1 + ATC: created function : 1 + 10(x-0)+0(y-0)+0(z-0) +variable perm equal 0.06 +variable nD equal 1.0e-4 +fix_modify AtC source electric_potential all ${nD} +fix_modify AtC source electric_potential all 0.00010000000000000000479 + +variable s equal 10 +thermo $s +thermo 10 +# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5] +thermo_modify format 1 %5i format 2 %7.2g +fix_modify AtC output no_atoms_ddmFE $s text +fix_modify AtC output no_atoms_ddmFE 10 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +fix_modify AtC extrinsic electron_integration implicit +run 40 +Setting up run ... +Memory usage per processor = 0.432198 Mbytes +Step CPU AtC[1] AtC[2] AtC[3] AtC[4] AtC[5] + 0 0 0.38734836 300 1.0987928e-07 300 0.011872454 + 10 2.3 0.3873484 300.00003 0.42381602 1.1554067e+09 0.011872454 + 20 3.8 0.38734851 300.00011 0.84762424 2.3107922e+09 0.011872453 + 30 4.9 0.38734869 300.00025 1.2714314 3.4661766e+09 0.011872354 + 40 6.2 0.38734894 300.00045 1.6952106 4.6215141e+09 0.011870471 +Loop time of 6.19604 on 4 procs for 40 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 5.73993e-05 (0.000926387) +Outpt time (%) = 0.0347454 (0.560768) +Other time (%) = 6.16123 (99.4383) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +# free electric field and allow shielding +fix_modify AtC unfix electric_potential all +fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 1 +fix_modify AtC fix electric_potential lbc linear 0 0 0 10 0 0 1 + ATC: created function : 1 + 10(x-0)+0(y-0)+0(z-0) +fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 1 +fix_modify AtC fix electric_potential rbc linear 0 0 0 10 0 0 1 + ATC: created function : 1 + 10(x-0)+0(y-0)+0(z-0) +fix_modify AtC extrinsic electron_integration implicit 10 +run 40 +Setting up run ... +Memory usage per processor = 0.432198 Mbytes +Step CPU AtC[1] AtC[2] AtC[3] AtC[4] AtC[5] + 40 0 0.38734894 300.00045 1.6952106 4.6215141e+09 0.011870471 + 50 6.1 0.38734927 300.0007 2.127197 5.798188e+09 0.012062369 + 60 20 0.38734967 300.00101 2.5636712 6.9867833e+09 0.01226417 + 70 26 0.38735014 300.00137 3.0038699 8.1852725e+09 0.01246759 + 80 32 0.38735069 300.0018 3.4468819 9.3912166e+09 0.012666742 +Loop time of 32.1279 on 4 procs for 40 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 9.63807e-05 (0.000299991) +Outpt time (%) = 0.0351226 (0.109321) +Other time (%) = 32.0926 (99.8904) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/drift_diffusion/null_material_ddm.screen b/examples/USER/atc/drift_diffusion/null_material_ddm.screen new file mode 100644 index 0000000000..be092412cf --- /dev/null +++ b/examples/USER/atc/drift_diffusion/null_material_ddm.screen @@ -0,0 +1,158 @@ +LAMMPS (14 Aug 2013) +units metal + +variable s equal 100 +variable T equal 20 +variable n equal 0.000004 +variable tol equal 0.1 +variable W equal 1000 + +atom_style atomic + +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region FE block -8 8 -6 6 0 3 +region MD block -7 7 -6 0 0 3 +region FREE block -4 4 -6 0 0 3 + +boundary f f p + +# create atoms +create_box 1 FE +Created orthogonal box = (-43.24 -32.43 0) to (43.24 32.43 16.215) + 2 by 2 by 1 MPI processor grid +mass 1 39.95 +atom_modify sort 0 1 + +timestep 0.002 +thermo $s +thermo 100 + +# ID group atc PhysicsType ParameterFile +fix AtC all atc drift_diffusion Ar_ddm.mat +ATC: constructing drift_diffusion coupling with parameter file Ar_ddm.mat + ATC: peratom PE compute created with ID: 3 + ATC: WARNING: material units real do not match lammps + ATC: WARNING: material units real do not match lammps + ATC: 2 materials defined from Ar_ddm.mat + ATC: creating drift_diffusion extrinsic model + ATC: WARNING: material units real do not match lammps + ATC: WARNING: material units real do not match lammps + ATC: 2 materials defined from Ar_ddm.mat + ATC: WARNING: material units real do not match lammps + ATC: WARNING: material units real do not match lammps + ATC: 2 materials defined from Ar_ddm.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 4 4 1 FE f f p + ATC: created uniform mesh with 50 nodes, 25 unique nodes, and 16 elements + +variable a equal $W+${tol} +variable a equal 1000+${tol} +variable a equal 1000+0.10000000000000000555 +fix_modify AtC mesh create_elementset wire -$a $a -INF ${tol} -INF INF +fix_modify AtC mesh create_elementset wire -1000.1000000000000227 $a -INF ${tol} -INF INF +fix_modify AtC mesh create_elementset wire -1000.1000000000000227 1000.1000000000000227 -INF ${tol} -INF INF +fix_modify AtC mesh create_elementset wire -1000.1000000000000227 1000.1000000000000227 -INF 0.10000000000000000555 -INF INF + ATC: created elementset wire with 8 elements +fix_modify AtC mesh create_elementset gap -$a $a -${tol} INF -INF INF +fix_modify AtC mesh create_elementset gap -1000.1000000000000227 $a -${tol} INF -INF INF +fix_modify AtC mesh create_elementset gap -1000.1000000000000227 1000.1000000000000227 -${tol} INF -INF INF +fix_modify AtC mesh create_elementset gap -1000.1000000000000227 1000.1000000000000227 -0.10000000000000000555 INF -INF INF + ATC: created elementset gap with 8 elements +# void is the complement of the wire nodeset +variable a equal $W-${tol} +variable a equal 1000-${tol} +variable a equal 1000-0.10000000000000000555 +fix_modify AtC mesh create_nodeset void -$a $a ${tol} INF -INF INF +fix_modify AtC mesh create_nodeset void -999.89999999999997726 $a ${tol} INF -INF INF +fix_modify AtC mesh create_nodeset void -999.89999999999997726 999.89999999999997726 ${tol} INF -INF INF +fix_modify AtC mesh create_nodeset void -999.89999999999997726 999.89999999999997726 0.10000000000000000555 INF -INF INF + ATC: created nodeset void with 10 nodes +fix_modify AtC mesh output null_material_ddmMESH binary + +fix_modify AtC control thermal none + +# fix a temperature +fix_modify AtC initial temperature all $T +fix_modify AtC initial temperature all 20 +fix_modify AtC initial electron_temperature all $T +fix_modify AtC initial electron_temperature all 20 +fix_modify AtC initial electron_density all $n +fix_modify AtC initial electron_density all 3.999999999999999819e-06 +fix_modify AtC initial electric_potential all 0.0 +fix_modify AtC initial temperature void 0.0 +fix_modify AtC initial electron_density void 0.0 +fix_modify AtC initial electric_potential void 0.0 + +# create vacuum +fix_modify AtC material gap Vacuum + +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] +fix_modify AtC output null_material_ddmFE $s full_text binary +fix_modify AtC output null_material_ddmFE 100 full_text binary + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +fix_modify AtC extrinsic electron_integration implicit + +# +fix_modify AtC mesh create_nodeset lbc -8.1 -7.9 -INF INF -INF INF + ATC: created nodeset lbc with 5 nodes +fix_modify AtC mesh create_nodeset rbc 7.9 8.1 -INF INF -INF INF + ATC: created nodeset rbc with 5 nodes +fix_modify AtC fix electron_temperature lbc $T +fix_modify AtC fix electron_temperature lbc 20 +fix_modify AtC fix electron_temperature rbc $T +fix_modify AtC fix electron_temperature rbc 20 +fix_modify AtC fix electron_density lbc $n +fix_modify AtC fix electron_density lbc 3.999999999999999819e-06 +fix_modify AtC fix electric_potential lbc 0.0 + +variable m equal $s*10 +variable m equal 100*10 +run $m +run 1000 +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [vacuum] cannot find electron_phonon_exchange + ATC: WARNING: physics model: [drift-diffusion], material: [vacuum] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [vacuum] cannot find electron_flux + ATC: WARNING: physics model: [drift-diffusion], material: [vacuum] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [vacuum] cannot find electron_heat_capacity + ATC: WARNING: physics model: [drift-diffusion], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 0.432121 Mbytes +Step CPU AtC[1] AtC[2] AtC[3] AtC[4] + 0 0 94.264519 12 94.264519 20 + 100 1.0169871 94.267978 12.000392 94.299245 20.003477 + 200 1.9957042 94.276498 12.001352 94.329947 20.006513 + 300 2.9752631 94.289291 12.002784 94.363814 20.009841 + 400 3.9508462 94.306379 12.004683 94.403041 20.013675 + 500 4.92396 94.328129 12.007084 94.449527 20.018196 + 600 5.896678 94.355216 12.010055 94.505534 20.023614 + 700 7.0118601 94.388659 12.0137 94.573962 20.030199 + 800 8.0023661 94.429901 12.01817 94.65867 20.03831 + 900 10.193833 94.480951 12.023673 94.764998 20.048448 + 1000 11.610713 94.544631 12.030506 94.900724 20.061365 +Loop time of 11.6118 on 4 procs for 1000 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 0.00087744 (0.00755644) +Outpt time (%) = 0.0343485 (0.295807) +Other time (%) = 11.5766 (99.6966) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + diff --git a/examples/USER/atc/drift_diffusion/poisson1d_noatoms.screen b/examples/USER/atc/drift_diffusion/poisson1d_noatoms.screen new file mode 100644 index 0000000000..b246c4863d --- /dev/null +++ b/examples/USER/atc/drift_diffusion/poisson1d_noatoms.screen @@ -0,0 +1,41 @@ +LAMMPS (14 Aug 2013) +Lattice spacing in x,y,z = 1 1 1 +Created orthogonal box = (0 0 0) to (10 1 1) + 4 by 1 by 1 MPI processor grid +ATC: constructing drift_diffusion coupling with parameter file Si_ddm.mat + ATC: peratom PE compute created with ID: 3 + ATC: 1 materials defined from Si_ddm.mat + ATC: creating drift_diffusion extrinsic model + ATC: 1 materials defined from Si_ddm.mat + ATC: 1 materials defined from Si_ddm.mat + ATC: created uniform mesh with 164 nodes, 41 unique nodes, and 40 elements + ATC: created nodeset lbc with 1 nodes + ATC: created faceset rbc with 1 faces + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +Setting up run ... +Memory usage per processor = 0.416939 Mbytes +Step CPU + 0 0 + 1 0.12138891 +Loop time of 0.132908 on 4 procs for 1 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 2.08616e-06 (0.00156963) +Outpt time (%) = 0.0033738 (2.53845) +Other time (%) = 0.129532 (97.46) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/drift_diffusion/poisson2d_noatoms.screen b/examples/USER/atc/drift_diffusion/poisson2d_noatoms.screen new file mode 100644 index 0000000000..ee9c31a228 --- /dev/null +++ b/examples/USER/atc/drift_diffusion/poisson2d_noatoms.screen @@ -0,0 +1,109 @@ +LAMMPS (14 Aug 2013) +variable nx equal 80 # 80 # 40 +variable ny equal ${nx} +variable ny equal 80 +variable nz equal 1 +variable h equal 1.0 +variable l equal -$h +variable l equal -1 +variable u equal $h +variable u equal 1 +#variable l equal -$h*${nx} +#variable u equal $h*${nx} +variable T equal 300 +variable n0 equal 0.005 +variable S equal 1 +variable V equal 5. +# STEP THE GATE VOLTAGE UP +atom_style atomic +timestep 0.0 +boundary f f f +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 +region BOX block $l $u $l $u 0 1 +region BOX block -1 $u $l $u 0 1 +region BOX block -1 1 $l $u 0 1 +region BOX block -1 1 -1 $u 0 1 +region BOX block -1 1 -1 1 0 1 +create_box 1 BOX +Created orthogonal box = (-1.5874 -1.5874 0) to (1.5874 1.5874 1.5874) + 2 by 2 by 1 MPI processor grid +mass * 12.01 +atom_modify sort 0 1 +# ID group atc PhysicsType ParameterFile +fix AtC all atc drift_diffusion CNT_ddm.mat +ATC: constructing drift_diffusion coupling with parameter file CNT_ddm.mat + ATC: peratom PE compute created with ID: 3 + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: 2 materials defined from CNT_ddm.mat + ATC: creating drift_diffusion extrinsic model + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: 2 materials defined from CNT_ddm.mat + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: 2 materials defined from CNT_ddm.mat +# ID part keywords nx ny nz region +fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p +fix_modify AtC mesh create 80 ${ny} ${nz} BOX f f p +fix_modify AtC mesh create 80 80 ${nz} BOX f f p +fix_modify AtC mesh create 80 80 1 BOX f f p + ATC: created uniform mesh with 13122 nodes, 6561 unique nodes, and 6400 elements +#fix_modify AtC extrinsic poisson_solver iterative +# boundary conditions +variable a equal $l-0.1 +variable a equal -1-0.1 +variable b equal $l+0.1 +variable b equal -1+0.1 +fix_modify AtC mesh create_nodeset bot -INF INF $a $b -INF INF +fix_modify AtC mesh create_nodeset bot -INF INF -1.1000000000000000888 $b -INF INF +fix_modify AtC mesh create_nodeset bot -INF INF -1.1000000000000000888 -0.9000000000000000222 -INF INF + ATC: created nodeset bot with 324 nodes +fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc -1.1000000000000000888 $b -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc -1.1000000000000000888 -0.9000000000000000222 -INF INF -INF INF + ATC: created nodeset rbc with 324 nodes +variable a equal $u-0.1 +variable a equal 1-0.1 +variable b equal $u+0.1 +variable b equal 1+0.1 +fix_modify AtC mesh create_nodeset top -INF INF $a $b -INF INF +fix_modify AtC mesh create_nodeset top -INF INF 0.9000000000000000222 $b -INF INF +fix_modify AtC mesh create_nodeset top -INF INF 0.9000000000000000222 1.1000000000000000888 -INF INF + ATC: created nodeset top with 324 nodes +fix_modify AtC mesh create_nodeset lbc $a $b -INF INF -INF INF +fix_modify AtC mesh create_nodeset lbc 0.9000000000000000222 $b -INF INF -INF INF +fix_modify AtC mesh create_nodeset lbc 0.9000000000000000222 1.1000000000000000888 -INF INF -INF INF + ATC: created nodeset lbc with 324 nodes +variable a equal -0.1 +variable b equal 0.1 +fix_modify AtC mesh create_nodeset origin -INF INF $a $b -INF INF +fix_modify AtC mesh create_nodeset origin -INF INF -0.10000000000000000555 $b -INF INF +fix_modify AtC mesh create_nodeset origin -INF INF -0.10000000000000000555 0.10000000000000000555 -INF INF + ATC: created nodeset origin with 648 nodes +variable a equal -2*$h +variable a equal -2*1 +variable b equal 2*$h +variable b equal 2*1 +variable a equal -8*$h +variable a equal -8*1 +variable b equal 8*$h +variable b equal 8*1 +fix_modify AtC mesh create_elementset wire -INF INF $a $b -INF INF +fix_modify AtC mesh create_elementset wire -INF INF -8 $b -INF INF +fix_modify AtC mesh create_elementset wire -INF INF -8 8 -INF INF + ATC: created elementset wire with 6400 elements +fix_modify AtC material wire C +# simplify +fix_modify AtC internal_quadrature off +fix_modify AtC control thermal none +fix_modify AtC extrinsic electron_integration explicit 1 +fix_modify AtC extrinsic poisson_solver iterative +ERROR: Illegal fix_modify command (../fix.cpp:104) diff --git a/examples/USER/atc/drift_diffusion/schrodinger-poisson2d_Jconstraint.screen b/examples/USER/atc/drift_diffusion/schrodinger-poisson2d_Jconstraint.screen new file mode 100644 index 0000000000..93b68c1582 --- /dev/null +++ b/examples/USER/atc/drift_diffusion/schrodinger-poisson2d_Jconstraint.screen @@ -0,0 +1,209 @@ +LAMMPS (14 Aug 2013) +#variable iter equal 2 # need two for potential to affect density +variable iter1 equal 4 # NOTE <<<< +variable iter2 equal 25 # NOTE <<<< +variable r equal 1 +variable nx equal 12 # 30 40 10 +variable mx equal 4 # 4 2 +#variable ny equal ${nx} +variable ny equal 12 # 30 40 +variable my equal 8 # 12 6 +variable nz equal 1 +variable hx equal 1.0 +variable hy equal ${hx}*${nx}/${ny} +variable hy equal 1*${nx}/${ny} +variable hy equal 1*12/${ny} +variable hy equal 1*12/12 +variable l equal -${hx}*${nx} +variable l equal -1*${nx} +variable l equal -1*12 +variable u equal ${hx}*${nx} +variable u equal 1*${nx} +variable u equal 1*12 +variable w equal ${hy}*${my} +variable w equal 1*${my} +variable w equal 1*8 +variable q equal ${hx}*${mx} +variable q equal 1*${mx} +variable q equal 1*4 +variable y equal ${nx}+1-${mx} +variable y equal 12+1-${mx} +variable y equal 12+1-4 +variable T equal 300 +variable S equal 1 +variable n0 equal 0.00007 +variable J0 equal 40.0 # 100.0 40.0 +variable Vs equal 1.0 +#variable Vg equal 1.0 # 10.0 0.0 +variable tol equal 0.01 +################################################# +atom_style atomic +timestep 0.001 +boundary f f f +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 +region BOX block ${l} ${u} ${l} ${u} 0 1 +region BOX block -12 ${u} ${l} ${u} 0 1 +region BOX block -12 12 ${l} ${u} 0 1 +region BOX block -12 12 -12 ${u} 0 1 +region BOX block -12 12 -12 12 0 1 +create_box 1 BOX +Created orthogonal box = (-19.0488 -19.0488 0) to (19.0488 19.0488 1.5874) + 2 by 2 by 1 MPI processor grid +mass * 12.01 +atom_modify sort 0 1 +# ID group atc PhysicsType ParameterFile +fix AtC all atc drift_diffusion-schrodinger-slice SiVacuum_ddm_schrodinger.mat +Constructing ATC transfer (drift_diffusion-schrodinger-slice) with parameter file SiVacuum_ddm_schrodinger.mat + ATC: peratom PE compute created with ID: 3 + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat + ATC: creating drift_diffusion extrinsic model + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat +# ID part keywords nx ny nz region +fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p +fix_modify AtC mesh create 12 ${ny} ${nz} BOX f f p +fix_modify AtC mesh create 12 12 ${nz} BOX f f p +fix_modify AtC mesh create 12 12 1 BOX f f p + ATC: created uniform mesh with 338 nodes, 169 unique nodes, and 144 elements +# surfaces & regions +variable a equal $l-${tol} +variable a equal -12-${tol} +variable a equal -12-0.010000000000000000208 +variable b equal $l+$q+${tol} +variable b equal -12+$q+${tol} +variable b equal -12+4+${tol} +variable b equal -12+4+0.010000000000000000208 +variable c equal -$w-${tol} +variable c equal -8-${tol} +variable c equal -8-0.010000000000000000208 +variable d equal $w+${tol} +variable d equal 8+${tol} +variable d equal 8+0.010000000000000000208 +variable e equal $l+$q-${tol} +variable e equal -12+$q-${tol} +variable e equal -12+4-${tol} +variable e equal -12+4-0.010000000000000000208 +fix_modify AtC mesh create_nodeset bot -INF INF $a $b -INF INF +fix_modify AtC mesh create_nodeset bot -INF INF -12.009999999999999787 $b -INF INF +fix_modify AtC mesh create_nodeset bot -INF INF -12.009999999999999787 -7.9900000000000002132 -INF INF + ATC: created nodeset bot with 39 nodes +fix_modify AtC mesh create_nodeset lbc $a $b -INF INF -INF INF +fix_modify AtC mesh create_nodeset lbc -12.009999999999999787 $b -INF INF -INF INF +fix_modify AtC mesh create_nodeset lbc -12.009999999999999787 -7.9900000000000002132 -INF INF -INF INF + ATC: created nodeset lbc with 39 nodes +variable a equal $u-$q-${tol} +variable a equal 12-$q-${tol} +variable a equal 12-4-${tol} +variable a equal 12-4-0.010000000000000000208 +variable b equal $u+${tol} +variable b equal 12+${tol} +variable b equal 12+0.010000000000000000208 +variable e equal $u-$q+${tol} +variable e equal 12-$q+${tol} +variable e equal 12-4+${tol} +variable e equal 12-4+0.010000000000000000208 +fix_modify AtC mesh create_nodeset top -INF INF $a $b -INF INF +fix_modify AtC mesh create_nodeset top -INF INF 7.9900000000000002132 $b -INF INF +fix_modify AtC mesh create_nodeset top -INF INF 7.9900000000000002132 12.009999999999999787 -INF INF + ATC: created nodeset top with 39 nodes +fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 7.9900000000000002132 $b -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 7.9900000000000002132 12.009999999999999787 -INF INF -INF INF + ATC: created nodeset rbc with 39 nodes +variable a equal -$w-${tol} +variable a equal -8-${tol} +variable a equal -8-0.010000000000000000208 +variable b equal $w+${tol} +variable b equal 8+${tol} +variable b equal 8+0.010000000000000000208 +variable c equal $l+$q-${tol} +variable c equal -12+$q-${tol} +variable c equal -12+4-${tol} +variable c equal -12+4-0.010000000000000000208 +variable d equal $u-$q+${tol} +variable d equal 12-$q+${tol} +variable d equal 12-4+${tol} +variable d equal 12-4+0.010000000000000000208 +fix_modify AtC mesh create_elementset wire $c $d $a $b -INF INF +fix_modify AtC mesh create_elementset wire -8.0099999999999997868 $d $a $b -INF INF +fix_modify AtC mesh create_elementset wire -8.0099999999999997868 8.0099999999999997868 $a $b -INF INF +fix_modify AtC mesh create_elementset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 $b -INF INF +fix_modify AtC mesh create_elementset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 8.0099999999999997868 -INF INF + ATC: created elementset wire with 64 elements +fix_modify AtC mesh create_nodeset wire $c $d $a $b -INF INF +fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 $d $a $b -INF INF +fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 8.0099999999999997868 $a $b -INF INF +fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 $b -INF INF +fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 8.0099999999999997868 -INF INF + ATC: created nodeset wire with 81 nodes +variable e equal $c+2*${tol} +variable e equal -8.0099999999999997868+2*${tol} +variable e equal -8.0099999999999997868+2*0.010000000000000000208 +variable f equal $c+${tol} +variable f equal -8.0099999999999997868+${tol} +variable f equal -8.0099999999999997868+0.010000000000000000208 +fix_modify AtC mesh create_nodeset lwire $c $e $a $b -INF INF +fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 $e $a $b -INF INF +fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 -7.9900000000000002132 $a $b -INF INF +fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 -7.9900000000000002132 -8.0099999999999997868 $b -INF INF +fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 -7.9900000000000002132 -8.0099999999999997868 8.0099999999999997868 -INF INF + ATC: created nodeset lwire with 9 nodes +fix_modify AtC mesh create_faceset lwire $f INF $a $b -INF INF +fix_modify AtC mesh create_faceset lwire -8 INF $a $b -INF INF +fix_modify AtC mesh create_faceset lwire -8 INF -8.0099999999999997868 $b -INF INF +fix_modify AtC mesh create_faceset lwire -8 INF -8.0099999999999997868 8.0099999999999997868 -INF INF + ATC: created faceset lwire with 8 faces +variable e equal $d-2*${tol} +variable e equal 8.0099999999999997868-2*${tol} +variable e equal 8.0099999999999997868-2*0.010000000000000000208 +variable f equal $d-${tol} +variable f equal 8.0099999999999997868-${tol} +variable f equal 8.0099999999999997868-0.010000000000000000208 +fix_modify AtC mesh create_nodeset rwire $e $d $a $b -INF INF +fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 $d $a $b -INF INF +fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 8.0099999999999997868 $a $b -INF INF +fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 8.0099999999999997868 -8.0099999999999997868 $b -INF INF +fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 8.0099999999999997868 -8.0099999999999997868 8.0099999999999997868 -INF INF + ATC: created nodeset rwire with 9 nodes +fix_modify AtC mesh create_faceset rwire -INF $f $a $b -INF INF +fix_modify AtC mesh create_faceset rwire -INF 8 $a $b -INF INF +fix_modify AtC mesh create_faceset rwire -INF 8 -8.0099999999999997868 $b -INF INF +fix_modify AtC mesh create_faceset rwire -INF 8 -8.0099999999999997868 8.0099999999999997868 -INF INF + ATC: created faceset rwire with 8 faces +variable e equal $a+2*${tol} +variable e equal -8.0099999999999997868+2*${tol} +variable e equal -8.0099999999999997868+2*0.010000000000000000208 +fix_modify AtC mesh create_nodeset bwire $c $d $a $e -INF INF +fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 $d $a $e -INF INF +fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 8.0099999999999997868 $a $e -INF INF +fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 $e -INF INF +fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 -7.9900000000000002132 -INF INF + ATC: created nodeset bwire with 9 nodes +variable e equal $b-2*${tol} +variable e equal 8.0099999999999997868-2*${tol} +variable e equal 8.0099999999999997868-2*0.010000000000000000208 +fix_modify AtC mesh create_nodeset twire $c $d $e $b -INF INF +fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 $d $e $b -INF INF +fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 8.0099999999999997868 $e $b -INF INF +fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 8.0099999999999997868 7.9900000000000002132 $b -INF INF +fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 8.0099999999999997868 7.9900000000000002132 8.0099999999999997868 -INF INF + ATC: created nodeset twire with 9 nodes +# new material +fix_modify AtC material wire Si +# simplify +fix_modify AtC extrinsic one_dimensional x wire $y +fix_modify AtC extrinsic one_dimensional x wire 9 +ERROR: Illegal fix_modify command (../fix.cpp:104) diff --git a/examples/USER/atc/drift_diffusion/schrodinger-poisson2d_convective.screen b/examples/USER/atc/drift_diffusion/schrodinger-poisson2d_convective.screen new file mode 100644 index 0000000000..ada034426b --- /dev/null +++ b/examples/USER/atc/drift_diffusion/schrodinger-poisson2d_convective.screen @@ -0,0 +1,219 @@ +LAMMPS (14 Aug 2013) +#variable iter equal 2 # need two for potential to affect density +variable iter1 equal 4 # NOTE <<<< +variable iter2 equal 25 # NOTE <<<< +variable r equal 1 +variable nx equal 12 # 30 40 10 +variable mx equal 4 # 4 2 +#variable ny equal ${nx} +variable ny equal 12 # 30 40 +variable my equal 8 # 12 6 +variable nz equal 1 +variable hx equal 1.0 +variable hy equal ${hx}*${nx}/${ny} +variable hy equal 1*${nx}/${ny} +variable hy equal 1*12/${ny} +variable hy equal 1*12/12 +variable l equal -${hx}*${nx} +variable l equal -1*${nx} +variable l equal -1*12 +variable u equal ${hx}*${nx} +variable u equal 1*${nx} +variable u equal 1*12 +variable w equal ${hy}*${my} +variable w equal 1*${my} +variable w equal 1*8 +variable q equal ${hx}*${mx} +variable q equal 1*${mx} +variable q equal 1*4 +variable y equal ${nx}+1-${mx} +variable y equal 12+1-${mx} +variable y equal 12+1-4 +variable T equal 300 +variable S equal 1 +variable n0 equal 0.00007 +variable v0 equal 1000.0 +variable J0 equal ${n0}*${v0} +variable J0 equal 6.9999999999999993868e-05*${v0} +variable J0 equal 6.9999999999999993868e-05*1000 +print "prescribed flux: ${J0}" +prescribed flux: 0.069999999999999992784 +variable Vs equal 1.0 +#variable Vg equal 1.0 # 10.0 0.0 +variable tol equal 0.01 +################################################# +atom_style atomic +timestep 0.001 +boundary f f f +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 +region BOX block ${l} ${u} ${l} ${u} 0 1 +region BOX block -12 ${u} ${l} ${u} 0 1 +region BOX block -12 12 ${l} ${u} 0 1 +region BOX block -12 12 -12 ${u} 0 1 +region BOX block -12 12 -12 12 0 1 +create_box 1 BOX +Created orthogonal box = (-19.0488 -19.0488 0) to (19.0488 19.0488 1.5874) + 2 by 2 by 1 MPI processor grid +mass * 12.01 +atom_modify sort 0 1 +# ID group atc PhysicsType ParameterFile +fix AtC all atc convective_drift_diffusion-schrodinger SiVacuum_cddm_schrodinger.mat +ATC: constructing convective_drift_diffusion-schrodinger coupling with parameter file SiVacuum_cddm_schrodinger.mat + ATC: peratom PE compute created with ID: 3 + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: 2 materials defined from SiVacuum_cddm_schrodinger.mat + ATC: creating convective_drift_diffusion extrinsic model + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: 2 materials defined from SiVacuum_cddm_schrodinger.mat + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: 2 materials defined from SiVacuum_cddm_schrodinger.mat + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: 2 materials defined from SiVacuum_cddm_schrodinger.mat +# ID part keywords nx ny nz region +fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p +fix_modify AtC mesh create 12 ${ny} ${nz} BOX f f p +fix_modify AtC mesh create 12 12 ${nz} BOX f f p +fix_modify AtC mesh create 12 12 1 BOX f f p + ATC: created uniform mesh with 338 nodes, 169 unique nodes, and 144 elements +# surfaces & regions +variable a equal $l-${tol} +variable a equal -12-${tol} +variable a equal -12-0.010000000000000000208 +variable b equal $l+$q+${tol} +variable b equal -12+$q+${tol} +variable b equal -12+4+${tol} +variable b equal -12+4+0.010000000000000000208 +variable c equal -$w-${tol} +variable c equal -8-${tol} +variable c equal -8-0.010000000000000000208 +variable d equal $w+${tol} +variable d equal 8+${tol} +variable d equal 8+0.010000000000000000208 +variable e equal $l+$q-${tol} +variable e equal -12+$q-${tol} +variable e equal -12+4-${tol} +variable e equal -12+4-0.010000000000000000208 +fix_modify AtC mesh create_nodeset bot -INF INF $a $b -INF INF +fix_modify AtC mesh create_nodeset bot -INF INF -12.009999999999999787 $b -INF INF +fix_modify AtC mesh create_nodeset bot -INF INF -12.009999999999999787 -7.9900000000000002132 -INF INF + ATC: created nodeset bot with 39 nodes +fix_modify AtC mesh create_nodeset lbc $a $b -INF INF -INF INF +fix_modify AtC mesh create_nodeset lbc -12.009999999999999787 $b -INF INF -INF INF +fix_modify AtC mesh create_nodeset lbc -12.009999999999999787 -7.9900000000000002132 -INF INF -INF INF + ATC: created nodeset lbc with 39 nodes +variable a equal $u-$q-${tol} +variable a equal 12-$q-${tol} +variable a equal 12-4-${tol} +variable a equal 12-4-0.010000000000000000208 +variable b equal $u+${tol} +variable b equal 12+${tol} +variable b equal 12+0.010000000000000000208 +variable e equal $u-$q+${tol} +variable e equal 12-$q+${tol} +variable e equal 12-4+${tol} +variable e equal 12-4+0.010000000000000000208 +fix_modify AtC mesh create_nodeset top -INF INF $a $b -INF INF +fix_modify AtC mesh create_nodeset top -INF INF 7.9900000000000002132 $b -INF INF +fix_modify AtC mesh create_nodeset top -INF INF 7.9900000000000002132 12.009999999999999787 -INF INF + ATC: created nodeset top with 39 nodes +fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 7.9900000000000002132 $b -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 7.9900000000000002132 12.009999999999999787 -INF INF -INF INF + ATC: created nodeset rbc with 39 nodes +variable a equal -$w-${tol} +variable a equal -8-${tol} +variable a equal -8-0.010000000000000000208 +variable b equal $w+${tol} +variable b equal 8+${tol} +variable b equal 8+0.010000000000000000208 +variable c equal $l+$q-${tol} +variable c equal -12+$q-${tol} +variable c equal -12+4-${tol} +variable c equal -12+4-0.010000000000000000208 +variable d equal $u-$q+${tol} +variable d equal 12-$q+${tol} +variable d equal 12-4+${tol} +variable d equal 12-4+0.010000000000000000208 +fix_modify AtC mesh create_elementset wire $c $d $a $b -INF INF +fix_modify AtC mesh create_elementset wire -8.0099999999999997868 $d $a $b -INF INF +fix_modify AtC mesh create_elementset wire -8.0099999999999997868 8.0099999999999997868 $a $b -INF INF +fix_modify AtC mesh create_elementset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 $b -INF INF +fix_modify AtC mesh create_elementset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 8.0099999999999997868 -INF INF + ATC: created elementset wire with 64 elements +fix_modify AtC mesh create_nodeset wire $c $d $a $b -INF INF +fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 $d $a $b -INF INF +fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 8.0099999999999997868 $a $b -INF INF +fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 $b -INF INF +fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 8.0099999999999997868 -INF INF + ATC: created nodeset wire with 81 nodes +variable e equal $c+2*${tol} +variable e equal -8.0099999999999997868+2*${tol} +variable e equal -8.0099999999999997868+2*0.010000000000000000208 +variable f equal $c+${tol} +variable f equal -8.0099999999999997868+${tol} +variable f equal -8.0099999999999997868+0.010000000000000000208 +fix_modify AtC mesh create_nodeset lwire $c $e $a $b -INF INF +fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 $e $a $b -INF INF +fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 -7.9900000000000002132 $a $b -INF INF +fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 -7.9900000000000002132 -8.0099999999999997868 $b -INF INF +fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 -7.9900000000000002132 -8.0099999999999997868 8.0099999999999997868 -INF INF + ATC: created nodeset lwire with 9 nodes +fix_modify AtC mesh create_faceset lwire $f INF $a $b -INF INF +fix_modify AtC mesh create_faceset lwire -8 INF $a $b -INF INF +fix_modify AtC mesh create_faceset lwire -8 INF -8.0099999999999997868 $b -INF INF +fix_modify AtC mesh create_faceset lwire -8 INF -8.0099999999999997868 8.0099999999999997868 -INF INF + ATC: created faceset lwire with 8 faces +variable e equal $d-2*${tol} +variable e equal 8.0099999999999997868-2*${tol} +variable e equal 8.0099999999999997868-2*0.010000000000000000208 +variable f equal $d-${tol} +variable f equal 8.0099999999999997868-${tol} +variable f equal 8.0099999999999997868-0.010000000000000000208 +fix_modify AtC mesh create_nodeset rwire $e $d $a $b -INF INF +fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 $d $a $b -INF INF +fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 8.0099999999999997868 $a $b -INF INF +fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 8.0099999999999997868 -8.0099999999999997868 $b -INF INF +fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 8.0099999999999997868 -8.0099999999999997868 8.0099999999999997868 -INF INF + ATC: created nodeset rwire with 9 nodes +fix_modify AtC mesh create_faceset rwire -INF $f $a $b -INF INF +fix_modify AtC mesh create_faceset rwire -INF 8 $a $b -INF INF +fix_modify AtC mesh create_faceset rwire -INF 8 -8.0099999999999997868 $b -INF INF +fix_modify AtC mesh create_faceset rwire -INF 8 -8.0099999999999997868 8.0099999999999997868 -INF INF + ATC: created faceset rwire with 8 faces +variable e equal $a+2*${tol} +variable e equal -8.0099999999999997868+2*${tol} +variable e equal -8.0099999999999997868+2*0.010000000000000000208 +fix_modify AtC mesh create_nodeset bwire $c $d $a $e -INF INF +fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 $d $a $e -INF INF +fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 8.0099999999999997868 $a $e -INF INF +fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 $e -INF INF +fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 -7.9900000000000002132 -INF INF + ATC: created nodeset bwire with 9 nodes +variable e equal $b-2*${tol} +variable e equal 8.0099999999999997868-2*${tol} +variable e equal 8.0099999999999997868-2*0.010000000000000000208 +fix_modify AtC mesh create_nodeset twire $c $d $e $b -INF INF +fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 $d $e $b -INF INF +fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 8.0099999999999997868 $e $b -INF INF +fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 8.0099999999999997868 7.9900000000000002132 $b -INF INF +fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 8.0099999999999997868 7.9900000000000002132 8.0099999999999997868 -INF INF + ATC: created nodeset twire with 9 nodes +# new material +fix_modify AtC material wire Si +# simplify +fix_modify AtC extrinsic one_dimensional x wire $y +fix_modify AtC extrinsic one_dimensional x wire 9 +ERROR: Illegal fix_modify command (../fix.cpp:104) diff --git a/examples/USER/atc/drift_diffusion/schrodinger-poisson2d_noatoms.screen b/examples/USER/atc/drift_diffusion/schrodinger-poisson2d_noatoms.screen new file mode 100644 index 0000000000..a76191f0ca --- /dev/null +++ b/examples/USER/atc/drift_diffusion/schrodinger-poisson2d_noatoms.screen @@ -0,0 +1,191 @@ +LAMMPS (14 Aug 2013) +#variable iter equal 2 # need two for potential to affect density +variable iter equal 1 # NOTE <<<< +variable r equal 1 +variable nx equal 30 # 30 # 40 10 +variable mx equal 4 # 4 2 +#variable ny equal ${nx} +variable ny equal 30 # 40 +variable my equal 12 # 6 +variable nz equal 1 +variable hx equal 1.0 +variable hy equal ${hx}*${nx}/${ny} +variable hy equal 1*${nx}/${ny} +variable hy equal 1*30/${ny} +variable hy equal 1*30/30 +variable l equal -${hx}*${nx} +variable l equal -1*${nx} +variable l equal -1*30 +variable u equal ${hx}*${nx} +variable u equal 1*${nx} +variable u equal 1*30 +variable w equal ${hy}*${my} +variable w equal 1*${my} +variable w equal 1*12 +variable q equal ${hx}*${mx} +variable q equal 1*${mx} +variable q equal 1*4 +variable y equal ${nx}+1-${mx} +variable y equal 30+1-${mx} +variable y equal 30+1-4 +variable T equal 300 +variable E equal 0.1 +variable S equal 1 +variable n0 equal 0.01 +variable V equal 5. +variable tol equal 0.01 +################################################# +atom_style atomic +timestep 0.001 +boundary f f f +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 +region BOX block ${l} ${u} ${l} ${u} 0 1 +region BOX block -30 ${u} ${l} ${u} 0 1 +region BOX block -30 30 ${l} ${u} 0 1 +region BOX block -30 30 -30 ${u} 0 1 +region BOX block -30 30 -30 30 0 1 +create_box 1 BOX +Created orthogonal box = (-47.622 -47.622 0) to (47.622 47.622 1.5874) + 2 by 2 by 1 MPI processor grid +mass * 12.01 +atom_modify sort 0 1 +# ID group atc PhysicsType ParameterFile +fix AtC all atc drift_diffusion-schrodinger-slice SiVacuum_ddm_schrodinger.mat +Constructing ATC transfer (drift_diffusion-schrodinger-slice) with parameter file SiVacuum_ddm_schrodinger.mat + ATC: peratom PE compute created with ID: 3 + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat + ATC: creating drift_diffusion extrinsic model + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e + ATC: WARNING: material units metal do not match lammps + ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat +# ID part keywords nx ny nz region +fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p +fix_modify AtC mesh create 30 ${ny} ${nz} BOX f f p +fix_modify AtC mesh create 30 30 ${nz} BOX f f p +fix_modify AtC mesh create 30 30 1 BOX f f p + ATC: created uniform mesh with 1922 nodes, 961 unique nodes, and 900 elements +# surfaces & regions +variable a equal $l-${tol} +variable a equal -30-${tol} +variable a equal -30-0.010000000000000000208 +variable b equal $l+$q+${tol} +variable b equal -30+$q+${tol} +variable b equal -30+4+${tol} +variable b equal -30+4+0.010000000000000000208 +variable c equal -$w-${tol} +variable c equal -12-${tol} +variable c equal -12-0.010000000000000000208 +variable d equal $w+${tol} +variable d equal 12+${tol} +variable d equal 12+0.010000000000000000208 +variable e equal $l+$q-${tol} +variable e equal -30+$q-${tol} +variable e equal -30+4-${tol} +variable e equal -30+4-0.010000000000000000208 +fix_modify AtC mesh create_nodeset bot -INF INF $a $b -INF INF +fix_modify AtC mesh create_nodeset bot -INF INF -30.010000000000001563 $b -INF INF +fix_modify AtC mesh create_nodeset bot -INF INF -30.010000000000001563 -25.989999999999998437 -INF INF + ATC: created nodeset bot with 93 nodes +fix_modify AtC mesh create_nodeset lbc $a $b -INF INF -INF INF +fix_modify AtC mesh create_nodeset lbc -30.010000000000001563 $b -INF INF -INF INF +fix_modify AtC mesh create_nodeset lbc -30.010000000000001563 -25.989999999999998437 -INF INF -INF INF + ATC: created nodeset lbc with 93 nodes +variable a equal $u-$q-${tol} +variable a equal 30-$q-${tol} +variable a equal 30-4-${tol} +variable a equal 30-4-0.010000000000000000208 +variable b equal $u+${tol} +variable b equal 30+${tol} +variable b equal 30+0.010000000000000000208 +variable e equal $u-$q+${tol} +variable e equal 30-$q+${tol} +variable e equal 30-4+${tol} +variable e equal 30-4+0.010000000000000000208 +fix_modify AtC mesh create_nodeset top -INF INF $a $b -INF INF +fix_modify AtC mesh create_nodeset top -INF INF 25.989999999999998437 $b -INF INF +fix_modify AtC mesh create_nodeset top -INF INF 25.989999999999998437 30.010000000000001563 -INF INF + ATC: created nodeset top with 93 nodes +fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 25.989999999999998437 $b -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 25.989999999999998437 30.010000000000001563 -INF INF -INF INF + ATC: created nodeset rbc with 93 nodes +variable a equal -$w-${tol} +variable a equal -12-${tol} +variable a equal -12-0.010000000000000000208 +variable b equal $w+${tol} +variable b equal 12+${tol} +variable b equal 12+0.010000000000000000208 +variable c equal $l+$q-${tol} +variable c equal -30+$q-${tol} +variable c equal -30+4-${tol} +variable c equal -30+4-0.010000000000000000208 +variable d equal $u-$q+${tol} +variable d equal 30-$q+${tol} +variable d equal 30-4+${tol} +variable d equal 30-4+0.010000000000000000208 +fix_modify AtC mesh create_elementset wire $c $d $a $b -INF INF +fix_modify AtC mesh create_elementset wire -26.010000000000001563 $d $a $b -INF INF +fix_modify AtC mesh create_elementset wire -26.010000000000001563 26.010000000000001563 $a $b -INF INF +fix_modify AtC mesh create_elementset wire -26.010000000000001563 26.010000000000001563 -12.009999999999999787 $b -INF INF +fix_modify AtC mesh create_elementset wire -26.010000000000001563 26.010000000000001563 -12.009999999999999787 12.009999999999999787 -INF INF + ATC: created elementset wire with 312 elements +fix_modify AtC mesh create_nodeset wire $c $d $a $b -INF INF +fix_modify AtC mesh create_nodeset wire -26.010000000000001563 $d $a $b -INF INF +fix_modify AtC mesh create_nodeset wire -26.010000000000001563 26.010000000000001563 $a $b -INF INF +fix_modify AtC mesh create_nodeset wire -26.010000000000001563 26.010000000000001563 -12.009999999999999787 $b -INF INF +fix_modify AtC mesh create_nodeset wire -26.010000000000001563 26.010000000000001563 -12.009999999999999787 12.009999999999999787 -INF INF + ATC: created nodeset wire with 351 nodes +variable e equal $c+2*${tol} +variable e equal -26.010000000000001563+2*${tol} +variable e equal -26.010000000000001563+2*0.010000000000000000208 +fix_modify AtC mesh create_nodeset lwire $c $e $a $b -INF INF +fix_modify AtC mesh create_nodeset lwire -26.010000000000001563 $e $a $b -INF INF +fix_modify AtC mesh create_nodeset lwire -26.010000000000001563 -25.99000000000000199 $a $b -INF INF +fix_modify AtC mesh create_nodeset lwire -26.010000000000001563 -25.99000000000000199 -12.009999999999999787 $b -INF INF +fix_modify AtC mesh create_nodeset lwire -26.010000000000001563 -25.99000000000000199 -12.009999999999999787 12.009999999999999787 -INF INF + ATC: created nodeset lwire with 13 nodes +variable e equal $d-2*${tol} +variable e equal 26.010000000000001563-2*${tol} +variable e equal 26.010000000000001563-2*0.010000000000000000208 +fix_modify AtC mesh create_nodeset rwire $e $d $a $b -INF INF +fix_modify AtC mesh create_nodeset rwire 25.99000000000000199 $d $a $b -INF INF +fix_modify AtC mesh create_nodeset rwire 25.99000000000000199 26.010000000000001563 $a $b -INF INF +fix_modify AtC mesh create_nodeset rwire 25.99000000000000199 26.010000000000001563 -12.009999999999999787 $b -INF INF +fix_modify AtC mesh create_nodeset rwire 25.99000000000000199 26.010000000000001563 -12.009999999999999787 12.009999999999999787 -INF INF + ATC: created nodeset rwire with 13 nodes +variable e equal $a+2*${tol} +variable e equal -12.009999999999999787+2*${tol} +variable e equal -12.009999999999999787+2*0.010000000000000000208 +fix_modify AtC mesh create_nodeset bwire $c $d $a $e -INF INF +fix_modify AtC mesh create_nodeset bwire -26.010000000000001563 $d $a $e -INF INF +fix_modify AtC mesh create_nodeset bwire -26.010000000000001563 26.010000000000001563 $a $e -INF INF +fix_modify AtC mesh create_nodeset bwire -26.010000000000001563 26.010000000000001563 -12.009999999999999787 $e -INF INF +fix_modify AtC mesh create_nodeset bwire -26.010000000000001563 26.010000000000001563 -12.009999999999999787 -11.990000000000000213 -INF INF + ATC: created nodeset bwire with 27 nodes +variable e equal $b-2*${tol} +variable e equal 12.009999999999999787-2*${tol} +variable e equal 12.009999999999999787-2*0.010000000000000000208 +fix_modify AtC mesh create_nodeset twire $c $d $e $b -INF INF +fix_modify AtC mesh create_nodeset twire -26.010000000000001563 $d $e $b -INF INF +fix_modify AtC mesh create_nodeset twire -26.010000000000001563 26.010000000000001563 $e $b -INF INF +fix_modify AtC mesh create_nodeset twire -26.010000000000001563 26.010000000000001563 11.990000000000000213 $b -INF INF +fix_modify AtC mesh create_nodeset twire -26.010000000000001563 26.010000000000001563 11.990000000000000213 12.009999999999999787 -INF INF + ATC: created nodeset twire with 27 nodes +# new material +fix_modify AtC material wire Si +# simplify +fix_modify AtC extrinsic one_dimensional x wire $y +fix_modify AtC extrinsic one_dimensional x wire 27 +ERROR: Illegal fix_modify command (../fix.cpp:104) diff --git a/examples/USER/atc/dxa/in.eam_tension_frame b/examples/USER/atc/dxa/in.eam_tension_frame new file mode 100644 index 0000000000..fba7728663 --- /dev/null +++ b/examples/USER/atc/dxa/in.eam_tension_frame @@ -0,0 +1,73 @@ +echo both +### PARAMETERS ----------------------------------------------- +# NOTE: dislocation and stacking fault formation occurs +# at frame 21 +variable frame equal 21 +log eam_tension_frame.log +variable origLx equal 10 # 10 40 +variable Ly equal 10 # 10 40 +variable Lz equal 3 # 3 4 5 +variable hx equal 10 # 4 10 20 +variable hy equal 10 # 4 10 20 +variable L equal 2 +variable tol equal 1.e-4 +variable n equal 25 # 2 25 20 +variable delta equal 0.005*${origLx} +variable totdelta equal ${delta}*${frame} +variable Lx equal ${origLx}+${totdelta} +variable alat equal 4.08 +variable Rc equal (${origLx}/${hx}+${Ly}/${hy})*${alat} +variable rtol equal 0.5*(1.0+1.0/sqrt(2.0))*${alat} +### ---------------------------------------------------------- +boundary p p p +atom_style atomic +units metal +dimension 3 +# create system +lattice fcc ${alat} origin 0.01 0.01 0.01 orient x 1 1 0 orient y 0 0 1 orient z 1 -1 0 +region SYSTEM block -${Lx} ${Lx} -${Ly} ${Ly} 0 ${Lz} +region REFSYSTEM block -${origLx} ${origLx} -${Ly} ${Ly} 0 ${Lz} +read_data eam_tension_${frame}.data +group internal region SYSTEM +pair_style eam/alloy +pair_coeff * * au2.set Au Au + +# define "roller" region +variable a equal -${Ly}+$L +region ROLLER1 block INF INF INF $a INF INF +variable a equal ${Ly}-$L +region ROLLER2 block INF INF $a INF INF INF +region ROLLER union 2 ROLLER1 ROLLER2 +group ROLLER region ROLLER +fix ROLLER ROLLER setforce NULL 0.0 NULL +group free subtract internal ROLLER + +neighbor 1.0 bin +neigh_modify delay 1000000 +atom_modify sort 0 1 + +thermo 20 +variable pe equal pe/count(all) +thermo_style custom step cpu pe press lx v_pe +timestep 0.0 +fix PK1 internal atc hardy +fix_modify PK1 kernel quartic_cylinder ${Rc} +fix_modify PK1 mesh create ${hx} ${hy} 1 SYSTEM f p p +fix_modify PK1 reset_atomic_reference_positions eam_tension_0.data +fix_modify PK1 set reference_potential_energy +fix_modify PK1 atom_element_map eulerian 1 +fix_modify PK1 fields add mass_density energy displacement +fix_modify PK1 fields add dislocation_density +fix_modify PK1 output eam_tension_frameFE 1 text binary tensor_components +fix_modify PK1 output index step +fix_modify PK1 on_the_fly bond on +fix_modify PK1 dxa_exact_mode on +variable u1 atom x-f_PK1[1] +variable u2 atom y-f_PK1[2] +variable u3 atom z-f_PK1[3] +compute CS all centro/atom fcc +compute CNA all cna/atom ${rtol} +dump CONFIG all custom 1 eam_tension_frame.dump id type x y z v_u1 v_u2 v_u3 c_CS c_CNA +# fix myDXA all dxa 1 ${rtol} eam_tension_frame${frame}.dxa # NOTE: dxa fix is NOT needed to use within ATC + +run 1 diff --git a/examples/USER/atc/dxa/in.eam_tension_mesh_frame b/examples/USER/atc/dxa/in.eam_tension_mesh_frame new file mode 100644 index 0000000000..e5cc4df57f --- /dev/null +++ b/examples/USER/atc/dxa/in.eam_tension_mesh_frame @@ -0,0 +1,71 @@ +echo both +### PARAMETERS ----------------------------------------------- +# NOTE: dislocation and stacking fault formation occurs +# at frame 21 +variable frame equal 21 +log eam_tension_mesh_frame.log +variable origLx equal 10 # 10 40 +variable Ly equal 10 # 10 40 +variable Lz equal 3 # 3 4 5 +variable hx equal 10 # 4 10 20 +variable hy equal 10 # 4 10 20 +variable L equal 2 +variable tol equal 1.e-4 +variable n equal 25 # 2 25 20 +variable delta equal 0.005*${origLx} +variable totdelta equal ${delta}*${frame} +variable Lx equal ${origLx}+${totdelta} +variable alat equal 4.08 +variable rtol equal 0.5*(1.0+1.0/sqrt(2.0))*${alat} +### ---------------------------------------------------------- +boundary p p p +atom_style atomic +units metal +dimension 3 +# create system +lattice fcc ${alat} origin 0.01 0.01 0.01 orient x 1 1 0 orient y 0 0 1 orient z 1 -1 0 +region SYSTEM block -${Lx} ${Lx} -${Ly} ${Ly} 0 ${Lz} +region REFSYSTEM block -${origLx} ${origLx} -${Ly} ${Ly} 0 ${Lz} +read_data eam_tension_${frame}.data +group internal region SYSTEM +pair_style eam/alloy +pair_coeff * * au2.set Au Au + +# define "roller" region +variable a equal -${Ly}+$L +region ROLLER1 block INF INF INF $a INF INF +variable a equal ${Ly}-$L +region ROLLER2 block INF INF $a INF INF INF +region ROLLER union 2 ROLLER1 ROLLER2 +group ROLLER region ROLLER +fix ROLLER ROLLER setforce NULL 0.0 NULL +group free subtract internal ROLLER + +neighbor 1.0 bin +neigh_modify delay 1000000 +atom_modify sort 0 1 + +thermo 20 +variable pe equal pe/count(all) +thermo_style custom step cpu pe press lx v_pe +timestep 0.0 +fix PK1 internal atc field +fix_modify PK1 mesh create ${hx} ${hy} 1 SYSTEM p p p +fix_modify PK1 reset_atomic_reference_positions eam_tension_0.data +fix_modify PK1 set reference_potential_energy +fix_modify PK1 atom_element_map eulerian 1 +fix_modify PK1 fields add mass_density energy displacement +fix_modify PK1 fields add dislocation_density +fix_modify PK1 output eam_tension_mesh_frameFE 1 text binary tensor_components +fix_modify PK1 output index step +# fix_modify PK1 on_the_fly bond on +fix_modify PK1 dxa_exact_mode on +variable u1 atom x-f_PK1[1] +variable u2 atom y-f_PK1[2] +variable u3 atom z-f_PK1[3] +compute CS all centro/atom fcc +compute CNA all cna/atom ${rtol} +dump CONFIG all custom 1 eam_tension_mesh_frame.dump id type x y z v_u1 v_u2 v_u3 c_CS c_CNA +# fix myDXA all dxa 1 ${rtol} eam_tension_mesh_frame${frame}.dxa # NOTE: dxa fix is NOT needed to use within ATC + +run 1 diff --git a/examples/USER/atc/elastic/Ar_CauchyBorn.mat b/examples/USER/atc/elastic/Ar_CauchyBorn.mat new file mode 100644 index 0000000000..b139841b6a --- /dev/null +++ b/examples/USER/atc/elastic/Ar_CauchyBorn.mat @@ -0,0 +1,8 @@ +material Ar real + stress cauchy-born + pair_style lj/cut 13.5 #pair_style lj/cut r_cut + pair_coeff 0.238 3.405 #pair_coeff epsilon sigma + end + mass_density + body_force +end diff --git a/examples/USER/atc/elastic/Ar_CauchyBornLinear.mat b/examples/USER/atc/elastic/Ar_CauchyBornLinear.mat new file mode 100644 index 0000000000..9f58245fc0 --- /dev/null +++ b/examples/USER/atc/elastic/Ar_CauchyBornLinear.mat @@ -0,0 +1,9 @@ +material Ar real + stress cauchy-born + pair_style lj/cut 13.5 #pair_style lj/cut r_cut + pair_coeff 0.238 3.405 #pair_coeff epsilon sigma + linear + end + mass_density + body_force +end diff --git a/examples/USER/atc/elastic/Ar_damped.mat b/examples/USER/atc/elastic/Ar_damped.mat new file mode 100644 index 0000000000..e5e226f2d6 --- /dev/null +++ b/examples/USER/atc/elastic/Ar_damped.mat @@ -0,0 +1,37 @@ +material Ar metal +stress linear + modulus 0.00025e6 + possions_ratio 0.25 +end +mass_density constant + density 1.01202 +end +body_force +end + +material cubic metal +stress cubic + c11 0.00030e6 + c12 0.00010e6 + c44 0.00010e6 +end +mass_density constant + density 1.01202 +end +body_force viscous + gamma 1e0 +end +end + +material damped metal +stress damped_cubic + c11 0.00030e6 + c12 0.00010e6 + c44 0.00010e6 + gamma 0.1e3 +end +mass_density constant + density 1.01202 +end +body_force +end diff --git a/examples/USER/atc/elastic/Ar_elastic.mat b/examples/USER/atc/elastic/Ar_elastic.mat new file mode 100644 index 0000000000..0db960291d --- /dev/null +++ b/examples/USER/atc/elastic/Ar_elastic.mat @@ -0,0 +1,29 @@ +material Ar real +stress linear + modulus 0.00025 + possions_ratio 0.25 +end +mass_density +body_force +end + +material cubic real +stress cubic + c11 0.00030 + c12 0.00010 + c44 0.00010 +end +mass_density +body_force +end + +material damped real +stress damped_cubic + c11 0.00030 + c12 0.00010 + c44 0.00010 + gamma 0.1 +end +mass_density +body_force +end diff --git a/examples/USER/atc/elastic/Ar_thermo_elastic.mat b/examples/USER/atc/elastic/Ar_thermo_elastic.mat new file mode 100644 index 0000000000..3862e7b3db --- /dev/null +++ b/examples/USER/atc/elastic/Ar_thermo_elastic.mat @@ -0,0 +1,11 @@ +material Ar real + stress linear + modulus 0.00025 + possions_ratio 0.25 + end + heat_flux linear + conductivity .00000000168 + end + mass_density + body_force +end diff --git a/examples/USER/atc/elastic/Au_elastic.mat b/examples/USER/atc/elastic/Au_elastic.mat new file mode 100644 index 0000000000..19c7a2c912 --- /dev/null +++ b/examples/USER/atc/elastic/Au_elastic.mat @@ -0,0 +1,18 @@ +material Au metal + stress cauchy-born + pair_style eam + #linear + end + mass_density + body_force +end + +material Au_cubic metal + stress cubic + c11 11020.5189657531 + c12 9575.20500303137 + c44 2709.96368010322 + end + mass_density + body_force +end diff --git a/examples/USER/atc/elastic/CNT.mat b/examples/USER/atc/elastic/CNT.mat new file mode 100644 index 0000000000..2832079c89 --- /dev/null +++ b/examples/USER/atc/elastic/CNT.mat @@ -0,0 +1,1315 @@ +material CNT0 metal +stress linear + modulus 0.00025 + possions_ratio 0.25 +end +electric_field linear + permittivity 1.0 +end +electron_density interpolation + number_of_points 3 + 0 0 -1.e-4 + 1.e0 -1.e-4 -1.e-4 + 2.e0 -2.e-4 -1.e-4 +end +mass_density +body_force +end +################################## +material CNT1 metal +stress linear + modulus 0.00025 + possions_ratio 0.25 +end +electric_field linear + permittivity 1.0 +end +electron_density linear + coefficient -1.e-4 +end +mass_density +body_force +end +################################## +material CNT2 metal +stress linear + modulus 0.00025 + possions_ratio 0.25 +end +electric_field linear + permittivity 1.0 +end +electron_density exponential + intrinsic_concentration -1.e-4 + intrinsic_energy 0.2 + reference_temperature 300 +end +mass_density +body_force +end +################################## +material CNT-quadratic metal +stress linear + modulus 0.00025 + possions_ratio 0.25 +end +electric_field linear + permittivity 1.0 +end +electron_density interpolation + number_of_points 3 + 0 0 0 + 1 -1 -2 + 2 -4 -4 +end +mass_density +body_force +end +################################## +material CNT-exp metal +stress linear + modulus 0.00025 + possions_ratio 0.25 +end +electric_field linear + permittivity 1.0 +end +electron_density interpolation + scale 1. + number_of_points 101 +0. 4.36668307825e-08 1.68910652168e-06 +0.030038331567317274 1.39563824966e-07 5.39856368588e-06 +0.06007666313463455 4.46060794658e-07 1.72543824184e-05 +0.09011499470195182 1.42565763428e-06 5.51468371893e-05 +0.1201533262692691 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+mass_density +body_force +end diff --git a/examples/USER/atc/elastic/CNT_electrostatic.mat b/examples/USER/atc/elastic/CNT_electrostatic.mat new file mode 100644 index 0000000000..2f7750bc1b --- /dev/null +++ b/examples/USER/atc/elastic/CNT_electrostatic.mat @@ -0,0 +1,18 @@ +material CNT metal +stress linear + modulus 0.00025 + possions_ratio 0.25 +end +electric_field linear +permittivity 1.0 +end +##electron_density identity +##end +mass_density +#electron_density exponential +# intrinsic_concentration 0.0001 +# intrinsic_energy 1.0 +# reference_temperature 300 +#end +body_force +end diff --git a/examples/USER/atc/elastic/CNT_electrostatic2.mat b/examples/USER/atc/elastic/CNT_electrostatic2.mat new file mode 100644 index 0000000000..86d1a68dc7 --- /dev/null +++ b/examples/USER/atc/elastic/CNT_electrostatic2.mat @@ -0,0 +1,20 @@ +material CNT metal +stress linear + modulus 0.0 + possions_ratio 0.25 +end +electric_field linear + permittivity 1.0 +end +electron_density linear + coefficient -1.e-2 # NOTE will not converge with +0.01, try smaller pos +end +mass_density +#electron_density interpolation +# number_of_points 3 +# 0 0 1.e-4 +# 1.e0 1.e-4 1.e-4 +# 3.e0 3.e-4 1.e-4 +#end +body_force +end diff --git a/examples/USER/atc/elastic/CNT_id.mat b/examples/USER/atc/elastic/CNT_id.mat new file mode 100644 index 0000000000..53c0db6e2a --- /dev/null +++ b/examples/USER/atc/elastic/CNT_id.mat @@ -0,0 +1,11 @@ +material CNT0 metal +stress linear + modulus 0.00025 + possions_ratio 0.25 +end +electric_field linear + permittivity 1.0 +end +mass_density +body_force +end diff --git a/examples/USER/atc/elastic/bar1d.screen b/examples/USER/atc/elastic/bar1d.screen new file mode 100644 index 0000000000..cbd105b0d8 --- /dev/null +++ b/examples/USER/atc/elastic/bar1d.screen @@ -0,0 +1,269 @@ +LAMMPS (14 Aug 2013) + +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 + +# create atoms +region simRegion block -12 12 -3 3 -3 3 +region atomRegion block -9 9 -3 3 -3 3 +region mdRegion block -8 8 -3 3 -3 3 +boundary f p p +create_box 1 simRegion +Created orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215) + 4 by 1 by 1 MPI processor grid +create_atoms 1 region mdRegion +Created 2304 atoms +mass 1 39.95 + +# specify interal/ghost atoms +region mdInternal block -6 6 -3 3 -3 3 +region leftghost block -8 -6 -3 3 -3 3 +region rightghost block 6 8 -3 3 -3 3 +group internal region mdInternal +1728 atoms in group internal +group Lghost region leftghost +288 atoms in group Lghost +group Rghost region rightghost +288 atoms in group Rghost +group ghosts union Lghost Rghost +576 atoms in group ghosts + +# velocities have Vcm = 0 +#velocity internal create 40. 87287 mom yes loop geom + +pair_style lj/cut 13.5 +#pair_coeff 1 1 0.010323166 3.405 13.5 +pair_coeff 1 1 .238 3.405 13.5 + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# define layer +# ID group atc PhysicsType ParameterFile +fix AtC internal atc elastic Ar_elastic.mat +ATC: constructing elastic coupling with parameter file Ar_elastic.mat + ATC: peratom PE compute created with ID: 3 + ATC: computed mass density : 1.01202 + ATC: computed mass density : 1.01202 + ATC: computed mass density : 1.01202 + ATC: 3 materials defined from Ar_elastic.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p + ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements + +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 + +# set node sets and bcs +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF + ATC: created nodeset lbc with 1 nodes +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF + ATC: created nodeset rbc with 1 nodes +fix_modify AtC fix velocity x rbc 0.00000004 +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix velocity x lbc 0. + +# specify atom types +#fix_modify AtC boundary Lghost +#fix_modify AtC boundary Rghost +fix_modify AtC boundary ghosts + +#fix_modify AtC output follow_ex.fe 50 +fix_modify AtC internal_quadrature off +fix_modify AtC control localized_lambda on +fix_modify AtC control momentum glc_velocity +fix_modify AtC filter type exponential +fix_modify AtC filter scale 1000.0 +fix_modify AtC filter on + +# run to extension +#fix_modify AtC output bar1dFE 50 text +timestep 5 +thermo 100 +run 1000 +Setting up run ... +Memory usage per processor = 93.2479 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -4406.6687 0 -4406.6687 -1155.1752 + 100 3.8434911e-14 -4406.6687 0 -4406.6687 -1155.1752 + 200 2.634669e-11 -4406.6687 0 -4406.6687 -1155.1754 + 300 6.909135e-10 -4406.6685 0 -4406.6685 -1155.1763 + 400 3.9413859e-09 -4406.6682 0 -4406.6682 -1155.1783 + 500 8.5603227e-09 -4406.6676 0 -4406.6676 -1155.181 + 600 1.0143684e-08 -4406.6671 0 -4406.6671 -1155.1835 + 700 9.8473676e-09 -4406.6667 0 -4406.6667 -1155.1854 + 800 9.9628095e-09 -4406.6663 0 -4406.6663 -1155.1871 + 900 1.1034555e-08 -4406.6659 0 -4406.6659 -1155.189 + 1000 1.2796459e-08 -4406.6655 0 -4406.6655 -1155.191 +Loop time of 71.7602 on 4 procs for 1000 steps with 2304 atoms + +Pair time (%) = 8.28353 (11.5433) +Neigh time (%) = 4.8737 (6.79165) +Comm time (%) = 23.4869 (32.7296) +Outpt time (%) = 0.14537 (0.202577) +Other time (%) = 34.9708 (48.7328) + +Nlocal: 576 ave 864 max 288 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5170 ave 6910 max 3430 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 178632 ave 288628 max 68417 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 357264 ave 577008 max 137520 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1429056 +Ave neighs/atom = 620.25 +Neighbor list builds = 100 +Dangerous builds = 0 + +# change nodes to fixed +fix_modify AtC fix velocity x rbc 0. +fix_modify AtC fix displacement x rbc 0.0002 + +fix_modify AtC output bar1dFE 500 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + + +# run to equilibrium +timestep 5 +thermo 100 +run 10000 +Setting up run ... +Memory usage per processor = 93.2479 Mbytes +Step Temp E_pair E_mol TotEng Press + 1000 1.2796459e-08 -4406.6655 0 -4406.6655 -1155.191 + 1100 1.3961782e-08 -4406.665 0 -4406.665 -1155.1929 + 1200 1.4156541e-08 -4406.6646 0 -4406.6646 -1155.1947 + 1300 1.1743161e-08 -4406.6643 0 -4406.6643 -1155.1961 + 1400 7.6261191e-09 -4406.6643 0 -4406.6643 -1155.1964 + 1500 5.4918861e-09 -4406.6644 0 -4406.6644 -1155.1955 + 1600 3.2067753e-09 -4406.6647 0 -4406.6647 -1155.1942 + 1700 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-1155.1947 + 7100 1.8115562e-09 -4406.6645 0 -4406.6645 -1155.1948 + 7200 7.4087342e-10 -4406.6645 0 -4406.6645 -1155.1952 + 7300 1.5779154e-09 -4406.6644 0 -4406.6644 -1155.1956 + 7400 2.7467977e-09 -4406.6644 0 -4406.6644 -1155.1955 + 7500 4.2123447e-10 -4406.6645 0 -4406.6645 -1155.195 + 7600 1.1615418e-09 -4406.6646 0 -4406.6646 -1155.1946 + 7700 2.5380373e-09 -4406.6646 0 -4406.6646 -1155.1945 + 7800 1.5068282e-09 -4406.6646 0 -4406.6646 -1155.1948 + 7900 6.0931799e-10 -4406.6645 0 -4406.6645 -1155.195 + 8000 2.0802965e-09 -4406.6645 0 -4406.6645 -1155.1951 + 8100 2.1544428e-09 -4406.6645 0 -4406.6645 -1155.1953 + 8200 4.4375899e-10 -4406.6644 0 -4406.6644 -1155.1955 + 8300 1.5879866e-09 -4406.6644 0 -4406.6644 -1155.1954 + 8400 2.1255967e-09 -4406.6645 0 -4406.6645 -1155.1949 + 8500 8.5066547e-10 -4406.6646 0 -4406.6646 -1155.1945 + 8600 4.9764713e-10 -4406.6646 0 -4406.6646 -1155.1945 + 8700 2.4032931e-09 -4406.6646 0 -4406.6646 -1155.1949 + 8800 1.5506272e-09 -4406.6645 0 -4406.6645 -1155.1951 + 8900 2.156996e-10 -4406.6645 0 -4406.6645 -1155.1952 + 9000 1.5053583e-09 -4406.6645 0 -4406.6645 -1155.1953 + 9100 2.2313062e-09 -4406.6645 0 -4406.6645 -1155.1954 + 9200 6.5295769e-10 -4406.6645 0 -4406.6645 -1155.1953 + 9300 7.1214495e-10 -4406.6646 0 -4406.6646 -1155.1949 + 9400 2.2525879e-09 -4406.6646 0 -4406.6646 -1155.1945 + 9500 1.2940878e-09 -4406.6646 0 -4406.6646 -1155.1945 + 9600 3.7619117e-10 -4406.6645 0 -4406.6645 -1155.195 + 9700 1.9605412e-09 -4406.6645 0 -4406.6645 -1155.1953 + 9800 1.7828694e-09 -4406.6645 0 -4406.6645 -1155.1953 + 9900 5.2324205e-10 -4406.6645 0 -4406.6645 -1155.1952 + 10000 1.1770899e-09 -4406.6645 0 -4406.6645 -1155.1952 + 10100 2.0621304e-09 -4406.6645 0 -4406.6645 -1155.1951 + 10200 9.4046414e-10 -4406.6646 0 -4406.6646 -1155.1948 + 10300 3.3301061e-10 -4406.6646 0 -4406.6646 -1155.1945 + 10400 2.2075407e-09 -4406.6646 0 -4406.6646 -1155.1946 + 10500 1.3556476e-09 -4406.6645 0 -4406.6645 -1155.1951 + 10600 3.1056944e-10 -4406.6645 0 -4406.6645 -1155.1954 + 10700 1.2113659e-09 -4406.6645 0 -4406.6645 -1155.1953 + 10800 2.0914266e-09 -4406.6645 0 -4406.6645 -1155.1951 + 10900 5.1353017e-10 -4406.6645 0 -4406.6645 -1155.1951 + 11000 5.4707109e-10 -4406.6645 0 -4406.6645 -1155.195 +Loop time of 354.654 on 4 procs for 10000 steps with 2304 atoms + +Pair time (%) = 67.9127 (19.149) +Neigh time (%) = 31.8455 (8.97932) +Comm time (%) = 122.402 (34.513) +Outpt time (%) = 0.360688 (0.101702) +Other time (%) = 132.133 (37.2569) + +Nlocal: 576 ave 864 max 288 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5170 ave 6910 max 3430 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 178632 ave 289342 max 67274 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 357264 ave 577008 max 137520 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1429056 +Ave neighs/atom = 620.25 +Neighbor list builds = 1000 +Dangerous builds = 0 diff --git a/examples/USER/atc/elastic/bar1d_damped.screen b/examples/USER/atc/elastic/bar1d_damped.screen new file mode 100644 index 0000000000..bf21b7027b --- /dev/null +++ b/examples/USER/atc/elastic/bar1d_damped.screen @@ -0,0 +1,379 @@ +LAMMPS (14 Aug 2013) + +units metal +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 + +# create atoms +region simRegion block -12 12 -3 3 -3 3 +region atomRegion block -9 9 -3 3 -3 3 +region mdRegion block -8 8 -3 3 -3 3 +boundary f p p +create_box 2 simRegion +Created orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215) + 4 by 1 by 1 MPI processor grid +create_atoms 1 region mdRegion +Created 2304 atoms +mass * 39.95 + +# specify interal/ghost atoms +region mdInternal block -6 6 -3 3 -3 3 +region leftghost block -8 -6 -3 3 -3 3 +region rightghost block 6 8 -3 3 -3 3 +group internal region mdInternal +1728 atoms in group internal +group Lghost region leftghost +288 atoms in group Lghost +group Rghost region rightghost +288 atoms in group Rghost +group ghosts union Lghost Rghost +576 atoms in group ghosts + +# velocities have Vcm = 0 +#velocity internal create 40. 87287 mom yes loop geom + +pair_style lj/cut 13.5 +#pair_coeff * * .238 3.405 13.5 +pair_coeff * * 0.010323166 3.405 13.5 + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# define layer +# ID group atc PhysicsType ParameterFile +fix AtC internal atc elastic Ar_damped.mat +ATC: constructing elastic coupling with parameter file Ar_damped.mat + ATC: peratom PE compute created with ID: 3 + ATC: 3 materials defined from Ar_damped.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p + ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements + +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 + + +variable v equal 0.00000004e3 +variable n equal 1000 +variable dt equal 0.005 +variable u equal $v*$n*${dt} +variable u equal 4.0000000000000003272e-05*$n*${dt} +variable u equal 4.0000000000000003272e-05*1000*${dt} +variable u equal 4.0000000000000003272e-05*1000*0.0050000000000000001041 + +# set node sets and bcs +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF + ATC: created nodeset lbc with 1 nodes +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF + ATC: created nodeset rbc with 1 nodes +fix_modify AtC fix velocity x rbc $v +fix_modify AtC fix velocity x rbc 4.0000000000000003272e-05 +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix velocity x lbc 0. + +# specify atom types +fix_modify AtC boundary ghosts + +#fix_modify AtC output follow_ex.fe 50 +fix_modify AtC internal_quadrature off +fix_modify AtC control localized_lambda on +fix_modify AtC control momentum glc_velocity +#fix_modify AtC filter type exponential +#fix_modify AtC filter scale 1.0 +#fix_modify AtC filter on + +# run to extension +timestep 0.005 +thermo 100 +thermo_style custom step cpu ke pe +run 0 +Setting up run ... +Memory usage per processor = 93.2479 Mbytes +Step CPU KinEng PotEng + 0 0 0 -191.1377 +Loop time of 6.3777e-06 on 4 procs for 0 steps with 2304 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 0 (0) +Outpt time (%) = 0 (0) +Other time (%) = 6.3777e-06 (100) + +Nlocal: 576 ave 864 max 288 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5170 ave 6910 max 3430 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 178632 ave 288576 max 68400 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 357264 ave 577008 max 137520 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1429056 +Ave neighs/atom = 620.25 +Neighbor list builds = 0 +Dangerous builds = 0 +variable pe0 equal pe +variable pe equal pe-${pe0} +variable pe equal pe--191.13770127444766445 +thermo_style custom step cpu ke pe v_pe f_AtC[1] f_AtC[2] f_AtC[4] f_AtC[5] + +run $n +run 1000 +Setting up run ... +Memory usage per processor = 93.2479 Mbytes +Step CPU KinEng PotEng pe AtC[1] AtC[2] AtC[4] AtC[5] + 0 0 0 -191.1377 0 0 0 0 0 + 100 8.0390151 1.055851e-16 -191.1377 5.3847288e-08 5.5210093e-10 4.8838395e-10 5.5210086e-10 4.8838395e-10 + 200 11.493128 2.7309802e-13 -191.1377 1.505559e-06 1.1639949e-09 1.2827565e-09 1.1637935e-09 1.2827433e-09 + 300 19.35353 1.7311896e-11 -191.13769 8.8450898e-06 2.0715862e-09 2.022604e-09 2.0579272e-09 2.020558e-09 + 400 28.928974 2.1239086e-10 -191.13768 2.6114181e-05 2.9481123e-09 2.7362141e-09 2.7703215e-09 2.6871501e-09 + 500 33.919009 9.6058596e-10 -191.13765 5.1722206e-05 4.1041211e-09 3.33188e-09 3.253095e-09 2.9376729e-09 + 600 43.879017 2.2037311e-09 -191.13762 8.020941e-05 5.6140713e-09 4.0767895e-09 3.5687157e-09 2.5638486e-09 + 700 53.458615 3.2720323e-09 -191.13759 0.00010864588 6.9461579e-09 5.4103466e-09 3.8327109e-09 1.9736115e-09 + 800 59.149139 3.9667277e-09 -191.13756 0.0001382309 7.930912e-09 7.0706824e-09 4.1286537e-09 1.5663212e-09 + 900 65.676015 4.6276406e-09 -191.13753 0.00016977721 8.7852e-09 8.6120146e-09 4.3243149e-09 1.3090105e-09 + 1000 76.426912 5.4647857e-09 -191.1375 0.00020107009 9.4089083e-09 1.0142471e-08 4.111432e-09 1.1470431e-09 +Loop time of 76.4282 on 4 procs for 1000 steps with 2304 atoms + +Pair time (%) = 8.25247 (10.7977) +Neigh time (%) = 4.72959 (6.18828) +Comm time (%) = 23.9356 (31.3178) +Outpt time (%) = 0.304101 (0.397891) +Other time (%) = 39.2064 (51.2984) + +Nlocal: 576 ave 864 max 288 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5170 ave 6910 max 3430 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 178632 ave 289722 max 67420 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 357264 ave 577008 max 137520 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1429056 +Ave neighs/atom = 620.25 +Neighbor list builds = 100 +Dangerous builds = 0 + +fix_modify AtC output bar1d_dampedFE 500 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +dump CONFIG all custom 500 bar1d_damped.dmp id type x y z vx vy vz + +# change nodes to fixed +fix_modify AtC fix velocity x rbc 0. +fix_modify AtC fix displacement x rbc $u +fix_modify AtC fix displacement x rbc 0.00020000000000000000958 + +# run to equilibrium +thermo 100 +log bar1d_damped.log +run 2000 +Setting up run ... +Memory usage per processor = 93.4533 Mbytes +Step CPU KinEng PotEng pe AtC[1] AtC[2] AtC[4] AtC[5] + 1000 0 5.4647857e-09 -191.1375 0.00020107009 9.4089083e-09 0 4.111432e-09 -8.9954275e-09 + 1100 3.4263639 6.3421646e-09 -191.13747 0.00022971709 8.75085e-09 1.4153048e-09 2.5767395e-09 -9.3569477e-09 + 1200 10.368947 6.9778939e-09 -191.13745 0.00025458471 8.1727552e-09 3.1204783e-09 1.3697518e-09 -9.4201182e-09 + 1300 14.878477 7.1529752e-09 -191.13743 0.00027170434 7.5897544e-09 4.5095316e-09 6.3357843e-10 -9.4773618e-09 + 1400 24.373178 6.6395813e-09 -191.13743 0.00027466413 6.747478e-09 5.4996207e-09 2.8850325e-10 -9.1651904e-09 + 1500 26.945583 5.6922363e-09 -191.13744 0.00026126097 6.2562137e-09 5.3958429e-09 7.4259589e-10 -8.7642657e-09 + 1600 29.179645 4.7135957e-09 -191.13747 0.00023620822 5.9708984e-09 4.7989197e-09 1.5108282e-09 -8.165151e-09 + 1700 32.158633 3.4710553e-09 -191.1375 0.00020618074 5.3956633e-09 4.5850559e-09 2.1370382e-09 -7.4317528e-09 + 1800 34.59477 2.4145542e-09 -191.13753 0.0001751612 4.4014655e-09 4.6172904e-09 2.1438377e-09 -6.2667582e-09 + 1900 36.481867 2.1438948e-09 -191.13756 0.00014569893 3.408323e-09 4.1360716e-09 1.4726957e-09 -4.5311799e-09 + 2000 38.402959 2.1864605e-09 -191.13758 0.00012155208 2.5555543e-09 3.2626157e-09 6.5555529e-10 -2.5834443e-09 + 2100 40.302963 1.9032904e-09 -191.13759 0.00010654531 2.0211043e-09 2.3634891e-09 3.1602374e-10 -1.1813128e-09 + 2200 42.169921 1.9875147e-09 -191.1376 0.00010189892 2.0066398e-09 1.5638553e-09 1.4805596e-10 -4.8955277e-10 + 2300 44.033215 3.2414453e-09 -191.13759 0.00010629042 3.4949611e-09 6.0884607e-11 3.7071553e-10 -1.2166095e-09 + 2400 45.904622 5.4666452e-09 -191.13758 0.00011815334 6.4739473e-09 -2.0744242e-09 1.1628627e-09 -3.4626277e-09 + 2500 47.797741 7.1143087e-09 -191.13756 0.00013705246 9.1384443e-09 -3.3784529e-09 2.1796903e-09 -5.9902478e-09 + 2600 51.178232 7.1885602e-09 -191.13754 0.00016288238 1.0502632e-08 -3.4468822e-09 3.4466305e-09 -8.0921646e-09 + 2700 53.509233 6.4420688e-09 -191.13751 0.00019390227 1.0708869e-08 -2.5391386e-09 4.4412335e-09 -9.5081141e-09 + 2800 55.372385 5.6029945e-09 -191.13748 0.00022551631 9.3553209e-09 7.5058192e-11 3.8587617e-09 -9.3943471e-09 + 2900 57.239711 5.099105e-09 -191.13745 0.00025162655 6.936034e-09 3.8584367e-09 1.8989273e-09 -7.959387e-09 + 3000 59.118431 4.5349913e-09 -191.13743 0.00026783371 5.1180916e-09 6.6034959e-09 6.6351749e-10 -7.0089177e-09 +Loop time of 59.1197 on 4 procs for 2000 steps with 2304 atoms + +Pair time (%) = 13.3157 (22.5233) +Neigh time (%) = 5.97997 (10.115) +Comm time (%) = 17.5956 (29.7626) +Outpt time (%) = 0.0869119 (0.14701) +Other time (%) = 22.1415 (37.452) + +Nlocal: 576 ave 864 max 288 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5170 ave 6910 max 3430 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 178632 ave 288868 max 65686 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 357264 ave 577008 max 137520 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1429056 +Ave neighs/atom = 620.25 +Neighbor list builds = 200 +Dangerous builds = 0 +fix_modify AtC material all cubic # M damping +run 2000 +Setting up run ... +Memory usage per processor = 93.4533 Mbytes +Step CPU KinEng PotEng pe AtC[1] AtC[2] AtC[4] AtC[5] + 3000 0 4.5349913e-09 -191.13743 0.00026783371 5.1180916e-09 0 6.6351749e-10 -1.3612414e-08 + 3100 1.884902 3.1627635e-09 -191.13743 0.00027166541 3.3508276e-09 1.5163376e-09 2.9822385e-10 -1.3169543e-08 + 3200 3.7543039 2.1305486e-09 -191.13744 0.00026502967 2.292755e-09 1.9348144e-09 2.9322733e-10 -1.2923953e-08 + 3300 6.005461 1.7622321e-09 -191.13745 0.00025028487 2.1709597e-09 1.2092749e-09 5.6848039e-10 -1.3098658e-08 + 3400 16.302727 1.4627886e-09 -191.13747 0.00022947204 2.0542491e-09 2.4241837e-10 7.6881831e-10 -1.3269991e-08 + 3500 18.647849 1.1457596e-09 -191.13749 0.0002071953 1.7022137e-09 -6.8412058e-10 6.5328081e-10 -1.3186597e-08 + 3600 20.526815 1.5322847e-09 -191.13751 0.00018851151 1.9578951e-09 -2.5376549e-09 5.0945853e-10 -1.3161338e-08 + 3700 22.404343 2.7199727e-09 -191.13753 0.00017501297 2.8551124e-09 -5.3147303e-09 3.5995471e-10 -1.317891e-08 + 3800 24.280314 3.8255198e-09 -191.13754 0.00016517255 3.776711e-09 -7.8091811e-09 1.9270828e-10 -1.3125415e-08 + 3900 26.155669 4.7080092e-09 -191.13754 0.00015798858 4.6102461e-09 -9.4550009e-09 1.2287245e-10 -1.3138835e-08 + 4000 28.039841 5.3603485e-09 -191.13755 0.00015424854 5.3157594e-09 -1.0203778e-08 1.5542087e-10 -1.3330611e-08 + 4100 29.917995 5.3407666e-09 -191.13755 0.00015459539 5.6318354e-09 -1.0223896e-08 3.9327183e-10 -1.3777619e-08 + 4200 31.791416 4.5200859e-09 -191.13754 0.000158412 5.2283097e-09 -9.7612848e-09 7.3695415e-10 -1.4260955e-08 + 4300 33.665959 3.248288e-09 -191.13754 0.00016494668 4.2434602e-09 -9.1569844e-09 1.0215962e-09 -1.4755402e-08 + 4400 35.538211 1.9718426e-09 -191.13753 0.00017370613 3.0004575e-09 -8.5412539e-09 1.0485714e-09 -1.5191473e-08 + 4500 37.426718 1.0175326e-09 -191.13752 0.00018301345 1.8277045e-09 -8.0355833e-09 8.1451769e-10 -1.5385018e-08 + 4600 39.941118 4.528091e-10 -191.13751 0.00019011125 8.8800708e-10 -7.698949e-09 4.3848726e-10 -1.5198592e-08 + 4700 41.926014 1.813047e-10 -191.13751 0.00019345531 3.2820899e-10 -7.6270177e-09 1.6240525e-10 -1.4863017e-08 + 4800 43.768896 1.0257178e-10 -191.13751 0.00019385828 1.3812287e-10 -7.7900766e-09 5.3812979e-11 -1.4605952e-08 + 4900 46.766592 1.9853801e-10 -191.13751 0.00019285378 1.955715e-10 -8.0515951e-09 1.5537909e-11 -1.4450335e-08 + 5000 51.661613 4.4499498e-10 -191.13751 0.00019101535 4.6651548e-10 -8.4263349e-09 3.2542828e-11 -1.4479894e-08 +Loop time of 51.6629 on 4 procs for 2000 steps with 2304 atoms + +Pair time (%) = 12.642 (24.4702) +Neigh time (%) = 5.57654 (10.7941) +Comm time (%) = 15.4191 (29.8455) +Outpt time (%) = 0.130104 (0.251833) +Other time (%) = 17.8952 (34.6384) + +Nlocal: 576 ave 864 max 288 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5170 ave 6910 max 3430 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 178632 ave 288868 max 65664 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 357264 ave 577008 max 137520 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1429056 +Ave neighs/atom = 620.25 +Neighbor list builds = 200 +Dangerous builds = 0 +fix_modify AtC material all damped # K damping +run 2000 +Setting up run ... +Memory usage per processor = 93.4533 Mbytes +Step CPU KinEng PotEng pe AtC[1] AtC[2] AtC[4] AtC[5] + 5000 0 4.4499498e-10 -191.13751 0.00019101535 4.6651548e-10 0 3.2542828e-11 -6.0535591e-09 + 5100 4.6635571 7.7530221e-10 -191.13751 0.00018808779 8.8219827e-10 -5.1894954e-10 1.1477898e-10 -6.2656816e-09 + 5200 7.9799862 1.0914185e-09 -191.13752 0.00018469909 1.3356438e-09 -1.1167463e-09 2.5090286e-10 -6.5437879e-09 + 5300 9.832078 1.3329143e-09 -191.13752 0.00018160964 1.7365431e-09 -1.6964741e-09 4.0718828e-10 -6.8217529e-09 + 5400 16.735786 1.504171e-09 -191.13752 0.00017917616 1.9911092e-09 -2.1593835e-09 4.9328931e-10 -7.0385998e-09 + 5500 21.043345 1.594802e-09 -191.13752 0.00017766571 2.0494572e-09 -2.4260642e-09 4.6275872e-10 -7.138857e-09 + 5600 23.746816 1.5743105e-09 -191.13752 0.00017717238 1.929034e-09 -2.4892277e-09 3.6487504e-10 -7.1146385e-09 + 5700 25.625748 1.4221294e-09 -191.13752 0.00017729486 1.6665332e-09 -2.3656166e-09 2.5500829e-10 -6.9804167e-09 + 5800 30.389402 1.1720493e-09 -191.13752 0.00017753363 1.3116581e-09 -2.0608866e-09 1.5433624e-10 -6.7800184e-09 + 5900 32.585614 8.6077652e-10 -191.13752 0.00017794528 9.2235699e-10 -1.6102419e-09 7.7989231e-11 -6.5963868e-09 + 6000 35.173423 5.2708656e-10 -191.13752 0.0001789751 5.4942864e-10 -1.0882941e-09 3.5646667e-11 -6.4862104e-09 + 6100 40.119008 2.325476e-10 -191.13752 0.0001807569 2.4150687e-10 -5.8295363e-10 1.6542883e-11 -6.4439488e-09 + 6200 41.993394 4.6103001e-11 -191.13752 0.00018302227 5.3284568e-11 -2.125555e-10 9.264294e-12 -6.4611762e-09 + 6300 45.873721 1.6246443e-11 -191.13752 0.00018541173 2.4386805e-11 -8.566705e-11 9.9387033e-12 -6.5339312e-09 + 6400 49.424723 1.4744476e-10 -191.13751 0.00018750725 1.5460292e-10 -2.1854704e-10 1.2454671e-11 -6.6323029e-09 + 6500 52.764808 4.0670554e-10 -191.13751 0.00018887546 4.1540944e-10 -5.5265965e-10 2.0454523e-11 -6.7446848e-09 + 6600 57.161516 7.1997609e-10 -191.13751 0.00018914788 7.4785363e-10 -9.9312474e-10 4.429436e-11 -6.8751447e-09 + 6700 60.044641 1.011863e-09 -191.13751 0.00018817658 1.080257e-09 -1.4281411e-09 8.7264316e-11 -7.0103089e-09 + 6800 63.731949 1.2214055e-09 -191.13751 0.00018635915 1.3481402e-09 -1.7820613e-09 1.4383303e-10 -7.1419056e-09 + 6900 65.622758 1.3150127e-09 -191.13752 0.00018434046 1.5093341e-09 -2.0332173e-09 2.0695782e-10 -7.2501404e-09 + 7000 67.990237 1.2853182e-09 -191.13752 0.0001825143 1.5377643e-09 -2.1694031e-09 2.6084212e-10 -7.2971336e-09 +Loop time of 67.9915 on 4 procs for 2000 steps with 2304 atoms + +Pair time (%) = 13.7916 (20.2843) +Neigh time (%) = 6.20275 (9.12283) +Comm time (%) = 22.365 (32.8938) +Outpt time (%) = 0.24604 (0.361868) +Other time (%) = 25.3861 (37.3372) + +Nlocal: 576 ave 864 max 288 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5170 ave 6910 max 3430 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 178632 ave 288864 max 65670 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 357264 ave 577008 max 137520 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1429056 +Ave neighs/atom = 620.25 +Neighbor list builds = 200 +Dangerous builds = 0 +# ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 from Ar_CauchyBorn.mat +# real to metal 1 kcal/mol = 0.04336 eV +variable kCal2eV equal 0.04336 +variable k equal 1.e-3 # 7.56717*${kCal2eV} NOTE <<< +variable g equal 0.75*0.355649e3*${kCal2eV} +variable g equal 0.75*0.355649e3*0.043360000000000002707 +variable m equal 0.5*39.95 +fix_modify AtC boundary_dynamics damped_harmonic $k $g $m +fix_modify AtC boundary_dynamics damped_harmonic 0.0010000000000000000208 $g $m +fix_modify AtC boundary_dynamics damped_harmonic 0.0010000000000000000208 11.56570548000000187 $m +fix_modify AtC boundary_dynamics damped_harmonic 0.0010000000000000000208 11.56570548000000187 19.975000000000001421 +run 2000 +Setting up run ... +Memory usage per processor = 93.4533 Mbytes +Step CPU KinEng PotEng pe AtC[1] AtC[2] AtC[4] AtC[5] + 7000 0 1.2853182e-09 -191.13752 0.0001825143 1.5377643e-09 0 2.6084212e-10 -5.1277305e-09 + 7100 3.8653619 2.8903751e-05 -191.1374 0.00029857456 1.4261761e-09 -1.214748e-11 2.7859112e-10 -5.084773e-09 + 7200 5.7172129 3.8761799e-06 -191.13735 0.00035025356 1.1959825e-09 8.5346682e-11 2.5313036e-10 -4.9584954e-09 + 7300 7.596113 1.8769484e-06 -191.13737 0.0003337536 8.9086284e-10 2.6798239e-10 2.0084283e-10 -4.7692463e-09 + 7400 12.42461 1.245935e-05 -191.13743 0.00026909159 5.6202829e-10 5.0489219e-10 1.2878586e-10 -4.5511096e-09 + 7500 15.114735 1.6301032e-05 -191.13751 0.00018830281 2.7560343e-10 7.5207256e-10 5.694786e-11 -4.362424e-09 + 7600 19.876048 9.4676227e-06 -191.13758 0.00012208357 8.4877207e-11 9.6782588e-10 1.2617604e-11 -4.2488453e-09 + 7700 21.707406 1.6567809e-06 -191.13761 8.9858261e-05 1.0099305e-11 1.1176649e-09 1.4916291e-12 -4.2369828e-09 + 7800 24.205287 3.0391321e-07 -191.13761 9.5611994e-05 5.1427805e-11 1.1674588e-09 1.7611917e-11 -4.3302492e-09 + 7900 27.866901 3.2726602e-06 -191.13757 0.0001295863 1.905123e-10 1.1057791e-09 4.8229373e-11 -4.4960207e-09 + 8000 29.84634 4.7851826e-06 -191.13753 0.00017453181 3.9524144e-10 9.4866146e-10 7.738243e-11 -4.6918777e-09 + 8100 32.731688 3.0560115e-06 -191.13749 0.00021322134 6.2989738e-10 7.2412128e-10 9.7353433e-11 -4.8834384e-09 + 8200 36.727295 6.6407027e-07 -191.13747 0.00023416094 8.5464088e-10 4.6942869e-10 1.1187578e-10 -5.0480909e-09 + 8300 38.564577 3.8165674e-08 -191.13747 0.00023410509 1.0268939e-09 2.3847444e-10 1.2118336e-10 -5.1639054e-09 + 8400 41.031069 8.4495007e-07 -191.13748 0.00021748415 1.1122546e-09 8.8553406e-11 1.2219945e-10 -5.2187642e-09 + 8500 44.303455 1.3915225e-06 -191.13751 0.0001932998 1.0989984e-09 5.0075534e-11 1.2293817e-10 -5.2142527e-09 + 8600 46.136877 9.7448077e-07 -191.13753 0.00017115059 9.8587454e-10 1.1774103e-10 1.2176493e-10 -5.1569143e-09 + 8700 49.565115 2.5400881e-07 -191.13754 0.00015791542 7.9484554e-10 2.5817073e-10 1.1156472e-10 -5.0569238e-09 + 8800 52.407452 2.6471441e-09 -191.13755 0.00015589474 5.6635938e-10 4.2847179e-10 9.4176403e-11 -4.9223096e-09 + 8900 54.820348 2.1367306e-07 -191.13754 0.00016308046 3.4009704e-10 5.9208385e-10 7.0443086e-11 -4.7692236e-09 + 9000 59.598561 4.0089918e-07 -191.13753 0.00017492322 1.5426704e-10 7.172267e-10 4.311796e-11 -4.6253241e-09 +Loop time of 59.5999 on 4 procs for 2000 steps with 2304 atoms + +Pair time (%) = 13.6404 (22.8866) +Neigh time (%) = 5.86772 (9.84519) +Comm time (%) = 19.3873 (32.5292) +Outpt time (%) = 0.201972 (0.338879) +Other time (%) = 20.5024 (34.4001) + +Nlocal: 576 ave 864 max 288 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5170 ave 6910 max 3430 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 178632 ave 288850 max 65677 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 357264 ave 577008 max 137520 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1429056 +Ave neighs/atom = 620.25 +Neighbor list builds = 200 +Dangerous builds = 0 diff --git a/examples/USER/atc/elastic/bar1d_flux.screen b/examples/USER/atc/elastic/bar1d_flux.screen new file mode 100644 index 0000000000..259c78a3af --- /dev/null +++ b/examples/USER/atc/elastic/bar1d_flux.screen @@ -0,0 +1,280 @@ +LAMMPS (14 Aug 2013) + +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +lattice fcc 5.2582305 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.25823 5.25823 5.25823 + +# create atoms +region simRegion block -12 12 -3 3 -3 3 +region atomRegion block -9 9 -3 3 -3 3 +region mdRegion block -8 8 -3 3 -3 3 +boundary f p p +create_box 1 simRegion +Created orthogonal box = (-63.0988 -15.7747 -15.7747) to (63.0988 15.7747 15.7747) + 4 by 1 by 1 MPI processor grid +create_atoms 1 region mdRegion +Created 2304 atoms +mass 1 39.95 + +# specify interal/ghost atoms +region mdInternal block -6 6 -3 3 -3 3 +region leftghost block -8 -6 -3 3 -3 3 +region rightghost block 6 8 -3 3 -3 3 +group internal region mdInternal +1728 atoms in group internal +group Lghost region leftghost +288 atoms in group Lghost +group Rghost region rightghost +288 atoms in group Rghost +group ghosts union Lghost Rghost +576 atoms in group ghosts + +# velocities have Vcm = 0 +#velocity internal create 40. 87287 mom yes loop geom + +pair_style lj/cut 13. +#pair_coeff 1 1 0.010323166 3.405 13. +pair_coeff 1 1 .2381 3.405 13. + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# define layer +# ID group atc PhysicsType ParameterFile +fix AtC internal atc elastic Ar_elastic.mat +ATC: constructing elastic coupling with parameter file Ar_elastic.mat + ATC: peratom PE compute created with ID: 3 + ATC: computed mass density : 1.09915 + ATC: computed mass density : 1.09915 + ATC: computed mass density : 1.09915 + ATC: 3 materials defined from Ar_elastic.mat +#fix_modify AtC boundary Lghost +#fix_modify AtC boundary Rghost +fix_modify AtC boundary ghosts + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p + ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements +fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward + ATC: created faceset obndy with 2 faces + +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 + +# set node sets and bcs +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF + ATC: created nodeset lbc with 1 nodes +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF + ATC: created nodeset rbc with 1 nodes +fix_modify AtC fix velocity x rbc 0.00000004 +#fix_modify AtC fix velocity x rbc 0. +#fix_modify AtC fix displacement x rbc 0. +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix velocity x lbc 0. + + +#fix_modify AtC output follow_ex.fe 50 +fix_modify AtC internal_quadrature off +#fix_modify AtC control lumped_lambda_solve on +#fix_modify AtC momentum control glc_velocity +#fix_modify AtC momentum control flux faceset obndy +fix_modify AtC control momentum flux interpolate +#fix_modify AtC filter scale 1000.0 + +# run to extension +compute myTemp internal temp +compute atomStress internal stress/atom +compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3] +variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol) +thermo_style custom step c_myTemp v_myPres pe +fix_modify AtC output bar1d_fluxFE 10 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +timestep 5 +thermo 100 +run 1000 +Setting up run ... +Memory usage per processor = 93.0953 Mbytes +Step myTemp myPres PotEng + 0 0 -0.00072339042 -4509.8851 + 100 1.7485737e-12 -0.00065677838 -4509.8851 + 200 2.1209236e-12 -0.00058835409 -4509.8851 + 300 3.1757662e-11 -0.00088336321 -4509.8851 + 400 4.4437682e-10 -0.0022808215 -4509.8852 + 500 2.1276171e-09 -0.0055205162 -4509.8852 + 600 5.3746766e-09 -0.010513144 -4509.8852 + 700 9.3752238e-09 -0.016165157 -4509.8852 + 800 1.3218953e-08 -0.02139071 -4509.8852 + 900 1.6753544e-08 -0.026203391 -4509.8852 + 1000 2.0559423e-08 -0.031228823 -4509.8852 +Loop time of 77.9631 on 4 procs for 1000 steps with 2304 atoms + +Pair time (%) = 8.02545 (10.2939) +Neigh time (%) = 4.56744 (5.85847) +Comm time (%) = 22.9713 (29.4644) +Outpt time (%) = 0.286932 (0.368036) +Other time (%) = 42.1119 (54.0152) + +Nlocal: 576 ave 864 max 288 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5170 ave 6910 max 3430 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 178632 ave 288102 max 69229 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 357264 ave 577008 max 137520 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1429056 +Ave neighs/atom = 620.25 +Neighbor list builds = 100 +Dangerous builds = 0 + +# change nodes to fixed +fix_modify AtC fix velocity x rbc 0. +fix_modify AtC fix displacement x rbc 0.0002 + +fix_modify AtC output bar1d_fluxFE 500 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + + +# run to equilibrium +timestep 5 +thermo 100 +run 10000 +Setting up run ... +Memory usage per processor = 93.5532 Mbytes +Step myTemp myPres PotEng + 1000 2.0559423e-08 -0.031228823 -4509.8852 + 1100 2.4448613e-08 -0.036521719 -4509.8852 + 1200 2.7029986e-08 -0.040978057 -4509.8852 + 1300 2.7245337e-08 -0.042998684 -4509.8852 + 1400 2.5759549e-08 -0.041645718 -4509.8852 + 1500 2.2667557e-08 -0.037303114 -4509.8852 + 1600 1.8985753e-08 -0.031463351 -4509.8852 + 1700 1.6073802e-08 -0.025662764 -4509.8852 + 1800 1.2763714e-08 -0.020737937 -4509.8852 + 1900 7.2995795e-09 -0.01675253 -4509.8852 + 2000 2.1755431e-09 -0.013533314 -4509.8853 + 2100 1.1934319e-09 -0.011450448 -4509.8853 + 2200 5.1850465e-09 -0.011687818 -4509.8853 + 2300 1.1883622e-08 -0.015251299 -4509.8852 + 2400 1.6266667e-08 -0.021397871 -4509.8852 + 2500 1.9099042e-08 -0.02792249 -4509.8851 + 2600 2.184558e-08 -0.033185039 -4509.8852 + 2700 2.4595817e-08 -0.037175923 -4509.8852 + 2800 2.6643068e-08 -0.040355693 -4509.8852 + 2900 2.6394943e-08 -0.042183343 -4509.8852 + 3000 2.3989422e-08 -0.041411974 -4509.8852 + 3100 2.0979363e-08 -0.037465063 -4509.8851 + 3200 1.7427127e-08 -0.031310189 -4509.8852 + 3300 1.3963242e-08 -0.024887233 -4509.8852 + 3400 1.0069796e-08 -0.019686777 -4509.8852 + 3500 4.9395633e-09 -0.01603797 -4509.8853 + 3600 1.5407167e-09 -0.013620537 -4509.8853 + 3700 2.5284685e-09 -0.012392513 -4509.8853 + 3800 7.790979e-09 -0.012777012 -4509.8852 + 3900 1.3465317e-08 -0.015407232 -4509.8852 + 4000 1.7796468e-08 -0.02062936 -4509.8852 + 4100 2.137127e-08 -0.027628973 -4509.8852 + 4200 2.3606809e-08 -0.034315098 -4509.8852 + 4300 2.5221837e-08 -0.038703928 -4509.8852 + 4400 2.6247664e-08 -0.040548555 -4509.8852 + 4500 2.5017987e-08 -0.040839998 -4509.8852 + 4600 2.1628404e-08 -0.040012148 -4509.8852 + 4700 1.7878834e-08 -0.037370745 -4509.8851 + 4800 1.5934582e-08 -0.032277925 -4509.8851 + 4900 1.2990149e-08 -0.025549108 -4509.8852 + 5000 7.8316754e-09 -0.01918358 -4509.8853 + 5100 3.3266953e-09 -0.014887033 -4509.8853 + 5200 1.805252e-09 -0.01286358 -4509.8853 + 5300 4.2912871e-09 -0.012392579 -4509.8852 + 5400 9.9026848e-09 -0.013257092 -4509.8852 + 5500 1.6165255e-08 -0.015976619 -4509.8852 + 5600 2.1206295e-08 -0.020907339 -4509.8852 + 5700 2.4000025e-08 -0.027469529 -4509.8852 + 5800 2.5521345e-08 -0.034321126 -4509.8852 + 5900 2.5894586e-08 -0.039670766 -4509.8852 + 6000 2.5086791e-08 -0.042046228 -4509.8852 + 6100 2.360407e-08 -0.041352366 -4509.8852 + 6200 1.9586346e-08 -0.038824048 -4509.8852 + 6300 1.6684228e-08 -0.035608606 -4509.8852 + 6400 1.4893508e-08 -0.031584998 -4509.8852 + 6500 1.1127507e-08 -0.026164353 -4509.8852 + 6600 5.9884577e-09 -0.019764802 -4509.8853 + 6700 2.2391294e-09 -0.014210542 -4509.8853 + 6800 2.7797654e-09 -0.011431487 -4509.8853 + 6900 6.7664929e-09 -0.011810438 -4509.8852 + 7000 1.1980057e-08 -0.014206493 -4509.8852 + 7100 1.7989445e-08 -0.017536849 -4509.8852 + 7200 2.3218176e-08 -0.02190877 -4509.8852 + 7300 2.5628573e-08 -0.027653206 -4509.8852 + 7400 2.610839e-08 -0.034000347 -4509.8852 + 7500 2.4944322e-08 -0.039281243 -4509.8852 + 7600 2.2693765e-08 -0.042058723 -4509.8852 + 7700 1.9767428e-08 -0.041825858 -4509.8851 + 7800 1.6504232e-08 -0.039030684 -4509.8851 + 7900 1.4309561e-08 -0.03485307 -4509.8852 + 8000 1.3055145e-08 -0.030357952 -4509.8852 + 8100 9.5625542e-09 -0.025706075 -4509.8852 + 8200 4.6410355e-09 -0.02054295 -4509.8853 + 8300 3.2795872e-09 -0.015185677 -4509.8853 + 8400 5.509246e-09 -0.011181309 -4509.8853 + 8500 9.2654236e-09 -0.010336847 -4509.8852 + 8600 1.5169111e-08 -0.013152226 -4509.8852 + 8700 2.1124719e-08 -0.018237266 -4509.8852 + 8800 2.5607376e-08 -0.023635507 -4509.8852 + 8900 2.7829768e-08 -0.028664368 -4509.8853 + 9000 2.7490864e-08 -0.033752079 -4509.8853 + 9100 2.4629425e-08 -0.038717883 -4509.8852 + 9200 1.9856317e-08 -0.042074213 -4509.8851 + 9300 1.5754223e-08 -0.042397751 -4509.8851 + 9400 1.4158011e-08 -0.039645985 -4509.8851 + 9500 1.293562e-08 -0.034905375 -4509.8852 + 9600 1.0925115e-08 -0.029498287 -4509.8852 + 9700 8.2117111e-09 -0.024274276 -4509.8853 + 9800 4.2073503e-09 -0.019498803 -4509.8853 + 9900 3.6200071e-09 -0.015198764 -4509.8853 + 10000 7.3205984e-09 -0.011878546 -4509.8852 + 10100 1.2327605e-08 -0.010695702 -4509.8852 + 10200 1.7930358e-08 -0.012691556 -4509.8852 + 10300 2.4534101e-08 -0.017839785 -4509.8852 + 10400 2.8574489e-08 -0.024561434 -4509.8852 + 10500 2.944535e-08 -0.030655475 -4509.8852 + 10600 2.7962098e-08 -0.034958095 -4509.8852 + 10700 2.3119076e-08 -0.037998711 -4509.8852 + 10800 1.684499e-08 -0.040493081 -4509.8852 + 10900 1.2305474e-08 -0.041691151 -4509.8851 + 11000 1.1330272e-08 -0.040137729 -4509.8851 +Loop time of 371.175 on 4 procs for 10000 steps with 2304 atoms + +Pair time (%) = 66.4286 (17.8968) +Neigh time (%) = 31.4239 (8.46606) +Comm time (%) = 117.354 (31.617) +Outpt time (%) = 0.685033 (0.184558) +Other time (%) = 155.283 (41.8355) + +Nlocal: 576 ave 864 max 288 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5170 ave 6910 max 3430 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 178632 ave 289296 max 68184 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 357264 ave 577008 max 137520 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1429056 +Ave neighs/atom = 620.25 +Neighbor list builds = 1000 +Dangerous builds = 0 diff --git a/examples/USER/atc/elastic/bar1d_frac_step.screen b/examples/USER/atc/elastic/bar1d_frac_step.screen new file mode 100644 index 0000000000..f84c6d0f97 --- /dev/null +++ b/examples/USER/atc/elastic/bar1d_frac_step.screen @@ -0,0 +1,225 @@ +LAMMPS (14 Aug 2013) + +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +lattice fcc 5.2582305 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.25823 5.25823 5.25823 + +# create atoms +region simRegion block -12 12 -3 3 -3 3 +region atomRegion block -8 8 -3 3 -3 3 +region mdRegion block -6 6 -3 3 -3 3 +boundary f p p +create_box 1 simRegion +Created orthogonal box = (-63.0988 -15.7747 -15.7747) to (63.0988 15.7747 15.7747) + 4 by 1 by 1 MPI processor grid +create_atoms 1 region atomRegion +Created 2304 atoms +mass 1 39.95 + +# specify interal/ghost atoms +region mdInternal block -6 6 -3 3 -3 3 +region leftghost block -8 -6 -3 3 -3 3 +region rightghost block 6 8 -3 3 -3 3 +group internal region mdInternal +1728 atoms in group internal +group Lghost region leftghost +288 atoms in group Lghost +group Rghost region rightghost +288 atoms in group Rghost +group ghosts union Lghost Rghost +576 atoms in group ghosts + +pair_style lj/cut 13. +#pair_coeff 1 1 0.010323166 3.405 13.5 +pair_coeff 1 1 .2381 3.405 13. + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# define layer +# ID group atc PhysicsType ParameterFile +fix AtC internal atc elastic Ar_elastic.mat +ATC: constructing elastic coupling with parameter file Ar_elastic.mat + ATC: peratom PE compute created with ID: 3 + ATC: computed mass density : 1.09915 + ATC: computed mass density : 1.09915 + ATC: computed mass density : 1.09915 + ATC: 3 materials defined from Ar_elastic.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p + ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements + +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 +fix_modify AtC time_integration fractional_step + +# set node sets and bcs +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF + ATC: created nodeset lbc with 1 nodes +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF + ATC: created nodeset rbc with 1 nodes +fix_modify AtC fix velocity x rbc 0.00000004 +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix velocity x lbc 0. + +# specify atom types +#fix_modify AtC boundary Lghost +#fix_modify AtC boundary Rghost +fix_modify AtC boundary ghosts + +fix_modify AtC internal_quadrature off +fix_modify AtC control localized_lambda on +fix_modify AtC control momentum flux interpolate +#fix_modify AtC control momentum hoover # tested in this mode +#fix_modify AtC filter type exponential +#fix_modify AtC filter scale 1000.0 +#fix_modify AtC filter on + +# run to extension +#fix_modify AtC output bar1d_frac_step_initFE 50 text binary +#dump D1 all atom 50 bar1d_frac_step_init.dmp +timestep 5 +thermo 100 +run 1000 +Setting up run ... +Memory usage per processor = 92.6375 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -4509.8851 0 -4509.8851 26.948349 + 100 4.7374019e-13 -4509.8851 0 -4509.8851 26.94834 + 200 9.7683427e-13 -4509.8851 0 -4509.8851 26.94803 + 300 1.9565172e-11 -4509.8851 0 -4509.8851 26.946439 + 400 2.6411547e-10 -4509.8852 0 -4509.8852 26.942798 + 500 1.351766e-09 -4509.8852 0 -4509.8852 26.93773 + 600 3.6802148e-09 -4509.8852 0 -4509.8852 26.932648 + 700 6.6530697e-09 -4509.8852 0 -4509.8852 26.928033 + 800 9.5474556e-09 -4509.8852 0 -4509.8852 26.923147 + 900 1.2412323e-08 -4509.8852 0 -4509.8852 26.917542 + 1000 1.5423223e-08 -4509.8852 0 -4509.8852 26.911973 +Loop time of 69.3748 on 4 procs for 1000 steps with 2304 atoms + +Pair time (%) = 8.07954 (11.6462) +Neigh time (%) = 4.407 (6.35245) +Comm time (%) = 22.0263 (31.7496) +Outpt time (%) = 0.19482 (0.280822) +Other time (%) = 34.6672 (49.9709) + +Nlocal: 576 ave 864 max 288 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5170 ave 6910 max 3430 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 178632 ave 288910 max 68513 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 357264 ave 577008 max 137520 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1429056 +Ave neighs/atom = 620.25 +Neighbor list builds = 100 +Dangerous builds = 0 + +# reset time +fix_modify AtC reset_time 0. +reset_timestep 0 + +# change nodes to fixed +fix_modify AtC fix velocity x rbc 0. +fix_modify AtC fix displacement x rbc 0.0002 + +fix_modify AtC output bar1d_frac_stepFE 500 text #binary + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +#fix_modify AtC output index step +#undump D1 +#dump D1 all atom 500 bar1d_frac_step.dmp + +# run to equilibrium +timestep 5 +thermo 100 +run 5000 +Setting up run ... +Memory usage per processor = 92.6375 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5423223e-08 -4509.8852 0 -4509.8852 26.911973 + 100 1.809994e-08 -4509.8852 0 -4509.8852 26.907429 + 200 1.9777109e-08 -4509.8852 0 -4509.8852 26.904241 + 300 2.0275205e-08 -4509.8852 0 -4509.8852 26.902912 + 400 1.9266773e-08 -4509.8852 0 -4509.8852 26.904281 + 500 1.6821974e-08 -4509.8851 0 -4509.8851 26.908126 + 600 1.370661e-08 -4509.8852 0 -4509.8852 26.912761 + 700 1.0292223e-08 -4509.8852 0 -4509.8852 26.916838 + 800 6.5498338e-09 -4509.8853 0 -4509.8853 26.920715 + 900 3.1643856e-09 -4509.8853 0 -4509.8853 26.925094 + 1000 1.0112513e-09 -4509.8852 0 -4509.8852 26.928958 + 1100 4.4564547e-10 -4509.8852 0 -4509.8852 26.930177 + 1200 2.264627e-09 -4509.8852 0 -4509.8852 26.92803 + 1300 6.3325706e-09 -4509.8853 0 -4509.8853 26.923952 + 1400 1.1281983e-08 -4509.8853 0 -4509.8853 26.919616 + 1500 1.5582979e-08 -4509.8852 0 -4509.8852 26.915411 + 1600 1.8378446e-08 -4509.8852 0 -4509.8852 26.911278 + 1700 1.9544417e-08 -4509.8852 0 -4509.8852 26.907886 + 1800 1.993739e-08 -4509.8851 0 -4509.8851 26.905965 + 1900 1.9956722e-08 -4509.8851 0 -4509.8851 26.905229 + 2000 1.9225238e-08 -4509.8852 0 -4509.8852 26.905144 + 2100 1.6580757e-08 -4509.8853 0 -4509.8853 26.906419 + 2200 1.2058028e-08 -4509.8853 0 -4509.8853 26.910376 + 2300 7.4549951e-09 -4509.8852 0 -4509.8852 26.916716 + 2400 4.0264612e-09 -4509.8852 0 -4509.8852 26.923054 + 2500 1.8321195e-09 -4509.8852 0 -4509.8852 26.92718 + 2600 5.8894583e-10 -4509.8852 0 -4509.8852 26.92887 + 2700 1.1822868e-09 -4509.8853 0 -4509.8853 26.928935 + 2800 4.1199827e-09 -4509.8853 0 -4509.8853 26.927485 + 2900 8.3401571e-09 -4509.8853 0 -4509.8853 26.924202 + 3000 1.2795486e-08 -4509.8852 0 -4509.8852 26.91968 + 3100 1.656454e-08 -4509.8852 0 -4509.8852 26.915184 + 3200 1.8809835e-08 -4509.8852 0 -4509.8852 26.911167 + 3300 1.9524689e-08 -4509.8852 0 -4509.8852 26.907277 + 3400 1.9239653e-08 -4509.8852 0 -4509.8852 26.904028 + 3500 1.8306513e-08 -4509.8852 0 -4509.8852 26.903155 + 3600 1.6715381e-08 -4509.8852 0 -4509.8852 26.905573 + 3700 1.4633381e-08 -4509.8851 0 -4509.8851 26.909896 + 3800 1.1933216e-08 -4509.8851 0 -4509.8851 26.913983 + 3900 8.1608505e-09 -4509.8852 0 -4509.8852 26.917338 + 4000 4.081711e-09 -4509.8853 0 -4509.8853 26.920926 + 4100 1.5631282e-09 -4509.8853 0 -4509.8853 26.924958 + 4200 1.2262219e-09 -4509.8853 0 -4509.8853 26.928167 + 4300 2.985009e-09 -4509.8852 0 -4509.8852 26.929352 + 4400 6.8933386e-09 -4509.8852 0 -4509.8852 26.928435 + 4500 1.1278724e-08 -4509.8852 0 -4509.8852 26.925624 + 4600 1.4438096e-08 -4509.8852 0 -4509.8852 26.920742 + 4700 1.6779441e-08 -4509.8852 0 -4509.8852 26.914294 + 4800 1.8690218e-08 -4509.8853 0 -4509.8853 26.908349 + 4900 1.9317873e-08 -4509.8852 0 -4509.8852 26.905059 + 5000 1.8273072e-08 -4509.8851 0 -4509.8851 26.904542 +Loop time of 207.618 on 4 procs for 5000 steps with 2304 atoms + +Pair time (%) = 33.494 (16.1325) +Neigh time (%) = 16.7803 (8.08228) +Comm time (%) = 59.1908 (28.5094) +Outpt time (%) = 0.143787 (0.0692554) +Other time (%) = 98.0096 (47.2066) + +Nlocal: 576 ave 864 max 288 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5170 ave 6910 max 3430 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 178632 ave 288845 max 67924 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 357264 ave 577008 max 137520 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1429056 +Ave neighs/atom = 620.25 +Neighbor list builds = 500 +Dangerous builds = 0 diff --git a/examples/USER/atc/elastic/bar1d_ghost_flux.screen b/examples/USER/atc/elastic/bar1d_ghost_flux.screen new file mode 100644 index 0000000000..0b3f5cac60 --- /dev/null +++ b/examples/USER/atc/elastic/bar1d_ghost_flux.screen @@ -0,0 +1,208 @@ +LAMMPS (14 Aug 2013) + +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +lattice fcc 5.2582305 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.25823 5.25823 5.25823 + +region simRegion block -12 12 -3 3 -3 3 +region mdRegion block -8 8 -3 3 -3 3 +boundary f p p +create_box 1 simRegion +Created orthogonal box = (-63.0988 -15.7747 -15.7747) to (63.0988 15.7747 15.7747) + 4 by 1 by 1 MPI processor grid +create_atoms 1 region mdRegion +Created 2304 atoms +mass 1 39.95 + +# specify interal/ghost atoms +region mdInternal block -6 6 -3 3 -3 3 +region leftghost block -8 -6 -3 3 -3 3 +region rightghost block 6 8 -3 3 -3 3 +group internal region mdInternal +1728 atoms in group internal +group Lghost region leftghost +288 atoms in group Lghost +group Rghost region rightghost +288 atoms in group Rghost +group ghosts union Lghost Rghost +576 atoms in group ghosts + +# velocities have Vcm = 0, NOTE next for lines commented out for restart +pair_style lj/cut 13. +#pair_coeff 1 1 0.010323166 3.405 13. +pair_coeff 1 1 .2381 3.405 13. + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# define layer +# ID group atc PhysicsType ParameterFile +fix AtC internal atc elastic Ar_elastic.mat +ATC: constructing elastic coupling with parameter file Ar_elastic.mat + ATC: peratom PE compute created with ID: 3 + ATC: computed mass density : 1.09915 + ATC: computed mass density : 1.09915 + ATC: computed mass density : 1.09915 + ATC: 3 materials defined from Ar_elastic.mat +fix_modify AtC boundary ghosts + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p + ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements +fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward + ATC: created faceset obndy with 2 faces +fix_modify AtC internal_quadrature off + +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC fix displacement y all 0.0 +fix_modify AtC fix displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC fix velocity y all 0.0 +fix_modify AtC fix velocity z all 0.0 + +# set node sets and bcs +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF + ATC: created nodeset lbc with 1 nodes +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF + ATC: created nodeset rbc with 1 nodes +#fix_modify AtC fix velocity x rbc 0. +#fix_modify AtC fix displacement x rbc 0. +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix velocity x lbc 0. + +# turn on multiscale +fix_modify AtC control momentum ghost_flux + +# new boundary conditions +fix_modify AtC fix velocity x rbc 0.00000004 + + +#fix_modify AtC output follow_ex.fe 50 +#fix_modify AtC localized_lambda on +#fix_modify AtC momentum control glc_velocity +#fix_modify AtC momentum control flux faceset obndy +#fix_modify AtC control momentum flux +#fix_modify AtC control momentum ghost_flux +#fix_modify AtC filter scale 1000.0 + +# run to extension +compute myTemp internal temp +compute atomStress internal stress/atom +compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3] +variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol) +thermo_style custom step c_myTemp v_myPres pe +fix_modify AtC output bar1d_ghost_fluxFE 500 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +#dump D1 all atom 100 bar1d_ghost_flux.dmp +timestep 5 +thermo 100 +run 1000 +Setting up run ... +Memory usage per processor = 93.0953 Mbytes +Step myTemp myPres PotEng + 0 0 -0.00072339042 -4509.8851 + 100 7.1225566e-14 -0.00069609188 -4509.8851 + 200 3.7853133e-13 -0.00065829543 -4509.8851 + 300 1.6363911e-11 -0.00093014878 -4509.8851 + 400 2.6679578e-10 -0.0022162027 -4509.8852 + 500 1.616056e-09 -0.0053039586 -4509.8852 + 600 5.0333459e-09 -0.010270696 -4509.8852 + 700 9.7370581e-09 -0.016093983 -4509.8852 + 800 1.3809125e-08 -0.021486202 -4509.8852 + 900 1.6783957e-08 -0.026147268 -4509.8852 + 1000 1.9615527e-08 -0.030744945 -4509.8852 +Loop time of 61.3722 on 4 procs for 1000 steps with 2304 atoms + +Pair time (%) = 8.47621 (13.8112) +Neigh time (%) = 4.57113 (7.44821) +Comm time (%) = 21.3849 (34.8445) +Outpt time (%) = 0.0678592 (0.11057) +Other time (%) = 26.8721 (43.7855) + +Nlocal: 576 ave 864 max 288 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5170 ave 6910 max 3430 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 178632 ave 288581 max 68542 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 357264 ave 577008 max 137520 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1429056 +Ave neighs/atom = 620.25 +Neighbor list builds = 100 +Dangerous builds = 0 + +# change nodes to fixed +fix_modify AtC unfix velocity x rbc +#fix_modify AtC fix displacement x rbc 0.0002 + +#fix_modify AtC output bar1d_fluxFE 500 text binary + +# run to equilibrium +timestep 5 +thermo 100 +run 3000 +Setting up run ... +Memory usage per processor = 93.5532 Mbytes +Step myTemp myPres PotEng + 1000 1.9615527e-08 -0.030744945 -4509.8852 + 1100 2.3080841e-08 -0.035570103 -4509.8852 + 1200 2.6803382e-08 -0.039749355 -4509.8852 + 1300 2.8836885e-08 -0.041881649 -4509.8852 + 1400 2.7038886e-08 -0.04118176 -4509.8852 + 1500 2.247439e-08 -0.037776265 -4509.8852 + 1600 1.8021787e-08 -0.032491325 -4509.8852 + 1700 1.4774855e-08 -0.026754505 -4509.8852 + 1800 1.2061023e-08 -0.022034601 -4509.8852 + 1900 8.5768539e-09 -0.018709001 -4509.8852 + 2000 3.6373058e-09 -0.016114748 -4509.8852 + 2100 5.3669536e-10 -0.014163462 -4509.8853 + 2200 3.2454928e-09 -0.014205399 -4509.8853 + 2300 1.030702e-08 -0.017492992 -4509.8853 + 2400 1.6038797e-08 -0.023210717 -4509.8852 + 2500 1.7061988e-08 -0.029013462 -4509.8851 + 2600 1.9296258e-08 -0.03339452 -4509.8852 + 2700 2.2816944e-08 -0.036626152 -4509.8852 + 2800 2.6944075e-08 -0.039307649 -4509.8852 + 2900 2.8170813e-08 -0.040972921 -4509.8852 + 3000 2.7256286e-08 -0.040327211 -4509.8852 + 3100 2.445985e-08 -0.036617618 -4509.8852 + 3200 1.8787648e-08 -0.03049195 -4509.8852 + 3300 1.4750104e-08 -0.023629006 -4509.8852 + 3400 1.3515772e-08 -0.017473229 -4509.8852 + 3500 1.157919e-08 -0.012114855 -4509.8851 + 3600 9.6213234e-09 -0.0064144434 -4509.8851 + 3700 9.1781574e-09 0.00062376196 -4509.8851 + 3800 9.0938842e-09 0.0087100206 -4509.885 + 3900 7.7454581e-09 0.016669158 -4509.885 + 4000 9.3314606e-09 0.023405906 -4509.885 +Loop time of 109.051 on 4 procs for 3000 steps with 2304 atoms + +Pair time (%) = 20.2492 (18.5685) +Neigh time (%) = 9.8419 (9.02501) +Comm time (%) = 37.2858 (34.191) +Outpt time (%) = 0.421606 (0.386612) +Other time (%) = 41.2529 (37.8289) + +Nlocal: 576 ave 864 max 288 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5170 ave 6910 max 3430 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 178632 ave 288933 max 68141 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 357264 ave 577008 max 137520 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1429056 +Ave neighs/atom = 620.25 +Neighbor list builds = 300 +Dangerous builds = 0 diff --git a/examples/USER/atc/elastic/bar1d_thermo_elastic.screen b/examples/USER/atc/elastic/bar1d_thermo_elastic.screen new file mode 100644 index 0000000000..23e6d6ba2c --- /dev/null +++ b/examples/USER/atc/elastic/bar1d_thermo_elastic.screen @@ -0,0 +1,112 @@ +LAMMPS (14 Aug 2013) + +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +lattice fcc 5.2582305 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.25823 5.25823 5.25823 + +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13. +read_data temp.init +Reading data file ... + orthogonal box = (-47.3241 -15.7747 -15.7747) to (47.3241 15.7747 15.7747) + 4 by 1 by 1 MPI processor grid + 2304 atoms + 2304 velocities +region simRegion block -12 12 -3 3 -3 3 +# create atoms, NOTE commented out for restart +#region mdRegion block -8 8 -3 3 -3 3 +#boundary f p p +#region mdBox block -9 9 -3 3 -3 3 +#create_box 1 mdBox +#create_atoms 1 region mdRegion +#mass 1 39.95 + +# specify interal/ghost atoms +region mdInternal block -6 6 -3 3 -3 3 +region leftghost block -8 -6 -3 3 -3 3 +region rightghost block 6 8 -3 3 -3 3 +group internal region mdInternal +1728 atoms in group internal +group Lghost region leftghost +288 atoms in group Lghost +group Rghost region rightghost +288 atoms in group Rghost +group ghosts union Lghost Rghost +576 atoms in group ghosts + +# velocities have Vcm = 0, NOTE next for lines commented out for restart +#velocity internal create 40. 87287 mom yes loop geom +#pair_style lj/cut 13. +##pair_coeff 1 1 0.010323166 3.405 13. +#pair_coeff 1 1 .2381 3.405 13. + +neighbor 5. bin +neigh_modify every 10 delay 0 check no +#write_restart tinit.dat + +# zero initial momentum +fix AtC internal atc elastic Ar_thermo_elastic.mat +ATC: constructing elastic coupling with parameter file Ar_thermo_elastic.mat + ATC: peratom PE compute created with ID: 3 + ATC: computed mass density : 1.09915 + ATC: 1 materials defined from Ar_thermo_elastic.mat +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p + ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements +fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward + ATC: created faceset obndy with 2 faces +fix_modify AtC internal_quadrature off +fix_modify AtC fix displacement x all 0. +fix_modify AtC fix displacement y all 0. +fix_modify AtC fix displacement z all 0. +fix_modify AtC fix velocity x all 0. +fix_modify AtC fix velocity y all 0. +fix_modify AtC fix velocity z all 0. +fix_modify AtC control momentum glc_velocity +#fix_modify AtC output bar1d_thermo_elastic_initializeFE 1 text #binary +timestep 0 +thermo 1 +run 1 +Setting up run ... +Memory usage per processor = 56.6533 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 29.995658 -4509.8851 0 -4303.9707 135.84496 + 1 29.920966 -4509.8851 0 -4304.4835 135.59617 +Loop time of 0.161032 on 4 procs for 1 steps with 2304 atoms + +Pair time (%) = 0.013374 (8.3052) +Neigh time (%) = 0 (0) +Comm time (%) = 0.00626355 (3.88963) +Outpt time (%) = 0.027244 (16.9184) +Other time (%) = 0.11415 (70.8868) + +Nlocal: 576 ave 648 max 504 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5677 ave 7126 max 4228 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 178632 ave 218376 max 138456 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 357264 ave 436752 max 277776 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1429056 +Ave neighs/atom = 620.25 +Neighbor list builds = 0 +Dangerous builds = 0 +unfix AtC + +# define layer +# ID group atc PhysicsType ParameterFile +fix AtC internal atc thermo_elastic Ar_thermo_elastic.mat +ATC: constructing thermo-mechanical coupling with parameter file Ar_thermo_elastic.mat + ATC: peratom PE compute created with ID: 3 + ATC: computed mass density : 1.09915 + ATC: 1 materials defined from Ar_thermo_elastic.mat + ATC: peratom PE compute created with ID: 3 +fix_modify AtC boundary ghosts +ERROR: Illegal fix_modify command (../fix.cpp:104) diff --git a/examples/USER/atc/elastic/cnt_electrostatic.screen b/examples/USER/atc/elastic/cnt_electrostatic.screen new file mode 100644 index 0000000000..6171d59f68 --- /dev/null +++ b/examples/USER/atc/elastic/cnt_electrostatic.screen @@ -0,0 +1,1212 @@ +LAMMPS (14 Aug 2013) +units metal +atom_style atomic + +lattice diamond 3.6 +Lattice spacing in x,y,z = 3.6 3.6 3.6 +pair_style tersoff +boundary s s f + +read_data tube_8_4.data +Reading data file ... + orthogonal box = (-4.34588 -4.34588 0) to (4.34588 4.34588 104.296) + 1 by 1 by 4 MPI processor grid + 1008 atoms + 1008 velocities + +# PARAMETERS----------------------------- +variable L equal zhi-zlo +variable R equal 12.1/2 +variable xhiFE equal 5.0*$R +variable xhiFE equal 5.0*6.0499999999999998224 +variable xloFE equal -${xhiFE} +variable xloFE equal -30.25 +variable yhiFE equal $R +variable yhiFE equal 6.0499999999999998224 +variable yloFE equal -${xhiFE} +variable yloFE equal -30.25 +variable zhiFE equal zhi +variable zloFE equal zlo+10 +print "Length $L [${zloFE}, ${zhiFE}]" +Length 104.29551668000000575 [10, 104.29551668000000575] + +variable E equal 10.0 +print "Electric field $E" +Electric field 10 +variable drhodx equal 0.0001 +variable s equal 50 +# END ----------------------------------- + +#pair_coeff * * SiC.tersoff C +pair_coeff * * ../../../../potentials/SiC.tersoff C +mass * 12.01 + +# all atoms simulation +region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 -30.25 ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 -30.25 6.0499999999999998224 ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 -30.25 6.0499999999999998224 10 ${zhiFE} units box +region feRegion block -30.25 30.25 -30.25 6.0499999999999998224 10 104.29551668000000575 units box +group internal region feRegion +908 atoms in group internal + +variable nAll equal count(all) +variable nGhost equal count(all)-count(internal) +print ">>> number of stationary ghosts: ${nGhost} of ${nAll}" +>>> number of stationary ghosts: 100 of 1008 + +neighbor 5. bin +neigh_modify every 10 delay 0 check no +timestep 0.0005 + +# coupling +fix AtC internal atc electrostatic CNT_electrostatic.mat +ATC: constructing electrostatic mechanical coupling with parameter file CNT_electrostatic.mat + ATC: peratom PE compute created with ID: 3 + ATC: computed mass density : 2.05933 + ATC: 1 materials defined from CNT_electrostatic.mat + ATC: creating electrostatic extrinsic model + ATC: computed mass density : 2.05933 + ATC: 1 materials defined from CNT_electrostatic.mat + ATC: computed mass density : 2.05933 + ATC: 1 materials defined from CNT_electrostatic.mat +fix_modify AtC internal_quadrature off +fix_modify AtC omit atomic_charge +fix_modify AtC mesh create 5 1 12 feRegion f p f + ATC: created uniform mesh with 156 nodes, 78 unique nodes, and 60 elements + +# initial & boundary conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 +fix_modify AtC initial electric_potential all 0.0 + +variable a equal -$R-0.1 +variable a equal -6.0499999999999998224-0.1 +variable b equal $R+0.1 +variable b equal 6.0499999999999998224+0.1 +fix_modify AtC mesh create_nodeset tube $a $b $a $b ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset tube -6.1499999999999994671 $b $a $b ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset tube -6.1499999999999994671 6.1499999999999994671 $a $b ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset tube -6.1499999999999994671 6.1499999999999994671 -6.1499999999999994671 $b ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset tube -6.1499999999999994671 6.1499999999999994671 -6.1499999999999994671 6.1499999999999994671 ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset tube -6.1499999999999994671 6.1499999999999994671 -6.1499999999999994671 6.1499999999999994671 10 ${zhiFE} units box +fix_modify AtC mesh create_nodeset tube -6.1499999999999994671 6.1499999999999994671 -6.1499999999999994671 6.1499999999999994671 10 104.29551668000000575 units box + ATC: created nodeset tube with 26 nodes +variable a equal ${zloFE}-0.1 +variable a equal 10-0.1 +variable b equal ${zloFE}+0.1 +variable b equal 10+0.1 +fix_modify AtC mesh create_nodeset lbc ${xloFE} ${xhiFE} ${xloFE} ${xhiFE} $a $b units box +fix_modify AtC mesh create_nodeset lbc -30.25 ${xhiFE} ${xloFE} ${xhiFE} $a $b units box +fix_modify AtC mesh create_nodeset lbc -30.25 30.25 ${xloFE} ${xhiFE} $a $b units box +fix_modify AtC mesh create_nodeset lbc -30.25 30.25 -30.25 ${xhiFE} $a $b units box +fix_modify AtC mesh create_nodeset lbc -30.25 30.25 -30.25 30.25 $a $b units box +fix_modify AtC mesh create_nodeset lbc -30.25 30.25 -30.25 30.25 9.9000000000000003553 $b units box +fix_modify AtC mesh create_nodeset lbc -30.25 30.25 -30.25 30.25 9.9000000000000003553 10.099999999999999645 units box + ATC: created nodeset lbc with 6 nodes +variable a equal ${xhiFE}-0.1 +variable a equal 30.25-0.1 +variable b equal ${xhiFE}+0.1 +variable b equal 30.25+0.1 +fix_modify AtC mesh create_nodeset top $a $b ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset top 30.149999999999998579 $b ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset top 30.149999999999998579 30.350000000000001421 ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset top 30.149999999999998579 30.350000000000001421 -30.25 ${yhiFE} ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset top 30.149999999999998579 30.350000000000001421 -30.25 6.0499999999999998224 ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset top 30.149999999999998579 30.350000000000001421 -30.25 6.0499999999999998224 10 ${zhiFE} units box +fix_modify AtC mesh create_nodeset top 30.149999999999998579 30.350000000000001421 -30.25 6.0499999999999998224 10 104.29551668000000575 units box + ATC: created nodeset top with 13 nodes +variable a equal ${xloFE}-0.1 +variable a equal -30.25-0.1 +variable b equal ${xloFE}+0.1 +variable b equal -30.25+0.1 +fix_modify AtC mesh create_nodeset bot $a $b ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset bot -30.350000000000001421 $b ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset bot -30.350000000000001421 -30.149999999999998579 ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset bot -30.350000000000001421 -30.149999999999998579 -30.25 ${yhiFE} ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset bot -30.350000000000001421 -30.149999999999998579 -30.25 6.0499999999999998224 ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset bot -30.350000000000001421 -30.149999999999998579 -30.25 6.0499999999999998224 10 ${zhiFE} units box +fix_modify AtC mesh create_nodeset bot -30.350000000000001421 -30.149999999999998579 -30.25 6.0499999999999998224 10 104.29551668000000575 units box + ATC: created nodeset bot with 13 nodes + +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix displacement y lbc 0. +fix_modify AtC fix displacement z lbc 0. +fix_modify AtC fix velocity x lbc 0. +fix_modify AtC fix velocity y lbc 0. +fix_modify AtC fix velocity z lbc 0. +fix_modify AtC fix electron_density all 0.0 +#fix_modify AtC fix electron_density tube 0.2 +fix_modify AtC fix electron_density tube linear 0 0 0 0 0 ${drhodx} 0 +fix_modify AtC fix electron_density tube linear 0 0 0 0 0 0.00010000000000000000479 0 + ATC: created function : 0 + 0(x-0)+0(y-0)+0.0001(z-0) +fix_modify AtC fix electric_potential all linear 0 0 0 $E 0 0 0 0 +fix_modify AtC fix electric_potential all linear 0 0 0 10 0 0 0 0 + ATC: created function : 0 + 10(x-0)+0(y-0)+0(z-0) + +fix_modify AtC control momentum flux + +# run +thermo_style custom step cpu etotal ke +thermo 1#$s +fix_modify AtC output cnt_electrostaticFE $s full_text +fix_modify AtC output cnt_electrostaticFE 50 full_text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +fix_modify AtC output index step +# NOTE not recognized as vector by paraview +variable uX atom x-f_AtC[1] +variable uY atom y-f_AtC[2] +variable uZ atom z-f_AtC[3] +variable rho atom mass*f_AtC[4] +dump CONFIG all custom $s cnt_electrostatic.dmp id type x y z v_uX v_uY v_uZ v_rho +dump CONFIG all custom 50 cnt_electrostatic.dmp id type x y z v_uX v_uY v_uZ v_rho +log cnt_electrostatic.log +#run 1000 + +# fixed charge, bc on potential +fix_modify AtC unfix electric_potential all +fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 0 0 +fix_modify AtC fix electric_potential lbc linear 0 0 0 10 0 0 0 0 + ATC: created function : 0 + 10(x-0)+0(y-0)+0(z-0) +fix_modify AtC fix electric_potential top linear 0 0 0 $E 0 0 0 0 +fix_modify AtC fix electric_potential top linear 0 0 0 10 0 0 0 0 + ATC: created function : 0 + 10(x-0)+0(y-0)+0(z-0) +fix_modify AtC fix electric_potential bot linear 0 0 0 $E 0 0 0 0 +fix_modify AtC fix electric_potential bot linear 0 0 0 10 0 0 0 0 + ATC: created function : 0 + 10(x-0)+0(y-0)+0(z-0) +run 1000 +Setting up run ... + ATC: WARNING: material: [cnt] cannot find electron_flux + ATC: WARNING: physics model: [electrostatic], material: [cnt] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 53.947 Mbytes +Step CPU TotEng KinEng + 0 0 -7315.3918 4.2386027e-06 + 1 0.31967092 -7315.3918 8.3975109e-06 + 2 0.57961583 -7315.3918 1.4120368e-05 + 3 0.73119783 -7315.3918 2.1378868e-05 + 4 0.77118993 -7315.3918 3.0172501e-05 + 5 0.81124997 -7315.3918 4.0500585e-05 + 6 0.85121584 -7315.3918 5.2362272e-05 + 7 0.89118791 -7315.3918 6.5756548e-05 + 8 0.93097782 -7315.3918 8.0682245e-05 + 9 0.97063279 -7315.3918 9.713804e-05 + 10 1.0182109 -7315.3918 0.00011512246 + 11 1.0585999 -7315.3918 0.00013463391 + 12 1.0980539 -7315.3918 0.00015567063 + 13 1.13748 -7315.3918 0.00017823074 + 14 1.177192 -7315.3918 0.00020231225 + 15 1.2165098 -7315.3918 0.00022791303 + 16 1.2559309 -7315.3918 0.00025503085 + 17 1.2955098 -7315.3918 0.00028366338 + 18 1.334971 -7315.3918 0.00031380817 + 19 1.3744769 -7315.3918 0.0003454627 + 20 1.4319949 -7315.3918 0.00037862437 + 21 1.4716878 -7315.3918 0.0004132905 + 22 1.5113468 -7315.3918 0.00044945835 + 23 1.67961 -7315.3918 0.00048712513 + 24 1.718936 -7315.3918 0.00052628798 + 25 1.75843 -7315.3918 0.00056694404 + 26 1.7989509 -7315.3918 0.00060909036 + 27 1.930331 -7315.3918 0.00065272401 + 28 1.9778998 -7315.3918 0.00069784199 + 29 2.0358789 -7315.3917 0.00074444131 + 30 2.0961409 -7315.3917 0.00079251893 + 31 2.3385279 -7315.3917 0.00084207182 + 32 2.636704 -7315.3917 0.00089309691 + 33 2.714483 -7315.3917 0.00094559113 + 34 2.9397018 -7315.3917 0.00099955142 + 35 3.2066698 -7315.3917 0.0010549747 + 36 3.2912428 -7315.3917 0.0011118579 + 37 3.4499469 -7315.3917 0.0011701978 + 38 3.609957 -7315.3917 0.0012299916 + 39 3.694387 -7315.3917 0.001291236 + 40 3.774771 -7315.3917 0.001353928 + 41 3.814693 -7315.3917 0.0014180645 + 42 3.8544669 -7315.3917 0.0014836425 + 43 3.899441 -7315.3917 0.0015506588 + 44 3.9393668 -7315.3917 0.0016191104 + 45 4.1302609 -7315.3917 0.0016889941 + 46 4.2312019 -7315.3917 0.0017603069 + 47 4.3896489 -7315.3917 0.0018330457 + 48 4.4500258 -7315.3917 0.0019072073 + 49 4.5496428 -7315.3916 0.0019827887 + 50 5.0796728 -7315.3916 0.0020597866 + 51 5.3996999 -7315.3916 0.002138198 + 52 5.7496638 -7315.3916 0.0022180196 + 53 6.0696678 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0.21005832 + 864 89.165538 -7315.3598 0.21022108 + 865 89.184898 -7315.3597 0.21038301 + 866 89.204106 -7315.3597 0.21054411 + 867 89.251565 -7315.3596 0.21070436 + 868 89.290937 -7315.3595 0.21086378 + 869 89.330265 -7315.3595 0.21102234 + 870 89.377166 -7315.3594 0.21118007 + 871 89.414822 -7315.3594 0.21133694 + 872 89.434192 -7315.3593 0.21149296 + 873 89.453368 -7315.3593 0.21164813 + 874 89.472454 -7315.3592 0.21180245 + 875 89.491571 -7315.3591 0.2119559 + 876 89.510674 -7315.3591 0.2121085 + 877 89.529877 -7315.359 0.21226024 + 878 89.548996 -7315.359 0.21241111 + 879 89.568152 -7315.3589 0.21256112 + 880 89.595252 -7315.3588 0.21271026 + 881 89.6147 -7315.3588 0.21285853 + 882 89.633863 -7315.3587 0.21300594 + 883 89.65326 -7315.3587 0.21315246 + 884 89.672522 -7315.3586 0.21329812 + 885 89.69152 -7315.3586 0.2134429 + 886 89.71067 -7315.3585 0.2135868 + 887 89.729722 -7315.3584 0.21372982 + 888 89.749039 -7315.3584 0.21387196 + 889 89.768394 -7315.3583 0.21401322 + 890 89.796225 -7315.3583 0.21415359 + 891 89.815677 -7315.3582 0.21429308 + 892 89.834924 -7315.3581 0.21443167 + 893 89.854321 -7315.3581 0.21456938 + 894 89.873438 -7315.358 0.2147062 + 895 89.892655 -7315.358 0.21484212 + 896 89.911887 -7315.3579 0.21497714 + 897 89.931091 -7315.3579 0.21511127 + 898 89.950479 -7315.3578 0.2152445 + 899 89.969675 -7315.3577 0.21537683 + 900 90.01472 -7315.3577 0.21550825 + 901 90.034006 -7315.3576 0.21563876 + 902 90.053225 -7315.3576 0.21576837 + 903 90.072657 -7315.3575 0.21589707 + 904 90.09191 -7315.3574 0.21602485 + 905 90.111182 -7315.3574 0.21615172 + 906 90.130546 -7315.3573 0.21627767 + 907 90.149817 -7315.3573 0.2164027 + 908 90.169087 -7315.3572 0.21652681 + 909 90.188325 -7315.3572 0.21664999 + 910 90.215488 -7315.3571 0.21677224 + 911 90.234608 -7315.357 0.21689356 + 912 90.253716 -7315.357 0.21701394 + 913 90.272855 -7315.3569 0.21713339 + 914 90.292016 -7315.3569 0.21725189 + 915 90.311284 -7315.3568 0.21736946 + 916 90.330461 -7315.3567 0.21748607 + 917 90.349858 -7315.3567 0.21760173 + 918 90.369039 -7315.3566 0.21771644 + 919 90.388491 -7315.3566 0.21783019 + 920 90.415598 -7315.3565 0.21794298 + 921 90.434815 -7315.3564 0.2180548 + 922 90.453916 -7315.3564 0.21816566 + 923 90.473219 -7315.3563 0.21827554 + 924 90.492413 -7315.3563 0.21838445 + 925 90.511521 -7315.3562 0.21849238 + 926 90.530687 -7315.3561 0.21859933 + 927 90.549802 -7315.3561 0.21870529 + 928 90.568943 -7315.356 0.21881025 + 929 90.588114 -7315.356 0.21891423 + 930 90.615756 -7315.3559 0.2190172 + 931 90.635455 -7315.3558 0.21911918 + 932 90.654547 -7315.3558 0.21922015 + 933 90.673662 -7315.3557 0.21932011 + 934 90.692953 -7315.3557 0.21941906 + 935 90.722492 -7315.3556 0.21951699 + 936 90.761659 -7315.3556 0.2196139 + 937 90.800898 -7315.3555 0.21970979 + 938 90.842105 -7315.3554 0.21980465 + 939 90.871451 -7315.3554 0.21989848 + 940 90.907429 -7315.3553 0.21999128 + 941 90.926583 -7315.3553 0.22008304 + 942 90.945759 -7315.3552 0.22017376 + 943 90.964868 -7315.3551 0.22026344 + 944 90.984007 -7315.3551 0.22035207 + 945 91.003376 -7315.355 0.22043965 + 946 91.022951 -7315.355 0.22052618 + 947 91.042125 -7315.3549 0.22061165 + 948 91.061277 -7315.3548 0.22069606 + 949 91.080497 -7315.3548 0.22077941 + 950 91.125824 -7315.3547 0.2208617 + 951 91.14565 -7315.3547 0.22094292 + 952 91.164916 -7315.3546 0.22102306 + 953 91.184149 -7315.3545 0.22110214 + 954 91.203654 -7315.3545 0.22118014 + 955 91.222991 -7315.3544 0.22125706 + 956 91.242287 -7315.3544 0.2213329 + 957 91.261574 -7315.3543 0.22140765 + 958 91.280943 -7315.3542 0.22148132 + 959 91.300466 -7315.3542 0.22155391 + 960 91.327772 -7315.3541 0.2216254 + 961 91.347251 -7315.3541 0.2216958 + 962 91.366764 -7315.354 0.2217651 + 963 91.386025 -7315.3539 0.22183331 + 964 91.405696 -7315.3539 0.22190042 + 965 91.444902 -7315.3538 0.22196643 + 966 91.484422 -7315.3538 0.22203133 + 967 91.523745 -7315.3537 0.22209513 + 968 91.542982 -7315.3536 0.22215783 + 969 91.562239 -7315.3536 0.22221941 + 970 91.589686 -7315.3535 0.22227989 + 971 91.608996 -7315.3535 0.22233925 + 972 91.628347 -7315.3534 0.2223975 + 973 91.64762 -7315.3533 0.22245464 + 974 91.687025 -7315.3533 0.22251066 + 975 91.726483 -7315.3532 0.22256556 + 976 91.764825 -7315.3532 0.22261935 + 977 91.794284 -7315.3531 0.22267201 + 978 91.813812 -7315.353 0.22272356 + 979 91.833194 -7315.353 0.22277398 + 980 91.86054 -7315.3529 0.22282328 + 981 91.879813 -7315.3529 0.22287146 + 982 91.909218 -7315.3528 0.22291852 + 983 91.928486 -7315.3527 0.22296445 + 984 91.947786 -7315.3527 0.22300925 + 985 91.967084 -7315.3526 0.22305293 + 986 91.986393 -7315.3526 0.22309548 + 987 92.005611 -7315.3525 0.2231369 + 988 92.034917 -7315.3524 0.2231772 + 989 92.05426 -7315.3524 0.22321637 + 990 92.091415 -7315.3523 0.22325442 + 991 92.110668 -7315.3523 0.22329133 + 992 92.129978 -7315.3522 0.22332712 + 993 92.149484 -7315.3521 0.22336179 + 994 92.178741 -7315.3521 0.22339532 + 995 92.197915 -7315.352 0.22342773 + 996 92.227185 -7315.352 0.22345901 + 997 92.246618 -7315.3519 0.22348916 + 998 92.266071 -7315.3518 0.22351819 + 999 92.285487 -7315.3518 0.22354609 + 1000 92.330713 -7315.3517 0.22357286 +Loop time of 92.3283 on 4 procs for 1000 steps with 1008 atoms + +Pair time (%) = 4.14521 (4.48965) +Neigh time (%) = 0.636156 (0.689016) +Comm time (%) = 6.31341 (6.838) +Outpt time (%) = 10.2982 (11.1539) +Other time (%) = 70.9353 (76.8295) + +Nlocal: 252 ave 256 max 248 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 103 ave 140 max 68 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 15183 ave 15624 max 14492 min +Histogram: 1 0 0 0 1 0 0 0 0 2 + +Total # of neighbors = 60732 +Ave neighs/atom = 60.25 +Neighbor list builds = 100 +Dangerous builds = 0 diff --git a/examples/USER/atc/elastic/cnt_electrostatic2.screen b/examples/USER/atc/elastic/cnt_electrostatic2.screen new file mode 100644 index 0000000000..ff91703850 --- /dev/null +++ b/examples/USER/atc/elastic/cnt_electrostatic2.screen @@ -0,0 +1,214 @@ +LAMMPS (14 Aug 2013) +units metal +atom_style atomic + +lattice diamond 3.6 +Lattice spacing in x,y,z = 3.6 3.6 3.6 +boundary f f f + +#region box block -4.3458792459312239 4.3458792459312328 -4.3458792459312168 4.3458792459312203 0.0 104.29551668 units box +#region box block 0 10 0 10 0 10 +#create_box 1 box +#group box region box +#atom_modify sort 0 1 + +pair_style tersoff +read_data tube_8_4.data +Reading data file ... + orthogonal box = (-4.34588 -4.34588 0) to (4.34588 4.34588 104.296) + 1 by 1 by 4 MPI processor grid + 1008 atoms + 1008 velocities +pair_coeff * * ../../../../potentials/SiC.tersoff C +mass * 12.01 + +# PARAMETERS----------------------------- +variable L equal zhi-zlo +variable R equal 12.1/2 +variable xhiFE equal 5.0*$R +variable xhiFE equal 5.0*6.0499999999999998224 +variable xloFE equal -${xhiFE} +variable xloFE equal -30.25 +variable yhiFE equal $R +variable yhiFE equal 6.0499999999999998224 +variable yloFE equal -${xhiFE} +variable yloFE equal -30.25 +variable zhiFE equal zhi +variable zloFE equal zlo+10 +print "Length $L [${zloFE}, ${zhiFE}]" +Length 104.29551668000000575 [10, 104.29551668000000575] + +variable E equal 0.01 # 1.0 10.0 0.01 +variable V equal $E*${zloFE} +variable V equal 0.010000000000000000208*${zloFE} +variable V equal 0.010000000000000000208*10 +variable V equal 2 +print "Electric field $E ref.voltage $V" +Electric field 0.010000000000000000208 ref.voltage 2 +variable s equal 20 +# END ----------------------------------- + +# all atoms simulation +region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 -30.25 ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 -30.25 6.0499999999999998224 ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 -30.25 6.0499999999999998224 10 ${zhiFE} units box +region feRegion block -30.25 30.25 -30.25 6.0499999999999998224 10 104.29551668000000575 units box +group internal region feRegion +908 atoms in group internal + +variable nAll equal count(all) +variable nGhost equal count(all)-count(internal) +print ">>> number of stationary ghosts: ${nGhost} of ${nAll}" +>>> number of stationary ghosts: 100 of 1008 + +#neighbor 5. bin +#neigh_modify every 10 delay 0 check no +timestep 0.0005 + +# coupling +fix AtC internal atc electrostatic-equilibrium CNT_electrostatic2.mat +ATC: constructing equilibrium electrostatic coupling with parameter file CNT_electrostatic2.mat + ATC: peratom PE compute created with ID: 3 + ATC: computed mass density : 2.05933 + ATC: 1 materials defined from CNT_electrostatic2.mat + ATC: creating electrostatic extrinsic model + ATC: computed mass density : 2.05933 + ATC: 1 materials defined from CNT_electrostatic2.mat + ATC: computed mass density : 2.05933 + ATC: 1 materials defined from CNT_electrostatic2.mat +fix_modify AtC omit atomic_charge +#fix_modify AtC internal_quadrature off <<<< ??? +variable alat equal 1.42 +variable w equal ${alat}*${alat}*3.*sqrt(3.)/4.0 +variable w equal 1.4199999999999999289*${alat}*3.*sqrt(3.)/4.0 +variable w equal 1.4199999999999999289*1.4199999999999999289*3.*sqrt(3.)/4.0 +#variable w equal 10 +fix_modify AtC atom_weight constant internal $w +fix_modify AtC atom_weight constant internal 2.6193804362864128166 +fix_modify AtC source_integration atom +fix_modify AtC atom_element_map eulerian 1 +fix_modify AtC mesh create 5 1 12 feRegion f p f + ATC: created uniform mesh with 156 nodes, 78 unique nodes, and 60 elements +fix_modify AtC control momentum flux +#fix_modify AtC extrinsic poisson_solver max_iterations 5 + +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 + +#variable a equal -$R-0.1 +#variable b equal $R+0.1 +#fix_modify AtC mesh create_nodeset tube $a $b $a $b ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset lbc ${xloFE} ${xhiFE} ${xloFE} ${xhiFE} ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lbc -30.25 ${xhiFE} ${xloFE} ${xhiFE} ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lbc -30.25 30.25 ${xloFE} ${xhiFE} ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lbc -30.25 30.25 -30.25 ${xhiFE} ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lbc -30.25 30.25 -30.25 30.25 ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lbc -30.25 30.25 -30.25 30.25 10 ${zloFE} units box +fix_modify AtC mesh create_nodeset lbc -30.25 30.25 -30.25 30.25 10 10 units box + ATC: created nodeset lbc with 6 nodes +fix_modify AtC mesh create_nodeset rbc ${xloFE} ${xhiFE} ${xloFE} ${xhiFE} ${zhiFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset rbc -30.25 ${xhiFE} ${xloFE} ${xhiFE} ${zhiFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset rbc -30.25 30.25 ${xloFE} ${xhiFE} ${zhiFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset rbc -30.25 30.25 -30.25 ${xhiFE} ${zhiFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset rbc -30.25 30.25 -30.25 30.25 ${zhiFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset rbc -30.25 30.25 -30.25 30.25 104.29551668000000575 ${zhiFE} units box +fix_modify AtC mesh create_nodeset rbc -30.25 30.25 -30.25 30.25 104.29551668000000575 104.29551668000000575 units box + ATC: created nodeset rbc with 6 nodes +fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset bot -30.25 ${xloFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset bot -30.25 -30.25 ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset bot -30.25 -30.25 -30.25 ${yhiFE} ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset bot -30.25 -30.25 -30.25 6.0499999999999998224 ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset bot -30.25 -30.25 -30.25 6.0499999999999998224 10 ${zhiFE} units box +fix_modify AtC mesh create_nodeset bot -30.25 -30.25 -30.25 6.0499999999999998224 10 104.29551668000000575 units box + ATC: created nodeset bot with 13 nodes +fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset top 30.25 ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset top 30.25 30.25 ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset top 30.25 30.25 -30.25 ${yhiFE} ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset top 30.25 30.25 -30.25 6.0499999999999998224 ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset top 30.25 30.25 -30.25 6.0499999999999998224 10 ${zhiFE} units box +fix_modify AtC mesh create_nodeset top 30.25 30.25 -30.25 6.0499999999999998224 10 104.29551668000000575 units box + ATC: created nodeset top with 13 nodes + +# boundary conditions +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix displacement y lbc 0. +fix_modify AtC fix displacement z lbc 0. +fix_modify AtC fix velocity x lbc 0. +fix_modify AtC fix velocity y lbc 0. +fix_modify AtC fix velocity z lbc 0. +fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V +fix_modify AtC fix electric_potential lbc linear 0 0 0 0.010000000000000000208 0 0 $V +fix_modify AtC fix electric_potential lbc linear 0 0 0 0.010000000000000000208 0 0 2 + ATC: created function : 2 + 0.01(x-0)+0(y-0)+0(z-0) +#fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V +##fix_modify AtC fix electric_potential top linear 0 0 0 $E 0 0 $V +fix_modify AtC fix electric_potential bot linear 0 0 0 $E 0 0 $V +fix_modify AtC fix electric_potential bot linear 0 0 0 0.010000000000000000208 0 0 $V +fix_modify AtC fix electric_potential bot linear 0 0 0 0.010000000000000000208 0 0 2 + ATC: created function : 2 + 0.01(x-0)+0(y-0)+0(z-0) + +# run +thermo_style custom step cpu etotal ke +thermo $s +thermo 20 +fix_modify AtC output cnt_electrostatic2FE $s full_text # binary +fix_modify AtC output cnt_electrostatic2FE 20 full_text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +fix_modify AtC output index step +# NOTE not recognized as vector by paraview +variable uX atom x-f_AtC[1] +variable uY atom y-f_AtC[2] +variable uZ atom z-f_AtC[3] +variable rho atom mass*f_AtC[4] +dump CONFIG all custom $s cnt_electrostatic2.dmp id type x y z v_uX v_uY v_uZ v_rho +dump CONFIG all custom 20 cnt_electrostatic2.dmp id type x y z v_uX v_uY v_uZ v_rho +log cnt_electrostatic2.log + +#run $s +run 100 +Setting up run ... + ATC: WARNING: all initial conditions for electron_density have not been defined and the undefined are assumed zero + ATC: WARNING: all initial conditions for electric_potential have not been defined and the undefined are assumed zero +Memory usage per processor = 53.9593 Mbytes +Step CPU TotEng KinEng + 0 0 -7315.3918 4.2386027e-06 + 20 7.0248148 -7315.3918 0.0003453277 + 40 8.5434699 -7315.3918 0.0012274403 + 60 14.682407 -7315.3918 0.0026370119 + 80 21.289801 -7315.3918 0.004552872 + 100 29.208281 -7315.3918 0.0069472253 +Loop time of 29.2009 on 4 procs for 100 steps with 1008 atoms + +Pair time (%) = 0.305472 (1.04611) +Neigh time (%) = 0 (0) +Comm time (%) = 0.435163 (1.49024) +Outpt time (%) = 0.202401 (0.693134) +Other time (%) = 28.2578 (96.7705) + +Nlocal: 252 ave 256 max 248 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 59 ave 80 max 40 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 4456 ave 4608 max 4304 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 17824 +Ave neighs/atom = 17.6825 +Neighbor list builds = 0 +Dangerous builds = 0 + +# NOTE try fix charge on tip diff --git a/examples/USER/atc/elastic/cnt_fixed_charge.screen b/examples/USER/atc/elastic/cnt_fixed_charge.screen new file mode 100644 index 0000000000..d0cfef0994 --- /dev/null +++ b/examples/USER/atc/elastic/cnt_fixed_charge.screen @@ -0,0 +1,350 @@ +LAMMPS (14 Aug 2013) +units metal +atom_style charge +dielectric 1. + +variable type string "_charge" +boundary s s f +# read in CNT +read_data cnt_9_0_100${type}.data +read_data cnt_9_0_100_charge.data +Reading data file ... + orthogonal box = (-7.04598 -7.04598 0) to (7.04598 7.04598 100) + 1 by 1 by 4 MPI processor grid + 846 atoms +lattice diamond 3.6 # NOTE ??? +Lattice spacing in x,y,z = 3.6 3.6 3.6 +pair_style airebo 3.0 +pair_coeff * * ./CH.airebo C +mass * 12.01 + +# PARAMETERS----------------------------- +variable dt equal 0.0005 +variable L equal zhi-zlo +variable zhi equal zhi +variable zTip equal ${zhi}-2.0 +variable zTip equal 100-2.0 +variable zFree equal zhi +variable R equal 12.1/2 +variable xhiFE equal 5.0*$R +variable xhiFE equal 5.0*6.0499999999999998224 +variable xloFE equal -${xhiFE} +variable xloFE equal -30.25 +variable yhiFE equal $R +variable yhiFE equal 6.0499999999999998224 +variable yloFE equal -${yhiFE} +variable yloFE equal -6.0499999999999998224 +variable zloFE equal zlo+10 # create fixed ghosts +variable zhiFE equal zhi+(zhi-${zloFE})/12*2 +variable zhiFE equal zhi+(zhi-10)/12*2 +variable Lfree equal zhi-${zloFE} +variable Lfree equal zhi-10 +variable nx equal 10 # 5 +variable nz equal 14 # 12 +print "Length $L [${zloFE}, ${zhiFE}] ${zTip}" +Length 100 [10, 115] 98 + +#variable E equal 0.1 # bias 1.0 +variable Vb equal 0.0 # bias +variable Vg equal 0.5 # gate/modulation +print "bias voltage ${Vb}, gate voltage ${Vg}" +bias voltage 0, gate voltage 0.5 + +variable n equal 100000 +variable s equal 250 +# END ----------------------------------- + +# all atoms simulation +region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 -6.0499999999999998224 ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 -6.0499999999999998224 6.0499999999999998224 ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 -6.0499999999999998224 6.0499999999999998224 10 ${zhiFE} units box +region feRegion block -30.25 30.25 -6.0499999999999998224 6.0499999999999998224 10 115 units box +group internal region feRegion +756 atoms in group internal +group fixed subtract all internal +90 atoms in group fixed +fix FIX fixed setforce 0 0 0 +thermo 100 +#minimize 0 0 1000 1000 +#write_restart cnt_in_box0.rst + +region TIP block INF INF INF INF ${zTip} INF units box +region TIP block INF INF INF INF 98 INF units box +group TIP region TIP +9 atoms in group TIP + +variable nAll equal count(all) +variable nGhost equal count(all)-count(internal) +variable nTip equal count(TIP) +print ">>> number of stationary ghosts: ${nGhost} of ${nAll}" +>>> number of stationary ghosts: 90 of 846 +print ">>> number of tip atoms : ${nTip}" +>>> number of tip atoms : 9 + +neighbor 5. bin +neigh_modify every 10 delay 0 check no +timestep ${dt} +timestep 0.00050000000000000001041 +variable tag string "cnt_fixed_charge" + +# set charge on tip +variable C equal -0.1 # -0.01 -0.0001102 +print "charge $C [e]" +charge -0.10000000000000000555 [e] +variable c equal $C/${nTip} +variable c equal -0.10000000000000000555/${nTip} +variable c equal -0.10000000000000000555/9 +set group TIP charge $c +set group TIP charge -0.011111111111111111535 +Setting atom values ... + 9 settings made for charge + +# coupling +fix AtC internal atc electrostatic CNT_id.mat +ATC: constructing electrostatic mechanical coupling with parameter file CNT_id.mat + ATC: peratom PE compute created with ID: 3 + ATC: computed mass density : 2.05933 + ATC: 1 materials defined from CNT_id.mat + ATC: creating electrostatic extrinsic model + ATC: computed mass density : 2.05933 + ATC: 1 materials defined from CNT_id.mat + ATC: computed mass density : 2.05933 + ATC: 1 materials defined from CNT_id.mat +fix_modify AtC include atomic_charge +fix_modify AtC internal_quadrature off +# note weights don't affect phi or f +fix_modify AtC atom_weight constant internal 1.0 +fix_modify AtC extrinsic short_range off +#fix_modify AtC atom_element_map eulerian 1 +fix_modify AtC control momentum flux + + +fix_modify AtC mesh create ${nx} 1 ${nz} feRegion f p f +fix_modify AtC mesh create 10 1 ${nz} feRegion f p f +fix_modify AtC mesh create 10 1 14 feRegion f p f + ATC: created uniform mesh with 330 nodes, 165 unique nodes, and 140 elements + +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 +fix_modify AtC initial electric_potential all 0.0 + +# node sets +variable t equal 1.1*$R +variable t equal 1.1*6.0499999999999998224 +fix_modify AtC mesh create_nodeset tube -$t $t -$t $t ${zloFE} ${zFree} units box +fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 $t -$t $t ${zloFE} ${zFree} units box +fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -$t $t ${zloFE} ${zFree} units box +fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 $t ${zloFE} ${zFree} units box +fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 ${zloFE} ${zFree} units box +fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 ${zFree} units box +fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 100 units box + ATC: created nodeset tube with 39 nodes +fix_modify AtC mesh create_nodeset lefttube -$t $t -$t $t ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 $t -$t $t ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -$t $t ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 $t ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 ${zloFE} units box +fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 10 units box + ATC: created nodeset lefttube with 3 nodes +fix_modify AtC mesh create_nodeset rbc INF INF INF INF ${zhiFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset rbc INF INF INF INF 115 ${zhiFE} units box +fix_modify AtC mesh create_nodeset rbc INF INF INF INF 115 115 units box + ATC: created nodeset rbc with 11 nodes +fix_modify AtC mesh create_nodeset lbc INF INF INF INF ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lbc INF INF INF INF 10 ${zloFE} units box +fix_modify AtC mesh create_nodeset lbc INF INF INF INF 10 10 units box + ATC: created nodeset lbc with 11 nodes +fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} INF INF INF INF units box +fix_modify AtC mesh create_nodeset top 30.25 ${xhiFE} INF INF INF INF units box +fix_modify AtC mesh create_nodeset top 30.25 30.25 INF INF INF INF units box + ATC: created nodeset top with 15 nodes +fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} INF INF INF INF units box +fix_modify AtC mesh create_nodeset bot -30.25 ${xloFE} INF INF INF INF units box +fix_modify AtC mesh create_nodeset bot -30.25 -30.25 INF INF INF INF units box + ATC: created nodeset bot with 15 nodes + +# boundary conditions +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix displacement y lbc 0. +fix_modify AtC fix displacement z lbc 0. +fix_modify AtC fix velocity x lbc 0. +fix_modify AtC fix velocity y lbc 0. +fix_modify AtC fix velocity z lbc 0. +# ground +fix_modify AtC fix electric_potential lbc 0 +# bias +fix_modify AtC fix electric_potential rbc ${Vb} +fix_modify AtC fix electric_potential rbc 0 +# gate +fix_modify AtC fix electric_potential bot ${Vg} +fix_modify AtC fix electric_potential bot 0.5 + +# run +compute CM TIP com +compute q all property/atom q +compute Q all reduce sum c_q +compute FSUM all reduce sum fx fy fz +thermo_style custom step etotal ke c_CM[1] c_CM[2] c_CM[3] c_Q f_AtC[4] f_AtC[5] f_AtC[6] f_AtC[7] f_FIX[1] f_FIX[2] f_FIX[3] f_AtC c_FSUM[1] +thermo $s +thermo 250 +log ${tag}.log +log cnt_fixed_charge.log +#run $n +#run $n +thermo 10 +timestep 0.0 +min_modify line quadratic +minimize 0 0 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: WARNING: all initial conditions for electron_density have not been defined and the undefined are assumed zero + ATC: WARNING: material: [cnt0] cannot find electron_flux + ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 54.7522 Mbytes +Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1] + 0 -6146.2653 0 -1.2222229e-10 1.1111297e-10 98.69 -0.1 0 0 0 -0.00094915808 9.0465829e-16 -2.9442594e-15 8.5762791 0.26756106 -0.00094915808 + 10 -6148.5953 0 -2.4439829e-05 -2.2098859e-10 98.493704 -0.1 0 0 0 -0.00094915808 1.2097899e-09 -1.5843514e-09 8.9290595 0.26659976 -0.00094915929 + 20 -6149.6563 0 -0.0001026377 -1.2280254e-10 98.220511 -0.1 0 0 0 -0.00094915808 -1.2490271e-10 1.3882666e-11 9.0170586 0.26585869 -0.00094915796 + 30 -6150.5918 0 -0.00018409212 -1.5241986e-10 98.082714 -0.1 0 0 0 -0.00094915808 1.1496787e-09 -5.0626918e-10 8.9773134 0.26549134 -0.00094915923 + 40 -6151.5228 0 -0.00028729352 -1.255161e-10 97.911408 -0.1 0 0 0 -0.00094915808 -7.0229746e-12 2.277342e-10 8.9692427 0.26498393 -0.00094915808 + 50 -6152.4762 0 -0.00040932626 -1.3818574e-12 97.725058 -0.1 0 0 0 -0.00094915808 6.9526046e-11 1.9786892e-10 8.9900875 0.26449594 -0.00094915815 + 60 -6153.4274 0 -0.00055067345 1.805009e-10 97.514368 -0.1 0 0 0 -0.00094915808 -2.4739767e-10 5.8424452e-10 8.9790629 0.26387994 -0.00094915784 + 70 -6154.3557 0 -0.00070066137 1.0114613e-10 97.330744 -0.1 0 0 0 -0.00094915808 -2.6211632e-10 7.052493e-10 8.9849075 0.26339716 -0.00094915782 + 80 -6155.267 0 -0.00085596687 -1.0710927e-10 97.147959 -0.1 0 0 0 -0.00094915808 4.4143026e-07 1.6718385e-10 5.3206144 0.26285936 -0.00094959951 + 90 -6155.4335 0 -0.00088765763 -1.7962733e-11 97.118985 -0.1 0 0 0 -0.00094915808 -3.2852156e-07 -2.142539e-10 1.9421081 0.2627935 -0.00094882956 + 100 -6155.4688 0 -0.00092338115 4.3179489e-12 97.108467 -0.1 0 0 0 -0.00094915808 2.1921637e-06 3.277627e-10 1.8128583 0.26276227 -0.00095135025 + 110 -6155.4937 0 -0.0009583995 2.7080132e-11 97.099066 -0.1 0 0 0 -0.00094915808 -6.6593497e-07 3.1466135e-10 1.6760028 0.26273976 -0.00094849215 + 120 -6155.5192 0 -0.0010096681 7.5495905e-12 97.084131 -0.1 0 0 0 -0.00094915808 4.1925486e-06 -3.3057391e-10 0.84688966 0.26269582 -0.00095335063 + 130 -6155.5475 0 -0.0010984064 -2.2204658e-11 97.037469 -0.1 0 0 0 -0.00094915808 1.6487881e-05 7.877601e-10 -0.24391523 0.26256701 -0.00096564596 + 140 -6155.5674 0 -0.0011643139 -5.8625528e-12 96.997016 -0.1 0 0 0 -0.00094915808 1.9922307e-05 2.8145019e-10 0.21107429 0.26245307 -0.00096908039 + 150 -6155.5802 0 -0.0012261174 1.6615978e-12 96.978462 -0.1 0 0 0 -0.00094915808 2.3564757e-05 -6.1453672e-10 0.34197533 0.26240133 -0.00097272284 + 160 -6155.5842 0 -0.0012567683 4.1015453e-12 96.969841 -0.1 0 0 0 -0.00094915808 -1.8048071e-05 -7.4358615e-10 0.24350595 0.26237804 -0.00093111001 + 170 -6155.5848 0 -0.0012749252 3.2100637e-12 96.96678 -0.1 0 0 0 -0.00094915808 -5.8709343e-05 -1.0101609e-10 0.23678759 0.26236915 -0.00089044874 + 180 -6155.5863 0 -0.0013921995 9.5094171e-12 96.955174 -0.1 0 0 0 -0.00094915808 -0.00026288245 2.257e-09 0.27067485 0.2623373 -0.00068627564 + 190 -6155.5869 0 -0.001448131 2.9297299e-11 96.95023 -0.1 0 0 0 -0.00094915808 -0.00022357532 -5.3015481e-10 0.25119591 0.26232192 -0.00072558276 + 200 -6155.5875 0 -0.0015072261 1.2995721e-11 96.946996 -0.1 0 0 0 -0.00094915808 3.676363e-06 -1.6247639e-09 0.14855078 0.26231405 -0.00095283445 + 210 -6155.5884 0 -0.0016446609 -5.6541246e-11 96.941051 -0.1 0 0 0 -0.00094915808 0.00012779831 5.5608749e-09 0.071556101 0.2622972 -0.0010769564 + 220 -6155.5885 0 -0.0016649389 -1.4916073e-11 96.940172 -0.1 0 0 0 -0.00094915808 2.8769126e-05 7.3325474e-10 0.072836172 0.26229459 -0.00097792721 + 230 -6155.5886 0 -0.0016840656 3.0271757e-11 96.93972 -0.1 0 0 0 -0.00094915808 -8.2275147e-05 -3.2732419e-09 0.038242471 0.26229362 -0.00086688294 + 240 -6155.5886 0 -0.0017104776 1.1844187e-12 96.939312 -0.1 0 0 0 -0.00094915808 1.3323934e-06 4.6833365e-10 0.029894245 0.2622922 -0.00095049048 + 250 -6155.5886 0 -0.001782375 -5.1737556e-11 96.938585 -0.1 0 0 0 -0.00094915808 0.00010776134 5.532132e-09 0.015593573 0.26229021 -0.0010569194 + 260 -6155.5886 0 -0.0018325003 1.4170213e-11 96.938021 -0.1 0 0 0 -0.00094915808 -0.00011466701 -1.8404319e-09 0.0074676942 0.26228875 -0.00083449107 + 270 -6155.5887 0 -0.0018909045 4.5008271e-12 96.93745 -0.1 0 0 0 -0.00094915808 0.00013183246 -4.7505827e-10 0.012466474 0.26228709 -0.0010809905 + 280 -6155.5887 0 -0.0019654593 -2.0855882e-11 96.936554 -0.1 0 0 0 -0.00094915808 0.000169485 -5.926811e-11 -0.0067531896 0.26228461 -0.0011186431 + 290 -6155.5887 0 -0.0020221999 -8.6767858e-12 96.935891 -0.1 0 0 0 -0.00094915808 -5.3692915e-05 1.0159278e-09 -0.0018194713 0.26228254 -0.00089546517 + 300 -6155.5887 0 -0.0020344145 -5.607299e-14 96.935775 -0.1 0 0 0 -0.00094915808 -1.5062541e-05 3.3229655e-10 0.0029236218 0.26228228 -0.00093409554 + 310 -6155.5887 0 -0.0020565506 -8.9663374e-12 96.935684 -0.1 0 0 0 -0.00094915808 0.00020002046 -1.267435e-09 0.003519094 0.26228199 -0.0011491785 + 320 -6155.5887 0 -0.0021315555 -1.4536397e-11 96.93549 -0.1 0 0 0 -0.00094915808 0.00011130878 1.691832e-10 0.0035264974 0.26228133 -0.0010604669 + 330 -6155.5887 0 -0.0021892704 2.8975537e-12 96.935359 -0.1 0 0 0 -0.00094915808 2.1304961e-05 -6.0918033e-10 0.0032239388 0.26228087 -0.00097046304 + 340 -6155.5887 0 -0.002267819 2.8726725e-12 96.935208 -0.1 0 0 0 -0.00094915808 -0.00012295621 1.4278825e-09 0.0015958494 0.26228031 -0.00082620188 + 350 -6155.5887 0 -0.0023365018 7.5696565e-12 96.935104 -0.1 0 0 0 -0.00094915808 -3.8319531e-05 2.8702501e-10 -0.00070205167 0.26227999 -0.00091083855 + 360 -6155.5887 0 -0.00237721 -9.4045843e-12 96.935064 -0.1 0 0 0 -0.00094915808 0.00015892958 -1.1733697e-09 -0.0021409156 0.26227985 -0.0011080877 + 370 -6155.5887 0 -0.0024126534 -1.8974906e-11 96.935058 -0.1 0 0 0 -0.00094915808 0.00013759568 4.1426828e-10 -0.0021373479 0.26227982 -0.0010867538 + 380 -6155.5887 0 -0.0024420366 3.1870067e-12 96.93505 -0.1 0 0 0 -0.00094915808 6.0222094e-05 -4.9318939e-10 -0.0021696981 0.26227978 -0.0010093802 + 390 -6155.5887 0 -0.0024987512 -6.1806174e-12 96.935034 -0.1 0 0 0 -0.00094915808 -2.1228292e-06 2.8515227e-10 -0.0022646942 0.2622797 -0.00094703525 + 400 -6155.5887 0 -0.002653766 -1.4619372e-11 96.93499 -0.1 0 0 0 -0.00094915808 0.00013021546 1.1233177e-09 -0.0033420787 0.26227949 -0.0010793735 + 410 -6155.5887 0 -0.0028422882 -1.292254e-11 96.934928 -0.1 0 0 0 -0.00094915808 0.00020536826 -5.0886e-10 -0.0049198922 0.26227921 -0.0011545263 + 420 -6155.5887 0 -0.0030173435 -1.0655446e-11 96.934865 -0.1 0 0 0 -0.00094915808 0.00011114747 -2.5969168e-10 -0.0048225266 0.2622789 -0.0010603056 + 430 -6155.5887 0 -0.0032602753 -2.4154772e-11 96.934789 -0.1 0 0 0 -0.00094915808 0.00035483493 1.6053604e-10 -0.0043785731 0.26227846 -0.001303993 + 440 -6155.5887 0 -0.0036112872 -5.6473718e-11 96.934705 -0.1 0 0 0 -0.00094915808 0.00043425018 1.8745787e-10 -0.0038812537 0.26227785 -0.0013834083 + 450 -6155.5887 0 -0.0038611908 -1.9242305e-12 96.934666 -0.1 0 0 0 -0.00094915808 0.0001243155 -3.6471408e-10 -0.0050455501 0.26227745 -0.0010734736 + 460 -6155.5887 0 -0.0042622211 -1.1948937e-11 96.93463 -0.1 0 0 0 -0.00094915808 0.00017733896 -5.9650038e-10 -0.005090118 0.26227685 -0.001126497 + 470 -6155.5887 0 -0.0051704959 -6.5555834e-11 96.93456 -0.1 0 0 0 -0.00094915808 0.00044796055 2.0162891e-09 -0.0063013863 0.26227558 -0.0013971186 + 480 -6155.5887 0 -0.0058774787 8.0639107e-12 96.934537 -0.1 0 0 0 -0.00094915808 0.00030232037 -4.1063286e-10 -0.0063827796 0.26227474 -0.0012514785 + 490 -6155.5887 0 -0.0071402115 -4.9061812e-11 96.934554 -0.1 0 0 0 -0.00094915808 0.00014674646 -1.4276993e-09 -0.0085602294 0.26227356 -0.0010959045 + 500 -6155.5887 0 -0.0089111607 -5.2606473e-11 96.934565 -0.1 0 0 0 -0.00094915808 0.00062500656 6.8011742e-10 -0.0084420596 0.26227196 -0.0015741646 +Loop time of 106.653 on 4 procs for 500 steps with 846 atoms + +Minimization stats: + Stopping criterion = max force evaluations + Energy initial, next-to-last, final = + -6146.26527937 -6155.58874802 -6155.58874805 + Force two-norm initial, final = 9.08614 0.00211093 + Force max component initial, final = 2.35984 0.000212848 + Final line search alpha, max atom move = 1 0.000212848 + Iterations, force evaluations = 500 1000 + +Pair time (%) = 9.67218 (9.06879) +Neigh time (%) = 0 (0) +Comm time (%) = 6.7444 (6.32366) +Outpt time (%) = 2.93299 (2.75002) +Other time (%) = 87.3039 (81.8575) + +Nlocal: 211.5 ave 216 max 207 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 191.25 ave 261 max 126 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 47313 ave 52056 max 42570 min +Histogram: 1 0 1 0 0 0 0 1 0 1 + +Total # of neighbors = 189252 +Ave neighs/atom = 223.702 +Neighbor list builds = 0 +Dangerous builds = 0 + +# u = F L^3 / 3 EI --> EI = F L^3 / 3 u +variable u equal c_CM[1] +variable F equal f_AtC[5] +# [eV/A * A^2] --> [N m] +variable eV2J equal 1.60217646e-19 +variable A2m equal 1.e-10 +variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u +variable EI equal 0*${Lfree}*${Lfree}*${Lfree}/3./$u +variable EI equal 0*90*${Lfree}*${Lfree}/3./$u +variable EI equal 0*90*90*${Lfree}/3./$u +variable EI equal 0*90*90*90/3./$u +variable EI equal 0*90*90*90/3./-0.0089111606622158945346 +variable EI equal ${EI}*${eV2J}*${A2m} +variable EI equal -0*${eV2J}*${A2m} +variable EI equal -0*1.6021764600000000642e-19*${A2m} +variable EI equal -0*1.6021764600000000642e-19*1.0000000000000000364e-10 +print "flexural rigidity ${EI} [Nm^2] NOTE z force" +flexural rigidity -0 [Nm^2] NOTE z force +# flexural rigidity 6.716732985e-25 [Nm^2] + +fix_modify AtC output ${tag}FE 1 full_text +fix_modify AtC output cnt_fixed_chargeFE 1 full_text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +fix_modify AtC output index step +run 1 +Setting up run ... + ATC: WARNING: material: [cnt0] cannot find electron_flux + ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 54.1206 Mbytes +Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1] + 500 -6155.5887 0 -0.0089111607 -5.2606424e-11 96.934565 -0.1 0 0 0 -0.00094915808 0.00062500656 6.8011742e-10 -0.0084420596 0.26227196 -0.0015741646 + 501 -6155.5887 0 -0.0089111607 -5.2606424e-11 96.934565 -0.1 0 0 0 -0.00094915808 0.00062500656 6.8011742e-10 -0.0084420596 0.26227196 -0.0015741646 +Loop time of 0.0591159 on 4 procs for 1 steps with 846 atoms + +Pair time (%) = 0.00747705 (12.6481) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000546396 (0.924278) +Outpt time (%) = 0.0172972 (29.2598) +Other time (%) = 0.0337953 (57.1678) + +Nlocal: 211.5 ave 216 max 198 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 195.75 ave 261 max 126 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 48199.5 ave 53136 max 41085 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 192798 +Ave neighs/atom = 227.894 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/elastic/eam_energy.screen b/examples/USER/atc/elastic/eam_energy.screen new file mode 100644 index 0000000000..4f035ca858 --- /dev/null +++ b/examples/USER/atc/elastic/eam_energy.screen @@ -0,0 +1,333 @@ +LAMMPS (14 Aug 2013) +units metal +atom_style atomic +atom_modify map hash +boundary p p p + +variable l equal 3 +variable l2 equal 0.5*$l +variable l2 equal 0.5*3 +variable L equal 10 +variable L2 equal 0.5*$L +variable L2 equal 0.5*10 +variable h equal $L +variable h equal 10 + +lattice fcc 4.08 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 4.08 4.08 4.08 +region BOX block -${l2} ${l2} -${L2} ${L2} -${l2} ${l2} +region BOX block -1.5 ${l2} -${L2} ${L2} -${l2} ${l2} +region BOX block -1.5 1.5 -${L2} ${L2} -${l2} ${l2} +region BOX block -1.5 1.5 -5 ${L2} -${l2} ${l2} +region BOX block -1.5 1.5 -5 5 -${l2} ${l2} +region BOX block -1.5 1.5 -5 5 -1.5 ${l2} +region BOX block -1.5 1.5 -5 5 -1.5 1.5 +create_box 1 BOX +Created orthogonal box = (-6.12 -20.4 -6.12) to (6.12 20.4 6.12) + 1 by 4 by 1 MPI processor grid +create_atoms 1 region BOX +Created 360 atoms + +pair_style eam +pair_coeff * * Au_u3.eam +mass * 196.97 + + +### NOTE change to CB -linear +fix PP all atc field Au_elastic.mat +ATC: constructing shape function field estimate with parameter file Au_elastic.mat + ATC: peratom PE compute created with ID: 3 +fix_modify PP mesh create 1 $h 1 BOX p f p +fix_modify PP mesh create 1 10 1 BOX p f p + ATC: created uniform mesh with 44 nodes, 11 unique nodes, and 10 elements +fix_modify PP fields add displacement velocity potential_energy cauchy_born_energy # kinetic_energy +fix_modify PP gradients add displacement +fix_modify PP set reference_potential_energy +fix_modify PP output counter step +fix_modify PP output eam_energyPP 1 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + + +fix ATC all atc elastic Au_elastic.mat +ATC: constructing elastic coupling with parameter file Au_elastic.mat + ATC: peratom PE compute created with ID: 3 + ATC: computed mass density : 11.6006 + ATC: computed mass density : 11.6006 + ATC: 2 materials defined from Au_elastic.mat +fix_modify ATC mesh create 1 $h 1 BOX p f p +fix_modify ATC mesh create 1 10 1 BOX p f p + ATC: created uniform mesh with 44 nodes, 11 unique nodes, and 10 elements +fix_modify ATC internal_quadrature off +fix_modify ATC control momentum none +#fix_modify ATC consistent_fe_initialization on +fix_modify ATC output counter step +fix_modify ATC output eam_energyFE 1 text binary + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +fix_modify ATC material all Au_cubic + + +dump CONFIG all custom 1 eam_energy.dmp id type x y z +thermo 1 + +timestep 0 # 1.e-20 # 0 + +variable e0 equal pe +variable L0 equal ly +run 0 +Setting up run ... + ATC: CB stiffness: 11.5362 Einstein freq: 4682.34 + ATC: CB stiffness: 11.5362 Einstein freq: 4682.34 + ATC: WARNING: all initial conditions for displacement have not been defined and the undefined are assumed zero + ATC: WARNING: all initial conditions for velocity have not been defined and the undefined are assumed zero +Memory usage per processor = 70.4928 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1414.8 0 -1414.8 0.022463201 +Loop time of 5.76973e-05 on 4 procs for 0 steps with 360 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 0 (0) +Outpt time (%) = 0 (0) +Other time (%) = 5.76973e-05 (100) + +Nlocal: 90 ave 90 max 90 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1184 ave 1184 max 1184 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 3870 ave 3870 max 3870 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 7740 ave 7740 max 7740 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 30960 +Ave neighs/atom = 86 +Neighbor list builds = 0 +Dangerous builds = 0 +variable pe equal pe-${e0} +variable pe equal pe--1414.8000000636002369 +variable dL equal ly-${L0} +variable dL equal ly-40.799999999999997158 +variable strain equal v_dL/${L0} +variable strain equal v_dL/40.799999999999997158 + +variable x equal y[1] +variable x2 equal y[2] +variable v equal vy[1] +thermo_style custom step etotal v_pe ke f_ATC[1] f_ATC[2] v_x v_v v_x2 ly v_dL v_strain +thermo_modify format 2 %15.8g + +############################################################################### +log eam_energy.log +run 1 +Setting up run ... +Memory usage per processor = 70.4928 Mbytes +Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain + 0 -1414.8 0 0 0 0 -19.38 0 -19.38 40.8 0 0 + 1 -1414.8 0 0 0 0 -19.38 0 -19.38 40.8 0 0 +Loop time of 0.220009 on 4 procs for 1 steps with 360 atoms + +Pair time (%) = 0.010402 (4.72801) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0269095 (12.2311) +Outpt time (%) = 0.0771807 (35.0808) +Other time (%) = 0.105516 (47.9601) + +Nlocal: 90 ave 90 max 90 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1184 ave 1184 max 1184 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 3870 ave 3870 max 3870 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 7740 ave 7740 max 7740 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 30960 +Ave neighs/atom = 86 +Neighbor list builds = 0 +Dangerous builds = 0 +velocity all set 0 0.1 0 units box +fix_modify ATC fix velocity y all 0.1 +run 1 +Setting up run ... +Memory usage per processor = 70.4928 Mbytes +Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain + 1 -1414.7633 0 0.036746101 0 0 -19.38 0.1 -19.38 40.8 0 0 + 2 -1414.7633 0 0.036746101 0.036746101 0 -19.38 0.1 -19.38 40.8 0 0 +Loop time of 0.305193 on 4 procs for 1 steps with 360 atoms + +Pair time (%) = 0.0104025 (3.4085) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0294241 (9.64114) +Outpt time (%) = 0.132358 (43.3686) +Other time (%) = 0.133008 (43.5818) + +Nlocal: 90 ave 90 max 90 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1184 ave 1184 max 1184 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 3870 ave 3870 max 3870 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 7740 ave 7740 max 7740 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 30960 +Ave neighs/atom = 86 +Neighbor list builds = 0 +Dangerous builds = 0 +velocity all set 0 0.2 0 units box +fix_modify ATC fix velocity y all 0.2 +run 1 +Setting up run ... +Memory usage per processor = 70.4928 Mbytes +Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain + 2 -1414.653 0 0.1469844 0.036746101 0 -19.38 0.2 -19.38 40.8 0 0 + 3 -1414.653 0 0.1469844 0.1469844 0 -19.38 0.2 -19.38 40.8 0 0 +Loop time of 0.49256 on 4 procs for 1 steps with 360 atoms + +Pair time (%) = 0.0226828 (4.60508) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0572202 (11.6169) +Outpt time (%) = 0.15985 (32.4529) +Other time (%) = 0.252807 (51.3251) + +Nlocal: 90 ave 90 max 90 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1184 ave 1184 max 1184 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 3870 ave 3870 max 3870 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 7740 ave 7740 max 7740 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 30960 +Ave neighs/atom = 86 +Neighbor list builds = 0 +Dangerous builds = 0 +velocity all set 0 0.3 0 units box +fix_modify ATC fix velocity y all 0.3 +run 1 +Setting up run ... +Memory usage per processor = 70.4928 Mbytes +Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain + 3 -1414.4693 0 0.33071491 0.1469844 0 -19.38 0.3 -19.38 40.8 0 0 + 4 -1414.4693 0 0.33071491 0.33071491 0 -19.38 0.3 -19.38 40.8 0 0 +Loop time of 0.4925 on 4 procs for 1 steps with 360 atoms + +Pair time (%) = 0.0401872 (8.15985) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0840666 (17.0694) +Outpt time (%) = 0.122344 (24.8415) +Other time (%) = 0.245902 (49.9293) + +Nlocal: 90 ave 90 max 90 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1184 ave 1184 max 1184 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 3870 ave 3870 max 3870 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 7740 ave 7740 max 7740 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 30960 +Ave neighs/atom = 86 +Neighbor list builds = 0 +Dangerous builds = 0 +change_box all y scale 1.01 remap +Changing box ... + orthogonal box = (-6.12 -20.604 -6.12) to (6.12 20.604 6.12) +fix_modify ATC fix displacement y all linear 0 0 0 0 0.01 0 0 + ATC: created function : 0 + 0(x-0)+0.01(y-0)+0(z-0) +run 1 +Setting up run ... +Memory usage per processor = 70.4928 Mbytes +Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain + 4 -1414.1262 0.34311553 0.33071491 0.33071491 0 -19.5738 0.3 -19.5738 41.208 0.408 0.01 + 5 -1414.1262 0.34311553 0.33071491 0.33071491 0.34908704 -19.5738 0.3 -19.5738 41.208 0.408 0.01 +Loop time of 0.406034 on 4 procs for 1 steps with 360 atoms + +Pair time (%) = 0.0312375 (7.69333) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0279282 (6.87828) +Outpt time (%) = 0.107298 (26.4259) +Other time (%) = 0.23957 (59.0025) + +Nlocal: 90 ave 90 max 90 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1184 ave 1184 max 1184 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 3870 ave 3870 max 3870 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 7740 ave 7740 max 7740 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 30960 +Ave neighs/atom = 86 +Neighbor list builds = 0 +Dangerous builds = 0 +change_box all y scale 1.01 remap +Changing box ... + orthogonal box = (-6.12 -20.81 -6.12) to (6.12 20.81 6.12) +fix_modify ATC fix displacement y all linear 0 0 0 0 0.0201 0 0 + ATC: created function : 0 + 0(x-0)+0.0201(y-0)+0(z-0) +run 1 +Setting up run ... +Memory usage per processor = 70.4928 Mbytes +Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain + 5 -1413.1082 1.3610604 0.33071491 0.33071491 0 -19.769538 0.3 -19.769538 41.62008 0.82008 0.0201 + 6 -1413.1082 1.3610604 0.33071491 0.33071491 1.0612595 -19.769538 0.3 -19.769538 41.62008 0.82008 0.0201 +Loop time of 0.0288442 on 4 procs for 1 steps with 360 atoms + +Pair time (%) = 0.000436962 (1.5149) +Neigh time (%) = 0 (0) +Comm time (%) = 0.00012219 (0.423618) +Outpt time (%) = 0.0219155 (75.9788) +Other time (%) = 0.00636959 (22.0827) + +Nlocal: 90 ave 90 max 90 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1184 ave 1184 max 1184 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 3870 ave 3870 max 3870 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 7740 ave 7740 max 7740 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 30960 +Ave neighs/atom = 86 +Neighbor list builds = 0 +Dangerous builds = 0 +change_box all y scale 1.01 remap +Changing box ... + orthogonal box = (-6.12 -21.0181 -6.12) to (6.12 21.0181 6.12) +fix_modify ATC fix displacement y all linear 0 0 0 0 0.030301 0 0 + ATC: created function : 0 + 0(x-0)+0.030301(y-0)+0(z-0) +run 1 +Setting up run ... +Memory usage per processor = 70.4928 Mbytes +Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain + 6 -1411.4328 3.0364818 0.33071491 0.33071491 0 -19.967233 0.3 -19.967233 42.036281 1.2362808 0.030301 + 7 -1411.4328 3.0364818 0.33071491 0.33071491 1.7947982 -19.967233 0.3 -19.967233 42.036281 1.2362808 0.030301 +Loop time of 0.0317271 on 4 procs for 1 steps with 360 atoms + +Pair time (%) = 0.00369978 (11.6613) +Neigh time (%) = 0 (0) +Comm time (%) = 0.00984788 (31.0394) +Outpt time (%) = 0.00181496 (5.72054) +Other time (%) = 0.0163645 (51.5788) + +Nlocal: 90 ave 90 max 90 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1184 ave 1184 max 1184 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 3870 ave 3870 max 3870 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 7740 ave 7740 max 7740 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 30960 +Ave neighs/atom = 86 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/elastic/electron_density.screen b/examples/USER/atc/elastic/electron_density.screen new file mode 100644 index 0000000000..0a9e41a71a --- /dev/null +++ b/examples/USER/atc/elastic/electron_density.screen @@ -0,0 +1,266 @@ +LAMMPS (14 Aug 2013) +units metal +# PARAMETERS----------------------------- +variable s equal 1 +variable L equal 10 +variable e equal 4 +variable E equal 0.0001 +variable V equal $E*$L +variable V equal 0.00010000000000000000479*$L +variable V equal 0.00010000000000000000479*10 +# END ----------------------------------- + +atom_style atomic +lattice diamond 1.0 +Lattice spacing in x,y,z = 1 1 1 +boundary f p p +region box block -$L $L 0 1 0 1 +region box block -10 $L 0 1 0 1 +region box block -10 10 0 1 0 1 +create_box 1 box +Created orthogonal box = (-10 0 0) to (10 1 1) + 4 by 1 by 1 MPI processor grid +group box region box +0 atoms in group box +atom_modify sort 0 1 +timestep 0.0 +mass * 12.01 + +# coupling +### NOTE ATC: material cnt does not provide all interfaces for charge_density physics and will be treated as null +fix AtC box atc electrostatic-equilibrium CNT.mat +ATC: constructing equilibrium electrostatic coupling with parameter file CNT.mat + ATC: peratom PE compute created with ID: 3 + ATC: computed mass density : 96.08 + ATC: computed mass density : 96.08 + ATC: computed mass density : 96.08 + ATC: computed mass density : 96.08 + ATC: computed mass density : 96.08 + ATC: computed mass density : 96.08 + ATC: computed mass density : 96.08 + ATC: 7 materials defined from CNT.mat + ATC: creating electrostatic extrinsic model + ATC: computed mass density : 96.08 + ATC: computed mass density : 96.08 + ATC: computed mass density : 96.08 + ATC: computed mass density : 96.08 + ATC: computed mass density : 96.08 + ATC: computed mass density : 96.08 + ATC: computed mass density : 96.08 + ATC: 7 materials defined from CNT.mat + ATC: computed mass density : 96.08 + ATC: computed mass density : 96.08 + ATC: computed mass density : 96.08 + ATC: computed mass density : 96.08 + ATC: computed mass density : 96.08 + ATC: computed mass density : 96.08 + ATC: computed mass density : 96.08 + ATC: 7 materials defined from CNT.mat +fix_modify AtC internal_quadrature off +#fix_modify AtC atom_weight constant internal 1.0 NOTE penultimate is a group +fix_modify AtC atom_weight constant box 1.0 +fix_modify AtC omit atomic_charge +fix_modify AtC mesh create $e 1 1 box f p p +fix_modify AtC mesh create 4 1 1 box f p p + ATC: created uniform mesh with 20 nodes, 5 unique nodes, and 4 elements +#fix_modify AtC control momentum flux +fix_modify AtC mesh create_elementset all -INF INF -INF INF -INF INF + ATC: created elementset all with 4 elements + +# bcs/ics conditions +fix_modify AtC fix displacement x all 0.0 +fix_modify AtC fix displacement y all 0.0 +fix_modify AtC fix displacement z all 0.0 +fix_modify AtC fix velocity x all 0.0 +fix_modify AtC fix velocity y all 0.0 +fix_modify AtC fix velocity z all 0.0 + +fix_modify AtC mesh create_nodeset lbc -10 -10 INF INF INF INF + ATC: created nodeset lbc with 1 nodes +fix_modify AtC mesh create_nodeset rbc 10 10 INF INF INF INF + ATC: created nodeset rbc with 1 nodes +fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V +fix_modify AtC fix electric_potential lbc linear 0 0 0 0.00010000000000000000479 0 0 $V +fix_modify AtC fix electric_potential lbc linear 0 0 0 0.00010000000000000000479 0 0 0.0010000000000000000208 + ATC: created function : 0.001 + 0.0001(x-0)+0(y-0)+0(z-0) +fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V +fix_modify AtC fix electric_potential rbc linear 0 0 0 0.00010000000000000000479 0 0 $V +fix_modify AtC fix electric_potential rbc linear 0 0 0 0.00010000000000000000479 0 0 0.0010000000000000000208 + ATC: created function : 0.001 + 0.0001(x-0)+0(y-0)+0(z-0) + +# run +thermo_style custom step cpu etotal ke +thermo $s +thermo 1 +fix_modify AtC output electron_densityFE $s text +fix_modify AtC output electron_densityFE 1 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +fix_modify AtC output index step +log electron_density.log + +# run default material +print "default material - table linear" +default material - table linear +run $s +run 1 +Setting up run ... + ATC: WARNING: material: [cnt-exp] cannot find body_force + ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [cnt] cannot find body_force + ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: all initial conditions for electron_density have not been defined and the undefined are assumed zero + ATC: WARNING: all initial conditions for electric_potential have not been defined and the undefined are assumed zero + ATC: WARNING: material: [cnt-exp] cannot find body_force + ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [cnt] cannot find body_force + ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 0.432442 Mbytes +Step CPU TotEng KinEng + 0 0 0 -0 + 1 0.01880908 0 -0 +Loop time of 0.018833 on 4 procs for 1 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 2.5034e-06 (0.0132926) +Outpt time (%) = 0.017292 (91.8175) +Other time (%) = 0.00153852 (8.16923) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +# run CNT1 material +print "CNT1 material - analytical linear" +CNT1 material - analytical linear +fix_modify AtC material all CNT1 +run $s +run 1 +Setting up run ... + ATC: WARNING: material: [cnt-exp] cannot find body_force + ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [cnt] cannot find body_force + ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [cnt-exp] cannot find body_force + ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [cnt] cannot find body_force + ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 0.432442 Mbytes +Step CPU TotEng KinEng + 1 0 0 -0 + 2 0.11045408 0 -0 +Loop time of 0.110485 on 4 procs for 1 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 1.54972e-06 (0.00140265) +Outpt time (%) = 0.00781226 (7.07087) +Other time (%) = 0.102671 (92.9277) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +# run CNT2 material +print "CNT2 material - analytical exponetial" +CNT2 material - analytical exponetial +fix_modify AtC material all CNT2 +run $s +run 1 +Setting up run ... + ATC: WARNING: material: [cnt-exp] cannot find body_force + ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [cnt] cannot find body_force + ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [cnt-exp] cannot find body_force + ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [cnt] cannot find body_force + ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 0.432442 Mbytes +Step CPU TotEng KinEng + 2 0 0 -0 + 3 0.10601687 0 -0 +Loop time of 0.123864 on 4 procs for 1 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 2.02656e-06 (0.00163611) +Outpt time (%) = 0.0475852 (38.4172) +Other time (%) = 0.0762771 (61.5812) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +# run CNT material +print "CNT material - table DOS" +CNT material - table DOS +fix_modify AtC material all CNT +#variable E equal 10*$E +#fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V +#fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V +run $s +run 1 +Setting up run ... + ATC: WARNING: material: [cnt-exp] cannot find body_force + ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [cnt] cannot find body_force + ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [cnt-exp] cannot find body_force + ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [cnt] cannot find body_force + ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 0.432442 Mbytes +Step CPU TotEng KinEng + 3 0 0 -0 + 4 0.0015778542 0 -0 +Loop time of 0.00159025 on 4 procs for 1 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 7.15256e-07 (0.0449775) +Outpt time (%) = 0.00022918 (14.4115) +Other time (%) = 0.00136036 (85.5435) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + diff --git a/examples/USER/atc/elastic/electrostatic_bending.screen b/examples/USER/atc/elastic/electrostatic_bending.screen new file mode 100644 index 0000000000..3d584b2277 --- /dev/null +++ b/examples/USER/atc/elastic/electrostatic_bending.screen @@ -0,0 +1,845 @@ +LAMMPS (14 Aug 2013) +units metal +atom_style charge +dielectric 1. + +variable type string "_charge" + +boundary s s f +# read in CNT +read_data cnt_9_0_100${type}.data +read_data cnt_9_0_100_charge.data +Reading data file ... + orthogonal box = (-7.04598 -7.04598 0) to (7.04598 7.04598 100) + 1 by 1 by 4 MPI processor grid + 846 atoms +lattice diamond 3.6 # NOTE ??? +Lattice spacing in x,y,z = 3.6 3.6 3.6 +pair_style airebo 3.0 +pair_coeff * * ./CH.airebo C +mass * 12.01 + +# PARAMETERS----------------------------- +variable dt equal 0.0005 +variable L equal zhi-zlo +variable zhi equal zhi +variable zTip equal ${zhi}-2.0 # 2 4 +variable zTip equal 100-2.0 +variable zFree equal zhi +variable R equal 12.1/2 +variable xhiFE equal 5.0*$R +variable xhiFE equal 5.0*6.0499999999999998224 +variable xloFE equal -${xhiFE} +variable xloFE equal -30.25 +variable yhiFE equal $R +variable yhiFE equal 6.0499999999999998224 +variable yloFE equal -${yhiFE} +variable yloFE equal -6.0499999999999998224 +variable zloFE equal zlo+10 # create fixed ghosts +variable zhiFE equal zhi+(zhi-${zloFE})/12*2 +variable zhiFE equal zhi+(zhi-10)/12*2 +variable Lfree equal zhi-${zloFE} +variable Lfree equal zhi-10 +variable nx equal 10 # 5 +variable nz equal 14 # 12 +print "Length $L [${zloFE}, ${zhiFE}] ${zTip}" +Length 100 [10, 115] 98 + +#variable E equal 0.1 # bias 1.0 +variable Vb equal 0.1 # 0.1 #0.5 #0.0 # bias +variable Vg equal 0.5 # 1.0 # 5.0 0.5 #50.0 # 0.5 # gate/modulation +print "bias voltage ${Vb}, gate voltage ${Vg}" +bias voltage 0.10000000000000000555, gate voltage 0.5 + +variable ng equal 20 # 80 # 10 +variable nb equal 2 # 3 + +variable n equal 100000 +variable s equal 250 +# END ----------------------------------- + +region TIP block INF INF INF INF ${zTip} INF units box +region TIP block INF INF INF INF 98 INF units box +group TIP region TIP +9 atoms in group TIP + +#region FIXED block INF INF INF INF INF ${zLoFE} units box +#group FIXED region FIXED + +#group FREE subtract all FIXED + +region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 -6.0499999999999998224 ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 -6.0499999999999998224 6.0499999999999998224 ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 -6.0499999999999998224 6.0499999999999998224 10 ${zhiFE} units box +region feRegion block -30.25 30.25 -6.0499999999999998224 6.0499999999999998224 10 115 units box +group internal region feRegion +756 atoms in group internal +group FIXED subtract all internal +90 atoms in group FIXED +fix FIX FIXED setforce 0 0 0 + +variable nAll equal count(all) +variable nGhost equal count(all)-count(internal) +variable nTip equal count(TIP) +print ">>> number of stationary ghosts: ${nGhost} of ${nAll}" +>>> number of stationary ghosts: 90 of 846 +print ">>> number of tip atoms : ${nTip}" +>>> number of tip atoms : 9 + +neighbor 5. bin +neigh_modify every 10 delay 0 check no +timestep ${dt} +timestep 0.00050000000000000001041 +thermo 100 +variable tag string "electrostatic_bending" + +# set charge on tip +variable C equal -0.025 +print "charge $C [e]" +charge -0.025000000000000001388 [e] +variable c equal $C/${nTip} +variable c equal -0.025000000000000001388/${nTip} +variable c equal -0.025000000000000001388/9 +set group TIP charge $c +set group TIP charge -0.0027777777777777778838 +Setting atom values ... + 9 settings made for charge + +# coupling +fix AtC internal atc electrostatic CNT_id.mat +ATC: constructing electrostatic mechanical coupling with parameter file CNT_id.mat + ATC: peratom PE compute created with ID: 3 + ATC: computed mass density : 2.05933 + ATC: 1 materials defined from CNT_id.mat + ATC: creating electrostatic extrinsic model + ATC: computed mass density : 2.05933 + ATC: 1 materials defined from CNT_id.mat + ATC: computed mass density : 2.05933 + ATC: 1 materials defined from CNT_id.mat +fix_modify AtC include atomic_charge +fix_modify AtC internal_quadrature off +# note weights don't affect phi or f +fix_modify AtC atom_weight constant internal 1.0 +fix_modify AtC extrinsic short_range off +#fix_modify AtC atom_element_map eulerian 1 +fix_modify AtC control momentum flux + +fix_modify AtC mesh create ${nx} 1 ${nz} feRegion f p f +fix_modify AtC mesh create 10 1 ${nz} feRegion f p f +fix_modify AtC mesh create 10 1 14 feRegion f p f + ATC: created uniform mesh with 330 nodes, 165 unique nodes, and 140 elements + +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 +fix_modify AtC initial electric_potential all 0.0 + +# node sets +variable t equal 1.1*$R +variable t equal 1.1*6.0499999999999998224 +fix_modify AtC mesh create_nodeset tube -$t $t -$t $t ${zloFE} ${zFree} units box +fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 $t -$t $t ${zloFE} ${zFree} units box +fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -$t $t ${zloFE} ${zFree} units box +fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 $t ${zloFE} ${zFree} units box +fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 ${zloFE} ${zFree} units box +fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 ${zFree} units box +fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 100 units box + ATC: created nodeset tube with 39 nodes +fix_modify AtC mesh create_nodeset lefttube -$t $t -$t $t ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 $t -$t $t ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -$t $t ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 $t ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 ${zloFE} units box +fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 10 units box + ATC: created nodeset lefttube with 3 nodes +fix_modify AtC mesh create_nodeset rbc INF INF INF INF ${zhiFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset rbc INF INF INF INF 115 ${zhiFE} units box +fix_modify AtC mesh create_nodeset rbc INF INF INF INF 115 115 units box + ATC: created nodeset rbc with 11 nodes +fix_modify AtC mesh create_nodeset lbc INF INF INF INF ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lbc INF INF INF INF 10 ${zloFE} units box +fix_modify AtC mesh create_nodeset lbc INF INF INF INF 10 10 units box + ATC: created nodeset lbc with 11 nodes +fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} INF INF INF INF units box +fix_modify AtC mesh create_nodeset top 30.25 ${xhiFE} INF INF INF INF units box +fix_modify AtC mesh create_nodeset top 30.25 30.25 INF INF INF INF units box + ATC: created nodeset top with 15 nodes +fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} INF INF INF INF units box +fix_modify AtC mesh create_nodeset bot -30.25 ${xloFE} INF INF INF INF units box +fix_modify AtC mesh create_nodeset bot -30.25 -30.25 INF INF INF INF units box + ATC: created nodeset bot with 15 nodes + +# boundary conditions +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix displacement y lbc 0. +fix_modify AtC fix displacement z lbc 0. +fix_modify AtC fix velocity x lbc 0. +fix_modify AtC fix velocity y lbc 0. +fix_modify AtC fix velocity z lbc 0. +# ground +fix_modify AtC fix electric_potential lbc 0 +# bias +fix_modify AtC fix electric_potential rbc ${Vb} +fix_modify AtC fix electric_potential rbc 0.10000000000000000555 +# gate +fix_modify AtC fix electric_potential bot ${Vg} +fix_modify AtC fix electric_potential bot 0.5 + +# run +compute CM TIP com +compute q all property/atom q +compute Q all reduce sum c_q +compute FSUM all reduce sum fx fy fz +compute RSUM internal reduce sum fx fy fz + +thermo_style custom step etotal ke c_CM[1] c_CM[2] c_CM[3] c_Q f_AtC[4] f_AtC[5] f_AtC[6] f_AtC[7] f_FIX[1] f_FIX[2] f_FIX[3] f_AtC c_FSUM[1] c_RSUM[1] +thermo $s +thermo 250 +fix_modify AtC output ${tag}FE 100000000 full_text # $s full_text #binary +fix_modify AtC output electrostatic_bendingFE 100000000 full_text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +fix_modify AtC output index step +# NOTE not recognized as vector by paraview +variable uX atom x-f_AtC[1] +variable uY atom y-f_AtC[2] +variable uZ atom z-f_AtC[3] +variable rho atom mass*f_AtC[4] +dump CONFIG all custom $s ${tag}.dmp id type x y z v_uX v_uY v_uZ v_rho +dump CONFIG all custom 250 ${tag}.dmp id type x y z v_uX v_uY v_uZ v_rho +dump CONFIG all custom 250 electrostatic_bending.dmp id type x y z v_uX v_uY v_uZ v_rho + +reset_timestep 0 +log ${tag}.log +log electrostatic_bending.log + +# [eV/A * A^2] --> [N m] +variable eV2J equal 1.60217646e-19 +variable A2m equal 1.e-10 +thermo 10 +timestep 0.0 +min_modify line quadratic +variable Vg equal 0.1 +variable Lx equal 1.0 +variable ng equal 4 +#compute RSUM FREE reduce sum fx fy fz +#dump CONFIG all custom 10000 ${tag}.dmp id type x y z c_U[1] c_U[2] c_U[3] fx fy fz +variable a equal 0 + variable i loop ${ng} + variable i loop 4 + label loop_i + variable b equal ($i-1)*${Vg}/(${ng}-1)/${Lx} + variable b equal (1-1)*${Vg}/(${ng}-1)/${Lx} + variable b equal (1-1)*0.10000000000000000555/(${ng}-1)/${Lx} + variable b equal (1-1)*0.10000000000000000555/(4-1)/${Lx} + variable b equal (1-1)*0.10000000000000000555/(4-1)/1 + + fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a 0 + fix_modify AtC fix electric_potential all linear 0 0 0 0 0 $a 0 + fix_modify AtC fix electric_potential all linear 0 0 0 0 0 0 0 + ATC: created function : 0 + 0(x-0)+0(y-0)+0(z-0) + min_style cg + min_modify line quadratic + #minimize 0 0 100000 100000 + minimize 0 0 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: WARNING: all initial conditions for electron_density have not been defined and the undefined are assumed zero + ATC: WARNING: material: [cnt0] cannot find electron_flux + ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 55.2354 Mbytes +Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1] RSUM[1] + 0 -6146.5328 0 -1.2222229e-10 1.1111297e-10 98.69 -0.025 0 0 0 0 9.0465829e-16 -2.9442594e-15 8.5762791 0 6.8998626e-16 6.8998626e-16 + 10 -6148.8618 0 4.940931e-12 -2.2100035e-10 98.493762 -0.025 0 0 0 0 1.2098779e-09 -1.5844069e-09 8.9290499 0 -1.209881e-09 -1.209881e-09 + 20 -6149.9222 0 2.3540796e-12 -1.2223531e-10 98.220638 -0.025 0 0 0 0 -1.255241e-10 1.3853794e-11 9.0170496 0 1.2552811e-10 1.2552811e-10 + 30 -6150.857 0 -5.8780008e-12 -1.5206673e-10 98.082897 -0.025 0 0 0 0 1.1490666e-09 -5.0591806e-10 8.9773205 0 -1.149063e-09 -1.149063e-09 + 40 -6151.7874 0 6.0788906e-12 -1.2585104e-10 97.911664 -0.025 0 0 0 0 -7.6226226e-12 2.2822122e-10 8.969255 0 7.6276741e-12 7.6276741e-12 + 50 -6152.7403 0 -8.5868587e-12 -2.1662548e-12 97.725384 -0.025 0 0 0 0 6.8901152e-11 1.9872572e-10 8.9900713 0 -6.8910336e-11 -6.8910336e-11 + 60 -6153.6909 0 -2.3882229e-11 1.8005686e-10 97.514756 -0.025 0 0 0 0 -2.4792216e-10 5.8505025e-10 8.9790647 0 2.4791056e-10 2.4791056e-10 + 70 -6154.6186 0 -1.4341604e-11 1.0186267e-10 97.331185 -0.025 0 0 0 0 -2.5377242e-10 7.0580372e-10 8.9849053 0 2.5377634e-10 2.5377634e-10 + 80 -6155.5294 0 3.317641e-12 -1.0628218e-10 97.148448 -0.025 0 0 0 0 -3.6329208e-10 1.6682668e-10 5.3213166 0 3.6329e-10 3.6329e-10 + 90 -6155.6958 0 -7.4051845e-13 -1.7958969e-11 97.119481 -0.025 0 0 0 0 -2.6610771e-10 -2.1459841e-10 1.9442496 0 2.6610824e-10 2.6610824e-10 + 100 -6155.7311 0 -1.7366193e-12 4.0895485e-12 97.108958 -0.025 0 0 0 0 -2.2828441e-12 3.2760579e-10 1.8155088 0 2.2768396e-12 2.2768396e-12 + 110 -6155.7559 0 -3.7182375e-12 2.7076944e-11 97.099557 -0.025 0 0 0 0 -2.7283076e-10 3.148088e-10 1.6786296 0 2.7283883e-10 2.7283883e-10 + 120 -6155.7815 0 -1.6001509e-12 7.7718611e-12 97.084625 -0.025 0 0 0 0 -2.3085834e-10 -3.3010689e-10 0.84988485 0 2.3084659e-10 2.3084659e-10 + 130 -6155.8097 0 6.1918255e-12 -2.2013612e-11 97.037986 -0.025 0 0 0 0 3.8781477e-10 7.8589814e-10 -0.24071684 0 -3.8781011e-10 -3.8781011e-10 + 140 -6155.8296 0 9.1649429e-13 -5.8772777e-12 96.997528 -0.025 0 0 0 0 -2.9271952e-10 2.8177507e-10 0.21373041 0 2.9272128e-10 2.9272128e-10 + 150 -6155.8424 0 1.2990133e-12 1.6560103e-12 96.978985 -0.025 0 0 0 0 1.8917465e-10 -6.1365804e-10 0.34484179 0 -1.8917478e-10 -1.8917478e-10 + 160 -6155.8465 0 -8.7514622e-13 4.204932e-12 96.970352 -0.025 0 0 0 0 5.4505837e-10 -7.430968e-10 0.24626587 0 -5.4506486e-10 -5.4506486e-10 + 170 -6155.8471 0 -3.1964234e-12 3.3010755e-12 96.967294 -0.025 0 0 0 0 2.2410803e-10 -1.016244e-10 0.23959213 0 -2.2410755e-10 -2.2410755e-10 + 180 -6155.8485 0 -1.5534979e-11 9.5624334e-12 96.955682 -0.025 0 0 0 0 -2.0043328e-09 2.2585906e-09 0.27363173 0 2.0043342e-09 2.0043342e-09 + 190 -6155.8492 0 -2.0892941e-11 2.9371598e-11 96.950738 -0.025 0 0 0 0 3.8637701e-10 -5.3578627e-10 0.2536299 0 -3.8637116e-10 -3.8637116e-10 + 200 -6155.8498 0 -7.8964312e-12 1.3090003e-11 96.947508 -0.025 0 0 0 0 1.5603734e-09 -1.6272208e-09 0.15118948 0 -1.5603738e-09 -1.5603738e-09 + 210 -6155.8506 0 3.2330911e-11 -5.680355e-11 96.941553 -0.025 0 0 0 0 -5.1954511e-09 5.6107173e-09 0.074902549 0 5.1954505e-09 5.1954505e-09 + 220 -6155.8508 0 1.291125e-11 -1.4639389e-11 96.940685 -0.025 0 0 0 0 -7.2531212e-10 7.1522033e-10 0.075697866 0 7.253091e-10 7.253091e-10 + 230 -6155.8508 0 -2.1539062e-11 3.0981675e-11 96.940234 -0.025 0 0 0 0 3.4501174e-09 -3.3448009e-09 0.040836048 0 -3.4501143e-09 -3.4501143e-09 + 240 -6155.8508 0 -2.6136061e-12 1.0779917e-12 96.939825 -0.025 0 0 0 0 -6.485948e-10 4.904014e-10 0.032769742 0 6.4859596e-10 6.4859596e-10 + 250 -6155.8509 0 5.4062908e-11 -5.4847092e-11 96.939069 -0.025 0 0 0 0 -6.3245546e-09 5.8679399e-09 0.01865975 0 6.3245566e-09 6.3245566e-09 + 260 -6155.8509 0 1.9938451e-12 1.3745327e-11 96.938535 -0.025 0 0 0 0 2.8230301e-09 -1.7880768e-09 0.010102843 0 -2.8230281e-09 -2.8230281e-09 + 270 -6155.8509 0 -1.1673108e-11 7.7225918e-12 96.937968 -0.025 0 0 0 0 4.3671364e-10 -8.0304089e-10 0.01529266 0 -4.3670395e-10 -4.3670395e-10 + 280 -6155.851 0 3.1090928e-11 -2.3740814e-11 96.93705 -0.025 0 0 0 0 -1.2298254e-09 2.371559e-10 -0.0040591525 0 1.2298302e-09 1.2298302e-09 + 290 -6155.851 0 6.6834666e-12 -9.0749829e-12 96.936403 -0.025 0 0 0 0 -7.3137352e-10 1.0983283e-09 0.0010075626 0 7.3137798e-10 7.3137798e-10 + 300 -6155.851 0 9.4443218e-13 5.2069655e-13 96.936293 -0.025 0 0 0 0 4.9924787e-12 3.5018175e-10 0.0057823754 0 -4.9956751e-12 -4.9956751e-12 + 310 -6155.851 0 4.9457364e-11 -2.183241e-11 96.936135 -0.025 0 0 0 0 5.5646397e-10 -3.1013634e-09 0.0066174421 0 -5.5646838e-10 -5.5646838e-10 + 320 -6155.851 0 1.1303802e-11 -1.5610116e-11 96.935999 -0.025 0 0 0 0 9.3725597e-11 -2.0834063e-10 0.0066461623 0 -9.3720589e-11 -9.3720589e-11 + 330 -6155.851 0 -8.7492205e-11 5.0132409e-11 96.935781 -0.025 0 0 0 0 1.5034892e-09 4.8824636e-09 0.0058982085 0 -1.5034817e-09 -1.5034817e-09 + 340 -6155.851 0 1.4386338e-10 -4.2580912e-11 96.935678 -0.025 0 0 0 0 -4.4942366e-09 -4.8008051e-09 0.0019740498 0 4.4942601e-09 4.4942601e-09 + 350 -6155.851 0 -1.5770775e-12 -1.5554503e-11 96.935641 -0.025 0 0 0 0 -1.789129e-09 4.3210504e-10 0.0016260173 0 1.7891285e-09 1.7891285e-09 + 360 -6155.851 0 -1.3297897e-10 5.1630323e-11 96.935622 -0.025 0 0 0 0 9.3219024e-09 5.9535856e-10 0.00082004967 0 -9.3218922e-09 -9.3218922e-09 + 370 -6155.851 0 5.4333939e-11 -2.6192184e-11 96.935617 -0.025 0 0 0 0 -4.3663676e-10 -5.1620423e-10 0.0012789335 0 4.3664737e-10 4.3664737e-10 + 380 -6155.851 0 -6.6039258e-12 -7.5609136e-12 96.935612 -0.025 0 0 0 0 -8.3813595e-09 4.7199823e-09 0.0011369214 0 8.3813612e-09 8.3813612e-09 + 390 -6155.851 0 -1.0040056e-10 8.5325014e-11 96.935587 -0.025 0 0 0 0 1.1171651e-08 -1.0037805e-08 0.00012469127 0 -1.1171646e-08 -1.1171646e-08 + 400 -6155.851 0 5.0853732e-11 -4.2801835e-11 96.935572 -0.025 0 0 0 0 -1.9340418e-09 1.74979e-09 0.00019466711 0 1.9340627e-09 1.9340627e-09 + 410 -6155.851 0 1.2049586e-10 -9.9618548e-11 96.935543 -0.025 0 0 0 0 -2.0243059e-08 1.9356236e-08 0.0002523799 0 2.0243046e-08 2.0243046e-08 + 420 -6155.851 0 1.7899642e-11 3.5995836e-12 96.935531 -0.025 0 0 0 0 3.5620666e-09 -2.7057846e-09 0.00024873544 0 -3.5620556e-09 -3.5620556e-09 + 430 -6155.851 0 -2.3941392e-11 2.3004815e-11 96.935527 -0.025 0 0 0 0 9.3931782e-09 -8.5349023e-09 0.0001591579 0 -9.3931752e-09 -9.3931752e-09 + 440 -6155.851 0 1.3054108e-10 -1.2689303e-10 96.935522 -0.025 0 0 0 0 -2.63239e-08 2.3190494e-08 0.00014838156 0 2.6323909e-08 2.6323909e-08 + 450 -6155.851 0 -3.3583974e-12 2.1841662e-11 96.93552 -0.025 0 0 0 0 7.9211719e-09 -6.7971069e-09 0.00012051248 0 -7.921168e-09 -7.921168e-09 + 460 -6155.851 0 -6.7930456e-10 6.424851e-10 96.935514 -0.025 0 0 0 0 1.2429227e-07 -1.0630871e-07 0.00014409432 0 -1.2429226e-07 -1.2429226e-07 + 470 -6155.851 0 5.649524e-10 -5.6453071e-10 96.935512 -0.025 0 0 0 0 -1.0735848e-07 8.9872405e-08 0.00010631061 0 1.0735848e-07 1.0735848e-07 + 480 -6155.851 0 6.13809e-10 -4.9012022e-10 96.935509 -0.025 0 0 0 0 -5.5839534e-08 4.5710027e-08 8.7271236e-05 0 5.5839543e-08 5.5839543e-08 + 490 -6155.851 0 -6.1673512e-10 5.8106663e-10 96.935508 -0.025 0 0 0 0 8.9417248e-08 -6.795396e-08 4.2860856e-05 0 -8.941724e-08 -8.941724e-08 + 500 -6155.851 0 -1.4672717e-11 -1.0669776e-11 96.935508 -0.025 0 0 0 0 -1.9116216e-08 1.6870874e-08 3.2008126e-05 0 1.9116217e-08 1.9116217e-08 +Loop time of 100.289 on 4 procs for 500 steps with 846 atoms + +Minimization stats: + Stopping criterion = max force evaluations + Energy initial, next-to-last, final = + -6146.53284043 -6155.85100774 -6155.85100774 + Force two-norm initial, final = 9.08523 6.13752e-06 + Force max component initial, final = 2.35947 4.97842e-07 + Final line search alpha, max atom move = 1 4.97842e-07 + Iterations, force evaluations = 500 1000 + +Pair time (%) = 9.67277 (9.6449) +Neigh time (%) = 0 (0) +Comm time (%) = 6.21171 (6.19381) +Outpt time (%) = 2.68868 (2.68093) +Other time (%) = 81.7159 (81.4804) + +Nlocal: 211.5 ave 216 max 207 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 191.25 ave 261 max 126 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 47313 ave 52056 max 42570 min +Histogram: 1 0 1 0 0 0 0 1 0 1 + +Total # of neighbors = 189252 +Ave neighs/atom = 223.702 +Neighbor list builds = 0 +Dangerous builds = 0 + min_style sd + min_modify line backtrack + #minimize 0 0 100000 100000 + minimize 0 0 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: WARNING: material: [cnt0] cannot find electron_flux + ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 55.3135 Mbytes +Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1] RSUM[1] + 500 -6155.851 0 -1.4672652e-11 -1.0669743e-11 96.935508 -0.025 0 0 0 0 -1.9116216e-08 1.6870874e-08 3.2008126e-05 0 1.9116216e-08 1.9116216e-08 + 501 -6155.851 0 -1.4672652e-11 -1.0669743e-11 96.935508 -0.025 0 0 0 0 -1.9116216e-08 1.6870874e-08 3.2008126e-05 0 1.9116216e-08 1.9116216e-08 +Loop time of 0.124472 on 4 procs for 1 steps with 846 atoms + +Minimization stats: + Stopping criterion = linesearch alpha is zero + Energy initial, next-to-last, final = + -6155.85100774 -6155.85100774 -6155.85100774 + Force two-norm initial, final = 6.13752e-06 6.13752e-06 + Force max component initial, final = 4.97842e-07 4.97842e-07 + Final line search alpha, max atom move = 0.5 2.48921e-07 + Iterations, force evaluations = 1 2 + +Pair time (%) = 0.0223783 (17.9785) +Neigh time (%) = 0 (0) +Comm time (%) = 0.00169677 (1.36317) +Outpt time (%) = 0 (0) +Other time (%) = 0.100397 (80.6583) + +Nlocal: 211.5 ave 216 max 198 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 195.75 ave 261 max 126 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 48199.5 ave 53136 max 41085 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 192798 +Ave neighs/atom = 227.894 +Neighbor list builds = 0 +Dangerous builds = 0 + fix_modify AtC output now + + # u = F L^3 / 3 EI --> EI = F L^3 / 3 u + variable u equal c_CM[1] + variable uz equal c_CM[3] +# variable F equal f_AtC[5] +# variable Fz equal f_AtC[7] + variable F equal c_RSUM[1] + variable Fz equal c_RSUM[3] + variable R equal $F-$C*$b + variable R equal 1.9116216109081213915e-08-$C*$b + variable R equal 1.9116216109081213915e-08--0.025000000000000001388*$b + variable R equal 1.9116216109081213915e-08--0.025000000000000001388*0 + variable Rz equal ${Fz}-$C*$a + variable Rz equal -3.2008125606681979403e-05-$C*$a + variable Rz equal -3.2008125606681979403e-05--0.025000000000000001388*$a + variable Rz equal -3.2008125606681979403e-05--0.025000000000000001388*0 + variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u + variable EI equal 1.9116216109081213915e-08*${Lfree}*${Lfree}*${Lfree}/3./$u + variable EI equal 1.9116216109081213915e-08*90*${Lfree}*${Lfree}/3./$u + variable EI equal 1.9116216109081213915e-08*90*90*${Lfree}/3./$u + variable EI equal 1.9116216109081213915e-08*90*90*90/3./$u + variable EI equal 1.9116216109081213915e-08*90*90*90/3./-1.4672651617664272549e-11 + variable EI equal ${EI}*${eV2J}*${A2m} + variable EI equal -316591754.20715177059*${eV2J}*${A2m} + variable EI equal -316591754.20715177059*1.6021764600000000642e-19*${A2m} + variable EI equal -316591754.20715177059*1.6021764600000000642e-19*1.0000000000000000364e-10 + #print "flexural rigidity ${EI} [Nm^2] NOTE z force" + + print ">> V $b $a F $F ${Fz} u $u ${uz} c $c phi 0 EI ${EI} R $R ${Rz}" +>> V 0 0 F 1.9116216109081213915e-08 -3.2008125606681979403e-05 u -1.4672651617664272549e-11 96.935507997738042718 c -0.0027777777777777778838 phi 0 EI -5.072358560208045613e-21 R 1.9116216109081213915e-08 -3.2008125606681979403e-05 + next i + jump SELF loop_i + variable b equal ($i-1)*${Vg}/(${ng}-1)/${Lx} + variable b equal (2-1)*${Vg}/(${ng}-1)/${Lx} + variable b equal (2-1)*0.10000000000000000555/(${ng}-1)/${Lx} + variable b equal (2-1)*0.10000000000000000555/(4-1)/${Lx} + variable b equal (2-1)*0.10000000000000000555/(4-1)/1 + + fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a 0 + fix_modify AtC fix electric_potential all linear 0 0 0 0.033333333333333332871 0 $a 0 + fix_modify AtC fix electric_potential all linear 0 0 0 0.033333333333333332871 0 0 0 + ATC: created function : 0 + 0.0333333(x-0)+0(y-0)+0(z-0) + min_style cg + min_modify line quadratic + #minimize 0 0 100000 100000 + minimize 0 0 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: WARNING: material: [cnt0] cannot find electron_flux + ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 55.3135 Mbytes +Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1] RSUM[1] + 501 -6155.851 0 -1.4672652e-11 -1.0669743e-11 96.935508 -0.025 0 0 0 0.00083333333 -1.9116216e-08 1.6870874e-08 3.2008126e-05 1.222715e-14 0.00083335245 0.00083335245 + 510 -6155.851 0 7.5244067e-05 -1.3502021e-11 96.935508 -0.025 0 0 0 0.00083333333 3.2438701e-08 -3.0416424e-08 -1.4566602e-05 -6.2703389e-08 0.00083330089 0.00083330089 + 520 -6155.851 0 0.00023596516 2.4216597e-11 96.935508 -0.025 0 0 0 0.00083333333 -9.6655814e-09 1.7834635e-08 3.5959276e-05 -1.9663763e-07 0.000833343 0.000833343 + 530 -6155.851 0 0.0004521778 -1.8488146e-10 96.935507 -0.025 0 0 0 0.00083333333 -2.8087999e-08 1.4373107e-08 2.6399328e-05 -3.7681483e-07 0.00083336142 0.00083336142 + 540 -6155.851 0 0.00068686652 2.2560925e-10 96.935506 -0.025 0 0 0 0.00083333333 5.1280851e-08 -4.944283e-08 -2.3516917e-05 -5.7238876e-07 0.00083328205 0.00083328205 + 550 -6155.851 0 0.00097528387 -6.0249475e-11 96.935505 -0.025 0 0 0 0.00083333333 -3.0869719e-08 4.6053248e-08 -9.2849468e-06 -8.1273656e-07 0.0008333642 0.0008333642 + 560 -6155.851 0 0.0012888546 -4.7543618e-10 96.935504 -0.025 0 0 0 0.00083333333 -1.4084137e-08 -6.9499793e-09 3.5765609e-05 -1.0740455e-06 0.00083334742 0.00083334742 + 570 -6155.851 0 0.0016207689 7.8821517e-10 96.935503 -0.025 0 0 0 0.00083333333 2.0767366e-08 -2.5348885e-08 -4.7729297e-05 -1.3506408e-06 0.00083331257 0.00083331257 + 580 -6155.851 0 0.00198597 -5.3637299e-10 96.935501 -0.025 0 0 0 0.00083333333 -5.4517718e-06 9.2340557e-09 -4.9488581e-05 -1.654975e-06 0.00083878511 0.00083878511 + 590 -6155.851 0 0.0023856369 -4.1449046e-10 96.9355 -0.025 0 0 0 0.00083333333 -3.8437452e-05 2.7829132e-08 -6.8439705e-05 -1.9880307e-06 0.00087177079 0.00087177079 + 600 -6155.851 0 0.0028044617 1.0997501e-09 96.935499 -0.025 0 0 0 0.00083333333 2.0036119e-05 -2.8313041e-08 -0.00038373515 -2.3370514e-06 0.00081329721 0.00081329721 + 610 -6155.851 0 0.0032615703 -9.438232e-10 96.935498 -0.025 0 0 0 0.00083333333 -6.721699e-05 -1.6094486e-08 0.00026852221 -2.7179752e-06 0.00090055032 0.00090055032 + 620 -6155.851 0 0.0037228155 -9.8658553e-11 96.935498 -0.025 0 0 0 0.00083333333 -5.0356472e-05 6.6220662e-08 -0.00016057488 -3.1023462e-06 0.00088368981 0.00088368981 + 630 -6155.851 0 0.0042063596 4.5342852e-10 96.935499 -0.025 0 0 0 0.00083333333 -0.00024149697 -6.6311642e-08 -0.00013128121 -3.5052997e-06 0.0010748303 0.0010748303 + 640 -6155.851 0 0.0047053923 -4.4915583e-12 96.935498 -0.025 0 0 0 0.00083333333 0.00018476866 8.5931516e-09 -1.0920921e-05 -3.9211602e-06 0.00064856468 0.00064856468 + 650 -6155.851 0 0.0051780729 -5.9267245e-10 96.9355 -0.025 0 0 0 0.00083333333 0.0012250879 4.6153937e-08 0.00016791897 -4.3150607e-06 -0.00039175458 -0.00039175458 + 660 -6155.851 0 0.005528704 2.0178848e-10 96.935499 -0.025 0 0 0 0.00083333333 0.0023386089 -4.9920568e-08 -0.00030153107 -4.6072533e-06 -0.0015052756 -0.0015052756 + 670 -6155.851 0 0.0067930159 2.0337825e-09 96.935504 -0.025 0 0 0 0.00083333333 0.00277847 9.6153354e-08 -0.001427071 -5.6608465e-06 -0.0019451367 -0.0019451367 + 680 -6155.851 0 0.0091353864 -1.2005671e-09 96.935506 -0.025 0 0 0 0.00083333333 -0.00098634606 -5.6084108e-09 -0.0001949811 -7.612822e-06 0.0018196794 0.0018196794 + 690 -6155.851 0 0.0092720897 -6.6192949e-11 96.935506 -0.025 0 0 0 0.00083333333 -0.0015552585 -8.6270391e-10 9.3688022e-05 -7.7267414e-06 0.0023885919 0.0023885919 + 699 -6155.851 0 0.0093583676 1.0464746e-09 96.935509 -0.025 0 0 0 0.00083333333 -0.0017464739 2.5209399e-08 7.7398462e-05 -7.7986397e-06 0.0025798072 0.0025798072 +Loop time of 14.1081 on 4 procs for 198 steps with 846 atoms + +Minimization stats: + Stopping criterion = linesearch alpha is zero + Energy initial, next-to-last, final = + -6155.85100774 -6155.85101159 -6155.85101159 + Force two-norm initial, final = 0.000277846 0.0011336 + Force max component initial, final = 9.26371e-05 0.00012545 + Final line search alpha, max atom move = 0.0078125 9.80074e-07 + Iterations, force evaluations = 198 409 + +Pair time (%) = 3.19903 (22.6752) +Neigh time (%) = 0 (0) +Comm time (%) = 0.348575 (2.47075) +Outpt time (%) = 0.160979 (1.14104) +Other time (%) = 10.3995 (73.713) + +Nlocal: 211.5 ave 216 max 198 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 195.75 ave 261 max 126 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 48199.5 ave 53136 max 41085 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 192798 +Ave neighs/atom = 227.894 +Neighbor list builds = 0 +Dangerous builds = 0 + min_style sd + min_modify line backtrack + #minimize 0 0 100000 100000 + minimize 0 0 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: WARNING: material: [cnt0] cannot find electron_flux + ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 55.3135 Mbytes +Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1] RSUM[1] + 699 -6155.851 0 0.0093583676 1.0464746e-09 96.935509 -0.025 0 0 0 0.00083333333 -0.0017464739 2.5209399e-08 7.7398462e-05 -7.7986397e-06 0.0025798072 0.0025798072 + 700 -6155.851 0 0.0093585294 1.0053739e-09 96.935509 -0.025 0 0 0 0.00083333333 -0.0017544129 2.4247674e-08 5.1686313e-05 -7.7987745e-06 0.0025877462 0.0025877462 + 701 -6155.851 0 0.0093585294 1.0053739e-09 96.935509 -0.025 0 0 0 0.00083333333 -0.0017544129 2.4247674e-08 5.1686313e-05 -7.7987745e-06 0.0025877462 0.0025877462 +Loop time of 0.5394 on 4 procs for 2 steps with 846 atoms + +Minimization stats: + Stopping criterion = linesearch alpha is zero + Energy initial, next-to-last, final = + -6155.85101159 -6155.8510116 -6155.8510116 + Force two-norm initial, final = 0.0011336 0.000872834 + Force max component initial, final = 0.00012545 8.10661e-05 + Final line search alpha, max atom move = 0.015625 1.26666e-06 + Iterations, force evaluations = 2 14 + +Pair time (%) = 0.111926 (20.7502) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0156116 (2.89425) +Outpt time (%) = 0.0084697 (1.57021) +Other time (%) = 0.403392 (74.7853) + +Nlocal: 211.5 ave 216 max 198 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 195.75 ave 261 max 126 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 48199.5 ave 53136 max 41085 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 192798 +Ave neighs/atom = 227.894 +Neighbor list builds = 0 +Dangerous builds = 0 + fix_modify AtC output now + + # u = F L^3 / 3 EI --> EI = F L^3 / 3 u + variable u equal c_CM[1] + variable uz equal c_CM[3] +# variable F equal f_AtC[5] +# variable Fz equal f_AtC[7] + variable F equal c_RSUM[1] + variable Fz equal c_RSUM[3] + variable R equal $F-$C*$b + variable R equal 0.0025877461923070671154-$C*$b + variable R equal 0.0025877461923070671154--0.025000000000000001388*$b + variable R equal 0.0025877461923070671154--0.025000000000000001388*0.033333333333333332871 + variable Rz equal ${Fz}-$C*$a + variable Rz equal -5.16863129458517475e-05-$C*$a + variable Rz equal -5.16863129458517475e-05--0.025000000000000001388*$a + variable Rz equal -5.16863129458517475e-05--0.025000000000000001388*0 + variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u + variable EI equal 0.0025877461923070671154*${Lfree}*${Lfree}*${Lfree}/3./$u + variable EI equal 0.0025877461923070671154*90*${Lfree}*${Lfree}/3./$u + variable EI equal 0.0025877461923070671154*90*90*${Lfree}/3./$u + variable EI equal 0.0025877461923070671154*90*90*90/3./$u + variable EI equal 0.0025877461923070671154*90*90*90/3./0.0093585293597155689432 + variable EI equal ${EI}*${eV2J}*${A2m} + variable EI equal 67192.429553881200263*${eV2J}*${A2m} + variable EI equal 67192.429553881200263*1.6021764600000000642e-19*${A2m} + variable EI equal 67192.429553881200263*1.6021764600000000642e-19*1.0000000000000000364e-10 + #print "flexural rigidity ${EI} [Nm^2] NOTE z force" + + print ">> V $b $a F $F ${Fz} u $u ${uz} c $c phi 0 EI ${EI} R $R ${Rz}" +>> V 0.033333333333333332871 0 F 0.0025877461923070671154 -5.16863129458517475e-05 u 0.0093585293597155689432 96.935509332376838643 c -0.0027777777777777778838 phi 0 EI 1.0765412892143675813e-24 R 0.0034210795256404006107 -5.16863129458517475e-05 + next i + jump SELF loop_i + variable b equal ($i-1)*${Vg}/(${ng}-1)/${Lx} + variable b equal (3-1)*${Vg}/(${ng}-1)/${Lx} + variable b equal (3-1)*0.10000000000000000555/(${ng}-1)/${Lx} + variable b equal (3-1)*0.10000000000000000555/(4-1)/${Lx} + variable b equal (3-1)*0.10000000000000000555/(4-1)/1 + + fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a 0 + fix_modify AtC fix electric_potential all linear 0 0 0 0.066666666666666665741 0 $a 0 + fix_modify AtC fix electric_potential all linear 0 0 0 0.066666666666666665741 0 0 0 + ATC: created function : 0 + 0.0666667(x-0)+0(y-0)+0(z-0) + min_style cg + min_modify line quadratic + #minimize 0 0 100000 100000 + minimize 0 0 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: WARNING: material: [cnt0] cannot find electron_flux + ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 55.3135 Mbytes +Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1] RSUM[1] + 701 -6155.851 0 0.0093585294 1.0053739e-09 96.935509 -0.025 0 0 0 0.0016666667 -0.0017544129 2.4247674e-08 5.1686313e-05 -1.5597549e-05 0.0034210795 0.0034210795 + 710 -6155.851 0 0.0093927498 -5.1805658e-10 96.935509 -0.025 0 0 0 0.0016666667 -0.001496399 -1.5573071e-08 7.0866631e-05 -1.5654583e-05 0.0031630657 0.0031630657 + 720 -6155.851 0 0.0095888777 -5.6216657e-11 96.935505 -0.025 0 0 0 0.0016666667 -0.0012004213 3.8090266e-08 -0.00014799652 -1.5981463e-05 0.002867088 0.002867088 + 730 -6155.851 0 0.0099072785 4.4310767e-10 96.935503 -0.025 0 0 0 0.0016666667 -0.0012734816 3.5022383e-09 -0.00014979591 -1.6512131e-05 0.0029401483 0.0029401483 + 740 -6155.851 0 0.010283518 -1.5173013e-09 96.935504 -0.025 0 0 0 0.0016666667 -0.0010070513 -1.0777316e-07 8.9852513e-05 -1.7139197e-05 0.0026737179 0.0026737179 + 750 -6155.851 0 0.010683953 1.4747556e-09 96.935501 -0.025 0 0 0 0.0016666667 -0.00089533919 1.3811485e-07 -6.6972671e-05 -1.7806589e-05 0.0025620059 0.0025620059 + 760 -6155.851 0 0.011131302 -8.2231093e-10 96.9355 -0.025 0 0 0 0.0016666667 -0.00011238797 -3.2303593e-08 -3.3022463e-06 -1.855217e-05 0.0017790546 0.0017790546 + 770 -6155.851 0 0.011585226 1.1357581e-10 96.9355 -0.025 0 0 0 0.0016666667 -0.0008139296 -1.0279988e-07 7.672706e-05 -1.9308709e-05 0.0024805963 0.0024805963 + 780 -6155.851 0 0.012015856 -1.7079649e-11 96.935492 -0.025 0 0 0 0.0016666667 -0.00011750039 1.4724756e-07 2.6085857e-05 -2.0026427e-05 0.0017841671 0.0017841671 + 790 -6155.851 0 0.012432647 -5.7454545e-10 96.935489 -0.025 0 0 0 0.0016666667 -2.6583326e-05 -5.8164597e-08 -0.00024192986 -2.0721078e-05 0.00169325 0.00169325 + 800 -6155.851 0 0.012864332 1.1612045e-09 96.935494 -0.025 0 0 0 0.0016666667 -0.00013922996 -7.3129958e-08 0.00017322782 -2.1440553e-05 0.0018058966 0.0018058966 + 810 -6155.851 0 0.013534631 -1.599629e-09 96.935497 -0.025 0 0 0 0.0016666667 0.00021713244 2.0110132e-07 -0.00011691578 -2.2557718e-05 0.0014495342 0.0014495342 + 820 -6155.851 0 0.014473048 1.4920287e-09 96.935488 -0.025 0 0 0 0.0016666667 0.00072740903 -2.2264896e-07 -0.00025826088 -2.4121746e-05 0.00093925764 0.00093925764 + 830 -6155.851 0 0.015814165 9.9540852e-10 96.935488 -0.025 0 0 0 0.0016666667 -0.00020150428 -1.4648382e-07 5.1213137e-05 -2.6356941e-05 0.0018681709 0.0018681709 + 840 -6155.851 0 0.017960316 -3.6691752e-09 96.935483 -0.025 0 0 0 0.0016666667 0.00095321447 6.0691053e-07 0.00078150564 -2.993386e-05 0.0007134522 0.0007134522 + 850 -6155.851 0 0.020433235 1.5826068e-09 96.935477 -0.025 0 0 0 0.0016666667 0.0035255313 -2.7216094e-07 -0.0011364529 -3.4055392e-05 -0.0018588646 -0.0018588646 + 860 -6155.851 0 0.023085812 3.1475892e-09 96.935486 -0.025 0 0 0 0.0016666667 0.01015645 -5.3450364e-07 -0.00055909791 -3.8476354e-05 -0.0084897836 -0.0084897836 + 870 -6155.851 0 0.027552884 -1.0798686e-08 96.935526 -0.025 0 0 0 0.0016666667 0.016481473 2.2189423e-06 0.0016007847 -4.5921473e-05 -0.014814807 -0.014814807 + 880 -6155.8511 0 0.055457179 -1.535611e-08 96.935606 -0.025 0 0 0 0.0016666667 0.013469024 1.8368724e-06 0.007644777 -9.2428631e-05 -0.011802357 -0.011802357 + 890 -6155.8511 0 0.070355074 3.8023025e-09 96.93559 -0.025 0 0 0 0.0016666667 0.0045123223 -1.0894883e-06 0.0012650095 -0.00011725846 -0.0028456556 -0.0028456556 + 900 -6155.8511 0 0.071239511 -9.5003883e-11 96.935566 -0.025 0 0 0 0.0016666667 0.0041482123 5.3052778e-08 0.0013631978 -0.00011873252 -0.0024815456 -0.0024815456 + 910 -6155.8511 0 0.071770633 1.2925244e-09 96.935508 -0.025 0 0 0 0.0016666667 0.0041066236 3.455464e-07 -4.7637007e-05 -0.00011961772 -0.0024399569 -0.0024399569 + 920 -6155.8511 0 0.07241886 -3.7163732e-10 96.935444 -0.025 0 0 0 0.0016666667 0.0043614531 -4.0071843e-07 -0.0020847574 -0.0001206981 -0.0026947864 -0.0026947864 + 930 -6155.8511 0 0.08035653 -8.2019055e-09 96.935169 -0.025 0 0 0 0.0016666667 0.0030840679 -1.6577238e-06 -0.0028722541 -0.00013392755 -0.0014174012 -0.0014174012 + 940 -6155.8511 0 0.10233759 1.4658533e-09 96.934738 -0.025 0 0 0 0.0016666667 0.0030986023 6.3718151e-07 0.0075147368 -0.00017056265 -0.0014319357 -0.0014319357 + 950 -6155.8511 0 0.1091589 4.8592844e-10 96.934799 -0.025 0 0 0 0.0016666667 0.0019854702 -1.4318185e-07 0.012415464 -0.00018193149 -0.00031880356 -0.00031880356 + 960 -6155.8511 0 0.12158268 2.8258211e-09 96.935015 -0.025 0 0 0 0.0016666667 0.0013596908 -1.5767032e-06 0.0030979015 -0.00020263779 0.00030697591 0.00030697591 + 970 -6155.8511 0 0.12403838 -1.3425882e-09 96.935054 -0.025 0 0 0 0.0016666667 0.0017582125 -2.2550336e-07 -0.0026021546 -0.00020673063 -9.1545869e-05 -9.1545869e-05 + 972 -6155.8511 0 0.12405405 -2.2177075e-10 96.935054 -0.025 0 0 0 0.0016666667 0.0017724415 -1.7549598e-07 -0.0025842017 -0.00020675674 -0.00010577487 -0.00010577487 +Loop time of 25.365 on 4 procs for 271 steps with 846 atoms + +Minimization stats: + Stopping criterion = linesearch alpha is zero + Energy initial, next-to-last, final = + -6155.8510194 -6155.85111851 -6155.85111851 + Force two-norm initial, final = 0.000910877 0.000855978 + Force max component initial, final = 9.24024e-05 8.83791e-05 + Final line search alpha, max atom move = 0.015625 1.38092e-06 + Iterations, force evaluations = 271 553 + +Pair time (%) = 4.51795 (17.8118) +Neigh time (%) = 0 (0) +Comm time (%) = 1.02193 (4.0289) +Outpt time (%) = 0.702078 (2.7679) +Other time (%) = 19.123 (75.3914) + +Nlocal: 211.5 ave 216 max 198 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 195.75 ave 261 max 126 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 48199.5 ave 53136 max 41085 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 192798 +Ave neighs/atom = 227.894 +Neighbor list builds = 0 +Dangerous builds = 0 + min_style sd + min_modify line backtrack + #minimize 0 0 100000 100000 + minimize 0 0 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: WARNING: material: [cnt0] cannot find electron_flux + ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 55.3135 Mbytes +Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1] RSUM[1] + 972 -6155.8511 0 0.12405405 -2.2177075e-10 96.935054 -0.025 0 0 0 0.0016666667 0.0017724415 -1.7549598e-07 -0.0025842017 -0.00020675674 -0.00010577487 -0.00010577487 + 973 -6155.8511 0 0.12405405 -2.2177075e-10 96.935054 -0.025 0 0 0 0.0016666667 0.0017724415 -1.7549598e-07 -0.0025842017 -0.00020675674 -0.00010577487 -0.00010577487 +Loop time of 0.277416 on 4 procs for 1 steps with 846 atoms + +Minimization stats: + Stopping criterion = linesearch alpha is zero + Energy initial, next-to-last, final = + -6155.85111851 -6155.85111851 -6155.85111851 + Force two-norm initial, final = 0.000855978 0.000855978 + Force max component initial, final = 8.83791e-05 8.83791e-05 + Final line search alpha, max atom move = 0.015625 1.38092e-06 + Iterations, force evaluations = 1 7 + +Pair time (%) = 0.0593559 (21.396) +Neigh time (%) = 0 (0) +Comm time (%) = 0.00413132 (1.48921) +Outpt time (%) = 0 (0) +Other time (%) = 0.213929 (77.1148) + +Nlocal: 211.5 ave 216 max 198 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 195.75 ave 261 max 126 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 48199.5 ave 53136 max 41085 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 192798 +Ave neighs/atom = 227.894 +Neighbor list builds = 0 +Dangerous builds = 0 + fix_modify AtC output now + + # u = F L^3 / 3 EI --> EI = F L^3 / 3 u + variable u equal c_CM[1] + variable uz equal c_CM[3] +# variable F equal f_AtC[5] +# variable Fz equal f_AtC[7] + variable F equal c_RSUM[1] + variable Fz equal c_RSUM[3] + variable R equal $F-$C*$b + variable R equal -0.00010577487498249815213-$C*$b + variable R equal -0.00010577487498249815213--0.025000000000000001388*$b + variable R equal -0.00010577487498249815213--0.025000000000000001388*0.066666666666666665741 + variable Rz equal ${Fz}-$C*$a + variable Rz equal 0.0025842016931355718881-$C*$a + variable Rz equal 0.0025842016931355718881--0.025000000000000001388*$a + variable Rz equal 0.0025842016931355718881--0.025000000000000001388*0 + variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u + variable EI equal -0.00010577487498249815213*${Lfree}*${Lfree}*${Lfree}/3./$u + variable EI equal -0.00010577487498249815213*90*${Lfree}*${Lfree}/3./$u + variable EI equal -0.00010577487498249815213*90*90*${Lfree}/3./$u + variable EI equal -0.00010577487498249815213*90*90*90/3./$u + variable EI equal -0.00010577487498249815213*90*90*90/3./0.12405404654784669971 + variable EI equal ${EI}*${eV2J}*${A2m} + variable EI equal -207.1943264731270915*${eV2J}*${A2m} + variable EI equal -207.1943264731270915*1.6021764600000000642e-19*${A2m} + variable EI equal -207.1943264731270915*1.6021764600000000642e-19*1.0000000000000000364e-10 + #print "flexural rigidity ${EI} [Nm^2] NOTE z force" + + print ">> V $b $a F $F ${Fz} u $u ${uz} c $c phi 0 EI ${EI} R $R ${Rz}" +>> V 0.066666666666666665741 0 F -0.00010577487498249815213 0.0025842016931355718881 u 0.12405404654784669971 96.935053768033569099 c -0.0027777777777777778838 phi 0 EI -3.3196187252079907596e-27 R 0.0015608917916841685402 0.0025842016931355718881 + next i + jump SELF loop_i + variable b equal ($i-1)*${Vg}/(${ng}-1)/${Lx} + variable b equal (4-1)*${Vg}/(${ng}-1)/${Lx} + variable b equal (4-1)*0.10000000000000000555/(${ng}-1)/${Lx} + variable b equal (4-1)*0.10000000000000000555/(4-1)/${Lx} + variable b equal (4-1)*0.10000000000000000555/(4-1)/1 + + fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a 0 + fix_modify AtC fix electric_potential all linear 0 0 0 0.10000000000000001943 0 $a 0 + fix_modify AtC fix electric_potential all linear 0 0 0 0.10000000000000001943 0 0 0 + ATC: created function : 0 + 0.1(x-0)+0(y-0)+0(z-0) + min_style cg + min_modify line quadratic + #minimize 0 0 100000 100000 + minimize 0 0 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: WARNING: material: [cnt0] cannot find electron_flux + ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 55.3135 Mbytes +Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1] RSUM[1] + 973 -6155.8512 0 0.12405405 -2.2177075e-10 96.935054 -0.025 0 0 0 0.0025 0.0017724415 -1.7549598e-07 -0.0025842017 -0.00031013512 0.00072755846 0.00072755846 + 977 -6155.8512 0 0.12406088 -1.0970139e-09 96.935055 -0.025 0 0 0 0.0025 0.0017262049 -1.3531203e-07 -0.0026622077 -0.0003101522 0.00077379508 0.00077379508 +Loop time of 1.007 on 4 procs for 4 steps with 846 atoms + +Minimization stats: + Stopping criterion = linesearch alpha is zero + Energy initial, next-to-last, final = + -6155.85122189 -6155.85122188 -6155.85122188 + Force two-norm initial, final = 0.000891466 0.000702795 + Force max component initial, final = 0.000104825 6.49275e-05 + Final line search alpha, max atom move = 0.015625 1.01449e-06 + Iterations, force evaluations = 4 19 + +Pair time (%) = 0.155607 (15.4525) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0349094 (3.46666) +Outpt time (%) = 0 (0) +Other time (%) = 0.816487 (81.0808) + +Nlocal: 211.5 ave 216 max 198 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 195.75 ave 261 max 126 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 48199.5 ave 53136 max 41085 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 192798 +Ave neighs/atom = 227.894 +Neighbor list builds = 0 +Dangerous builds = 0 + min_style sd + min_modify line backtrack + #minimize 0 0 100000 100000 + minimize 0 0 1000 1000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) +Setting up minimization ... + ATC: WARNING: material: [cnt0] cannot find electron_flux + ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 55.3135 Mbytes +Step TotEng KinEng CM[1] CM[2] CM[3] Q AtC[4] AtC[5] AtC[6] AtC[7] FIX[1] FIX[2] FIX[3] AtC FSUM[1] RSUM[1] + 977 -6155.8512 0 0.12406088 -1.0970139e-09 96.935055 -0.025 0 0 0 0.0025 0.0017262049 -1.3531203e-07 -0.0026622077 -0.0003101522 0.00077379508 0.00077379508 + 978 -6155.8512 0 0.12406088 -1.0970139e-09 96.935055 -0.025 0 0 0 0.0025 0.0017262049 -1.3531203e-07 -0.0026622077 -0.0003101522 0.00077379508 0.00077379508 +Loop time of 0.277741 on 4 procs for 1 steps with 846 atoms + +Minimization stats: + Stopping criterion = linesearch alpha is zero + Energy initial, next-to-last, final = + -6155.85122188 -6155.85122188 -6155.85122188 + Force two-norm initial, final = 0.000702795 0.000702795 + Force max component initial, final = 6.49275e-05 6.49275e-05 + Final line search alpha, max atom move = 0.015625 1.01449e-06 + Iterations, force evaluations = 1 7 + +Pair time (%) = 0.0594354 (21.3995) +Neigh time (%) = 0 (0) +Comm time (%) = 0.00418288 (1.50603) +Outpt time (%) = 0 (0) +Other time (%) = 0.214123 (77.0944) + +Nlocal: 211.5 ave 216 max 198 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 195.75 ave 261 max 126 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 48199.5 ave 53136 max 41085 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 192798 +Ave neighs/atom = 227.894 +Neighbor list builds = 0 +Dangerous builds = 0 + fix_modify AtC output now + + # u = F L^3 / 3 EI --> EI = F L^3 / 3 u + variable u equal c_CM[1] + variable uz equal c_CM[3] +# variable F equal f_AtC[5] +# variable Fz equal f_AtC[7] + variable F equal c_RSUM[1] + variable Fz equal c_RSUM[3] + variable R equal $F-$C*$b + variable R equal 0.00077379508410631867108-$C*$b + variable R equal 0.00077379508410631867108--0.025000000000000001388*$b + variable R equal 0.00077379508410631867108--0.025000000000000001388*0.10000000000000001943 + variable Rz equal ${Fz}-$C*$a + variable Rz equal 0.0026622076933775122923-$C*$a + variable Rz equal 0.0026622076933775122923--0.025000000000000001388*$a + variable Rz equal 0.0026622076933775122923--0.025000000000000001388*0 + variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u + variable EI equal 0.00077379508410631867108*${Lfree}*${Lfree}*${Lfree}/3./$u + variable EI equal 0.00077379508410631867108*90*${Lfree}*${Lfree}/3./$u + variable EI equal 0.00077379508410631867108*90*90*${Lfree}/3./$u + variable EI equal 0.00077379508410631867108*90*90*90/3./$u + variable EI equal 0.00077379508410631867108*90*90*90/3./0.12406087903930071437 + variable EI equal ${EI}*${eV2J}*${A2m} + variable EI equal 1515.6446326506320474*${eV2J}*${A2m} + variable EI equal 1515.6446326506320474*1.6021764600000000642e-19*${A2m} + variable EI equal 1515.6446326506320474*1.6021764600000000642e-19*1.0000000000000000364e-10 + #print "flexural rigidity ${EI} [Nm^2] NOTE z force" + + print ">> V $b $a F $F ${Fz} u $u ${uz} c $c phi 0 EI ${EI} R $R ${Rz}" +>> V 0.10000000000000001943 0 F 0.00077379508410631867108 0.0026622076933775122923 u 0.12406087903930071437 96.935055022011525239 c -0.0027777777777777778838 phi 0 EI 2.4283301521581904147e-26 R 0.0032737950841063190484 0.0026622076933775122923 + next i + jump SELF loop_i + diff --git a/examples/USER/atc/elastic/electrostatic_bending_dos.screen b/examples/USER/atc/elastic/electrostatic_bending_dos.screen new file mode 100644 index 0000000000..67c07ee0a9 --- /dev/null +++ b/examples/USER/atc/elastic/electrostatic_bending_dos.screen @@ -0,0 +1,632 @@ +LAMMPS (14 Aug 2013) +units metal +atom_style charge +dielectric 1. + +boundary s s f +# read in CNT +read_data min_CNT_dos.data +Reading data file ... + orthogonal box = (-3.72623 -3.66963 0) to (3.60284 3.66963 100) + 1 by 1 by 4 MPI processor grid + 846 atoms + 846 velocities +set group all charge 0 +Setting atom values ... + 846 settings made for charge +lattice diamond 3.6 +Lattice spacing in x,y,z = 3.6 3.6 3.6 +pair_style airebo 3.0 +pair_coeff * * ./CH.airebo C +mass * 12.01 + +compute q all property/atom q +compute Q all reduce sum c_q + +# PARAMETERS----------------------------- +# [eV/A * A^2] --> [N m] +variable eV2J equal 1.60217646e-19 +variable A2m equal 1.e-10 + +variable Lx equal xhi-xlo +variable L equal zhi-zlo +variable zTip equal zhi-3.5 +variable zFree equal zhi +variable R equal 12.1/2 +variable xhiFE equal 5.0*$R +variable xhiFE equal 5.0*6.0499999999999998224 +variable xloFE equal -${xhiFE} +variable xloFE equal -30.25 +variable yhiFE equal $R +variable yhiFE equal 6.0499999999999998224 +variable yloFE equal -${yhiFE} +variable yloFE equal -6.0499999999999998224 +variable zloFE equal zlo+10 # create fixed ghosts +variable zhiFE equal zhi+(zhi-${zloFE})/12*2 +variable zhiFE equal zhi+(zhi-10)/12*2 +variable Lfree equal zhi-${zloFE} +variable Lfree equal zhi-10 +variable nx equal 10 # 5 +variable nz equal 14 # 12 +print "Length $L [${zloFE}, ${zhiFE}] ${zTip}" +Length 100 [10, 115] 96.5 + +variable Vb equal 0.1 +variable Vg equal 0.15 +variable V0 equal 1. # 2. +print "bias voltage ${Vb}, gate voltage ${Vg}" +bias voltage 0.10000000000000000555, gate voltage 0.14999999999999999445 + +variable ng equal 3 + +variable n equal 100000 +variable s equal 250 +# END ----------------------------------- + +region TIP block INF INF INF INF ${zTip} INF units box +region TIP block INF INF INF INF 96.5 INF units box +group TIP region TIP +9 atoms in group TIP + +region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 -6.0499999999999998224 ${yhiFE} ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 -6.0499999999999998224 6.0499999999999998224 ${zloFE} ${zhiFE} units box +region feRegion block -30.25 30.25 -6.0499999999999998224 6.0499999999999998224 10 ${zhiFE} units box +region feRegion block -30.25 30.25 -6.0499999999999998224 6.0499999999999998224 10 115 units box +group internal region feRegion +756 atoms in group internal +group FIXED subtract all internal +90 atoms in group FIXED +fix FIX FIXED setforce 0 0 0 + +thermo 10 +set group all image 0 0 0 +Setting atom values ... + 846 settings made for image +compute CM TIP com +thermo_style custom step c_Q etotal c_CM[1] c_CM[3] +#minimize 0 0 1000 1000 +#write_restart min_CNT_dos.rst +run 0 +Setting up run ... +Memory usage per processor = 2.45103 Mbytes +Step Q TotEng CM[1] CM[3] + 0 0 -6155.851 -3752.4867 -51103.063 +Loop time of 0.00996494 on 4 procs for 0 steps with 846 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 0 (0) +Outpt time (%) = 0 (0) +Other time (%) = 0.00996494 (100) + +Nlocal: 211.5 ave 216 max 198 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 159.75 ave 216 max 108 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 37714.5 ave 40824 max 32904 min +Histogram: 1 0 0 0 1 0 0 0 0 2 + +Total # of neighbors = 150858 +Ave neighs/atom = 178.319 +Neighbor list builds = 0 +Dangerous builds = 0 +#EXIT +variable L equal c_CM[1] +variable Lx equal $L +variable Lx equal -3752.4866657778384251 +variable dx equal c_CM[1]-${Lx} +variable dx equal c_CM[1]--3752.4866657778384251 +variable L equal c_CM[3] +variable Lz equal $L +variable Lz equal -51103.063299276320322 +variable dz equal c_CM[3]-${Lz} +variable dz equal c_CM[3]--51103.063299276320322 +print "initial ${Lx} ${Lz} " +initial -3752.4866657778384251 -51103.063299276320322 + +variable nAll equal count(all) +variable nGhost equal count(all)-count(internal) +print ">>> number of stationary ghosts: ${nGhost} of ${nAll}" +>>> number of stationary ghosts: 90 of 846 + +neighbor 5. bin +neigh_modify every 10 delay 0 check no +timestep 0 +thermo 100 + +# coupling ............................................................ +fix AtC internal atc electrostatic CNT_electrostatic2.mat +ATC: constructing electrostatic mechanical coupling with parameter file CNT_electrostatic2.mat + ATC: peratom PE compute created with ID: 6 + ATC: computed mass density : 2.05933 + ATC: 1 materials defined from CNT_electrostatic2.mat + ATC: creating electrostatic extrinsic model + ATC: computed mass density : 2.05933 + ATC: 1 materials defined from CNT_electrostatic2.mat + ATC: computed mass density : 2.05933 + ATC: 1 materials defined from CNT_electrostatic2.mat +fix_modify AtC omit atomic_charge +#fix_modify AtC internal_quadrature off ## NOTE active -> error +# note weights don't affect phi or f i.e. they divide out +fix_modify AtC atom_weight constant internal 1.0 +fix_modify AtC extrinsic short_range off +fix_modify AtC source_integration atom +fix_modify AtC atom_element_map eulerian 1 +fix_modify AtC control momentum none # flux + +fix_modify AtC mesh create ${nx} 1 ${nz} feRegion f p f +fix_modify AtC mesh create 10 1 ${nz} feRegion f p f +fix_modify AtC mesh create 10 1 14 feRegion f p f + ATC: created uniform mesh with 330 nodes, 165 unique nodes, and 140 elements + +# node sets ............................................................ +variable t equal 1.1*$R +variable t equal 1.1*6.0499999999999998224 +fix_modify AtC mesh create_nodeset tube -$t $t -$t $t ${zloFE} ${zFree} units box +fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 $t -$t $t ${zloFE} ${zFree} units box +fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -$t $t ${zloFE} ${zFree} units box +fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 $t ${zloFE} ${zFree} units box +fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 ${zloFE} ${zFree} units box +fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 ${zFree} units box +fix_modify AtC mesh create_nodeset tube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 100 units box + ATC: created nodeset tube with 39 nodes +fix_modify AtC mesh create_nodeset lefttube -$t $t -$t $t ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 $t -$t $t ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -$t $t ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 $t ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 ${zloFE} units box +fix_modify AtC mesh create_nodeset lefttube -6.6550000000000002487 6.6550000000000002487 -6.6550000000000002487 6.6550000000000002487 10 10 units box + ATC: created nodeset lefttube with 3 nodes +fix_modify AtC mesh create_nodeset rbc INF INF INF INF ${zhiFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset rbc INF INF INF INF 115 ${zhiFE} units box +fix_modify AtC mesh create_nodeset rbc INF INF INF INF 115 115 units box + ATC: created nodeset rbc with 11 nodes +fix_modify AtC mesh create_nodeset lbc INF INF INF INF ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset lbc INF INF INF INF 10 ${zloFE} units box +fix_modify AtC mesh create_nodeset lbc INF INF INF INF 10 10 units box + ATC: created nodeset lbc with 11 nodes +fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} INF INF INF INF units box +fix_modify AtC mesh create_nodeset top 30.25 ${xhiFE} INF INF INF INF units box +fix_modify AtC mesh create_nodeset top 30.25 30.25 INF INF INF INF units box + ATC: created nodeset top with 15 nodes +fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} INF INF INF INF units box +fix_modify AtC mesh create_nodeset bot -30.25 ${xloFE} INF INF INF INF units box +fix_modify AtC mesh create_nodeset bot -30.25 -30.25 INF INF INF INF units box + ATC: created nodeset bot with 15 nodes + +# boundary conditions .................................................. +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix displacement y lbc 0. +fix_modify AtC fix displacement z lbc 0. +fix_modify AtC fix velocity x lbc 0. +fix_modify AtC fix velocity y lbc 0. +fix_modify AtC fix velocity z lbc 0. + +# minimize ............................................................. +compute FSUM all reduce sum fx fy fz +compute RSUM internal reduce sum fx fy fz + +thermo $s +thermo 250 +fix_modify AtC output electrostatic_bending_dosFE 100000000 full_text binary + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +fix_modify AtC output index step + +# store original (reference) coordinates +fix X all store/state 0 x y z + +# NOTE not recognized as vector by paraview - due to dump2ensight +variable uX atom x-f_X[1] +variable uY atom y-f_X[2] +variable uZ atom z-f_X[3] +#variable uX atom x-f_AtC[1] +#variable uY atom y-f_AtC[2] +#variable uZ atom z-f_AtC[3] +variable rho atom mass*f_AtC[4] +dump CONFIG all custom 100000 electrostatic_bending_dos.dmp id type x y z c_q v_uX v_uY v_uZ v_rho + +reset_timestep 0 +log electrostatic_bending_dos.log + +thermo 10 # 1 # 10 +min_modify line quadratic +variable a equal 0 +variable i loop ${ng} +variable i loop 3 +thermo_style custom step c_Q pe v_dx v_dz f_FIX[1] f_FIX[3] +label loop_i + variable b equal ($i-1)*${Vg}/${ng}/${Lz} + variable b equal (1-1)*${Vg}/${ng}/${Lz} + variable b equal (1-1)*0.14999999999999999445/${ng}/${Lz} + variable b equal (1-1)*0.14999999999999999445/3/${Lz} + variable b equal (1-1)*0.14999999999999999445/3/-51103.063299276320322 + fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a ${V0} # << physics and will be treated as null +Memory usage per processor = 51.8077 Mbytes +Step Q PotEng dx dz FIX[1] FIX[3] + 0 0 -6155.851 0 0 2.2200304e-11 0.010686876 + 10 0 -6155.851 2.7284841e-12 -0.00060946523 5.7770455e-11 0.0091922227 + 20 0 -6155.851 4.0927262e-12 -0.0011905579 -4.4327736e-13 0.0001153156 + 30 0 -6155.851 4.5474735e-12 -0.0011946243 2.1081175e-11 1.3099811e-05 + 40 0 -6155.851 4.5474735e-12 -0.0011946457 2.2032078e-11 6.8020645e-06 + 50 0 -6155.851 5.4569682e-12 -0.0011947265 2.2896851e-11 6.476084e-06 + 60 0 -6155.851 7.730705e-12 -0.0011953427 2.2953812e-11 3.5758304e-06 + 70 0 -6155.851 8.1854523e-12 -0.0011954794 1.9801188e-11 8.3950483e-07 + 80 0 -6155.851 8.1854523e-12 -0.0011954783 1.8441963e-11 2.9804539e-07 + 90 0 -6155.851 7.2759576e-12 -0.0011954747 2.1744013e-11 -3.8789192e-08 + 100 0 -6155.851 7.730705e-12 -0.0011954732 1.9237549e-11 -2.8935894e-09 + 110 0 -6155.851 7.2759576e-12 -0.0011954716 1.9095805e-11 1.6112378e-09 + 120 0 -6155.851 8.1854523e-12 -0.0011954714 1.9817977e-11 4.6976383e-09 + 130 0 -6155.851 7.730705e-12 -0.0011954714 1.7488642e-11 3.2517748e-09 + 140 0 -6155.851 1.0004442e-11 -0.0011954717 1.5207016e-11 2.7887026e-11 + 150 0 -6155.851 1.0459189e-11 -0.0011954718 1.7530141e-11 6.6725403e-11 + 160 0 -6155.851 1.0913936e-11 -0.0011954718 1.7545739e-11 8.9193097e-12 + 170 0 -6155.851 1.0913936e-11 -0.0011954718 1.7562698e-11 8.2844842e-12 + 180 0 -6155.851 1.0913936e-11 -0.0011954718 1.7454236e-11 8.3764107e-12 + 190 0 -6155.851 1.0913936e-11 -0.0011954718 1.7391744e-11 8.3804075e-12 + 200 0 -6155.851 1.0913936e-11 -0.0011954718 1.7363343e-11 8.2092111e-12 + 210 0 -6155.851 1.0913936e-11 -0.0011954718 1.7510129e-11 8.3804075e-12 + 220 0 -6155.851 1.0913936e-11 -0.0011954718 1.7388087e-11 8.3107965e-12 + 230 0 -6155.851 1.0913936e-11 -0.0011954718 1.7328517e-11 8.3658636e-12 + 240 0 -6155.851 1.0913936e-11 -0.0011954718 1.7553941e-11 8.2239771e-12 + 250 0 -6155.851 1.0913936e-11 -0.0011954718 1.7431705e-11 7.9389828e-12 + 260 0 -6155.851 1.0913936e-11 -0.0011954718 1.7440851e-11 8.2803764e-12 + 270 0 -6155.851 1.0913936e-11 -0.0011954718 1.7502551e-11 8.4340313e-12 + 280 0 -6155.851 1.0913936e-11 -0.0011954718 1.7509039e-11 8.2114315e-12 + 290 0 -6155.851 1.0913936e-11 -0.0011954718 1.7563475e-11 8.2074347e-12 + 300 0 -6155.851 1.0913936e-11 -0.0011954718 1.7385805e-11 8.4339202e-12 + 310 0 -6155.851 1.0913936e-11 -0.0011954718 1.7432996e-11 8.3754115e-12 + 320 0 -6155.851 1.0913936e-11 -0.0011954718 1.7523174e-11 8.472778e-12 + 330 0 -6155.851 1.0913936e-11 -0.0011954718 1.7343221e-11 8.1784579e-12 + 340 0 -6155.851 1.0913936e-11 -0.0011954718 1.7426002e-11 8.1481488e-12 + 350 0 -6155.851 1.0913936e-11 -0.0011954718 1.74698e-11 8.3067997e-12 + 360 0 -6155.851 1.0913936e-11 -0.0011954718 1.738067e-11 8.5164098e-12 + 370 0 -6155.851 1.0913936e-11 -0.0011954718 1.753599e-11 8.3784091e-12 + 380 0 -6155.851 1.0913936e-11 -0.0011954718 1.7339446e-11 8.3465457e-12 + 390 0 -6155.851 1.0913936e-11 -0.0011954718 1.7437576e-11 8.5182972e-12 + 400 0 -6155.851 1.0913936e-11 -0.0011954718 1.7300047e-11 8.1350482e-12 + 410 0 -6155.851 1.0913936e-11 -0.0011954718 1.7222838e-11 8.2779339e-12 + 420 0 -6155.851 1.0913936e-11 -0.0011954718 1.7421602e-11 8.0918605e-12 + 430 0 -6155.851 1.0913936e-11 -0.0011954718 1.7416773e-11 8.3816287e-12 + 440 0 -6155.851 1.0913936e-11 -0.0011954718 1.7347863e-11 8.4523499e-12 + 450 0 -6155.851 1.0913936e-11 -0.0011954718 1.7408828e-11 8.1795681e-12 + 460 0 -6155.851 1.0913936e-11 -0.0011954718 1.7534991e-11 8.308576e-12 + 470 0 -6155.851 1.0913936e-11 -0.0011954718 1.7459565e-11 8.2645002e-12 + 480 0 -6155.851 1.0913936e-11 -0.0011954718 1.7273457e-11 8.5179641e-12 + 490 0 -6155.851 1.0913936e-11 -0.0011954718 1.7452029e-11 8.4042773e-12 + 500 0 -6155.851 1.0913936e-11 -0.0011954718 1.7463576e-11 8.1070706e-12 +Loop time of 154.975 on 4 procs for 500 steps with 846 atoms + +Minimization stats: + Stopping criterion = max force evaluations + Energy initial, next-to-last, final = + -6155.85097822 -6155.8510078 -6155.8510078 + Force two-norm initial, final = 0.00144775 6.46495e-12 + Force max component initial, final = 0.000150789 6.70891e-13 + Final line search alpha, max atom move = 1 6.70891e-13 + Iterations, force evaluations = 500 1000 + +Pair time (%) = 10.2259 (6.59839) +Neigh time (%) = 0 (0) +Comm time (%) = 7.76684 (5.01167) +Outpt time (%) = 0.783488 (0.505557) +Other time (%) = 136.199 (87.8844) + +Nlocal: 211.5 ave 216 max 198 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 195.75 ave 261 max 126 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 48199.5 ave 53136 max 41085 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 192798 +Ave neighs/atom = 227.894 +Neighbor list builds = 0 +Dangerous builds = 0 + #min_style sd + #min_modify line backtrack + #minimize 0 0 1000 1000 + fix_modify AtC output now + + # u = F L^3 / 3 EI --> EI = F L^3 / 3 u + variable Q equal c_Q + variable ux equal ${dx} + variable ux equal 1.0913936421275138855e-11 + variable uz equal ${dz} + variable uz equal -0.0011954718283959664404 + variable Fx equal f_FIX[1] + variable Fz equal f_FIX[3] + variable EI equal ${Fx}*${Lfree}*${Lfree}*${Lfree}/3./${ux} + variable EI equal 1.7463575724407931489e-11*${Lfree}*${Lfree}*${Lfree}/3./${ux} + variable EI equal 1.7463575724407931489e-11*90*${Lfree}*${Lfree}/3./${ux} + variable EI equal 1.7463575724407931489e-11*90*90*${Lfree}/3./${ux} + variable EI equal 1.7463575724407931489e-11*90*90*90/3./${ux} + variable EI equal 1.7463575724407931489e-11*90*90*90/3./1.0913936421275138855e-11 + variable EI equal ${EI}*${eV2J}*${A2m} + variable EI equal 388828.44257354736328*${eV2J}*${A2m} + variable EI equal 388828.44257354736328*1.6021764600000000642e-19*${A2m} + variable EI equal 388828.44257354736328*1.6021764600000000642e-19*1.0000000000000000364e-10 + print ">> V $b $a F ${Fx} ${Fz} u ${ux} ${uz} Q $Q EI ${EI}" +>> V -0 0 F 1.7463575724407931489e-11 8.1070705704178180895e-12 u 1.0913936421275138855e-11 -0.0011954718283959664404 Q 0 EI 6.2297177766979946381e-24 + + next i +jump SELF loop_i + variable b equal ($i-1)*${Vg}/${ng}/${Lz} + variable b equal (2-1)*${Vg}/${ng}/${Lz} + variable b equal (2-1)*0.14999999999999999445/${ng}/${Lz} + variable b equal (2-1)*0.14999999999999999445/3/${Lz} + variable b equal (2-1)*0.14999999999999999445/3/-51103.063299276320322 + fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a ${V0} # << physics and will be treated as null +Memory usage per processor = 51.8077 Mbytes +Step Q PotEng dx dz FIX[1] FIX[3] + 500 0 -6155.851 0.0003179655 -0.0011954718 1.7463576e-11 8.1070706e-12 + 510 0 -6155.851 0.0003179655 -0.0011954718 1.7251516e-11 8.5466079e-12 + 520 0 -6155.851 0.0003179655 -0.0011954718 1.7276357e-11 8.2207574e-12 + 530 0 -6155.851 0.0003179655 -0.0011954718 1.75636e-11 8.4386942e-12 + 540 0 -6155.851 0.0003179655 -0.0011954718 1.7522834e-11 8.5189633e-12 + 550 0 -6155.851 0.0003179655 -0.0011954718 1.7338121e-11 8.1677998e-12 + 560 0 -6155.851 0.0003179655 -0.0011954718 1.7448248e-11 8.4081631e-12 + 570 0 -6155.851 0.0003179655 -0.0011954718 1.7392986e-11 8.5064178e-12 + 580 0 -6155.851 0.0003179655 -0.0011954718 1.7444438e-11 8.5607077e-12 + 590 0 -6155.851 0.0003179655 -0.0011954718 1.7296425e-11 8.4051655e-12 + 600 0 -6155.851 0.0003179655 -0.0011954718 1.7447616e-11 8.3621998e-12 + 610 0 -6155.851 0.0003179655 -0.0011954718 1.7417904e-11 8.3870688e-12 + 620 0 -6155.851 0.0003179655 -0.0011954718 1.7328212e-11 8.6393115e-12 + 630 0 -6155.851 0.0003179655 -0.0011954718 1.7411971e-11 8.4993124e-12 + 640 0 -6155.851 0.0003179655 -0.0011954718 1.7426383e-11 8.6461949e-12 + 650 0 -6155.851 0.0003179655 -0.0011954718 1.7399009e-11 8.3740792e-12 + 660 0 -6155.851 0.0003179655 -0.0011954718 1.737387e-11 8.4294793e-12 + 670 0 -6155.851 0.0003179655 -0.0011954718 1.7378914e-11 8.7023722e-12 + 680 0 -6155.851 0.0003179655 -0.0011954718 1.734771e-11 8.80096e-12 + 690 0 -6155.851 0.0003179655 -0.0011954718 1.7320447e-11 8.8147267e-12 + 700 0 -6155.851 0.0003179655 -0.0011954718 1.7359548e-11 8.7029273e-12 + 710 0 -6155.851 0.0003179655 -0.0011954718 1.7191474e-11 8.8338226e-12 + 720 0 -6155.851 0.0003179655 -0.0011954718 1.7362872e-11 8.7141405e-12 + 730 0 -6155.851 0.0003179655 -0.0011954718 1.7459898e-11 8.5019769e-12 + 740 0 -6155.851 0.0003179655 -0.0011954718 1.724575e-11 8.7195806e-12 + 750 0 -6155.851 0.0003179655 -0.0011954718 1.7368686e-11 8.9750429e-12 + 760 0 -6155.851 0.0003179655 -0.0011954718 1.7282762e-11 8.5165208e-12 + 770 0 -6155.851 0.0003179655 -0.0011954718 1.7351915e-11 8.6922691e-12 + 780 0 -6155.851 0.0003179655 -0.0011954718 1.7261335e-11 8.8746788e-12 + 790 0 -6155.851 0.0003179655 -0.0011954718 1.7332431e-11 8.4021679e-12 + 800 0 -6155.851 0.0003179655 -0.0011954718 1.7336011e-11 8.6323171e-12 + 810 0 -6155.851 0.0003179655 -0.0011954718 1.7329544e-11 8.656631e-12 + 820 0 -6155.851 0.0003179655 -0.0011954718 1.7118616e-11 8.7636565e-12 + 830 0 -6155.851 0.0003179655 -0.0011954718 1.7304474e-11 8.7291285e-12 + 840 0 -6155.851 0.0003179655 -0.0011954718 1.7398697e-11 8.7205798e-12 + 850 0 -6155.851 0.0003179655 -0.0011954718 1.7366813e-11 8.8165031e-12 + 860 0 -6155.851 0.0003179655 -0.0011954718 1.7268856e-11 8.8138385e-12 + 870 0 -6155.851 0.0003179655 -0.0011954718 1.7315867e-11 9.0394359e-12 + 880 0 -6155.851 0.0003179655 -0.0011954718 1.7205706e-11 8.9996899e-12 + 890 0 -6155.851 0.0003179655 -0.0011954718 1.7218945e-11 9.0571994e-12 + 900 0 -6155.851 0.0003179655 -0.0011954718 1.7313557e-11 8.9475094e-12 + 910 0 -6155.851 0.0003179655 -0.0011954718 1.7205095e-11 8.8882235e-12 + 920 0 -6155.851 0.0003179655 -0.0011954718 1.7258906e-11 8.6174401e-12 + 930 0 -6155.851 0.0003179655 -0.0011954718 1.7300519e-11 9.1007202e-12 + 940 0 -6155.851 0.0003179655 -0.0011954718 1.7295516e-11 8.8616892e-12 + 950 0 -6155.851 0.0003179655 -0.0011954718 1.7298798e-11 8.9259711e-12 + 960 0 -6155.851 0.0003179655 -0.0011954718 1.7154941e-11 8.7637675e-12 + 970 0 -6155.851 0.0003179655 -0.0011954718 1.7201674e-11 9.0283336e-12 + 980 0 -6155.851 0.0003179655 -0.0011954718 1.7269717e-11 8.5640384e-12 + 990 0 -6155.851 0.0003179655 -0.0011954718 1.7215684e-11 8.985479e-12 + 1000 0 -6155.851 0.0003179655 -0.0011954718 1.7359402e-11 9.1016084e-12 +Loop time of 58.7288 on 4 procs for 500 steps with 846 atoms + +Minimization stats: + Stopping criterion = max force evaluations + Energy initial, next-to-last, final = + -6155.8510078 -6155.8510078 -6155.8510078 + Force two-norm initial, final = 6.46495e-12 6.71492e-12 + Force max component initial, final = 6.70891e-13 6.69757e-13 + Final line search alpha, max atom move = 1 6.69757e-13 + Iterations, force evaluations = 500 1000 + +Pair time (%) = 7.65567 (13.0356) +Neigh time (%) = 0 (0) +Comm time (%) = 1.17538 (2.00138) +Outpt time (%) = 0.144858 (0.246656) +Other time (%) = 49.7529 (84.7163) + +Nlocal: 211.5 ave 216 max 198 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 195.75 ave 261 max 126 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 48199.5 ave 53136 max 41085 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 192798 +Ave neighs/atom = 227.894 +Neighbor list builds = 0 +Dangerous builds = 0 + #min_style sd + #min_modify line backtrack + #minimize 0 0 1000 1000 + fix_modify AtC output now + + # u = F L^3 / 3 EI --> EI = F L^3 / 3 u + variable Q equal c_Q + variable ux equal ${dx} + variable ux equal 0.0003179654981977364514 + variable uz equal ${dz} + variable uz equal -0.0011954718283959664404 + variable Fx equal f_FIX[1] + variable Fz equal f_FIX[3] + variable EI equal ${Fx}*${Lfree}*${Lfree}*${Lfree}/3./${ux} + variable EI equal 1.7359402110228572269e-11*${Lfree}*${Lfree}*${Lfree}/3./${ux} + variable EI equal 1.7359402110228572269e-11*90*${Lfree}*${Lfree}/3./${ux} + variable EI equal 1.7359402110228572269e-11*90*90*${Lfree}/3./${ux} + variable EI equal 1.7359402110228572269e-11*90*90*90/3./${ux} + variable EI equal 1.7359402110228572269e-11*90*90*90/3./0.0003179654981977364514 + variable EI equal ${EI}*${eV2J}*${A2m} + variable EI equal 0.013266642880109728517*${eV2J}*${A2m} + variable EI equal 0.013266642880109728517*1.6021764600000000642e-19*${A2m} + variable EI equal 0.013266642880109728517*1.6021764600000000642e-19*1.0000000000000000364e-10 + print ">> V $b $a F ${Fx} ${Fz} u ${ux} ${uz} Q $Q EI ${EI}" +>> V -9.7841492802855238901e-07 0 F 1.7359402110228572269e-11 9.1016083558770333184e-12 u 0.0003179654981977364514 -0.0011954718283959664404 Q 0 EI 2.125550292573840973e-31 + + next i +jump SELF loop_i + variable b equal ($i-1)*${Vg}/${ng}/${Lz} + variable b equal (3-1)*${Vg}/${ng}/${Lz} + variable b equal (3-1)*0.14999999999999999445/${ng}/${Lz} + variable b equal (3-1)*0.14999999999999999445/3/${Lz} + variable b equal (3-1)*0.14999999999999999445/3/-51103.063299276320322 + fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a ${V0} # << physics and will be treated as null +Memory usage per processor = 51.8077 Mbytes +Step Q PotEng dx dz FIX[1] FIX[3] + 1000 0 -6155.851 0.00031796548 -0.0011954718 1.7359402e-11 9.1016084e-12 + 1010 0 -6155.851 0.00031796548 -0.0011954718 1.72647e-11 8.9737107e-12 + 1020 0 -6155.851 0.00031796548 -0.0011954718 1.7298243e-11 9.3161034e-12 + 1030 0 -6155.851 0.00031796548 -0.0011954718 1.7292941e-11 8.7504448e-12 + 1040 0 -6155.851 0.00031796548 -0.0011954718 1.7324222e-11 8.9780405e-12 + 1050 0 -6155.851 0.00031796548 -0.0011954718 1.7239831e-11 8.8595797e-12 + 1060 0 -6155.851 0.00031796548 -0.0011954718 1.7318608e-11 8.6920471e-12 + 1070 0 -6155.851 0.00031796548 -0.0011954718 1.7192938e-11 8.8485885e-12 + 1080 0 -6155.851 0.00031796548 -0.0011954718 1.7274428e-11 8.8733465e-12 + 1090 0 -6155.851 0.00031796548 -0.0011954718 1.7129246e-11 9.0292218e-12 + 1100 0 -6155.851 0.00031796548 -0.0011954718 1.7195401e-11 9.1879837e-12 + 1110 0 -6155.851 0.00031796548 -0.0011954718 1.7221478e-11 8.9610541e-12 + 1120 0 -6155.851 0.00031796548 -0.0011954718 1.7302357e-11 9.2608143e-12 + 1130 0 -6155.851 0.00031796548 -0.0011954718 1.7290416e-11 9.0714103e-12 + 1140 0 -6155.851 0.00031796548 -0.0011954718 1.7198343e-11 9.21907e-12 + 1150 0 -6155.851 0.00031796548 -0.0011954718 1.7163059e-11 9.2147401e-12 + 1160 0 -6155.851 0.00031796548 -0.0011954718 1.7186443e-11 9.0759622e-12 + 1170 0 -6155.851 0.00031796548 -0.0011954718 1.7350291e-11 9.0307761e-12 + 1180 0 -6155.851 0.00031796548 -0.0011954718 1.7178033e-11 8.9124264e-12 + 1190 0 -6155.851 0.00031796548 -0.0011954718 1.7142825e-11 9.4578789e-12 + 1200 0 -6155.851 0.00031796548 -0.0011954718 1.7238853e-11 8.9984686e-12 + 1210 0 -6155.851 0.00031796548 -0.0011954718 1.7307909e-11 8.8733465e-12 + 1220 0 -6155.851 0.00031796548 -0.0011954718 1.7251884e-11 9.2414965e-12 + 1230 0 -6155.851 0.00031796548 -0.0011954718 1.7304682e-11 9.1451291e-12 + 1240 0 -6155.851 0.00031796548 -0.0011954718 1.7177992e-11 9.1870955e-12 + 1250 0 -6155.851 0.00031796548 -0.0011954718 1.7087293e-11 9.1605612e-12 + 1260 0 -6155.851 0.00031796548 -0.0011954718 1.7135144e-11 9.0688568e-12 + 1270 0 -6155.851 0.00031796548 -0.0011954718 1.7224919e-11 9.0758512e-12 + 1280 0 -6155.851 0.00031796548 -0.0011954718 1.7203346e-11 9.1016084e-12 + 1290 0 -6155.851 0.00031796548 -0.0011954718 1.7203673e-11 9.2676977e-12 + 1300 0 -6155.851 0.00031796548 -0.0011954718 1.7155246e-11 9.1611163e-12 + 1310 0 -6155.851 0.00031796548 -0.0011954718 1.7048158e-11 9.2623686e-12 + 1320 0 -6155.851 0.00031796548 -0.0011954718 1.7049185e-11 9.2745811e-12 + 1330 0 -6155.851 0.00031796548 -0.0011954718 1.7226918e-11 9.383605e-12 + 1340 0 -6155.851 0.00031796548 -0.0011954718 1.7146114e-11 9.0593089e-12 + 1350 0 -6155.851 0.00031796548 -0.0011954718 1.7130807e-11 9.2582608e-12 + 1360 0 -6155.851 0.00031796548 -0.0011954718 1.7170206e-11 9.4171337e-12 + 1370 0 -6155.851 0.00031796548 -0.0011954718 1.7139155e-11 9.0635277e-12 + 1380 0 -6155.851 0.00031796548 -0.0011954718 1.7048789e-11 9.1849861e-12 + 1390 0 -6155.851 0.00031796548 -0.0011954718 1.7176548e-11 9.2297281e-12 + 1400 0 -6155.851 0.00031796548 -0.0011954718 1.7135373e-11 9.2431618e-12 + 1410 0 -6155.851 0.00031796548 -0.0011954718 1.7186665e-11 9.3181018e-12 + 1420 0 -6155.851 0.00031796548 -0.0011954718 1.7178928e-11 9.4295682e-12 + 1430 0 -6155.851 0.00031796548 -0.0011954718 1.7148834e-11 9.4859676e-12 + 1440 0 -6155.851 0.00031796548 -0.0011954718 1.715662e-11 9.3871577e-12 + 1450 0 -6155.851 0.00031796548 -0.0011954718 1.7190711e-11 9.3713926e-12 + 1460 0 -6155.851 0.00031796548 -0.0011954718 1.7210958e-11 9.5933261e-12 + 1470 0 -6155.851 0.00031796548 -0.0011954718 1.7199183e-11 9.4561026e-12 + 1480 0 -6155.851 0.00031796548 -0.0011954718 1.7054681e-11 9.3104413e-12 + 1490 0 -6155.851 0.00031796548 -0.0011954718 1.722188e-11 9.3294261e-12 + 1500 0 -6155.851 0.00031796548 -0.0011954718 1.7142694e-11 9.3715036e-12 +Loop time of 76.7522 on 4 procs for 500 steps with 846 atoms + +Minimization stats: + Stopping criterion = max force evaluations + Energy initial, next-to-last, final = + -6155.8510078 -6155.8510078 -6155.8510078 + Force two-norm initial, final = 6.71492e-12 6.81183e-12 + Force max component initial, final = 6.69757e-13 8.93204e-13 + Final line search alpha, max atom move = 1 8.93204e-13 + Iterations, force evaluations = 500 1000 + +Pair time (%) = 8.35572 (10.8866) +Neigh time (%) = 0 (0) +Comm time (%) = 2.23788 (2.91572) +Outpt time (%) = 0.0837539 (0.109123) +Other time (%) = 66.0748 (86.0885) + +Nlocal: 211.5 ave 216 max 198 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 195.75 ave 261 max 126 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 48199.5 ave 53136 max 41085 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 192798 +Ave neighs/atom = 227.894 +Neighbor list builds = 0 +Dangerous builds = 0 + #min_style sd + #min_modify line backtrack + #minimize 0 0 1000 1000 + fix_modify AtC output now + + # u = F L^3 / 3 EI --> EI = F L^3 / 3 u + variable Q equal c_Q + variable ux equal ${dx} + variable ux equal 0.0003179654813720844686 + variable uz equal ${dz} + variable uz equal -0.0011954718283959664404 + variable Fx equal f_FIX[1] + variable Fz equal f_FIX[3] + variable EI equal ${Fx}*${Lfree}*${Lfree}*${Lfree}/3./${ux} + variable EI equal 1.714269351471564562e-11*${Lfree}*${Lfree}*${Lfree}/3./${ux} + variable EI equal 1.714269351471564562e-11*90*${Lfree}*${Lfree}/3./${ux} + variable EI equal 1.714269351471564562e-11*90*90*${Lfree}/3./${ux} + variable EI equal 1.714269351471564562e-11*90*90*90/3./${ux} + variable EI equal 1.714269351471564562e-11*90*90*90/3./0.0003179654813720844686 + variable EI equal ${EI}*${eV2J}*${A2m} + variable EI equal 0.013101027526950992722*${eV2J}*${A2m} + variable EI equal 0.013101027526950992722*1.6021764600000000642e-19*${A2m} + variable EI equal 0.013101027526950992722*1.6021764600000000642e-19*1.0000000000000000364e-10 + print ">> V $b $a F ${Fx} ${Fz} u ${ux} ${uz} Q $Q EI ${EI}" +>> V -1.956829856057104778e-06 0 F 1.714269351471564562e-11 9.3715035731634088734e-12 u 0.0003179654813720844686 -0.0011954718283959664404 Q 0 EI 2.0990157905492896479e-31 + + next i +jump SELF loop_i diff --git a/examples/USER/atc/elastic/in.bar1d b/examples/USER/atc/elastic/in.bar1d new file mode 100644 index 0000000000..e7f1fa93af --- /dev/null +++ b/examples/USER/atc/elastic/in.bar1d @@ -0,0 +1,91 @@ +# needs description +#AtC Thermal Coupling +echo both + +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +lattice fcc 5.405 origin 0.25 0.25 0.25 + +# create atoms +region simRegion block -12 12 -3 3 -3 3 +region atomRegion block -9 9 -3 3 -3 3 +region mdRegion block -8 8 -3 3 -3 3 +boundary f p p +create_box 1 simRegion +create_atoms 1 region mdRegion +mass 1 39.95 + +# specify interal/ghost atoms +region mdInternal block -6 6 -3 3 -3 3 +region leftghost block -8 -6 -3 3 -3 3 +region rightghost block 6 8 -3 3 -3 3 +group internal region mdInternal +group Lghost region leftghost +group Rghost region rightghost +group ghosts union Lghost Rghost + +# velocities have Vcm = 0 +#velocity internal create 40. 87287 mom yes loop geom + +pair_style lj/cut 13.5 +#pair_coeff 1 1 0.010323166 3.405 13.5 +pair_coeff 1 1 .238 3.405 13.5 + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# define layer +# ID group atc PhysicsType ParameterFile +fix AtC internal atc elastic Ar_elastic.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p + +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 + +# set node sets and bcs +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF +fix_modify AtC fix velocity x rbc 0.00000004 +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix velocity x lbc 0. + +# specify atom types +#fix_modify AtC boundary Lghost +#fix_modify AtC boundary Rghost +fix_modify AtC boundary ghosts + +#fix_modify AtC output follow_ex.fe 50 +fix_modify AtC internal_quadrature off +fix_modify AtC control localized_lambda on +fix_modify AtC control momentum glc_velocity +fix_modify AtC filter type exponential +fix_modify AtC filter scale 1000.0 +fix_modify AtC filter on + +# run to extension +#fix_modify AtC output bar1dFE 50 text +timestep 5 +thermo 100 +run 1000 + +# change nodes to fixed +fix_modify AtC fix velocity x rbc 0. +fix_modify AtC fix displacement x rbc 0.0002 + +fix_modify AtC output bar1dFE 500 text + +# run to equilibrium +timestep 5 +thermo 100 +run 10000 diff --git a/examples/USER/atc/elastic/in.bar1d_damped b/examples/USER/atc/elastic/in.bar1d_damped new file mode 100644 index 0000000000..08263157e5 --- /dev/null +++ b/examples/USER/atc/elastic/in.bar1d_damped @@ -0,0 +1,112 @@ +# needs description +echo both + +units metal +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +lattice fcc 5.405 origin 0.25 0.25 0.25 + +# create atoms +region simRegion block -12 12 -3 3 -3 3 +region atomRegion block -9 9 -3 3 -3 3 +region mdRegion block -8 8 -3 3 -3 3 +boundary f p p +create_box 2 simRegion +create_atoms 1 region mdRegion +mass * 39.95 + +# specify interal/ghost atoms +region mdInternal block -6 6 -3 3 -3 3 +region leftghost block -8 -6 -3 3 -3 3 +region rightghost block 6 8 -3 3 -3 3 +group internal region mdInternal +group Lghost region leftghost +group Rghost region rightghost +group ghosts union Lghost Rghost + +# velocities have Vcm = 0 +#velocity internal create 40. 87287 mom yes loop geom + +pair_style lj/cut 13.5 +#pair_coeff * * .238 3.405 13.5 +pair_coeff * * 0.010323166 3.405 13.5 + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# define layer +# ID group atc PhysicsType ParameterFile +fix AtC internal atc elastic Ar_damped.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p + +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 + + +variable v equal 0.00000004e3 +variable n equal 1000 +variable dt equal 0.005 +variable u equal $v*$n*${dt} + +# set node sets and bcs +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF +fix_modify AtC fix velocity x rbc $v +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix velocity x lbc 0. + +# specify atom types +fix_modify AtC boundary ghosts + +#fix_modify AtC output follow_ex.fe 50 +fix_modify AtC internal_quadrature off +fix_modify AtC control localized_lambda on +fix_modify AtC control momentum glc_velocity +#fix_modify AtC filter type exponential +#fix_modify AtC filter scale 1.0 +#fix_modify AtC filter on + +# run to extension +timestep 0.005 +thermo 100 +thermo_style custom step cpu ke pe +run 0 +variable pe0 equal pe +variable pe equal pe-${pe0} +thermo_style custom step cpu ke pe v_pe f_AtC[1] f_AtC[2] f_AtC[4] f_AtC[5] + +run $n + +fix_modify AtC output bar1d_dampedFE 500 text +dump CONFIG all custom 500 bar1d_damped.dmp id type x y z vx vy vz + +# change nodes to fixed +fix_modify AtC fix velocity x rbc 0. +fix_modify AtC fix displacement x rbc $u + +# run to equilibrium +thermo 100 +log bar1d_damped.log +run 2000 +fix_modify AtC material all cubic # M damping +run 2000 +fix_modify AtC material all damped # K damping +run 2000 +# ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 from Ar_CauchyBorn.mat +# real to metal 1 kcal/mol = 0.04336 eV +variable kCal2eV equal 0.04336 +variable k equal 1.e-3 # 7.56717*${kCal2eV} NOTE <<< +variable g equal 0.75*0.355649e3*${kCal2eV} +variable m equal 0.5*39.95 +fix_modify AtC boundary_dynamics damped_harmonic $k $g $m +run 2000 diff --git a/examples/USER/atc/elastic/in.bar1d_flux b/examples/USER/atc/elastic/in.bar1d_flux new file mode 100644 index 0000000000..53750388cb --- /dev/null +++ b/examples/USER/atc/elastic/in.bar1d_flux @@ -0,0 +1,98 @@ +# needs description +#AtC Thermal Coupling +echo both + +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +lattice fcc 5.2582305 origin 0.25 0.25 0.25 + +# create atoms +region simRegion block -12 12 -3 3 -3 3 +region atomRegion block -9 9 -3 3 -3 3 +region mdRegion block -8 8 -3 3 -3 3 +boundary f p p +create_box 1 simRegion +create_atoms 1 region mdRegion +mass 1 39.95 + +# specify interal/ghost atoms +region mdInternal block -6 6 -3 3 -3 3 +region leftghost block -8 -6 -3 3 -3 3 +region rightghost block 6 8 -3 3 -3 3 +group internal region mdInternal +group Lghost region leftghost +group Rghost region rightghost +group ghosts union Lghost Rghost + +# velocities have Vcm = 0 +#velocity internal create 40. 87287 mom yes loop geom + +pair_style lj/cut 13. +#pair_coeff 1 1 0.010323166 3.405 13. +pair_coeff 1 1 .2381 3.405 13. + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# define layer +# ID group atc PhysicsType ParameterFile +fix AtC internal atc elastic Ar_elastic.mat +#fix_modify AtC boundary Lghost +#fix_modify AtC boundary Rghost +fix_modify AtC boundary ghosts + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p +fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward + +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 + +# set node sets and bcs +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF +fix_modify AtC fix velocity x rbc 0.00000004 +#fix_modify AtC fix velocity x rbc 0. +#fix_modify AtC fix displacement x rbc 0. +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix velocity x lbc 0. + + +#fix_modify AtC output follow_ex.fe 50 +fix_modify AtC internal_quadrature off +#fix_modify AtC control lumped_lambda_solve on +#fix_modify AtC momentum control glc_velocity +#fix_modify AtC momentum control flux faceset obndy +fix_modify AtC control momentum flux interpolate +#fix_modify AtC filter scale 1000.0 + +# run to extension +compute myTemp internal temp +compute atomStress internal stress/atom +compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3] +variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol) +thermo_style custom step c_myTemp v_myPres pe +fix_modify AtC output bar1d_fluxFE 10 text +timestep 5 +thermo 100 +run 1000 + +# change nodes to fixed +fix_modify AtC fix velocity x rbc 0. +fix_modify AtC fix displacement x rbc 0.0002 + +fix_modify AtC output bar1d_fluxFE 500 text + +# run to equilibrium +timestep 5 +thermo 100 +run 10000 diff --git a/examples/USER/atc/elastic/in.bar1d_frac_step b/examples/USER/atc/elastic/in.bar1d_frac_step new file mode 100644 index 0000000000..fcdc785953 --- /dev/null +++ b/examples/USER/atc/elastic/in.bar1d_frac_step @@ -0,0 +1,97 @@ +# needs description +#AtC Elastic Coupling +echo both + +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +lattice fcc 5.2582305 origin 0.25 0.25 0.25 + +# create atoms +region simRegion block -12 12 -3 3 -3 3 +region atomRegion block -8 8 -3 3 -3 3 +region mdRegion block -6 6 -3 3 -3 3 +boundary f p p +create_box 1 simRegion +create_atoms 1 region atomRegion +mass 1 39.95 + +# specify interal/ghost atoms +region mdInternal block -6 6 -3 3 -3 3 +region leftghost block -8 -6 -3 3 -3 3 +region rightghost block 6 8 -3 3 -3 3 +group internal region mdInternal +group Lghost region leftghost +group Rghost region rightghost +group ghosts union Lghost Rghost + +pair_style lj/cut 13. +#pair_coeff 1 1 0.010323166 3.405 13.5 +pair_coeff 1 1 .2381 3.405 13. + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# define layer +# ID group atc PhysicsType ParameterFile +fix AtC internal atc elastic Ar_elastic.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p + +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 +fix_modify AtC time_integration fractional_step + +# set node sets and bcs +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF +fix_modify AtC fix velocity x rbc 0.00000004 +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix velocity x lbc 0. + +# specify atom types +#fix_modify AtC boundary Lghost +#fix_modify AtC boundary Rghost +fix_modify AtC boundary ghosts + +fix_modify AtC internal_quadrature off +fix_modify AtC control localized_lambda on +fix_modify AtC control momentum flux interpolate +#fix_modify AtC control momentum hoover # tested in this mode +#fix_modify AtC filter type exponential +#fix_modify AtC filter scale 1000.0 +#fix_modify AtC filter on + +# run to extension +#fix_modify AtC output bar1d_frac_step_initFE 50 text binary +#dump D1 all atom 50 bar1d_frac_step_init.dmp +timestep 5 +thermo 100 +run 1000 + +# reset time +fix_modify AtC reset_time 0. +reset_timestep 0 + +# change nodes to fixed +fix_modify AtC fix velocity x rbc 0. +fix_modify AtC fix displacement x rbc 0.0002 + +fix_modify AtC output bar1d_frac_stepFE 500 text #binary +#fix_modify AtC output index step +#undump D1 +#dump D1 all atom 500 bar1d_frac_step.dmp + +# run to equilibrium +timestep 5 +thermo 100 +run 5000 diff --git a/examples/USER/atc/elastic/in.bar1d_ghost_flux b/examples/USER/atc/elastic/in.bar1d_ghost_flux new file mode 100644 index 0000000000..a2fb603f12 --- /dev/null +++ b/examples/USER/atc/elastic/in.bar1d_ghost_flux @@ -0,0 +1,99 @@ +# Computes elastic waves propagating in and out of a finite temperature region +#AtC ThermoElastic Coupling +echo both + +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +lattice fcc 5.2582305 origin 0.25 0.25 0.25 + +region simRegion block -12 12 -3 3 -3 3 +region mdRegion block -8 8 -3 3 -3 3 +boundary f p p +create_box 1 simRegion +create_atoms 1 region mdRegion +mass 1 39.95 + +# specify interal/ghost atoms +region mdInternal block -6 6 -3 3 -3 3 +region leftghost block -8 -6 -3 3 -3 3 +region rightghost block 6 8 -3 3 -3 3 +group internal region mdInternal +group Lghost region leftghost +group Rghost region rightghost +group ghosts union Lghost Rghost + +# velocities have Vcm = 0, NOTE next for lines commented out for restart +pair_style lj/cut 13. +#pair_coeff 1 1 0.010323166 3.405 13. +pair_coeff 1 1 .2381 3.405 13. + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# define layer +# ID group atc PhysicsType ParameterFile +fix AtC internal atc elastic Ar_elastic.mat +fix_modify AtC boundary ghosts + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p +fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward +fix_modify AtC internal_quadrature off + +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC fix displacement y all 0.0 +fix_modify AtC fix displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC fix velocity y all 0.0 +fix_modify AtC fix velocity z all 0.0 + +# set node sets and bcs +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF +#fix_modify AtC fix velocity x rbc 0. +#fix_modify AtC fix displacement x rbc 0. +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix velocity x lbc 0. + +# turn on multiscale +fix_modify AtC control momentum ghost_flux + +# new boundary conditions +fix_modify AtC fix velocity x rbc 0.00000004 + + +#fix_modify AtC output follow_ex.fe 50 +#fix_modify AtC localized_lambda on +#fix_modify AtC momentum control glc_velocity +#fix_modify AtC momentum control flux faceset obndy +#fix_modify AtC control momentum flux +#fix_modify AtC control momentum ghost_flux +#fix_modify AtC filter scale 1000.0 + +# run to extension +compute myTemp internal temp +compute atomStress internal stress/atom +compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3] +variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol) +thermo_style custom step c_myTemp v_myPres pe +fix_modify AtC output bar1d_ghost_fluxFE 500 text +#dump D1 all atom 100 bar1d_ghost_flux.dmp +timestep 5 +thermo 100 +run 1000 + +# change nodes to fixed +fix_modify AtC unfix velocity x rbc +#fix_modify AtC fix displacement x rbc 0.0002 + +#fix_modify AtC output bar1d_fluxFE 500 text binary + +# run to equilibrium +timestep 5 +thermo 100 +run 3000 diff --git a/examples/USER/atc/elastic/in.bar1d_thermo_elastic b/examples/USER/atc/elastic/in.bar1d_thermo_elastic new file mode 100644 index 0000000000..5d2e56db9a --- /dev/null +++ b/examples/USER/atc/elastic/in.bar1d_thermo_elastic @@ -0,0 +1,139 @@ +# Computes elastic waves propagating in and out of a finite temperature region +#AtC ThermoElastic Coupling +echo both + +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +lattice fcc 5.2582305 origin 0.25 0.25 0.25 + +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13. +read_data temp.init +region simRegion block -12 12 -3 3 -3 3 +# create atoms, NOTE commented out for restart +#region mdRegion block -8 8 -3 3 -3 3 +#boundary f p p +#region mdBox block -9 9 -3 3 -3 3 +#create_box 1 mdBox +#create_atoms 1 region mdRegion +#mass 1 39.95 + +# specify interal/ghost atoms +region mdInternal block -6 6 -3 3 -3 3 +region leftghost block -8 -6 -3 3 -3 3 +region rightghost block 6 8 -3 3 -3 3 +group internal region mdInternal +group Lghost region leftghost +group Rghost region rightghost +group ghosts union Lghost Rghost + +# velocities have Vcm = 0, NOTE next for lines commented out for restart +#velocity internal create 40. 87287 mom yes loop geom +#pair_style lj/cut 13. +##pair_coeff 1 1 0.010323166 3.405 13. +#pair_coeff 1 1 .2381 3.405 13. + +neighbor 5. bin +neigh_modify every 10 delay 0 check no +#write_restart tinit.dat + +# zero initial momentum +fix AtC internal atc elastic Ar_thermo_elastic.mat +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p +fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward +fix_modify AtC internal_quadrature off +fix_modify AtC fix displacement x all 0. +fix_modify AtC fix displacement y all 0. +fix_modify AtC fix displacement z all 0. +fix_modify AtC fix velocity x all 0. +fix_modify AtC fix velocity y all 0. +fix_modify AtC fix velocity z all 0. +fix_modify AtC control momentum glc_velocity +#fix_modify AtC output bar1d_thermo_elastic_initializeFE 1 text #binary +timestep 0 +thermo 1 +run 1 +unfix AtC + +# define layer +# ID group atc PhysicsType ParameterFile +fix AtC internal atc thermo_elastic Ar_thermo_elastic.mat +fix_modify AtC boundary ghosts + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p +fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward +fix_modify AtC internal_quadrature off + +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC fix displacement y all 0.0 +fix_modify AtC fix displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC fix velocity y all 0.0 +fix_modify AtC fix velocity z all 0.0 +fix_modify AtC fix temperature all 20. + +# set node sets and bcs +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF +#fix_modify AtC fix velocity x rbc 0. +#fix_modify AtC fix displacement x rbc 0. +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix velocity x lbc 0. + +# rescale thermostat for initial atomic temperatures +fix_modify AtC control thermal rescale 10 +fix_modify AtC control momentum ghost_flux +fix_modify AtC output bar1d_thermo_elasticFE 100 text #binary +timestep 5 +thermo 100 +run 1000 + +# free all nodes +#fix_modify AtC unfix displacement x all +#fix_modify AtC unfix velocity x all +fix_modify AtC unfix temperature all + +# new boundary conditions +fix_modify AtC fix velocity x rbc 0.00000004 +fix_modify AtC fix temperature lbc 20. + + +#fix_modify AtC output follow_ex.fe 50 +#fix_modify AtC localized_lambda on +#fix_modify AtC momentum control glc_velocity +#fix_modify AtC momentum control flux faceset obndy +#fix_modify AtC control momentum flux +#fix_modify AtC control momentum ghost_flux +fix_modify AtC control thermal flux +#fix_modify AtC filter scale 1000.0 + +# run to extension +compute myTemp internal temp +compute atomStress internal stress/atom +compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3] +variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol) +thermo_style custom step c_myTemp v_myPres pe +fix_modify AtC output bar1d_thermo_elasticFE 500 text +#dump D1 all custom 100 bar1d_thermo_elastic.dmp id type x y z vx vy vz +timestep 5 +thermo 100 +run 1000 + +# change nodes to fixed +fix_modify AtC unfix velocity x rbc 0. +#fix_modify AtC fix displacement x rbc 0.0002 + +#fix_modify AtC output bar1d_fluxFE 500 text binary + +# run to equilibrium +timestep 5 +thermo 100 +run 3000 diff --git a/examples/USER/atc/elastic/in.cnt_electrostatic b/examples/USER/atc/elastic/in.cnt_electrostatic new file mode 100644 index 0000000000..2c313bad23 --- /dev/null +++ b/examples/USER/atc/elastic/in.cnt_electrostatic @@ -0,0 +1,107 @@ +# needs description +# E = - grad \phi +# f = q E +echo both +units metal +atom_style atomic + +lattice diamond 3.6 +pair_style tersoff +boundary s s f + +read_data tube_8_4.data + +# PARAMETERS----------------------------- +variable L equal zhi-zlo +variable R equal 12.1/2 +variable xhiFE equal 5.0*$R +variable xloFE equal -${xhiFE} +variable yhiFE equal $R +variable yloFE equal -${xhiFE} +variable zhiFE equal zhi +variable zloFE equal zlo+10 +print "Length $L [${zloFE}, ${zhiFE}]" + +variable E equal 10.0 +print "Electric field $E" +variable drhodx equal 0.0001 +variable s equal 50 +# END ----------------------------------- + +#pair_coeff * * SiC.tersoff C +pair_coeff * * ../../../../potentials/SiC.tersoff C +mass * 12.01 + +# all atoms simulation +region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +group internal region feRegion + +variable nAll equal count(all) +variable nGhost equal count(all)-count(internal) +print ">>> number of stationary ghosts: ${nGhost} of ${nAll}" + +neighbor 5. bin +neigh_modify every 10 delay 0 check no +timestep 0.0005 + +# coupling +fix AtC internal atc electrostatic CNT_electrostatic.mat +fix_modify AtC internal_quadrature off +fix_modify AtC omit atomic_charge +fix_modify AtC mesh create 5 1 12 feRegion f p f + +# initial & boundary conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 +fix_modify AtC initial electric_potential all 0.0 + +variable a equal -$R-0.1 +variable b equal $R+0.1 +fix_modify AtC mesh create_nodeset tube $a $b $a $b ${zloFE} ${zhiFE} units box +variable a equal ${zloFE}-0.1 +variable b equal ${zloFE}+0.1 +fix_modify AtC mesh create_nodeset lbc ${xloFE} ${xhiFE} ${xloFE} ${xhiFE} $a $b units box +variable a equal ${xhiFE}-0.1 +variable b equal ${xhiFE}+0.1 +fix_modify AtC mesh create_nodeset top $a $b ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +variable a equal ${xloFE}-0.1 +variable b equal ${xloFE}+0.1 +fix_modify AtC mesh create_nodeset bot $a $b ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box + +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix displacement y lbc 0. +fix_modify AtC fix displacement z lbc 0. +fix_modify AtC fix velocity x lbc 0. +fix_modify AtC fix velocity y lbc 0. +fix_modify AtC fix velocity z lbc 0. +fix_modify AtC fix electron_density all 0.0 +#fix_modify AtC fix electron_density tube 0.2 +fix_modify AtC fix electron_density tube linear 0 0 0 0 0 ${drhodx} 0 +fix_modify AtC fix electric_potential all linear 0 0 0 $E 0 0 0 0 + +fix_modify AtC control momentum flux + +# run +thermo_style custom step cpu etotal ke +thermo 1#$s +fix_modify AtC output cnt_electrostaticFE $s full_text +fix_modify AtC output index step +# NOTE not recognized as vector by paraview +variable uX atom x-f_AtC[1] +variable uY atom y-f_AtC[2] +variable uZ atom z-f_AtC[3] +variable rho atom mass*f_AtC[4] +dump CONFIG all custom $s cnt_electrostatic.dmp id type x y z v_uX v_uY v_uZ v_rho +log cnt_electrostatic.log +#run 1000 + +# fixed charge, bc on potential +fix_modify AtC unfix electric_potential all +fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 0 0 +fix_modify AtC fix electric_potential top linear 0 0 0 $E 0 0 0 0 +fix_modify AtC fix electric_potential bot linear 0 0 0 $E 0 0 0 0 +run 1000 diff --git a/examples/USER/atc/elastic/in.cnt_electrostatic2 b/examples/USER/atc/elastic/in.cnt_electrostatic2 new file mode 100644 index 0000000000..7edd8e0f73 --- /dev/null +++ b/examples/USER/atc/elastic/in.cnt_electrostatic2 @@ -0,0 +1,118 @@ +# needs description +# E = - grad \phi +# f = q E + +# NOTE tangent is constant for LAGRANGIAN but not exact... +# NOTE try one atom and one free node + +# issue is one of magnitude of E since +# tangent = perm BB - dn/dphi NN +# CHECK CONDITIONING? + +echo both +units metal +atom_style atomic + +lattice diamond 3.6 +boundary f f f + +#region box block -4.3458792459312239 4.3458792459312328 -4.3458792459312168 4.3458792459312203 0.0 104.29551668 units box +#region box block 0 10 0 10 0 10 +#create_box 1 box +#group box region box +#atom_modify sort 0 1 + +pair_style tersoff +read_data tube_8_4.data +pair_coeff * * ../../../../potentials/SiC.tersoff C +mass * 12.01 + +# PARAMETERS----------------------------- +variable L equal zhi-zlo +variable R equal 12.1/2 +variable xhiFE equal 5.0*$R +variable xloFE equal -${xhiFE} +variable yhiFE equal $R +variable yloFE equal -${xhiFE} +variable zhiFE equal zhi +variable zloFE equal zlo+10 +print "Length $L [${zloFE}, ${zhiFE}]" + +variable E equal 0.01 # 1.0 10.0 0.01 +variable V equal $E*${zloFE} +variable V equal 2 +print "Electric field $E ref.voltage $V" +variable s equal 20 +# END ----------------------------------- + +# all atoms simulation +region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +group internal region feRegion + +variable nAll equal count(all) +variable nGhost equal count(all)-count(internal) +print ">>> number of stationary ghosts: ${nGhost} of ${nAll}" + +#neighbor 5. bin +#neigh_modify every 10 delay 0 check no +timestep 0.0005 + +# coupling +fix AtC internal atc electrostatic-equilibrium CNT_electrostatic2.mat +fix_modify AtC omit atomic_charge +#fix_modify AtC internal_quadrature off <<<< ??? +variable alat equal 1.42 +variable w equal ${alat}*${alat}*3.*sqrt(3.)/4.0 +#variable w equal 10 +fix_modify AtC atom_weight constant internal $w +fix_modify AtC source_integration atom +fix_modify AtC atom_element_map eulerian 1 +fix_modify AtC mesh create 5 1 12 feRegion f p f +fix_modify AtC control momentum flux +#fix_modify AtC extrinsic poisson_solver max_iterations 5 + +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 + +#variable a equal -$R-0.1 +#variable b equal $R+0.1 +#fix_modify AtC mesh create_nodeset tube $a $b $a $b ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset lbc ${xloFE} ${xhiFE} ${xloFE} ${xhiFE} ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset rbc ${xloFE} ${xhiFE} ${xloFE} ${xhiFE} ${zhiFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box + +# boundary conditions +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix displacement y lbc 0. +fix_modify AtC fix displacement z lbc 0. +fix_modify AtC fix velocity x lbc 0. +fix_modify AtC fix velocity y lbc 0. +fix_modify AtC fix velocity z lbc 0. +fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V +#fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V +##fix_modify AtC fix electric_potential top linear 0 0 0 $E 0 0 $V +fix_modify AtC fix electric_potential bot linear 0 0 0 $E 0 0 $V + +# run +thermo_style custom step cpu etotal ke +thermo $s +fix_modify AtC output cnt_electrostatic2FE $s full_text # binary +fix_modify AtC output index step +# NOTE not recognized as vector by paraview +variable uX atom x-f_AtC[1] +variable uY atom y-f_AtC[2] +variable uZ atom z-f_AtC[3] +variable rho atom mass*f_AtC[4] +dump CONFIG all custom $s cnt_electrostatic2.dmp id type x y z v_uX v_uY v_uZ v_rho +log cnt_electrostatic2.log + +#run $s +run 100 + +# NOTE try fix charge on tip diff --git a/examples/USER/atc/elastic/in.cnt_fixed_charge b/examples/USER/atc/elastic/in.cnt_fixed_charge new file mode 100644 index 0000000000..76e3340d68 --- /dev/null +++ b/examples/USER/atc/elastic/in.cnt_fixed_charge @@ -0,0 +1,145 @@ +echo both +units metal +atom_style charge +dielectric 1. + +variable type string "_charge" +boundary s s f +# read in CNT +read_data cnt_9_0_100${type}.data +lattice diamond 3.6 # NOTE ??? +pair_style airebo 3.0 +pair_coeff * * ./CH.airebo C +mass * 12.01 + +# PARAMETERS----------------------------- +variable dt equal 0.0005 +variable L equal zhi-zlo +variable zhi equal zhi +variable zTip equal ${zhi}-2.0 +variable zFree equal zhi +variable R equal 12.1/2 +variable xhiFE equal 5.0*$R +variable xloFE equal -${xhiFE} +variable yhiFE equal $R +variable yloFE equal -${yhiFE} +variable zloFE equal zlo+10 # create fixed ghosts +variable zhiFE equal zhi+(zhi-${zloFE})/12*2 +variable Lfree equal zhi-${zloFE} +variable nx equal 10 # 5 +variable nz equal 14 # 12 +print "Length $L [${zloFE}, ${zhiFE}] ${zTip}" + +#variable E equal 0.1 # bias 1.0 +variable Vb equal 0.0 # bias +variable Vg equal 0.5 # gate/modulation +print "bias voltage ${Vb}, gate voltage ${Vg}" + +variable n equal 100000 +variable s equal 250 +# END ----------------------------------- + +# all atoms simulation +region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +group internal region feRegion +group fixed subtract all internal +fix FIX fixed setforce 0 0 0 +thermo 100 +#minimize 0 0 1000 1000 +#write_restart cnt_in_box0.rst + +region TIP block INF INF INF INF ${zTip} INF units box +group TIP region TIP + +variable nAll equal count(all) +variable nGhost equal count(all)-count(internal) +variable nTip equal count(TIP) +print ">>> number of stationary ghosts: ${nGhost} of ${nAll}" +print ">>> number of tip atoms : ${nTip}" + +neighbor 5. bin +neigh_modify every 10 delay 0 check no +timestep ${dt} +variable tag string "cnt_fixed_charge" + +# set charge on tip +variable C equal -0.1 # -0.01 -0.0001102 +print "charge $C [e]" +variable c equal $C/${nTip} +set group TIP charge $c + +# coupling +fix AtC internal atc electrostatic CNT_id.mat +fix_modify AtC include atomic_charge +fix_modify AtC internal_quadrature off +# note weights don't affect phi or f +fix_modify AtC atom_weight constant internal 1.0 +fix_modify AtC extrinsic short_range off +#fix_modify AtC atom_element_map eulerian 1 +fix_modify AtC control momentum flux + + +fix_modify AtC mesh create ${nx} 1 ${nz} feRegion f p f + +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 +fix_modify AtC initial electric_potential all 0.0 + +# node sets +variable t equal 1.1*$R +fix_modify AtC mesh create_nodeset tube -$t $t -$t $t ${zloFE} ${zFree} units box +fix_modify AtC mesh create_nodeset lefttube -$t $t -$t $t ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset rbc INF INF INF INF ${zhiFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset lbc INF INF INF INF ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} INF INF INF INF units box +fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} INF INF INF INF units box + +# boundary conditions +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix displacement y lbc 0. +fix_modify AtC fix displacement z lbc 0. +fix_modify AtC fix velocity x lbc 0. +fix_modify AtC fix velocity y lbc 0. +fix_modify AtC fix velocity z lbc 0. +# ground +fix_modify AtC fix electric_potential lbc 0 +# bias +fix_modify AtC fix electric_potential rbc ${Vb} +# gate +fix_modify AtC fix electric_potential bot ${Vg} + +# run +compute CM TIP com +compute q all property/atom q +compute Q all reduce sum c_q +compute FSUM all reduce sum fx fy fz +thermo_style custom step etotal ke c_CM[1] c_CM[2] c_CM[3] & + c_Q f_AtC[4] f_AtC[5] f_AtC[6] f_AtC[7] f_FIX[1] f_FIX[2] f_FIX[3] f_AtC c_FSUM[1] +thermo $s +log ${tag}.log +#run $n +#run $n +thermo 10 +timestep 0.0 +min_modify line quadratic +minimize 0 0 1000 1000 + +# u = F L^3 / 3 EI --> EI = F L^3 / 3 u +variable u equal c_CM[1] +variable F equal f_AtC[5] +# [eV/A * A^2] --> [N m] +variable eV2J equal 1.60217646e-19 +variable A2m equal 1.e-10 +variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u +variable EI equal ${EI}*${eV2J}*${A2m} +print "flexural rigidity ${EI} [Nm^2] NOTE z force" +# flexural rigidity 6.716732985e-25 [Nm^2] + +fix_modify AtC output ${tag}FE 1 full_text +fix_modify AtC output index step +run 1 diff --git a/examples/USER/atc/elastic/in.eam_energy b/examples/USER/atc/elastic/in.eam_energy new file mode 100644 index 0000000000..62398b4e23 --- /dev/null +++ b/examples/USER/atc/elastic/in.eam_energy @@ -0,0 +1,80 @@ +echo both +units metal +atom_style atomic +atom_modify map hash +boundary p p p + +variable l equal 3 +variable l2 equal 0.5*$l +variable L equal 10 +variable L2 equal 0.5*$L +variable h equal $L + +lattice fcc 4.08 origin 0.25 0.25 0.25 +region BOX block -${l2} ${l2} -${L2} ${L2} -${l2} ${l2} +create_box 1 BOX +create_atoms 1 region BOX + +pair_style eam +pair_coeff * * Au_u3.eam +mass * 196.97 + + +### NOTE change to CB -linear +fix PP all atc field Au_elastic.mat +fix_modify PP mesh create 1 $h 1 BOX p f p +fix_modify PP fields add displacement velocity potential_energy cauchy_born_energy # kinetic_energy +fix_modify PP gradients add displacement +fix_modify PP set reference_potential_energy +fix_modify PP output counter step +fix_modify PP output eam_energyPP 1 text + +fix ATC all atc elastic Au_elastic.mat +fix_modify ATC mesh create 1 $h 1 BOX p f p +fix_modify ATC internal_quadrature off +fix_modify ATC control momentum none +#fix_modify ATC consistent_fe_initialization on +fix_modify ATC output counter step +fix_modify ATC output eam_energyFE 1 text binary +fix_modify ATC material all Au_cubic + + +dump CONFIG all custom 1 eam_energy.dmp id type x y z +thermo 1 + +timestep 0 # 1.e-20 # 0 + +variable e0 equal pe +variable L0 equal ly +run 0 +variable pe equal pe-${e0} +variable dL equal ly-${L0} +variable strain equal v_dL/${L0} + +variable x equal y[1] +variable x2 equal y[2] +variable v equal vy[1] +thermo_style custom step etotal v_pe ke f_ATC[1] f_ATC[2] v_x v_v v_x2 ly v_dL v_strain +thermo_modify format 2 %15.8g + +############################################################################### +log eam_energy.log +run 1 +velocity all set 0 0.1 0 units box +fix_modify ATC fix velocity y all 0.1 +run 1 +velocity all set 0 0.2 0 units box +fix_modify ATC fix velocity y all 0.2 +run 1 +velocity all set 0 0.3 0 units box +fix_modify ATC fix velocity y all 0.3 +run 1 +change_box all y scale 1.01 remap +fix_modify ATC fix displacement y all linear 0 0 0 0 0.01 0 0 +run 1 +change_box all y scale 1.01 remap +fix_modify ATC fix displacement y all linear 0 0 0 0 0.0201 0 0 +run 1 +change_box all y scale 1.01 remap +fix_modify ATC fix displacement y all linear 0 0 0 0 0.030301 0 0 +run 1 diff --git a/examples/USER/atc/elastic/in.electron_density b/examples/USER/atc/elastic/in.electron_density new file mode 100644 index 0000000000..bd56f8cdd3 --- /dev/null +++ b/examples/USER/atc/elastic/in.electron_density @@ -0,0 +1,74 @@ +# needs description +echo both +units metal +# PARAMETERS----------------------------- +variable s equal 1 +variable L equal 10 +variable e equal 4 +variable E equal 0.0001 +variable V equal $E*$L +# END ----------------------------------- + +atom_style atomic +lattice diamond 1.0 +boundary f p p +region box block -$L $L 0 1 0 1 +create_box 1 box +group box region box +atom_modify sort 0 1 +timestep 0.0 +mass * 12.01 + +# coupling +### NOTE ATC: material cnt does not provide all interfaces for charge_density physics and will be treated as null +fix AtC box atc electrostatic-equilibrium CNT.mat +fix_modify AtC internal_quadrature off +#fix_modify AtC atom_weight constant internal 1.0 NOTE penultimate is a group +fix_modify AtC atom_weight constant box 1.0 +fix_modify AtC omit atomic_charge +fix_modify AtC mesh create $e 1 1 box f p p +#fix_modify AtC control momentum flux +fix_modify AtC mesh create_elementset all -INF INF -INF INF -INF INF + +# bcs/ics conditions +fix_modify AtC fix displacement x all 0.0 +fix_modify AtC fix displacement y all 0.0 +fix_modify AtC fix displacement z all 0.0 +fix_modify AtC fix velocity x all 0.0 +fix_modify AtC fix velocity y all 0.0 +fix_modify AtC fix velocity z all 0.0 + +fix_modify AtC mesh create_nodeset lbc -10 -10 INF INF INF INF +fix_modify AtC mesh create_nodeset rbc 10 10 INF INF INF INF +fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V +fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V + +# run +thermo_style custom step cpu etotal ke +thermo $s +fix_modify AtC output electron_densityFE $s text +fix_modify AtC output index step +log electron_density.log + +# run default material +print "default material - table linear" +run $s + +# run CNT1 material +print "CNT1 material - analytical linear" +fix_modify AtC material all CNT1 +run $s + +# run CNT2 material +print "CNT2 material - analytical exponetial" +fix_modify AtC material all CNT2 +run $s + +# run CNT material +print "CNT material - table DOS" +fix_modify AtC material all CNT +#variable E equal 10*$E +#fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V +#fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V +run $s + diff --git a/examples/USER/atc/elastic/in.electrostatic_bending b/examples/USER/atc/elastic/in.electrostatic_bending new file mode 100644 index 0000000000..686e7778a7 --- /dev/null +++ b/examples/USER/atc/elastic/in.electrostatic_bending @@ -0,0 +1,186 @@ +echo both +units metal +atom_style charge +dielectric 1. + +variable type string "_charge" + +boundary s s f +# read in CNT +read_data cnt_9_0_100${type}.data +lattice diamond 3.6 # NOTE ??? +pair_style airebo 3.0 +pair_coeff * * ./CH.airebo C +mass * 12.01 + +# PARAMETERS----------------------------- +variable dt equal 0.0005 +variable L equal zhi-zlo +variable zhi equal zhi +variable zTip equal ${zhi}-2.0 # 2 4 +variable zFree equal zhi +variable R equal 12.1/2 +variable xhiFE equal 5.0*$R +variable xloFE equal -${xhiFE} +variable yhiFE equal $R +variable yloFE equal -${yhiFE} +variable zloFE equal zlo+10 # create fixed ghosts +variable zhiFE equal zhi+(zhi-${zloFE})/12*2 +variable Lfree equal zhi-${zloFE} +variable nx equal 10 # 5 +variable nz equal 14 # 12 +print "Length $L [${zloFE}, ${zhiFE}] ${zTip}" + +#variable E equal 0.1 # bias 1.0 +variable Vb equal 0.1 # 0.1 #0.5 #0.0 # bias +variable Vg equal 0.5 # 1.0 # 5.0 0.5 #50.0 # 0.5 # gate/modulation +print "bias voltage ${Vb}, gate voltage ${Vg}" + +variable ng equal 20 # 80 # 10 +variable nb equal 2 # 3 + +variable n equal 100000 +variable s equal 250 +# END ----------------------------------- + +region TIP block INF INF INF INF ${zTip} INF units box +group TIP region TIP + +#region FIXED block INF INF INF INF INF ${zLoFE} units box +#group FIXED region FIXED + +#group FREE subtract all FIXED + +region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +group internal region feRegion +group FIXED subtract all internal +fix FIX FIXED setforce 0 0 0 + +variable nAll equal count(all) +variable nGhost equal count(all)-count(internal) +variable nTip equal count(TIP) +print ">>> number of stationary ghosts: ${nGhost} of ${nAll}" +print ">>> number of tip atoms : ${nTip}" + +neighbor 5. bin +neigh_modify every 10 delay 0 check no +timestep ${dt} +thermo 100 +variable tag string "electrostatic_bending" + +# set charge on tip +variable C equal -0.025 +print "charge $C [e]" +variable c equal $C/${nTip} +set group TIP charge $c + +# coupling +fix AtC internal atc electrostatic CNT_id.mat +fix_modify AtC include atomic_charge +fix_modify AtC internal_quadrature off +# note weights don't affect phi or f +fix_modify AtC atom_weight constant internal 1.0 +fix_modify AtC extrinsic short_range off +#fix_modify AtC atom_element_map eulerian 1 +fix_modify AtC control momentum flux + +fix_modify AtC mesh create ${nx} 1 ${nz} feRegion f p f + +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 +fix_modify AtC initial electric_potential all 0.0 + +# node sets +variable t equal 1.1*$R +fix_modify AtC mesh create_nodeset tube -$t $t -$t $t ${zloFE} ${zFree} units box +fix_modify AtC mesh create_nodeset lefttube -$t $t -$t $t ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset rbc INF INF INF INF ${zhiFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset lbc INF INF INF INF ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} INF INF INF INF units box +fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} INF INF INF INF units box + +# boundary conditions +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix displacement y lbc 0. +fix_modify AtC fix displacement z lbc 0. +fix_modify AtC fix velocity x lbc 0. +fix_modify AtC fix velocity y lbc 0. +fix_modify AtC fix velocity z lbc 0. +# ground +fix_modify AtC fix electric_potential lbc 0 +# bias +fix_modify AtC fix electric_potential rbc ${Vb} +# gate +fix_modify AtC fix electric_potential bot ${Vg} + +# run +compute CM TIP com +compute q all property/atom q +compute Q all reduce sum c_q +compute FSUM all reduce sum fx fy fz +compute RSUM internal reduce sum fx fy fz + +thermo_style custom step etotal ke c_CM[1] c_CM[2] c_CM[3] & + c_Q f_AtC[4] f_AtC[5] f_AtC[6] f_AtC[7] f_FIX[1] f_FIX[2] f_FIX[3] f_AtC c_FSUM[1] c_RSUM[1] +thermo $s +fix_modify AtC output ${tag}FE 100000000 full_text # $s full_text #binary +fix_modify AtC output index step +# NOTE not recognized as vector by paraview +variable uX atom x-f_AtC[1] +variable uY atom y-f_AtC[2] +variable uZ atom z-f_AtC[3] +variable rho atom mass*f_AtC[4] +dump CONFIG all custom $s ${tag}.dmp id type x y z v_uX v_uY v_uZ v_rho + +reset_timestep 0 +log ${tag}.log + +# [eV/A * A^2] --> [N m] +variable eV2J equal 1.60217646e-19 +variable A2m equal 1.e-10 +thermo 10 +timestep 0.0 +min_modify line quadratic +variable Vg equal 0.1 +variable Lx equal 1.0 +variable ng equal 4 +#compute RSUM FREE reduce sum fx fy fz +#dump CONFIG all custom 10000 ${tag}.dmp id type x y z c_U[1] c_U[2] c_U[3] fx fy fz +variable a equal 0 + variable i loop ${ng} + label loop_i + variable b equal ($i-1)*${Vg}/(${ng}-1)/${Lx} + + fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a 0 + min_style cg + min_modify line quadratic + #minimize 0 0 100000 100000 + minimize 0 0 1000 1000 + min_style sd + min_modify line backtrack + #minimize 0 0 100000 100000 + minimize 0 0 1000 1000 + fix_modify AtC output now + + # u = F L^3 / 3 EI --> EI = F L^3 / 3 u + variable u equal c_CM[1] + variable uz equal c_CM[3] +# variable F equal f_AtC[5] +# variable Fz equal f_AtC[7] + variable F equal c_RSUM[1] + variable Fz equal c_RSUM[3] + variable R equal $F-$C*$b + variable Rz equal ${Fz}-$C*$a + variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u + variable EI equal ${EI}*${eV2J}*${A2m} + #print "flexural rigidity ${EI} [Nm^2] NOTE z force" + + print ">> V $b $a F $F ${Fz} u $u ${uz} c $c phi 0 EI ${EI} R $R ${Rz}" + next i + jump SELF loop_i + diff --git a/examples/USER/atc/elastic/in.electrostatic_bending_dos b/examples/USER/atc/elastic/in.electrostatic_bending_dos new file mode 100644 index 0000000000..1a37b6a702 --- /dev/null +++ b/examples/USER/atc/elastic/in.electrostatic_bending_dos @@ -0,0 +1,164 @@ +echo both +units metal +atom_style charge +dielectric 1. + +boundary s s f +# read in CNT +read_data min_CNT_dos.data +set group all charge 0 +lattice diamond 3.6 +pair_style airebo 3.0 +pair_coeff * * ./CH.airebo C +mass * 12.01 + +compute q all property/atom q +compute Q all reduce sum c_q + +# PARAMETERS----------------------------- +# [eV/A * A^2] --> [N m] +variable eV2J equal 1.60217646e-19 +variable A2m equal 1.e-10 + +variable Lx equal xhi-xlo +variable L equal zhi-zlo +variable zTip equal zhi-3.5 +variable zFree equal zhi +variable R equal 12.1/2 +variable xhiFE equal 5.0*$R +variable xloFE equal -${xhiFE} +variable yhiFE equal $R +variable yloFE equal -${yhiFE} +variable zloFE equal zlo+10 # create fixed ghosts +variable zhiFE equal zhi+(zhi-${zloFE})/12*2 +variable Lfree equal zhi-${zloFE} +variable nx equal 10 # 5 +variable nz equal 14 # 12 +print "Length $L [${zloFE}, ${zhiFE}] ${zTip}" + +variable Vb equal 0.1 +variable Vg equal 0.15 +variable V0 equal 1. # 2. +print "bias voltage ${Vb}, gate voltage ${Vg}" + +variable ng equal 3 + +variable n equal 100000 +variable s equal 250 +# END ----------------------------------- + +region TIP block INF INF INF INF ${zTip} INF units box +group TIP region TIP + +region feRegion block ${xloFE} ${xhiFE} ${yloFE} ${yhiFE} ${zloFE} ${zhiFE} units box +group internal region feRegion +group FIXED subtract all internal +fix FIX FIXED setforce 0 0 0 + +thermo 10 +set group all image 0 0 0 +compute CM TIP com +thermo_style custom step c_Q etotal c_CM[1] c_CM[3] +#minimize 0 0 1000 1000 +#write_restart min_CNT_dos.rst +run 0 +#EXIT +variable L equal c_CM[1] +variable Lx equal $L +variable dx equal c_CM[1]-${Lx} +variable L equal c_CM[3] +variable Lz equal $L +variable dz equal c_CM[3]-${Lz} +print "initial ${Lx} ${Lz} " + +variable nAll equal count(all) +variable nGhost equal count(all)-count(internal) +print ">>> number of stationary ghosts: ${nGhost} of ${nAll}" + +neighbor 5. bin +neigh_modify every 10 delay 0 check no +timestep 0 +thermo 100 + +# coupling ............................................................ +fix AtC internal atc electrostatic CNT_electrostatic2.mat +fix_modify AtC omit atomic_charge +#fix_modify AtC internal_quadrature off ## NOTE active -> error +# note weights don't affect phi or f i.e. they divide out +fix_modify AtC atom_weight constant internal 1.0 +fix_modify AtC extrinsic short_range off +fix_modify AtC source_integration atom +fix_modify AtC atom_element_map eulerian 1 +fix_modify AtC control momentum none # flux + +fix_modify AtC mesh create ${nx} 1 ${nz} feRegion f p f + +# node sets ............................................................ +variable t equal 1.1*$R +fix_modify AtC mesh create_nodeset tube -$t $t -$t $t ${zloFE} ${zFree} units box +fix_modify AtC mesh create_nodeset lefttube -$t $t -$t $t ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset rbc INF INF INF INF ${zhiFE} ${zhiFE} units box +fix_modify AtC mesh create_nodeset lbc INF INF INF INF ${zloFE} ${zloFE} units box +fix_modify AtC mesh create_nodeset top ${xhiFE} ${xhiFE} INF INF INF INF units box +fix_modify AtC mesh create_nodeset bot ${xloFE} ${xloFE} INF INF INF INF units box + +# boundary conditions .................................................. +fix_modify AtC fix displacement x lbc 0. +fix_modify AtC fix displacement y lbc 0. +fix_modify AtC fix displacement z lbc 0. +fix_modify AtC fix velocity x lbc 0. +fix_modify AtC fix velocity y lbc 0. +fix_modify AtC fix velocity z lbc 0. + +# minimize ............................................................. +compute FSUM all reduce sum fx fy fz +compute RSUM internal reduce sum fx fy fz + +thermo $s +fix_modify AtC output electrostatic_bending_dosFE 100000000 full_text binary +fix_modify AtC output index step + +# store original (reference) coordinates +fix X all store/state 0 x y z + +# NOTE not recognized as vector by paraview - due to dump2ensight +variable uX atom x-f_X[1] +variable uY atom y-f_X[2] +variable uZ atom z-f_X[3] +#variable uX atom x-f_AtC[1] +#variable uY atom y-f_AtC[2] +#variable uZ atom z-f_AtC[3] +variable rho atom mass*f_AtC[4] +dump CONFIG all custom 100000 electrostatic_bending_dos.dmp id type x y z c_q v_uX v_uY v_uZ v_rho + +reset_timestep 0 +log electrostatic_bending_dos.log + +thermo 10 # 1 # 10 +min_modify line quadratic +variable a equal 0 +variable i loop ${ng} +thermo_style custom step c_Q pe v_dx v_dz f_FIX[1] f_FIX[3] +label loop_i + variable b equal ($i-1)*${Vg}/${ng}/${Lz} + fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a ${V0} # << EI = F L^3 / 3 u + variable Q equal c_Q + variable ux equal ${dx} + variable uz equal ${dz} + variable Fx equal f_FIX[1] + variable Fz equal f_FIX[3] + variable EI equal ${Fx}*${Lfree}*${Lfree}*${Lfree}/3./${ux} + variable EI equal ${EI}*${eV2J}*${A2m} + print ">> V $b $a F ${Fx} ${Fz} u ${ux} ${uz} Q $Q EI ${EI}" + + next i +jump SELF loop_i diff --git a/examples/USER/atc/elastic/in.no_atoms b/examples/USER/atc/elastic/in.no_atoms new file mode 100755 index 0000000000..6e5a7b93c4 --- /dev/null +++ b/examples/USER/atc/elastic/in.no_atoms @@ -0,0 +1,42 @@ +# needs description +#AtC thermal Coupling +# DESCRIPTION: no atoms, FE region with full periodic boundary conditions. +units real +atom_style atomic +# create domain +lattice fcc 5.25623 origin 0.25 0.25 0.25 +region feRegion block 0 100 0 10 0 10 +boundary f p p +create_box 1 feRegion +atom_modify sort 0 1 +mass 1 39.95 # need to keep this +# ID group atc PhysicsType ParameterFile +fix AtC all atc elastic Ar_elastic.mat +# ID part keywords nx ny nz region +fix_modify AtC mesh create 25 1 1 feRegion f p p +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 +# set node sets and bcs +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -1 1 -1 11 -1 11 +fix_modify AtC mesh create_nodeset rbc1 83 85 -1 11 -1 11 +fix_modify AtC mesh create_nodeset rbc2 88 89 -1 11 -1 11 +fix_modify AtC mesh create_nodeset rbc3 92 93 -1 11 -1 11 +fix_modify AtC mesh create_nodeset rbc4 95 97 -1 11 -1 11 +fix_modify AtC mesh create_nodeset rbc5 99 101 -1 11 -1 11 +fix_modify AtC fix displacement x lbc 0.0 +fix_modify AtC initial displacement x rbc1 0.00004 +fix_modify AtC initial displacement x rbc2 0.00014 +fix_modify AtC initial displacement x rbc3 0.00026 +fix_modify AtC initial displacement x rbc4 0.00036 +fix_modify AtC initial displacement x rbc5 0.0004 +thermo_style custom step cpu +fix_modify AtC output no_atomsFE 500 text +timestep 20 +thermo 100 +run 3000 diff --git a/examples/USER/atc/elastic/in.no_atoms_cb b/examples/USER/atc/elastic/in.no_atoms_cb new file mode 100755 index 0000000000..4059916f42 --- /dev/null +++ b/examples/USER/atc/elastic/in.no_atoms_cb @@ -0,0 +1,43 @@ +# needs description +#AtC thermal Coupling +# DESCRIPTION: no atoms, FE region with full periodic boundary conditions. +units real +atom_style atomic +# create domain +lattice fcc 5.25623 origin 0.25 0.25 0.25 +region feRegion block 0 100 0 10 0 10 +boundary f p p +create_box 1 feRegion +atom_modify sort 0 1 +mass 1 39.95 # need to keep this +# ID group atc PhysicsType ParameterFile +fix AtC all atc elastic Ar_CauchyBorn.mat +# ID part keywords nx ny nz region +fix_modify AtC mesh create 25 1 1 feRegion f p p +fix_modify AtC mesh quadrature face +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 +# set node sets and bcs +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -1 1 -1 11 -1 11 +fix_modify AtC mesh create_nodeset rbc1 83 85 -1 11 -1 11 +fix_modify AtC mesh create_nodeset rbc2 88 89 -1 11 -1 11 +fix_modify AtC mesh create_nodeset rbc3 92 93 -1 11 -1 11 +fix_modify AtC mesh create_nodeset rbc4 95 97 -1 11 -1 11 +fix_modify AtC mesh create_nodeset rbc5 99 101 -1 11 -1 11 +fix_modify AtC fix displacement x lbc 0.0 +fix_modify AtC initial displacement x rbc1 0.0004 +fix_modify AtC initial displacement x rbc2 0.0014 +fix_modify AtC initial displacement x rbc3 0.0026 +fix_modify AtC initial displacement x rbc4 0.0036 +fix_modify AtC initial displacement x rbc5 0.004 +thermo_style custom step cpu +fix_modify AtC output no_atoms_cbFE 500 text +timestep 20 +thermo 100 +run 3000 diff --git a/examples/USER/atc/elastic/in.no_atoms_cb_linear b/examples/USER/atc/elastic/in.no_atoms_cb_linear new file mode 100755 index 0000000000..e7bc47182e --- /dev/null +++ b/examples/USER/atc/elastic/in.no_atoms_cb_linear @@ -0,0 +1,42 @@ +# needs description +#AtC thermal Coupling +# DESCRIPTION: no atoms, FE region with full periodic boundary conditions. +units real +atom_style atomic +# create domain +lattice fcc 5.25623 origin 0.25 0.25 0.25 +region feRegion block 0 100 0 10 0 10 +boundary f p p +create_box 1 feRegion +atom_modify sort 0 1 +mass 1 39.95 # need to keep this +# ID group atc PhysicsType ParameterFile +fix AtC all atc elastic Ar_CauchyBornLinear.mat +# ID part keywords nx ny nz region +fix_modify AtC mesh create 25 1 1 feRegion f p p +# initial conditions +fix_modify AtC initial displacement x all 0.0 +fix_modify AtC initial displacement y all 0.0 +fix_modify AtC initial displacement z all 0.0 +fix_modify AtC initial velocity x all 0.0 +fix_modify AtC initial velocity y all 0.0 +fix_modify AtC initial velocity z all 0.0 +# set node sets and bcs +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -1 1 -1 11 -1 11 +fix_modify AtC mesh create_nodeset rbc1 83 85 -1 11 -1 11 +fix_modify AtC mesh create_nodeset rbc2 88 89 -1 11 -1 11 +fix_modify AtC mesh create_nodeset rbc3 92 93 -1 11 -1 11 +fix_modify AtC mesh create_nodeset rbc4 95 97 -1 11 -1 11 +fix_modify AtC mesh create_nodeset rbc5 99 101 -1 11 -1 11 +fix_modify AtC fix displacement x lbc 0.0 +fix_modify AtC initial displacement x rbc1 0.00004 +fix_modify AtC initial displacement x rbc2 0.00014 +fix_modify AtC initial displacement x rbc3 0.00026 +fix_modify AtC initial displacement x rbc4 0.00036 +fix_modify AtC initial displacement x rbc5 0.0004 +thermo_style custom step cpu +fix_modify AtC output no_atoms_cb_linearFE 500 text +timestep 20 +thermo 100 +run 3000 diff --git a/examples/USER/atc/elastic/no_atoms.screen b/examples/USER/atc/elastic/no_atoms.screen new file mode 100644 index 0000000000..ccb287b366 --- /dev/null +++ b/examples/USER/atc/elastic/no_atoms.screen @@ -0,0 +1,74 @@ +LAMMPS (14 Aug 2013) +Lattice spacing in x,y,z = 5.25623 5.25623 5.25623 +Created orthogonal box = (0 0 0) to (525.623 52.5623 52.5623) + 4 by 1 by 1 MPI processor grid +ATC: constructing elastic coupling with parameter file Ar_elastic.mat + ATC: peratom PE compute created with ID: 3 + ATC: computed mass density : 1.10041 + ATC: computed mass density : 1.10041 + ATC: computed mass density : 1.10041 + ATC: 3 materials defined from Ar_elastic.mat + ATC: created uniform mesh with 104 nodes, 26 unique nodes, and 25 elements + ATC: created nodeset lbc with 1 nodes + ATC: created nodeset rbc1 with 1 nodes + ATC: created nodeset rbc2 with 1 nodes + ATC: created nodeset rbc3 with 1 nodes + ATC: created nodeset rbc4 with 1 nodes + ATC: created nodeset rbc5 with 1 nodes + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +Setting up run ... +Memory usage per processor = 0.432442 Mbytes +Step CPU + 0 0 + 100 0.28801608 + 200 0.60494804 + 300 1.9659522 + 400 5.8900452 + 500 8.2498631 + 600 8.6479681 + 700 10.04323 + 800 10.456577 + 900 10.742816 + 1000 11.104007 + 1100 11.349205 + 1200 11.689583 + 1300 11.902604 + 1400 12.098199 + 1500 12.934268 + 1600 19.349941 + 1700 22.496211 + 1800 23.167077 + 1900 24.027154 + 2000 24.235364 + 2100 24.432181 + 2200 24.628729 + 2300 25.034703 + 2400 28.890065 + 2500 31.916798 + 2600 33.219873 + 2700 34.139887 + 2800 34.52512 + 2900 34.766055 + 3000 35.032684 +Loop time of 35.0327 on 4 procs for 3000 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0106689 (0.030454) +Outpt time (%) = 0.0495699 (0.141496) +Other time (%) = 34.9725 (99.828) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/elastic/no_atoms_cb.screen b/examples/USER/atc/elastic/no_atoms_cb.screen new file mode 100644 index 0000000000..2f81c0d72f --- /dev/null +++ b/examples/USER/atc/elastic/no_atoms_cb.screen @@ -0,0 +1,77 @@ +LAMMPS (14 Aug 2013) +Lattice spacing in x,y,z = 5.25623 5.25623 5.25623 +Created orthogonal box = (0 0 0) to (525.623 52.5623 52.5623) + 4 by 1 by 1 MPI processor grid +ATC: constructing elastic coupling with parameter file Ar_CauchyBorn.mat + ATC: peratom PE compute created with ID: 3 + ATC: computed mass density : 1.10041 + ATC: 1 materials defined from Ar_CauchyBorn.mat +using face quad! +using face quad! +using face quad! + ATC: created uniform mesh with 104 nodes, 26 unique nodes, and 25 elements +using face quad! + ATC: created nodeset lbc with 1 nodes + ATC: created nodeset rbc1 with 1 nodes + ATC: created nodeset rbc2 with 1 nodes + ATC: created nodeset rbc3 with 1 nodes + ATC: created nodeset rbc4 with 1 nodes + ATC: created nodeset rbc5 with 1 nodes + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +Setting up run ... + ATC: CB stiffness: 7.56711 Einstein freq: 0.355647 +Memory usage per processor = 0.432442 Mbytes +Step CPU + 0 0 + 100 5.373224 + 200 13.156875 + 300 17.393315 + 400 23.759932 + 500 28.611823 + 600 36.396029 + 700 40.553676 + 800 47.000228 + 900 51.579739 + 1000 57.538064 + 1100 64.053463 + 1200 71.077067 + 1300 76.430127 + 1400 84.956777 + 1500 88.559395 + 1600 90.649106 + 1700 93.449754 + 1800 95.849976 + 1900 98.488277 + 2000 100.78877 + 2100 102.80799 + 2200 104.88818 + 2300 106.89208 + 2400 108.89542 + 2500 110.89934 + 2600 114.3289 + 2700 116.6514 + 2800 118.66646 + 2900 120.66124 + 3000 122.65321 +Loop time of 122.653 on 4 procs for 3000 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0159223 (0.0129816) +Outpt time (%) = 0.0753418 (0.0614267) +Other time (%) = 122.562 (99.9256) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/elastic/no_atoms_cb_linear.screen b/examples/USER/atc/elastic/no_atoms_cb_linear.screen new file mode 100644 index 0000000000..f69dff025a --- /dev/null +++ b/examples/USER/atc/elastic/no_atoms_cb_linear.screen @@ -0,0 +1,78 @@ +LAMMPS (14 Aug 2013) +Lattice spacing in x,y,z = 5.25623 5.25623 5.25623 +Created orthogonal box = (0 0 0) to (525.623 52.5623 52.5623) + 4 by 1 by 1 MPI processor grid +ATC: constructing elastic coupling with parameter file Ar_CauchyBornLinear.mat + ATC: peratom PE compute created with ID: 3 + ATC: computed mass density : 1.10041 + ATC: 1 materials defined from Ar_CauchyBornLinear.mat + ATC: created uniform mesh with 104 nodes, 26 unique nodes, and 25 elements + ATC: created nodeset lbc with 1 nodes + ATC: created nodeset rbc1 with 1 nodes + ATC: created nodeset rbc2 with 1 nodes + ATC: created nodeset rbc3 with 1 nodes + ATC: created nodeset rbc4 with 1 nodes + ATC: created nodeset rbc5 with 1 nodes + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +Setting up run ... + ATC: created cubic stress function: + lammps ATC units + c11=0.623221 0.000260756 + c12=0.355572 0.000148771 + c44=0.355572 0.000148771 + ATC: CB stiffness: 7.56711 Einstein freq: 0.355647 +Memory usage per processor = 0.432442 Mbytes +Step CPU + 0 0 + 100 5.2610211 + 200 8.207129 + 300 8.399112 + 400 8.590606 + 500 8.7906051 + 600 8.9944639 + 700 9.2591641 + 800 9.4823501 + 900 9.9786441 + 1000 10.218563 + 1100 10.442493 + 1200 10.63588 + 1300 12.651145 + 1400 17.621 + 1500 21.060829 + 1600 21.253883 + 1700 21.44572 + 1800 24.531154 + 1900 25.631172 + 2000 26.061068 + 2100 27.272422 + 2200 27.740018 + 2300 28.139088 + 2400 28.539013 + 2500 30.439943 + 2600 30.839081 + 2700 31.207394 + 2800 31.400084 + 2900 31.592798 + 3000 31.78627 +Loop time of 31.7863 on 4 procs for 3000 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0208905 (0.0657218) +Outpt time (%) = 0.0490193 (0.154215) +Other time (%) = 31.7164 (99.7801) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/fluids/Ar_elastic.mat b/examples/USER/atc/fluids/Ar_elastic.mat new file mode 100644 index 0000000000..1be69b61f6 --- /dev/null +++ b/examples/USER/atc/fluids/Ar_elastic.mat @@ -0,0 +1,8 @@ +material Ar real +stress linear + modulus 0.00025 + possions_ratio 0.25 +end +mass_density basis + 0 1 +end diff --git a/examples/USER/atc/fluids/Ar_electrostatic.mat b/examples/USER/atc/fluids/Ar_electrostatic.mat new file mode 100644 index 0000000000..6f9d029d5a --- /dev/null +++ b/examples/USER/atc/fluids/Ar_electrostatic.mat @@ -0,0 +1,8 @@ +material Ar real +mass_density constant + density 0.854258 +end +electric_field linear +permittivity +end +end diff --git a/examples/USER/atc/fluids/Ar_liquid.mat b/examples/USER/atc/fluids/Ar_liquid.mat new file mode 100644 index 0000000000..bd0681950c --- /dev/null +++ b/examples/USER/atc/fluids/Ar_liquid.mat @@ -0,0 +1,8 @@ +material Ar real + heat_flux linear + conductivity 0.00000000154 # computed using bar1d_fluids + end + #heat_capacity constant + #capacity 0.00000003422 + #end +end diff --git a/examples/USER/atc/fluids/Ar_species.mat b/examples/USER/atc/fluids/Ar_species.mat new file mode 100644 index 0000000000..ee0df476a0 --- /dev/null +++ b/examples/USER/atc/fluids/Ar_species.mat @@ -0,0 +1,5 @@ +material Ar real + electric_field linear + permittivity + end +end diff --git a/examples/USER/atc/fluids/Ar_species_dl.mat b/examples/USER/atc/fluids/Ar_species_dl.mat new file mode 100644 index 0000000000..f8def1277d --- /dev/null +++ b/examples/USER/atc/fluids/Ar_species_dl.mat @@ -0,0 +1,8 @@ +material Ar metal + mass_density constant + density 0. + end + electric_field linear + permittivity + end +end diff --git a/examples/USER/atc/fluids/Ar_thermal.mat b/examples/USER/atc/fluids/Ar_thermal.mat new file mode 100644 index 0000000000..97e5aff6bb --- /dev/null +++ b/examples/USER/atc/fluids/Ar_thermal.mat @@ -0,0 +1,9 @@ +material Ar real + heat_flux linear + #conductivity .00000000168 + conductivity 0. + end + heat_capacity constant + #capacity 0.00000003422 + end +end diff --git a/examples/USER/atc/fluids/Ar_visc_no_atoms.mat b/examples/USER/atc/fluids/Ar_visc_no_atoms.mat new file mode 100644 index 0000000000..955f8bb869 --- /dev/null +++ b/examples/USER/atc/fluids/Ar_visc_no_atoms.mat @@ -0,0 +1,6 @@ +material Ar real +viscous_stress constant + viscosity 1000. +end +mass_density +body_force null diff --git a/examples/USER/atc/fluids/Ar_viscosity.mat b/examples/USER/atc/fluids/Ar_viscosity.mat new file mode 100644 index 0000000000..7cdbf2e715 --- /dev/null +++ b/examples/USER/atc/fluids/Ar_viscosity.mat @@ -0,0 +1,9 @@ +material Ar real +viscous_stress constant + viscosity 1000. +end +mass_density constant + density 0.2756 +end +body_force null +end diff --git a/examples/USER/atc/fluids/bar1d_fluids.screen b/examples/USER/atc/fluids/bar1d_fluids.screen new file mode 100644 index 0000000000..9f8ceb7622 --- /dev/null +++ b/examples/USER/atc/fluids/bar1d_fluids.screen @@ -0,0 +1,164 @@ +LAMMPS (14 Aug 2013) +Reading data file ... + orthogonal box = (-37.835 -16.215 -16.215) to (37.835 16.215 16.215) + 4 by 1 by 1 MPI processor grid + 1288 atoms + 1288 velocities +Lattice spacing in x,y,z = 5.405 5.405 5.405 +1000 atoms in group internal +288 atoms in group ghost +Lattice spacing in x,y,z = 5.405 5.405 5.405 +ATC: constructing thermal coupling with parameter file Ar_thermal.mat + ATC: peratom PE compute created with ID: 3 + ATC: 1 materials defined from Ar_thermal.mat + ATC: created uniform mesh with 28 nodes, 7 unique nodes, and 6 elements + ATC: created nodeset lbc with 1 nodes + ATC: created nodeset rbc with 1 nodes +Setting up run ... +Memory usage per processor = 49.3207 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -994.32071 -1292.1036 1073.0916 99.9 100 + 200 1 -1039.357 -1337.438 1073.0916 100 100 + 400 1.9 -1063.9771 -1362.0581 1073.0916 100 100 + 600 2.9 -1077.6783 -1375.7593 1073.0916 100 100 + 800 3.8 -1088.068 -1386.149 1073.0916 100 100 + 1000 5.8 -1087.7336 -1385.8146 1073.0916 100 100 + 1200 6.7 -1093.3541 -1391.4351 1073.0916 100 100 + 1400 8 -1092.143 -1390.224 1073.0916 100 100 + 1600 8.9 -1092.6395 -1390.7205 1073.0916 100 100 + 1800 9.9 -1098.4744 -1396.5554 1073.0916 100 100 + 2000 11 -1096.3326 -1394.4136 1073.0916 100 100 +Loop time of 10.7926 on 4 procs for 2000 steps with 1288 atoms + +Pair time (%) = 4.54746 (42.1348) +Neigh time (%) = 1.91457 (17.7396) +Comm time (%) = 1.38715 (12.8527) +Outpt time (%) = 0.00288278 (0.0267106) +Other time (%) = 2.94058 (27.2462) + +Nlocal: 322 ave 349 max 294 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 3306 ave 4004 max 2612 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 59447.5 ave 61515 max 57250 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 118895 ave 123082 max 114432 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +Total # of neighbors = 475580 +Ave neighs/atom = 369.239 +Neighbor list builds = 200 +Dangerous builds = 0 + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +Setting up run ... +Memory usage per processor = 56.0218 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -1096.3326 -1394.4136 1073.0916 100 100 + 100 0.53 -1097.1297 -1393.4516 1075.1972 99.409862 100.23926 + 200 1 -1096.0757 -1399.305 1075.4399 101.72715 100.33007 + 300 1.6 -1092.2745 -1395.827 1078.6046 101.83557 100.65429 + 400 2.1 -1090.7478 -1387.1617 1078.4832 99.440713 100.71601 + 500 2.6 -1094.2309 -1405.4917 1082.77 104.42152 101.12986 + 600 3.1 -1092.5375 -1398.2596 1088.0437 102.56341 101.62253 + 700 3.7 -1092.1714 -1403.4837 1093.2974 104.43883 102.1136 + 800 4.2 -1088.0883 -1402.5474 1099.5467 105.4945 102.6842 + 900 4.7 -1096.5611 -1407.2614 1106.6337 104.2335 103.32171 + 1000 5.2 -1096.0664 -1410.5711 1107.5876 105.50984 103.46933 + 1100 5.7 -1093.3795 -1398.4056 1109.412 102.32995 103.68648 + 1200 6.9 -1094.9691 -1405.2381 1110.9358 104.08883 103.87963 + 1300 8.4 -1099.21 -1406.5076 1109.7276 103.09197 103.85455 + 1400 9.5 -1096.4599 -1409.163 1112.0859 104.9054 104.11435 + 1500 15 -1093.8693 -1402.2613 1115.3316 103.45912 104.44504 + 1600 16 -1099.7654 -1418.4301 1116.8226 106.90538 104.63556 + 1700 22 -1096.8766 -1410.0213 1122.0201 105.05356 105.12214 + 1800 26 -1097.6888 -1415.4839 1123.5055 106.61369 105.31222 + 1900 29 -1091.0457 -1407.4814 1127.847 106.15762 105.73043 + 2000 29 -1087.88 -1410.9303 1132.576 108.3767 106.17959 +Loop time of 29.4659 on 4 procs for 2000 steps with 1288 atoms + +Pair time (%) = 5.39338 (18.3038) +Neigh time (%) = 2.56404 (8.7017) +Comm time (%) = 6.58258 (22.3396) +Outpt time (%) = 0.115528 (0.392073) +Other time (%) = 14.8104 (50.2628) + +Nlocal: 322 ave 357 max 288 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Nghost: 3290.75 ave 4029 max 2581 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 59412.5 ave 63932 max 55464 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +FullNghs: 118825 ave 127926 max 110803 min +Histogram: 1 0 1 0 0 0 1 0 0 1 + +Total # of neighbors = 475300 +Ave neighs/atom = 369.022 +Neighbor list builds = 200 +Dangerous builds = 0 +Setting up run ... +Memory usage per processor = 56.0218 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 2000 0 -1087.88 -1410.9303 1132.576 108.3767 106.17959 + 2100 7.9 -1091.2838 -1411.7447 1136.7596 107.50799 106.51412 + 2200 9.3 -1087.4168 -1410.7195 1140.19 108.46135 106.78813 + 2300 10 -1083.8716 -1416.0271 1148.7049 111.43128 107.46826 + 2400 19 -1091.2629 -1419.2548 1154.945 110.0345 107.9667 + 2500 21 -1085.6579 -1412.5054 1159.6405 109.65056 108.34175 + 2600 22 -1087.4854 -1415.3304 1163.337 109.98522 108.63701 + 2700 23 -1085.9108 -1418.0071 1166.5382 111.4114 108.89271 + 2800 24 -1086.1867 -1409.9525 1170.0101 108.61673 109.17004 + 2900 26 -1087.6424 -1414.342 1170.7793 109.60095 109.23147 + 3000 28 -1086.4899 -1406.3424 1168.9883 107.30389 109.08841 + 3100 33 -1088.2206 -1415.602 1168.5555 109.82968 109.05384 + 3200 34 -1088.1639 -1405.8117 1167.0205 106.56424 108.93124 + 3300 35 -1092.1189 -1412.2062 1164.7511 107.38266 108.74997 + 3400 43 -1089.7001 -1409.1671 1163.2716 107.17456 108.63179 + 3500 45 -1096.5551 -1411.0879 1159.1282 105.51925 108.30083 + 3600 45 -1094.65 -1413.2194 1154.2549 106.87345 107.91157 + 3700 46 -1096.9933 -1406.3656 1150.9523 103.788 107.64778 + 3800 47 -1091.9401 -1404.356 1147.2503 104.80904 107.35207 + 3900 47 -1087.998 -1407.1701 1146.0989 107.07564 107.2601 + 4000 50 -1095.8818 -1411.8326 1144.6278 105.99494 107.1426 + 4100 54 -1097.5819 -1412.4007 1144.1232 105.61516 107.10229 + 4200 56 -1098.6452 -1408.5634 1143.4876 103.97114 107.05152 + 4300 57 -1092.6405 -1406.6538 1140.8735 105.34494 106.84272 + 4400 58 -1093.7564 -1406.7458 1139.2442 105.00146 106.71258 + 4500 58 -1095.6025 -1411.6037 1139.2304 106.01182 106.71148 + 4600 60 -1104.0547 -1417.3245 1140.0447 105.09552 106.77652 + 4700 69 -1099.1767 -1415.132 1138.1578 105.99644 106.6258 + 4800 70 -1104.7266 -1421.7194 1137.6765 106.34453 106.58735 + 4900 71 -1099.3521 -1416.1386 1139.6396 106.27528 106.74416 + 5000 73 -1102.0311 -1422.1342 1140.1617 107.38796 106.78586 + 5100 75 -1099.9553 -1423.0918 1142.2784 108.4056 106.95494 + 5200 80 -1097.3863 -1421.3598 1145.6828 108.68639 107.22687 + 5300 81 -1094.5474 -1415.4736 1148.3123 107.6641 107.4369 + 5400 82 -1101.9624 -1416.5216 1148.1412 105.52807 107.42323 + 5500 83 -1099.6507 -1418.3752 1146.1342 106.92544 107.26292 + 5600 91 -1085.351 -1412.4144 1149.2494 109.72299 107.51175 + 5700 92 -1089.1937 -1408.3714 1151.8951 107.0775 107.72308 + 5800 92 -1098.7444 -1422.1218 1152.7943 108.48641 107.7949 + 5900 94 -1089.3746 -1412.4578 1153.8446 108.3877 107.8788 + 6000 1e+02 -1095.5262 -1420.9521 1156.6272 109.17363 108.10106 +Loop time of 103.93 on 4 procs for 4000 steps with 1288 atoms + +Pair time (%) = 12.9055 (12.4175) +Neigh time (%) = 6.4635 (6.21906) +Comm time (%) = 23.7367 (22.839) +Outpt time (%) = 0.16248 (0.156335) +Other time (%) = 60.6623 (58.3681) + +Nlocal: 322 ave 379 max 280 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +Nghost: 3294 ave 4103 max 2559 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 59569 ave 71977 max 55076 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +FullNghs: 119138 ave 143935 max 110133 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 476552 +Ave neighs/atom = 369.994 +Neighbor list builds = 400 +Dangerous builds = 0 diff --git a/examples/USER/atc/fluids/concentration.screen b/examples/USER/atc/fluids/concentration.screen new file mode 100644 index 0000000000..800cd0a1d8 --- /dev/null +++ b/examples/USER/atc/fluids/concentration.screen @@ -0,0 +1,161 @@ +LAMMPS (14 Aug 2013) +units real +atom_style full # charge +### NOTE p p p is required for both lammps & atc since periodic images are employed in ExtrinsicModelElectrostatic::correct_electrostatic_forces +########### BEGIN PARAMETERS #################################### +variable T equal 300 +variable a equal 1.0 # 5.719025032 +variable i equal 10 # thermo +variable f equal 50 # neighbor & conc interval +variable s equal 100 # 10 # 100 # output +variable n equal 800 # 20 # 200 # 300 # duration +variable x equal 4 # 40 # 2 # 4 # exchanges +variable e equal 100. # 1. # 100. # 10. # energy +variable h equal 5 # nelems +variable dt equal 4. #1. # 0 # 4.0 +############## END PARAMETERS ################################# +dimension 3 +boundary p p p +pair_style lj/cut/coul/cut 13.0 +lattice sc $a +lattice sc 1 +Lattice spacing in x,y,z = 1 1 1 +read_data concentration_init.data +Scanning data file ... +Reading data file ... + orthogonal box = (0 0 0) to (114.381 22.8761 22.8761) + 4 by 1 by 1 MPI processor grid + 544 atoms + 544 velocities +Finding 1-2 1-3 1-4 neighbors ... + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors +atom_modify sort 0 1 +mass * 39.948 +pair_coeff * * 0.2381 3.405 +pair_coeff 1 * 0.4 3.405 +dielectric 80.0 +variable xlo equal xlo +variable xhi equal xhi +variable xmid equal 0.5*(${xhi}+${xlo}) +variable xmid equal 0.5*(114.38050064000000816+${xlo}) +variable xmid equal 0.5*(114.38050064000000816+0) +print "reservior x ${xmid}:${xhi}" +reservior x 57.190250320000004081:114.38050064000000816 +variable ylo equal ylo +variable yhi equal yhi +variable zlo equal zlo +variable zhi equal zhi +region BOX block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box +region BOX block 0 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box +region BOX block 0 114.38050064000000816 ${ylo} ${yhi} ${zlo} ${zhi} units box +region BOX block 0 114.38050064000000816 0 ${yhi} ${zlo} ${zhi} units box +region BOX block 0 114.38050064000000816 0 22.876100128000000922 ${zlo} ${zhi} units box +region BOX block 0 114.38050064000000816 0 22.876100128000000922 0 ${zhi} units box +region BOX block 0 114.38050064000000816 0 22.876100128000000922 0 22.876100128000000922 units box +region FLUID block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box +region FLUID block 0 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box +region FLUID block 0 114.38050064000000816 ${ylo} ${yhi} ${zlo} ${zhi} units box +region FLUID block 0 114.38050064000000816 0 ${yhi} ${zlo} ${zhi} units box +region FLUID block 0 114.38050064000000816 0 22.876100128000000922 ${zlo} ${zhi} units box +region FLUID block 0 114.38050064000000816 0 22.876100128000000922 0 ${zhi} units box +region FLUID block 0 114.38050064000000816 0 22.876100128000000922 0 22.876100128000000922 units box +region R block ${xmid} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box +region R block 57.190250320000004081 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box +region R block 57.190250320000004081 114.38050064000000816 ${ylo} ${yhi} ${zlo} ${zhi} units box +region R block 57.190250320000004081 114.38050064000000816 0 ${yhi} ${zlo} ${zhi} units box +region R block 57.190250320000004081 114.38050064000000816 0 22.876100128000000922 ${zlo} ${zhi} units box +region R block 57.190250320000004081 114.38050064000000816 0 22.876100128000000922 0 ${zhi} units box +region R block 57.190250320000004081 114.38050064000000816 0 22.876100128000000922 0 22.876100128000000922 units box +group SOLID type 1 +288 atoms in group SOLID +variable xdof equal 3*count(SOLID) +compute_modify thermo_temp extra ${xdof} +compute_modify thermo_temp extra 864 +#set group SOLID charge 0 +group NEUTRAL type 2 +114 atoms in group NEUTRAL +group FLUID type 2 3 4 +256 atoms in group FLUID +group NION type 3 +66 atoms in group NION +group PION type 4 +76 atoms in group PION +#group tPION type 5 # not dynamic +#group tNION type 6 # not dynamic +#variable typeP atom type[]==5 +set group PION charge 1 +Setting atom values ... + 76 settings made for charge +set group NION charge -1 +Setting atom values ... + 66 settings made for charge +variable O equal count(NEUTRAL) +variable S equal count(SOLID) +variable F equal count(FLUID) +variable P equal count(PION) +variable N equal count(NION) +variable Pr equal count(PION,R) +variable Nr equal count(NION,R) +#variable tP equal count(tPION) +#variable tN equal count(tNION) +variable V equal vol +variable cO equal v_O/v_V +variable cS equal v_S/v_V +variable cN equal v_N/v_V +variable cP equal v_P/v_V +compute q all property/atom q +compute m all property/atom mass +compute Q all reduce sum c_q +compute M all reduce sum c_m +compute Qf FLUID reduce sum c_q +compute Mf FLUID reduce sum c_m +compute PMIN PION reduce min x +compute PMAX PION reduce max x +compute NMIN NION reduce min x +compute NMAX NION reduce max x +timestep ${dt} +timestep 4 +#neighbor 13 bin +neigh_modify every $i check no +neigh_modify every 10 check no +# coulombic interactions +fix ATC FLUID atc species_electrostatic Ar_electrostatic.mat +ATC: constructing electrostatic species coupling with parameter file Ar_electrostatic.mat + ATC: peratom PE compute created with ID: 13 + ATC: 1 materials defined from Ar_electrostatic.mat + ATC: creating fem_efield extrinsic model + ATC: 1 materials defined from Ar_electrostatic.mat +#fix_modify ATC parallel_consistency off +fix_modify ATC extrinsic short_range off +#fix_modify ATC boundary SOLID +fix_modify ATC atom_element_map eulerian $i +fix_modify ATC atom_element_map eulerian 10 +fix_modify ATC internal_quadrature off +fix_modify ATC consistent_fe_initialization on +fix_modify ATC filter type exponential +fix_modify ATC filter scale $i +fix_modify ATC filter scale 10 +fix_modify ATC filter equilibrate +# mesh +print "x = ${xlo}:${xhi}" +x = 0:114.38050064000000816 +fix_modify ATC mesh create $h 1 1 BOX p p p # f p p ExtrinsicModelElectrostatic::correct_electrostatic_forces iterates through ghosts +fix_modify ATC mesh create 5 1 1 BOX p p p + ATC: created uniform mesh with 24 nodes, 5 unique nodes, and 5 elements +fix_modify ATC mesh create_nodeset LBC ${xlo} ${xlo} -INF INF -INF INF +fix_modify ATC mesh create_nodeset LBC 0 ${xlo} -INF INF -INF INF +fix_modify ATC mesh create_nodeset LBC 0 0 -INF INF -INF INF + ATC: created nodeset LBC with 1 nodes +fix_modify ATC mesh create_elementset FLUID FLUID + ATC: created elementset FLUID with 5 elements +fix_modify ATC mesh create_elementset R R + ATC: created elementset R with 2 elements +fix_modify ATC mesh create_elementset BOX BOX + ATC: created elementset BOX with 5 elements +## NOTE tag instead of type, what about transition tyme +fix_modify ATC mass_matrix fe +fix_modify ATC internal_element_set FLUID +ERROR: Illegal fix_modify command (../fix.cpp:104) diff --git a/examples/USER/atc/fluids/conducting_interface.screen b/examples/USER/atc/fluids/conducting_interface.screen new file mode 100644 index 0000000000..0ba180cdb7 --- /dev/null +++ b/examples/USER/atc/fluids/conducting_interface.screen @@ -0,0 +1,124 @@ +LAMMPS (14 Aug 2013) +units real +atom_style full +########### BEGIN PARAMETERS #################################### +variable a equal 5.719025032 +variable i equal 1 +variable s equal 100 +variable n equal 1000 # 500 2000 +variable dt equal 4.0 +variable W equal 4 +variable L equal 20 +variable Ls equal 4 # surface +variable h equal 10 +variable phiInf equal -1. # 0. 10 -10.0 +variable R equal 2*$a +variable R equal 2*5.7190250320000002304 +############## END PARAMETERS ################################# +dimension 3 +boundary f p p +pair_style lj/cut 13.0 +lattice fcc $a +lattice fcc 5.7190250320000002304 +Lattice spacing in x,y,z = 5.71903 5.71903 5.71903 +read_data interface_init.data +Scanning data file ... +Reading data file ... + orthogonal box = (0 0 0) to (114.381 22.8761 22.8761) + 4 by 1 by 1 MPI processor grid + 544 atoms + 544 velocities +Finding 1-2 1-3 1-4 neighbors ... + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors +atom_modify sort 0 1 +mass * 39.948 +pair_coeff * * 0.2381 3.405 +dielectric 1.0 +region BOX block 0 $L 0 $W 0 $W +region BOX block 0 20 0 $W 0 $W +region BOX block 0 20 0 4 0 $W +region BOX block 0 20 0 4 0 4 +group SOLID type 1 +288 atoms in group SOLID +group FLUID type 2 3 4 +256 atoms in group FLUID +group P type 3 +66 atoms in group P +group N type 4 +76 atoms in group N +set group SOLID charge 0 # use ATC to provide charge to the surface +Setting atom values ... + 288 settings made for charge +# charged layer -- NOTE on an element boundary +variable b equal ${Ls}-0.1 +variable b equal 4-0.1 +variable c equal ${Ls}+0.1 +variable c equal 4+0.1 +region LAYER block $b $c INF INF INF INF +region LAYER block 3.8999999999999999112 $c INF INF INF INF +region LAYER block 3.8999999999999999112 4.0999999999999996447 INF INF INF INF +group LAYER region LAYER +32 atoms in group LAYER +timestep ${dt} +timestep 4 +neigh_modify every $i check no +neigh_modify every 1 check no +fix WALLS all wall/reflect xlo EDGE xhi EDGE +fix PP all atc field +ATC: constructing shape function field estimate + ATC: peratom PE compute created with ID: 3 +fix_modify PP add_species IONS type 1 2 3 4 +fix_modify PP fields add species_concentration mass_density charge_density # temperature +fix_modify PP output volume_integral all mass_density +fix_modify PP output volume_integral all charge_density +fix_modify PP atom_element_map eulerian $s +fix_modify PP atom_element_map eulerian 100 +fix_modify PP mesh create $h 1 1 BOX f p p +fix_modify PP mesh create 10 1 1 BOX f p p + ATC: created uniform mesh with 44 nodes, 11 unique nodes, and 10 elements +fix ATC FLUID atc species_electrostatic Ar_electrostatic.mat +ATC: constructing electrostatic species coupling with parameter file Ar_electrostatic.mat + ATC: peratom PE compute created with ID: 3 + ATC: 1 materials defined from Ar_electrostatic.mat + ATC: creating fem_efield extrinsic model + ATC: 1 materials defined from Ar_electrostatic.mat +fix_modify ATC add_species P type 3 +fix_modify ATC add_species N type 4 +fix_modify ATC boundary SOLID +#fix_modify ATC kernel cell $R $R $W +fix_modify ATC atom_element_map eulerian $i +fix_modify ATC atom_element_map eulerian 1 +fix_modify ATC internal_quadrature off # on creates a nasty error (NOTE trap error) +fix_modify ATC mass_matrix fe +fix_modify ATC include atomic_charge +# mesh : 2x2 tosses an atom to infinity and beyond +#fix_modify ATC mesh create $h 4 1 BOX f p p dx piecewise_linear 0 0 0 1 0 0 0.0 1.0 1.0 1.0 +#fix_modify ATC mesh create $h 1 1 BOX f p p dx piecewise_linear 0 0 0 1 0 0 # 0.0 1.0 0.2 1.0 0.207812 0.1 1.0 1.0 +### >>> node h vs list reepat and scale to box +fix_modify ATC mesh create $h 4 1 BOX f p p dx 2 2 0.5 0.5 0.5 0.5 2 3 4 5 +fix_modify ATC mesh create 10 4 1 BOX f p p dx 2 2 0.5 0.5 0.5 0.5 2 3 4 5 + ATC: created structured mesh with 110 nodes, 44 unique nodes, and 40 elements +fix_modify ATC mesh create_nodeset lbc 0 0 -INF INF -INF INF + ATC: created nodeset lbc with 4 nodes +fix_modify ATC mesh create_nodeset rbc $L $L -INF INF -INF INF +fix_modify ATC mesh create_nodeset rbc 20 $L -INF INF -INF INF +fix_modify ATC mesh create_nodeset rbc 20 20 -INF INF -INF INF + ATC: created nodeset rbc with 4 nodes +fix_modify ATC mesh create_nodeset wall 0 ${Ls} 0 4 0 4 +fix_modify ATC mesh create_nodeset wall 0 4 0 4 0 4 + ATC: created nodeset wall with 12 nodes +fix_modify ATC mesh create_elementset wall 0 ${Ls} 0 4 0 4 +fix_modify ATC mesh create_elementset wall 0 4 0 4 0 4 + ATC: created elementset wall with 8 elements +#fix_modify ATC mesh create_faceset lbc plane x 0 +fix_modify ATC mesh create_faceset surface -INF ${Ls} -INF INF -INF INF +fix_modify ATC mesh create_faceset surface -INF 4 -INF INF -INF INF + ATC: created faceset surface with 4 faces +fix_modify ATC mesh create_elementset fluidElts ${Ls} INF -INF INF -INF INF +fix_modify ATC mesh create_elementset fluidElts 4 INF -INF INF -INF INF + ATC: created elementset fluidElts with 32 elements +fix_modify ATC internal_element_set fluidElts +ERROR: Illegal fix_modify command (../fix.cpp:104) diff --git a/examples/USER/atc/fluids/dielectric.mat b/examples/USER/atc/fluids/dielectric.mat new file mode 100644 index 0000000000..16b730bb0b --- /dev/null +++ b/examples/USER/atc/fluids/dielectric.mat @@ -0,0 +1,15 @@ +material Fluid real +electric_field linear +permittivity 1. +end +electron_density null +end +end + +material Solid real +electric_field linear +permittivity 4. +end +electron_density null +end +end diff --git a/examples/USER/atc/fluids/dielectric_interface.screen b/examples/USER/atc/fluids/dielectric_interface.screen new file mode 100644 index 0000000000..30b1f734cc --- /dev/null +++ b/examples/USER/atc/fluids/dielectric_interface.screen @@ -0,0 +1,106 @@ +LAMMPS (14 Aug 2013) +units real +atom_style full +########### BEGIN PARAMETERS #################################### +variable a equal 5.719025032 +variable i equal 1 +variable s equal 100 +variable n equal 1000 # 500 2000 +variable dt equal 4.0 +variable W equal 4 +variable L equal 20 +variable Ls equal 4 # surface +variable h equal 10 +variable phiInf equal -1. # 0. 10 -10.0 +variable perm2 equal 2. +variable depth equal 17.1571 +# 1 1 0.1 0.1 1 1 +variable w1 equal 4/$L # relative wall width +variable w1 equal 4/20 +variable w2 equal ${w1}+2/$L # relative wall width +variable w2 equal 0.2000000000000000111+2/$L +variable w2 equal 0.2000000000000000111+2/20 +variable w3 equal ${w2}+2/$L +variable w3 equal 0.30000000000000004441+2/$L +variable w3 equal 0.30000000000000004441+2/20 +variable w4 equal ${w3}+2/$L +variable w4 equal 0.4000000000000000222+2/$L +variable w4 equal 0.4000000000000000222+2/20 +############## END PARAMETERS ################################# +dimension 3 +boundary f p p +pair_style lj/cut 13.0 +lattice fcc $a +lattice fcc 5.7190250320000002304 +Lattice spacing in x,y,z = 5.71903 5.71903 5.71903 +read_data interface_init.data +Scanning data file ... +Reading data file ... + orthogonal box = (0 0 0) to (114.381 22.8761 22.8761) + 4 by 1 by 1 MPI processor grid + 544 atoms + 544 velocities +Finding 1-2 1-3 1-4 neighbors ... + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors +atom_modify sort 0 1 +mass * 39.948 +pair_coeff * * 0.2381 3.405 +dielectric 1.0 +region BOX block 0 $L 0 $W 0 $W +region BOX block 0 20 0 $W 0 $W +region BOX block 0 20 0 4 0 $W +region BOX block 0 20 0 4 0 4 +group SOLID type 1 +288 atoms in group SOLID +group FLUID type 2 3 4 +256 atoms in group FLUID +group P type 3 +66 atoms in group P +group N type 4 +76 atoms in group N +set group SOLID charge 0 # use ATC to provide charge to the surface +Setting atom values ... + 288 settings made for charge +timestep ${dt} +timestep 4 +neigh_modify every $i check no +neigh_modify every 1 check no +fix WALLS all wall/reflect xlo EDGE xhi EDGE +fix PP all atc field +ATC: constructing shape function field estimate + ATC: peratom PE compute created with ID: 3 +fix_modify PP add_species IONS type 1 2 3 4 +fix_modify PP fields add species_concentration mass_density charge_density +fix_modify PP atom_element_map eulerian $s +fix_modify PP atom_element_map eulerian 100 +fix_modify PP mesh create $h 1 1 BOX f p p +fix_modify PP mesh create 10 1 1 BOX f p p + ATC: created uniform mesh with 44 nodes, 11 unique nodes, and 10 elements +fix_modify PP output volume_integral all mass_density +fix_modify PP output volume_integral all charge_density +fix ATC FLUID atc species_electrostatic Ar_electrostatic.mat +ATC: constructing electrostatic species coupling with parameter file Ar_electrostatic.mat + ATC: peratom PE compute created with ID: 3 + ATC: 1 materials defined from Ar_electrostatic.mat + ATC: creating fem_efield extrinsic model + ATC: 1 materials defined from Ar_electrostatic.mat +fix_modify ATC add_species P type 3 +fix_modify ATC add_species N type 4 +fix_modify ATC boundary SOLID +fix_modify ATC atom_element_map eulerian $i +fix_modify ATC atom_element_map eulerian 1 +fix_modify ATC internal_quadrature off # on creates a nasty error (NOTE trap error) +fix_modify ATC mass_matrix fe +fix_modify ATC include atomic_charge +# mesh +fix_modify ATC mesh create $h 2 2 BOX f p p dx piecewise_linear 0 0 0 1 0 0 0.0 1.0 1.0 1.0 +fix_modify ATC mesh create 10 2 2 BOX f p p dx piecewise_linear 0 0 0 1 0 0 0.0 1.0 1.0 1.0 + ATC: created structured mesh with 99 nodes, 44 unique nodes, and 40 elements +fix_modify ATC mesh create_elementset fluidElts ${Ls} INF -INF INF -INF INF +fix_modify ATC mesh create_elementset fluidElts 4 INF -INF INF -INF INF + ATC: created elementset fluidElts with 32 elements +fix_modify ATC internal_element_set fluidElts +ERROR: Illegal fix_modify command (../fix.cpp:104) diff --git a/examples/USER/atc/fluids/double_layer.screen b/examples/USER/atc/fluids/double_layer.screen new file mode 100644 index 0000000000..b54c341688 --- /dev/null +++ b/examples/USER/atc/fluids/double_layer.screen @@ -0,0 +1,202 @@ +LAMMPS (14 Aug 2013) + +units metal +atom_style full +dimension 3 +neighbor 2 bin +neigh_modify every 1 check yes +boundary f f f + +timestep 0.0005 +thermo 100 +dielectric 81. + +newton off + +pair_style lj/cut 13.000000 +pair_modify mix arithmetic +read_data waternve.atm +Scanning data file ... +Reading data file ... + orthogonal box = (-19.38 -19.38 -21.88) to (19.38 19.38 23.94) + 1 by 2 by 2 MPI processor grid + 1982 atoms + 1982 velocities +Finding 1-2 1-3 1-4 neighbors ... + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors +reset_timestep 0 + +variable nsteps equal 1000 +variable dumpfreq equal ${nsteps}/10 +variable dumpfreq equal 1000/10 +variable nx equal 4 +variable ny equal 4 +variable nz equal 4 +variable x_min equal -19.38 +variable x_max equal 19.38 +variable x_goldmin equal -11.22 +variable x_goldmax equal 11.22 +variable x_fluidmin equal ${x_goldmin} +variable x_fluidmin equal -11.220000000000000639 +variable x_fluidmax equal ${x_goldmax} +variable x_fluidmax equal 11.220000000000000639 +variable x_wallmin equal ${x_goldmin}-1.5 +variable x_wallmin equal -11.220000000000000639-1.5 +variable x_wallmax equal ${x_goldmax}+1.5 +variable x_wallmax equal 11.220000000000000639+1.5 +variable y_min equal -19.38 +variable y_max equal 19.38 +variable y_goldmin equal -11.22 +variable y_goldmax equal 11.22 +variable surface_charge equal -0.3125/(4.08*4.08) +variable y_fluidmin equal ${y_goldmin} +variable y_fluidmin equal -11.220000000000000639 +variable y_fluidmax equal ${y_goldmax} +variable y_fluidmax equal 11.220000000000000639 +variable y_wallmin equal ${y_goldmin}-1.5 +variable y_wallmin equal -11.220000000000000639-1.5 +variable y_wallmax equal ${y_goldmax}+1.5 +variable y_wallmax equal 11.220000000000000639+1.5 +variable downshift equal 2.5 +variable zshiftlatt equal 1-${downshift}/4.08 +variable zshiftlatt equal 1-2.5/4.08 +variable z_min equal -20.4-${downshift}+0.25*4.08 +variable z_min equal -20.4-2.5+0.25*4.08 +variable z_max equal 22.44+1.5 +variable z_goldmin equal -12.24-${downshift}+0.25*4.08 +variable z_goldmin equal -12.24-2.5+0.25*4.08 +variable z_goldmax equal -${downshift}+0.25*4.08 +variable z_goldmax equal -2.5+0.25*4.08 +variable z_goldtopmin equal ${z_goldmax}-0.5*4.08 +variable z_goldtopmin equal -1.4799999999999999822-0.5*4.08 +variable z_goldtopmax equal ${z_goldmax} +variable z_goldtopmax equal -1.4799999999999999822 +variable z_fluidmin equal 0. +variable z_fluidmax equal 22.44 +variable z_wallmax equal ${z_max} +variable z_wallmax equal 23.940000000000001279 + +lattice sc 8.16 origin 0 0 0.75 +Lattice spacing in x,y,z = 8.16 8.16 8.16 + +group pos type 4 +27 atoms in group pos +group neg type 5 +0 atoms in group neg +group allfluid type 3 4 5 +177 atoms in group allfluid + +compute fluidT allfluid temp +thermo_style custom step epair emol etotal press c_fluidT + +fix zhiwall allfluid wall/lj93 zhi ${z_wallmax} 0.0195 3.45 10.000000 units box +fix zhiwall allfluid wall/lj93 zhi 23.940000000000001279 0.0195 3.45 10.000000 units box +fix xlowall allfluid wall/lj93 xlo ${x_wallmin} 0.0195 3.45 10.000000 units box +fix xlowall allfluid wall/lj93 xlo -12.720000000000000639 0.0195 3.45 10.000000 units box +fix xhiwall allfluid wall/lj93 xhi ${x_wallmax} 0.0195 3.45 10.000000 units box +fix xhiwall allfluid wall/lj93 xhi 12.720000000000000639 0.0195 3.45 10.000000 units box +fix ylowall allfluid wall/lj93 ylo ${y_wallmin} 0.0195 3.45 10.000000 units box +fix ylowall allfluid wall/lj93 ylo -12.720000000000000639 0.0195 3.45 10.000000 units box +fix yhiwall allfluid wall/lj93 yhi ${y_wallmax} 0.0195 3.45 10.000000 units box +fix yhiwall allfluid wall/lj93 yhi 12.720000000000000639 0.0195 3.45 10.000000 units box + +group solvent type 3 +150 atoms in group solvent +fix fluidnvt solvent nvt temp 300.0 300.0 0.100 drag 0.2 + +########################################################################## +region ATC_BOX block ${x_wallmin} ${x_wallmax} ${y_wallmin} ${y_wallmax} ${z_goldtopmin} ${z_wallmax} units box +region ATC_BOX block -12.720000000000000639 ${x_wallmax} ${y_wallmin} ${y_wallmax} ${z_goldtopmin} ${z_wallmax} units box +region ATC_BOX block -12.720000000000000639 12.720000000000000639 ${y_wallmin} ${y_wallmax} ${z_goldtopmin} ${z_wallmax} units box +region ATC_BOX block -12.720000000000000639 12.720000000000000639 -12.720000000000000639 ${y_wallmax} ${z_goldtopmin} ${z_wallmax} units box +region ATC_BOX block -12.720000000000000639 12.720000000000000639 -12.720000000000000639 12.720000000000000639 ${z_goldtopmin} ${z_wallmax} units box +region ATC_BOX block -12.720000000000000639 12.720000000000000639 -12.720000000000000639 12.720000000000000639 -3.5200000000000000178 ${z_wallmax} units box +region ATC_BOX block -12.720000000000000639 12.720000000000000639 -12.720000000000000639 12.720000000000000639 -3.5200000000000000178 23.940000000000001279 units box +group ATC_ATOMS type 4 5 +27 atoms in group ATC_ATOMS +fix ATC ATC_ATOMS atc species_electrostatic Ar_species_dl.mat +ATC: constructing electrostatic species coupling with parameter file Ar_species_dl.mat + ATC: peratom PE compute created with ID: 5 + ATC: 1 materials defined from Ar_species_dl.mat + ATC: creating fem_efield extrinsic model + ATC: 1 materials defined from Ar_species_dl.mat +fix_modify ATC add_species P group pos +fix_modify ATC add_species N group neg +fix_modify ATC mesh create ${nx} ${ny} ${nz} ATC_BOX f f f +fix_modify ATC mesh create 4 ${ny} ${nz} ATC_BOX f f f +fix_modify ATC mesh create 4 4 ${nz} ATC_BOX f f f +fix_modify ATC mesh create 4 4 4 ATC_BOX f f f + ATC: created uniform mesh with 125 nodes, 125 unique nodes, and 64 elements +fix_modify ATC atom_element_map eulerian 1 +fix_modify ATC internal_quadrature off + +fix_modify ATC initial mass_density all 0. +fix_modify ATC mesh create_faceset BOTTOM_FACE -INF INF -INF INF ${z_goldtopmin} INF +fix_modify ATC mesh create_faceset BOTTOM_FACE -INF INF -INF INF -3.5200000000000000178 INF + ATC: created faceset BOTTOM_FACE with 16 faces +## OLD +fix_modify ATC extrinsic fix_charge BOTTOM_FACE ${surface_charge} +fix_modify ATC extrinsic fix_charge BOTTOM_FACE -0.018772827758554402194 +## NEW +# ERROR: Poisson solver needs Dirichlet data +#fix_modify ATC control charge conductor ${surface_charge} +#fix_modify ATC control charge effective_charge ATC_ATOMS BOTTOM_FACE +## END + +fix_modify ATC output double_layerFE ${dumpfreq} text binary +fix_modify ATC output double_layerFE 100 text binary + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: +NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationP +NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationN +species_concentration : species_concentrationP +species_concentration : species_concentrationN + +dump chargenve all atom ${dumpfreq} double_layer.dmp +dump chargenve all atom 100 double_layer.dmp + +run ${nsteps} +run 1000 +Setting up run ... + ATC: WARNING: all initial conditions for charge_density have not been defined and the undefined are assumed zero + ATC: WARNING: all initial conditions for species_concentration have not been defined and the undefined are assumed zero + ATC: WARNING: all initial conditions for electric_potential have not been defined and the undefined are assumed zero +Memory usage per processor = 54.1045 Mbytes +Step E_pair E_mol TotEng Press fluidT + 0 -9252.0858 0 -9228.1564 -55763.67 293.65526 + 100 -9252.3247 0 -9228.0784 -55827.581 307.58592 + 200 -9251.4752 0 -9227.7891 -55737.506 282.95787 + 300 -9251.4249 0 -9227.5267 -55707.319 292.28243 + 400 -9251.418 0 -9227.1803 -55676.42 307.20457 + 500 -9251.2317 0 -9226.4518 -55626.477 331.04006 + 600 -9251.0816 0 -9226.0561 -55592.086 341.83069 + 700 -9250.3998 0 -9226.2318 -55560.989 304.13946 + 800 -9251.0058 0 -9226.6944 -55690.148 310.44444 + 900 -9251.0001 0 -9227.2599 -55752.304 285.33992 + 1000 -9250.9076 0 -9227.1099 -55769.609 287.86493 +Loop time of 110.95 on 4 procs for 1000 steps with 1982 atoms + +Pair time (%) = 10.3921 (9.36645) +Bond time (%) = 0.000747621 (0.000673836) +Neigh time (%) = 0.0807644 (0.0727935) +Comm time (%) = 7.50919 (6.76808) +Outpt time (%) = 0.527695 (0.475615) +Other time (%) = 92.4396 (83.3164) + +Nlocal: 495.5 ave 976 max 63 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 916.5 ave 1083 max 778 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 132325 ave 269946 max 8208 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +FullNghs: 219343 ave 455925 max 9588 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 877372 +Ave neighs/atom = 442.67 +Ave special neighs/atom = 0 +Neighbor list builds = 4 +Dangerous builds = 0 diff --git a/examples/USER/atc/fluids/in.bar1d_fluids b/examples/USER/atc/fluids/in.bar1d_fluids new file mode 100644 index 0000000000..63ef0e2744 --- /dev/null +++ b/examples/USER/atc/fluids/in.bar1d_fluids @@ -0,0 +1,98 @@ +#AtC Thermal Coupling +# This benchmark tests heat conducting into and out of the MD region. The +# temperature is intially 20 everywhere and the left boundary BC is fixed at +# 40.# The result should show heat diffusing through the FEM to the MD and back +# out # to the FEM on the right. Insufficient time is captured to reach the +# linear # steady state, but heat crossing both boundaries should be observed. +log bar1d_fluids.log +units real +atom_style atomic +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init +#read_restart post_eq.dat +lattice fcc 5.405 origin 0.25 0.25 0.25 +# create atoms, NOTE commented out for restart +#region mdRegion block -7 7 -3 3 -3 3 +#boundary f p p +#create_box 2 mdRegion +#create_atoms 1 region mdRegion +#mass * 39.95 +# specify interal/ghost atoms +#region mdInternal block -6 6 -3 3 -3 3 +#region mdGhost block -6 6 -3 3 -3 3 side out +#create_atoms 1 region mdGhost +#lattice fcc 6.5 origin 0.25 0.25 0.25 +#create_atoms 2 region mdInternal +group internal type 2 +group ghost type 1 +# velocities have Vcm = 0, NOTE next four lines commented out for restart +#velocity internal create 100. 87287 mom yes loop geom +#pair_style lj/cut 13.5 +##pair_coeff 1 1 0.010323166 3.405 13.5 +#pair_coeff * * .238 3.405 13.5 +neighbor 5. bin +neigh_modify every 10 delay 0 check no +#write_restart tinit.dat +# ID group atc PhysicsType ParameterFile +lattice fcc 5.405 origin 0.25 0.25 0.25 +region atcRegion block -6.25 6.25 -3 3 -3 3 +fix AtC internal atc thermal Ar_thermal.mat +# ID part keywords nx ny nz region periodicity +fix_modify AtC mesh create 6 1 1 atcRegion f p p +fix_modify AtC time_integration fractional_step +fix_modify AtC atom_element_map eulerian 10 # NOTE this introduces a minor amount of time integration error tracking the atomic temperature +fix_modify AtC internal_quadrature off +#fix_modify AtC mass_matrix fe +# fix a temperature +fix_modify AtC fix temperature all 100. +# add nodesets +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -6.3 -6.2 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 6.2 6.3 -INF INF -INF INF +#fix_modify AtC fix temperature lbc 120. +#fix_modify AtC fix temperature rbc 100. +#used for restarting +#fix_modify AtC consistent_fe_initialization on +#fix_modify AtC initial temperature all 100. +# turn on thermostat +fix_modify AtC control thermal rescale 10 +# equilibrate MD field +variable xdof equal 3*count(ghost) +compute_modify thermo_temp extra ${xdof} +thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] +thermo_modify format 1 %6i format 2 %7.2g +#fix_modify AtC output bar1d_fluids_eqFE 200 text binary +#dump D1 all atom 200 dump_eq.bar1d +timestep 2 +thermo 200 +run 2000 +#write_restart post_eq.dat +# change thermostat to hoover +reset_timestep 0 +fix_modify AtC reset_time +fix_modify AtC unfix temperature all +variable deltaT equal 2.*2000. +fix_modify AtC fix temperature lbc temporal_ramp 100. 120. ${deltaT} +#fix_modify AtC fix temperature lbc 100. +fix_modify AtC fix temperature rbc 100. +fix_modify AtC control thermal flux no_boundary +fix_modify AtC control tolerance 1.e-14 +fix_modify AtC control localized_lambda on +fix_modify AtC filter type exponential +fix_modify AtC filter scale 1000.0 +fix_modify AtC filter on +# ouput commands +fix_modify AtC output bar1d_fluidsFE 100 text +#undump D1 +#dump D2 all atom 200 dump.bar1d +#dump D2 all custom 200 dump.bar1d id type xs ys zs vx vy vz +# set-up non-equilibrium IC +thermo 100 +run 2000 +# run non-equilibrium condition +fix_modify AtC fix temperature lbc 120. +run 4000 diff --git a/examples/USER/atc/fluids/in.concentration b/examples/USER/atc/fluids/in.concentration new file mode 100644 index 0000000000..255524bc0a --- /dev/null +++ b/examples/USER/atc/fluids/in.concentration @@ -0,0 +1,172 @@ +echo both +units real +atom_style full # charge +### NOTE p p p is required for both lammps & atc since periodic images are employed in ExtrinsicModelElectrostatic::correct_electrostatic_forces +########### BEGIN PARAMETERS #################################### +variable T equal 300 +variable a equal 1.0 # 5.719025032 +variable i equal 10 # thermo +variable f equal 50 # neighbor & conc interval +variable s equal 100 # 10 # 100 # output +variable n equal 800 # 20 # 200 # 300 # duration +variable x equal 4 # 40 # 2 # 4 # exchanges +variable e equal 100. # 1. # 100. # 10. # energy +variable h equal 5 # nelems +variable dt equal 4. #1. # 0 # 4.0 +############## END PARAMETERS ################################# +dimension 3 +boundary p p p +pair_style lj/cut/coul/cut 13.0 +lattice sc $a +read_data concentration_init.data +atom_modify sort 0 1 +mass * 39.948 +pair_coeff * * 0.2381 3.405 +pair_coeff 1 * 0.4 3.405 +dielectric 80.0 +variable xlo equal xlo +variable xhi equal xhi +variable xmid equal 0.5*(${xhi}+${xlo}) +print "reservior x ${xmid}:${xhi}" +variable ylo equal ylo +variable yhi equal yhi +variable zlo equal zlo +variable zhi equal zhi +region BOX block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box +region FLUID block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box +region R block ${xmid} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box +group SOLID type 1 +variable xdof equal 3*count(SOLID) +compute_modify thermo_temp extra ${xdof} +#set group SOLID charge 0 +group NEUTRAL type 2 +group FLUID type 2 3 4 +group NION type 3 +group PION type 4 +#group tPION type 5 # not dynamic +#group tNION type 6 # not dynamic +#variable typeP atom type[]==5 +set group PION charge 1 +set group NION charge -1 +variable O equal count(NEUTRAL) +variable S equal count(SOLID) +variable F equal count(FLUID) +variable P equal count(PION) +variable N equal count(NION) +variable Pr equal count(PION,R) +variable Nr equal count(NION,R) +#variable tP equal count(tPION) +#variable tN equal count(tNION) +variable V equal vol +variable cO equal v_O/v_V +variable cS equal v_S/v_V +variable cN equal v_N/v_V +variable cP equal v_P/v_V +compute q all property/atom q +compute m all property/atom mass +compute Q all reduce sum c_q +compute M all reduce sum c_m +compute Qf FLUID reduce sum c_q +compute Mf FLUID reduce sum c_m +compute PMIN PION reduce min x +compute PMAX PION reduce max x +compute NMIN NION reduce min x +compute NMAX NION reduce max x +timestep ${dt} +#neighbor 13 bin +neigh_modify every $i check no +# coulombic interactions +fix ATC FLUID atc species_electrostatic Ar_electrostatic.mat +#fix_modify ATC parallel_consistency off +fix_modify ATC extrinsic short_range off +#fix_modify ATC boundary SOLID +fix_modify ATC atom_element_map eulerian $i +fix_modify ATC internal_quadrature off +fix_modify ATC consistent_fe_initialization on +fix_modify ATC filter type exponential +fix_modify ATC filter scale $i +fix_modify ATC filter equilibrate +# mesh +print "x = ${xlo}:${xhi}" +fix_modify ATC mesh create $h 1 1 BOX p p p # f p p ExtrinsicModelElectrostatic::correct_electrostatic_forces iterates through ghosts +fix_modify ATC mesh create_nodeset LBC ${xlo} ${xlo} -INF INF -INF INF +fix_modify ATC mesh create_elementset FLUID FLUID +fix_modify ATC mesh create_elementset R R +fix_modify ATC mesh create_elementset BOX BOX +## NOTE tag instead of type, what about transition tyme +fix_modify ATC mass_matrix fe +fix_modify ATC include atomic_charge +fix_modify ATC add_species N type 3 +fix_modify ATC add_species P type 4 +fix_modify ATC add_species Nt type 5 +fix_modify ATC add_species Pt type 6 +## CC +fix_modify ATC control concentration N R 0.001 Nt # deletions R +fix_modify ATC control concentration N frequency $f +fix_modify ATC control concentration N max_energy $e +fix_modify ATC control concentration N max_attempts 100 +fix_modify ATC control concentration N max_exchanges $x +#- +fix_modify ATC control concentration P R 0.002 Pt # addtions R +fix_modify ATC control concentration P frequency $f +fix_modify ATC control concentration P max_energy $e +fix_modify ATC control concentration P max_attempts 100 +fix_modify ATC control concentration P max_exchanges $x +fix_modify ATC output volume_integral all mass_density +fix_modify ATC output volume_integral all charge_density +# data reduction +fix PP all atc field +#fix_modify PP add_species ions type 3 4 +#fix_modify PP add_species IONS type 3 4 1 2 +fix_modify PP add_species n type 3 +fix_modify PP add_species p type 4 +fix_modify PP add_species s type 1 +fix_modify PP add_species o type 2 +fix_modify PP fields add species_concentration mass_density charge_density temperature +fix_modify PP fields add charge_flux species_flux +fix_modify PP output volume_integral all mass_density +fix_modify PP output volume_integral all charge_density +fix_modify PP mesh create $h 1 1 BOX f p p +fix_modify PP atom_element_map eulerian $i +# output +thermo $i +variable dN equal f_ATC[1] +variable dP equal f_ATC[2] +variable Nc equal f_ATC[3] +variable Pc equal f_ATC[4] +variable Nt equal f_ATC[5] +variable Pt equal f_ATC[6] +# +variable Nu equal f_ATC[7] +variable Pu equal f_ATC[8] +variable Ng equal f_ATC[9] +variable Pg equal f_ATC[10] +thermo_style custom step temp etotal & +atoms v_F v_P v_N v_dP v_dN v_Pc v_Nc v_Pr v_Nr v_Pt v_Nt & +c_PMIN c_NMIN c_PMAX c_NMAX c_Q c_M c_Qf c_Mf v_Pu v_Nu v_Pg v_Ng +# NOTE this doesn't seem to work +#thermo_modify format 4 %5d format 5 %5d format 6 %5d format 7 %5d format 8 %5d +#thermo_modify format 4 %5d +#thermo_modify format 5 %5d +#thermo_modify format 6 %5d +#thermo_modify format 7 %5d +#thermo_modify format 8 %5d +#thermo_modify format 9 %5d +#thermo_modify format 10 %5d +#thermo_modify format 11 %5d +log concentration.log +fix_modify ATC output concentrationFE $s text binary +fix_modify PP output concentrationPP $s text +dump D all custom $s concentration.dmp id type x y z q vx vy vz fx fy fz +#fix_modify ATC fix temperature all $T +fix_modify ATC fix electric_potential LBC 0. +thermo_modify lost ignore # HACK, look at fix_gcmc or ask Paul C. +run $n +#print "average concentration S:${cS} O:${sO} N:${cN} P:${cP}" +print "average_concentration_S: ${cS}" +print "average_concentration_O: ${cO}" +print "average_concentration_N: ${cN}" +print "average_concentration_P: ${cP}" +print "volume: $V" +#write_restart concentration.rst +#shell "restart2data concentration.rst concentration.data" diff --git a/examples/USER/atc/fluids/in.conducting_interface b/examples/USER/atc/fluids/in.conducting_interface new file mode 100644 index 0000000000..7ee906e45a --- /dev/null +++ b/examples/USER/atc/fluids/in.conducting_interface @@ -0,0 +1,111 @@ +# simulation of negatively charge liquid argon-positively charged solid/frozen argon +# MAKE this conducting_interface then interface (major difference: non-uniform grid) +# START with extrinsic charges on both and then use an instrinsic charge density for frozen +echo both +units real +atom_style full +########### BEGIN PARAMETERS #################################### +variable a equal 5.719025032 +variable i equal 1 +variable s equal 100 +variable n equal 1000 # 500 2000 +variable dt equal 4.0 +variable W equal 4 +variable L equal 20 +variable Ls equal 4 # surface +variable h equal 10 +variable phiInf equal -1. # 0. 10 -10.0 +variable R equal 2*$a +############## END PARAMETERS ################################# +dimension 3 +boundary f p p +pair_style lj/cut 13.0 +lattice fcc $a +read_data interface_init.data +atom_modify sort 0 1 +mass * 39.948 +pair_coeff * * 0.2381 3.405 +dielectric 1.0 +region BOX block 0 $L 0 $W 0 $W +group SOLID type 1 +group FLUID type 2 3 4 +group P type 3 +group N type 4 +set group SOLID charge 0 # use ATC to provide charge to the surface +# charged layer -- NOTE on an element boundary +variable b equal ${Ls}-0.1 +variable c equal ${Ls}+0.1 +region LAYER block $b $c INF INF INF INF +group LAYER region LAYER +timestep ${dt} +neigh_modify every $i check no +fix WALLS all wall/reflect xlo EDGE xhi EDGE +fix PP all atc field +fix_modify PP add_species IONS type 1 2 3 4 +fix_modify PP fields add species_concentration mass_density charge_density # temperature +fix_modify PP output volume_integral all mass_density +fix_modify PP output volume_integral all charge_density +fix_modify PP atom_element_map eulerian $s +fix_modify PP mesh create $h 1 1 BOX f p p +fix ATC FLUID atc species_electrostatic Ar_electrostatic.mat +fix_modify ATC add_species P type 3 +fix_modify ATC add_species N type 4 +fix_modify ATC boundary SOLID +#fix_modify ATC kernel cell $R $R $W +fix_modify ATC atom_element_map eulerian $i +fix_modify ATC internal_quadrature off # on creates a nasty error (NOTE trap error) +fix_modify ATC mass_matrix fe +fix_modify ATC include atomic_charge +# mesh : 2x2 tosses an atom to infinity and beyond +#fix_modify ATC mesh create $h 4 1 BOX f p p dx piecewise_linear 0 0 0 1 0 0 0.0 1.0 1.0 1.0 +#fix_modify ATC mesh create $h 1 1 BOX f p p dx piecewise_linear 0 0 0 1 0 0 & +# 0.0 1.0 0.2 1.0 0.207812 0.1 1.0 1.0 +### >>> node h vs list reepat and scale to box +fix_modify ATC mesh create $h 4 1 BOX f p p dx 2 2 0.5 0.5 0.5 0.5 2 3 4 5 +fix_modify ATC mesh create_nodeset lbc 0 0 -INF INF -INF INF +fix_modify ATC mesh create_nodeset rbc $L $L -INF INF -INF INF +fix_modify ATC mesh create_nodeset wall 0 ${Ls} 0 4 0 4 +fix_modify ATC mesh create_elementset wall 0 ${Ls} 0 4 0 4 +#fix_modify ATC mesh create_faceset lbc plane x 0 +fix_modify ATC mesh create_faceset surface -INF ${Ls} -INF INF -INF INF +fix_modify ATC mesh output conducting_interfaceMESH full_text binary +fix_modify ATC output volume_integral all mass_density +fix_modify ATC output volume_integral all charge_density +# ic/bcs +#fix_modify ATC initial charge_density all 0. +fix_modify ATC initial mass_density all 0. +fix_modify ATC initial electric_potential all 0. +# output +thermo $s +variable cFLUID equal count(FLUID) +compute PAVE P reduce ave x +compute PMIN P reduce min x +compute PMAX P reduce max x +compute NAVE N reduce ave x +compute NMIN N reduce min x +compute NMAX N reduce max x +compute q all property/atom q +compute Q all reduce sum c_q +compute Qf FLUID reduce sum c_q +compute m all property/atom mass +compute M all reduce sum c_m +compute Mf FLUID reduce sum c_m +compute F FLUID reduce sum fx fy fz +thermo_style custom step temp press etotal pe c_Q c_M c_Qf c_Mf c_PMIN c_PAVE c_PMAX c_NMIN c_NAVE c_NMAX c_F[1] c_F[2] c_F[3] +compute T FLUID temp +thermo_modify temp T +thermo_modify flush yes +log conducting_interface.log +fix_modify ATC output conducting_interfaceFE $s full_text binary +fix_modify PP output conducting_interfacePP $s full_text binary +dump X all custom $s conducting_interface.dmp id type x y z q vx vy vz fx fy fz +fix_modify ATC fix electric_potential rbc 0. +# stage 1 : active source controlling far-field shielding +fix_modify ATC control charge LAYER conductor ${phiInf} +fix_modify ATC control charge LAYER feedback surface +# +run $n +# stage 2 : static source - i.e. above the mean like JCTC / "effective_charge" +fix_modify ATC source electric_potential wall 0.001 +fix_modify ATC fix electric_potential lbc ${phiInf} +#run $n diff --git a/examples/USER/atc/fluids/in.dielectric_interface b/examples/USER/atc/fluids/in.dielectric_interface new file mode 100644 index 0000000000..e9cbe7882a --- /dev/null +++ b/examples/USER/atc/fluids/in.dielectric_interface @@ -0,0 +1,106 @@ +# simulation of negatively charge liquid argon-positively charged solid/frozen argon +# MAKE this dielectric_interface then interface (major difference: non-uniform grid) +# START with extrinsic charges on both and then use an instrinsic charge density for frozen +echo both +units real +atom_style full +########### BEGIN PARAMETERS #################################### +variable a equal 5.719025032 +variable i equal 1 +variable s equal 100 +variable n equal 1000 # 500 2000 +variable dt equal 4.0 +variable W equal 4 +variable L equal 20 +variable Ls equal 4 # surface +variable h equal 10 +variable phiInf equal -1. # 0. 10 -10.0 +variable perm2 equal 2. +variable depth equal 17.1571 +# 1 1 0.1 0.1 1 1 +variable w1 equal 4/$L # relative wall width +variable w2 equal ${w1}+2/$L # relative wall width +variable w3 equal ${w2}+2/$L +variable w4 equal ${w3}+2/$L +############## END PARAMETERS ################################# +dimension 3 +boundary f p p +pair_style lj/cut 13.0 +lattice fcc $a +read_data interface_init.data +atom_modify sort 0 1 +mass * 39.948 +pair_coeff * * 0.2381 3.405 +dielectric 1.0 +region BOX block 0 $L 0 $W 0 $W +group SOLID type 1 +group FLUID type 2 3 4 +group P type 3 +group N type 4 +set group SOLID charge 0 # use ATC to provide charge to the surface +timestep ${dt} +neigh_modify every $i check no +fix WALLS all wall/reflect xlo EDGE xhi EDGE +fix PP all atc field +fix_modify PP add_species IONS type 1 2 3 4 +fix_modify PP fields add species_concentration mass_density charge_density +fix_modify PP atom_element_map eulerian $s +fix_modify PP mesh create $h 1 1 BOX f p p +fix_modify PP output volume_integral all mass_density +fix_modify PP output volume_integral all charge_density +fix ATC FLUID atc species_electrostatic Ar_electrostatic.mat +fix_modify ATC add_species P type 3 +fix_modify ATC add_species N type 4 +fix_modify ATC boundary SOLID +fix_modify ATC atom_element_map eulerian $i +fix_modify ATC internal_quadrature off # on creates a nasty error (NOTE trap error) +fix_modify ATC mass_matrix fe +fix_modify ATC include atomic_charge +# mesh +fix_modify ATC mesh create $h 2 2 BOX f p p dx piecewise_linear 0 0 0 1 0 0 0.0 1.0 1.0 1.0 +fix_modify ATC output volume_integral all mass_density +fix_modify ATC output volume_integral all charge_density +fix_modify ATC mesh create_nodeset lbc 0 0 -INF INF -INF INF +fix_modify ATC mesh create_nodeset rbc $L $L -INF INF -INF INF +fix_modify ATC mesh create_nodeset wall 0 ${Ls} 0 4 0 4 +fix_modify ATC mesh create_elementset wall 0 ${Ls} 0 4 0 4 +#fix_modify ATC mesh create_faceset lbc plane x 0 +fix_modify ATC mesh create_faceset surface -INF ${Ls} -INF INF -INF INF +fix_modify ATC mesh output dielectric_interfaceMESH text binary +# ic/bcs +#fix_modify ATC initial charge_density all 0. +fix_modify ATC initial mass_density all 0. +fix_modify ATC initial electric_potential all 0. +# output +thermo $s +variable cFLUID equal count(FLUID) +compute PAVE P reduce ave x +compute PMIN P reduce min x +compute PMAX P reduce max x +compute NAVE N reduce ave x +compute NMIN N reduce min x +compute NMAX N reduce max x +compute q all property/atom q +compute Q all reduce sum c_q +compute m all property/atom mass +compute M all reduce sum c_m +compute Qf FLUID reduce sum c_q +compute Mf FLUID reduce sum c_m +compute F FLUID reduce sum fx fy fz +thermo_style custom step temp press etotal pe c_Q c_M c_Qf c_Mf c_PMIN c_PAVE c_PMAX c_NMIN c_NAVE c_NMAX c_F[1] c_F[2] c_F[3] +compute T FLUID temp +thermo_modify temp T +thermo_modify flush yes +log dielectric_interface.log +fix_modify ATC output dielectric_interfaceFE $s full_text binary +fix_modify PP output dielectric_interfacePP $s full_text binary +dump X all custom $s dielectric_interface.dmp id type x y z q vx vy vz fx fy fz +fix_modify ATC fix electric_potential rbc 0. +# stage 1 : active source controlling far-field shielding +fix_modify ATC control charge FLUID dielectric ${phiInf} ${perm2} ${depth} +fix_modify ATC control charge FLUID image_charge surface +run $n +# stage 2 : static source - i.e. above the mean like JCTC / "effective_charge" +fix_modify ATC source electric_potential wall 0.001 +fix_modify ATC fix electric_potential lbc ${phiInf} +#run $n diff --git a/examples/USER/atc/fluids/in.double_layer b/examples/USER/atc/fluids/in.double_layer new file mode 100644 index 0000000000..eee9a9166c --- /dev/null +++ b/examples/USER/atc/fluids/in.double_layer @@ -0,0 +1,100 @@ +# AtC electric field module and BCs +# This benchmark using fix_charge to set up a charged surface +# and computes the resulting double layer dynamics +log double_layer.log +echo both + +units metal +atom_style full +dimension 3 +neighbor 2 bin +neigh_modify every 1 check yes +boundary f f f + +timestep 0.0005 +thermo 100 +dielectric 81. + +newton off + +pair_style lj/cut 13.000000 +pair_modify mix arithmetic +read_data waternve.atm +reset_timestep 0 + +variable nsteps equal 1000 +variable dumpfreq equal ${nsteps}/10 +variable nx equal 4 +variable ny equal 4 +variable nz equal 4 +variable x_min equal -19.38 +variable x_max equal 19.38 +variable x_goldmin equal -11.22 +variable x_goldmax equal 11.22 +variable x_fluidmin equal ${x_goldmin} +variable x_fluidmax equal ${x_goldmax} +variable x_wallmin equal ${x_goldmin}-1.5 +variable x_wallmax equal ${x_goldmax}+1.5 +variable y_min equal -19.38 +variable y_max equal 19.38 +variable y_goldmin equal -11.22 +variable y_goldmax equal 11.22 +variable surface_charge equal -0.3125/(4.08*4.08) +variable y_fluidmin equal ${y_goldmin} +variable y_fluidmax equal ${y_goldmax} +variable y_wallmin equal ${y_goldmin}-1.5 +variable y_wallmax equal ${y_goldmax}+1.5 +variable downshift equal 2.5 +variable zshiftlatt equal 1-${downshift}/4.08 +variable z_min equal -20.4-${downshift}+0.25*4.08 +variable z_max equal 22.44+1.5 +variable z_goldmin equal -12.24-${downshift}+0.25*4.08 +variable z_goldmax equal -${downshift}+0.25*4.08 +variable z_goldtopmin equal ${z_goldmax}-0.5*4.08 +variable z_goldtopmax equal ${z_goldmax} +variable z_fluidmin equal 0. +variable z_fluidmax equal 22.44 +variable z_wallmax equal ${z_max} + +lattice sc 8.16 origin 0 0 0.75 + +group pos type 4 +group neg type 5 +group allfluid type 3 4 5 + +compute fluidT allfluid temp +thermo_style custom step epair emol etotal press c_fluidT + +fix zhiwall allfluid wall/lj93 zhi ${z_wallmax} 0.0195 3.45 10.000000 units box +fix xlowall allfluid wall/lj93 xlo ${x_wallmin} 0.0195 3.45 10.000000 units box +fix xhiwall allfluid wall/lj93 xhi ${x_wallmax} 0.0195 3.45 10.000000 units box +fix ylowall allfluid wall/lj93 ylo ${y_wallmin} 0.0195 3.45 10.000000 units box +fix yhiwall allfluid wall/lj93 yhi ${y_wallmax} 0.0195 3.45 10.000000 units box + +group solvent type 3 +fix fluidnvt solvent nvt temp 300.0 300.0 0.100 drag 0.2 + +########################################################################## +region ATC_BOX block ${x_wallmin} ${x_wallmax} ${y_wallmin} ${y_wallmax} ${z_goldtopmin} ${z_wallmax} units box +group ATC_ATOMS type 4 5 +fix ATC ATC_ATOMS atc species_electrostatic Ar_species_dl.mat +fix_modify ATC add_species P group pos +fix_modify ATC add_species N group neg +fix_modify ATC mesh create ${nx} ${ny} ${nz} ATC_BOX f f f +fix_modify ATC atom_element_map eulerian 1 +fix_modify ATC internal_quadrature off + +fix_modify ATC initial mass_density all 0. +fix_modify ATC mesh create_faceset BOTTOM_FACE -INF INF -INF INF ${z_goldtopmin} INF +## OLD +fix_modify ATC extrinsic fix_charge BOTTOM_FACE ${surface_charge} +## NEW +# ERROR: Poisson solver needs Dirichlet data +#fix_modify ATC control charge conductor ${surface_charge} +#fix_modify ATC control charge effective_charge ATC_ATOMS BOTTOM_FACE +## END + +fix_modify ATC output double_layerFE ${dumpfreq} text binary +dump chargenve all atom ${dumpfreq} double_layer.dmp + +run ${nsteps} diff --git a/examples/USER/atc/fluids/in.liquid_electrostatic b/examples/USER/atc/fluids/in.liquid_electrostatic new file mode 100644 index 0000000000..dfa8a5b9b8 --- /dev/null +++ b/examples/USER/atc/fluids/in.liquid_electrostatic @@ -0,0 +1,63 @@ +# simulation of liquid argon with an electrostatic potential +# +# p | free | free | fixed | p +# real units: +# distance = Angstroms +# time = femtoseconds +# mass = grams/mole +# energy = Kcal/mole +# 1 kilocalorie = 4184 Joules +# mvv2e = 2390.057361533490 [g/mol A^2/fs^2] -> [kcal/mol] +echo both +units real +atom_style full +########### BEGIN PARAMETERS #################################### +variable T equal 115.607 +print "reference temperature $T [K]" +variable a equal 5.719025032 +variable i equal 1 +variable s equal 100 +variable dt equal 4.0 +############## END PARAMETERS ################################# +dimension 3 +boundary f p p +pair_style lj/cut 13.0 +lattice sc $a +region BOX block 0 12 0 4 0 4 +read_data velocities.init +mass * 39.948 +pair_coeff * * 0.2381 3.405 +set group all charge 0.1 +dielectric 80.0 +timestep ${dt} +neigh_modify every $i check no +thermo $s +# ------------- Equilibration and thermalisation ---------------- +fix WALL all wall/reflect xlo EDGE xhi EDGE +fix NVT all nvt temp $T $T 10 drag 0.2 +thermo_style custom step temp press etotal pe +#run 400 +unfix NVT +# ------------- Post processing --------------------------------- +fix PP all atc field +fix_modify PP fields add mass_density charge_density electric_potential velocity +#fix_modify PP mesh create 50 1 1 BOX f p p +fix_modify PP mesh create 25 1 1 BOX f p p +#fix_modify PP mesh create 6 1 1 BOX f p p +fix_modify PP atom_element_map eulerian $i +# ------------- Coupling ---------------------------------------- +fix AtC all atc species_electrostatic Ar_species.mat +fix_modify AtC add_species ALL group all +fix_modify AtC internal_quadrature off +fix_modify AtC mesh create 6 1 1 BOX f p p +fix_modify AtC atom_element_map eulerian $i +fix_modify AtC extrinsic short_range off +fix_modify AtC mesh create_nodeset rbc 12. 12. -INF INF -INF INF +fix_modify AtC mesh create_nodeset lbc 0. 0. -INF INF -INF INF +# ------------- run --------------------------------------------- +thermo_style custom step cpu etotal ke +fix_modify AtC output liquid_electrostaticFE $s full_text # binary +fix_modify PP output liquid_electrostaticPP $s full_text +log liquid_electrostatic.log +fix_modify AtC fix electric_potential lbc linear 0 0 0 0 0 0 0 +run 800 diff --git a/examples/USER/atc/fluids/in.opp_force b/examples/USER/atc/fluids/in.opp_force new file mode 100644 index 0000000000..daf11da73e --- /dev/null +++ b/examples/USER/atc/fluids/in.opp_force @@ -0,0 +1,70 @@ +# Tests Poisson solver, charge density restriction +# and electric field force prolongation +# Two groups of charged particles interact electrically +# using the long range electric field only, so they will +# move towards each other +echo both +units metal +variable E equal 20.0 +variable nx equal 16 +# allow charges +atom_style full +dielectric 1. +dimension 3 +boundary p p p +lattice fcc 4.08 origin 0.25 0.25 0.25 +region BOX block -8 8 0 3 0 3 +create_box 3 BOX +create_atoms 1 region BOX +pair_style lj/cut 10. +#pair_style lj/cut/coul/long 10. +#kspace_style pppm 1.e-4 +#kspace_style ewald 1.e-4 +pair_coeff * * 0.2381 3.405 +mass * 39.948 +group real region BOX +region LEFT block -5 -2 INF INF INF INF +region RIGHT block 2 5 INF INF INF INF +set region LEFT type 2 +set region RIGHT type 3 +set region LEFT charge -1. +set region RIGHT charge 1. +group NION region LEFT +group PION region RIGHT +neighbor 2. bin +########################################################################### +#fix EFIELD all efield $E 0.0 0.0 +########################################################################### +fix ATC real atc species_electrostatic Ar_species.mat +fix_modify ATC add_species N group NION +fix_modify ATC add_species P group PION +fix_modify ATC include atomic_charge +fix_modify ATC internal_quadrature off +fix_modify ATC extrinsic short_range off +fix_modify ATC mesh create ${nx} 1 1 BOX p p p +fix_modify ATC atom_element_map eulerian 1 +fix_modify ATC atom_weight multiscale +fix_modify ATC initial mass_density all 0. +#fix_modify ATC initial charge_density all 0. +fix_modify ATC initial electric_potential all 0. +fix_modify ATC mesh create_nodeset left_end -8.01 -7.99 -.1 .1 -.1 .1 +fix_modify ATC fix electric_potential left_end 0. +#fix_modify ATC mesh create_nodeset right_end 7.99 8.01 -.1 .1 -.1 .1 +#fix_modify ATC fix electric_potential right_end 0. +# quick test for charged surfaces +#fix_modify ATC mesh create_faceset left_end box -8 10 -10 10 -10 10 outward +#fix_modify ATC extrinsic fix_charge left_end 0. +fix_modify ATC add_species NION type 2 +fix_modify ATC add_species PION type 3 +########################################################################### +variable n equal count(real) +print "number of atoms: $n" +timestep 0.0005 +thermo 100 +compute Fn NION reduce sum fx +compute Fp PION reduce sum fx +thermo_style custom step etotal temp press pe c_Fn c_Fp +# initial thermo line should be: +#0 13699.992 0 12453927 13699.992 880.49388 -880.49388 +fix_modify ATC output opp_forceFE 100 text binary +run 1000 diff --git a/examples/USER/atc/fluids/in.poisson b/examples/USER/atc/fluids/in.poisson new file mode 100644 index 0000000000..0625077aaa --- /dev/null +++ b/examples/USER/atc/fluids/in.poisson @@ -0,0 +1,69 @@ +# test poisson solver +# * seems to have error in fix_flux +echo both +units metal +variable E equal 20.0 +variable nx equal 32 +# allow charges +atom_style full +dielectric 1. +dimension 3 +boundary f p p +lattice fcc 4.08 origin 0.25 0.25 0.25 +region BOX block 0 16 0 3 0 3 +create_box 1 BOX +create_atoms 1 region BOX +pair_style lj/cut 13. +pair_coeff * * 0.2381 3.405 +mass * 39.948 +group real region BOX +set group real charge 1 +########################################################################### +#fix EFIELD all efield $E 0.0 0.0 +########################################################################### +fix ATC real atc species_electrostatic Ar_species.mat +fix_modify ATC add_species ion type 1 ### <<<<< +#fix_modify ATC add_species REAL group real +fix_modify ATC include atomic_charge +fix_modify ATC internal_quadrature off +fix_modify ATC extrinsic short_range off +fix_modify ATC mesh create ${nx} 1 1 BOX f p p +fix_modify ATC atom_element_map eulerian 1 +fix_modify ATC atom_weight multiscale +fix_modify ATC initial mass_density all 0. +#fix_modify ATC initial charge_density all 0. +########################################################################### +variable n equal count(real) +print "number of atoms: $n" +timestep 0.0 +thermo 1 +compute Fx real reduce sum fx +compute Fy real reduce sum fy +thermo_style custom step etotal temp press pe c_Fx c_Fy +fix_modify ATC output poissonFE 1 text binary +# (1) all fixed +fix_modify ATC fix electric_potential all linear 0 0 0 $E 0 0 0 0 +run 1 +# (2) Dirichlet +# NOTE with correct density solution is very close +#fix_modify ATC fix charge_density all 0.0588951459091903 +fix_modify ATC unfix electric_potential all +fix_modify ATC mesh create_nodeset lbc 0.0 0.0 -INF INF -INF INF +fix_modify ATC mesh create_faceset lbc 0.0 INF -INF INF -INF INF +fix_modify ATC mesh create_faceset rbc -INF 16.0 -INF INF -INF INF +fix_modify ATC fix electric_potential lbc 100.0 +run 1 +# (3) Neumann +fix_modify ATC fix_flux electric_potential rbc 0.5 +run 1 +# (4) Robin eps_1 phi'_1 = eps_2/L_2 (phi_{L_2} - phi) +fix_modify ATC unfix_flux electric_potential rbc +fix_modify ATC fix_robin electric_potential rbc 0.5 -0.00001 +run 1 +# (5) Robins on the left and Robins on the right +fix_modify ATC unfix electric_potential lbc +fix_modify ATC fix_robin electric_potential rbc 0.01 -0.0001 +fix_modify ATC fix_robin electric_potential lbc 0.01 -0.0001 +run 1 +#fix_modify ATC fix charge_density all 0.0 +#run 1 diff --git a/examples/USER/atc/fluids/in.shear_flow b/examples/USER/atc/fluids/in.shear_flow new file mode 100644 index 0000000000..c5a53b1273 --- /dev/null +++ b/examples/USER/atc/fluids/in.shear_flow @@ -0,0 +1,84 @@ +#AtC Mechanical Coupling +# This benchmark tests momentum flux as a BC to the MD region to generate shear flow. +# Currently heat will be generated as it will have no where to go. +log shear_flow.log +units real +atom_style atomic +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13.5 +#read_data temp.init +read_data post_eq.init +lattice fcc 5.405 origin 0.25 0.25 0.25 +# create atoms, NOTE commented out for restart +#region mdRegion block -8 8 -3 3 -3 3 +#boundary f p p +#create_box 2 mdRegion +#create_atoms 1 region mdRegion +#mass * 39.95 +# specify interal/ghost atoms +#region mdInternal block -6 6 -3 3 -3 3 +#region mdGhost block -6 6 -3 3 -3 3 side out +#create_atoms 1 region mdGhost +#lattice fcc 6.5 origin 0.25 0.25 0.25 +#create_atoms 2 region mdInternal +group internal type 2 +group ghost type 1 +# velocities have Vcm = 0, NOTE next four lines commented out for restart +#velocity internal create 100. 87287 mom yes loop geom +#pair_style lj/cut 13.5 +##pair_coeff 1 1 0.010323166 3.405 13.5 +#pair_coeff * * .238 3.405 13.5 +#write_restart tinit.dat +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# equilibrate MD field +variable xdof equal 3*count(ghost) +compute_modify thermo_temp extra ${xdof} +thermo_style custom step cpu etotal pe temp +thermo_modify format 1 %6i format 2 %7.2g +#fix NVT internal nvt temp 100 100 10 drag 0.2 +#dump D1 all atom 200 shear_flow_init.dmp +timestep 2 +#thermo 200 +#run 2000 +#write_restart post_eq.dat + +# ID group atc PhysicsType ParameterFile +lattice fcc 5.405 origin 0.25 0.25 0.25 +region atcRegion block -6.25 6.25 -3 3 -3 3 +fix AtC internal atc shear Ar_viscosity.mat +# ID part keywords nx ny nz region periodicity +fix_modify AtC mesh create 6 1 1 atcRegion f p p +#fix_modify AtC time_integration fractional_step +##fix_modify AtC atom_element_map eulerian 10 # NOTE this introduces a minor amount of time integration error tracking the atomic temperature +fix_modify AtC internal_quadrature off +#fix_modify AtC mass_matrix fe +# add nodesets +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_elementset rbc 4.12 6.3 -INF INF -INF INF +#used for restarting +fix_modify AtC consistent_fe_initialization on +#fix_modify AtC initial velocity x all 0. + +# turn on kinetostat +reset_timestep 0 +fix_modify AtC reset_time +fix_modify AtC source velocity y rbc .0000001 +fix_modify AtC control momentum flux no_boundary +fix_modify AtC control tolerance 1.e-14 +fix_modify AtC control localized_lambda on +#fix_modify AtC filter type exponential +#fix_modify AtC filter scale 1000.0 +#fix_modify AtC filter on + +# ouput commands +fix_modify AtC output shear_flowFE 100 text #binary +#undump D1 +#dump D1 all custom 100 shear_flow.dmp id type xs ys zs vx vy vz +# set-up non-equilibrium IC +thermo 100 +run 2000 diff --git a/examples/USER/atc/fluids/in.shear_no_atoms b/examples/USER/atc/fluids/in.shear_no_atoms new file mode 100644 index 0000000000..8bd350f06c --- /dev/null +++ b/examples/USER/atc/fluids/in.shear_no_atoms @@ -0,0 +1,32 @@ +atom_style atomic +lattice fcc 1.0 +region simRegion block -50 50 0 1 0 1 +boundary f p p +create_box 1 simRegion +mass 1 39.95 # need to keep this +atom_modify sort 0 1 + +lattice fcc 5.405 origin 0.25 0.25 0.25 +region atcRegion block -6.25 19.25 -3 3 -3 3 +fix AtC all atc shear Ar_visc_no_atoms.mat +# ID part keywords nx ny nz region periodicity +fix_modify AtC mesh create 12 1 1 atcRegion f p p +# add nodesets +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset rbc 19.2 19.3 -INF INF -INF INF +fix_modify AtC mesh create_nodeset lbc -6.3 -6.2 -INF INF -INF INF +fix_modify AtC fix velocity x all 0. +fix_modify AtC initial velocity y all 0. +fix_modify AtC fix velocity z all 0. + +# turn on kinetostat +reset_timestep 0 +fix_modify AtC reset_time +fix_modify AtC fix velocity y rbc 0.1 +fix_modify AtC fix velocity y lbc 0. + +# ouput commands +fix_modify AtC output shear_no_atomsFE 200 text binary +# set-up non-equilibrium IC +thermo 100 +run 5000 diff --git a/examples/USER/atc/fluids/liquid_electrostatic.screen b/examples/USER/atc/fluids/liquid_electrostatic.screen new file mode 100644 index 0000000000..7489b3146c --- /dev/null +++ b/examples/USER/atc/fluids/liquid_electrostatic.screen @@ -0,0 +1,141 @@ +LAMMPS (14 Aug 2013) +units real +atom_style full +########### BEGIN PARAMETERS #################################### +variable T equal 115.607 +print "reference temperature $T [K]" +reference temperature 115.60699999999999932 [K] +variable a equal 5.719025032 +variable i equal 1 +variable s equal 100 +variable dt equal 4.0 +############## END PARAMETERS ################################# +dimension 3 +boundary f p p +pair_style lj/cut 13.0 +lattice sc $a +lattice sc 5.7190250320000002304 +Lattice spacing in x,y,z = 5.71903 5.71903 5.71903 +region BOX block 0 12 0 4 0 4 +read_data velocities.init +Scanning data file ... +Reading data file ... + orthogonal box = (0 0 0) to (68.6283 22.8761 22.8761) + 4 by 1 by 1 MPI processor grid + 192 atoms + 192 velocities +Finding 1-2 1-3 1-4 neighbors ... + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors +mass * 39.948 +pair_coeff * * 0.2381 3.405 +set group all charge 0.1 +Setting atom values ... + 192 settings made for charge +dielectric 80.0 +timestep ${dt} +timestep 4 +neigh_modify every $i check no +neigh_modify every 1 check no +thermo $s +thermo 100 +# ------------- Equilibration and thermalisation ---------------- +fix WALL all wall/reflect xlo EDGE xhi EDGE +fix NVT all nvt temp $T $T 10 drag 0.2 +fix NVT all nvt temp 115.60699999999999932 $T 10 drag 0.2 +fix NVT all nvt temp 115.60699999999999932 115.60699999999999932 10 drag 0.2 +thermo_style custom step temp press etotal pe +#run 400 +unfix NVT +# ------------- Post processing --------------------------------- +fix PP all atc field +ATC: constructing shape function field estimate + ATC: peratom PE compute created with ID: 3 +fix_modify PP fields add mass_density charge_density electric_potential velocity +#fix_modify PP mesh create 50 1 1 BOX f p p +fix_modify PP mesh create 25 1 1 BOX f p p + ATC: created uniform mesh with 104 nodes, 26 unique nodes, and 25 elements +#fix_modify PP mesh create 6 1 1 BOX f p p +fix_modify PP atom_element_map eulerian $i +fix_modify PP atom_element_map eulerian 1 +# ------------- Coupling ---------------------------------------- +fix AtC all atc species_electrostatic Ar_species.mat +ATC: constructing electrostatic species coupling with parameter file Ar_species.mat + ATC: peratom PE compute created with ID: 3 + ATC: 1 materials defined from Ar_species.mat + ATC: creating fem_efield extrinsic model + ATC: 1 materials defined from Ar_species.mat +fix_modify AtC add_species ALL group all +fix_modify AtC internal_quadrature off +fix_modify AtC mesh create 6 1 1 BOX f p p + ATC: created uniform mesh with 28 nodes, 7 unique nodes, and 6 elements +fix_modify AtC atom_element_map eulerian $i +fix_modify AtC atom_element_map eulerian 1 +fix_modify AtC extrinsic short_range off +fix_modify AtC mesh create_nodeset rbc 12. 12. -INF INF -INF INF + ATC: created nodeset rbc with 1 nodes +fix_modify AtC mesh create_nodeset lbc 0. 0. -INF INF -INF INF + ATC: created nodeset lbc with 1 nodes +# ------------- run --------------------------------------------- +thermo_style custom step cpu etotal ke +fix_modify AtC output liquid_electrostaticFE $s full_text # binary +fix_modify AtC output liquid_electrostaticFE 100 full_text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: +NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationALL +species_concentration : species_concentrationALL + +fix_modify PP output liquid_electrostaticPP $s full_text +fix_modify PP output liquid_electrostaticPP 100 full_text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +log liquid_electrostatic.log +fix_modify AtC fix electric_potential lbc linear 0 0 0 0 0 0 0 + ATC: created function : 0 + 0(x-0)+0(y-0)+0(z-0) +run 800 +Setting up run ... + ATC: WARNING: material: [ar] cannot find mass_density + ATC: WARNING: physics model: [species], material: [ar] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: all initial conditions for mass_density have not been defined and the undefined are assumed zero + ATC: WARNING: all initial conditions for charge_density have not been defined and the undefined are assumed zero + ATC: WARNING: all initial conditions for species_concentration have not been defined and the undefined are assumed zero + ATC: WARNING: all initial conditions for electric_potential have not been defined and the undefined are assumed zero + ATC: WARNING: material: [ar] cannot find mass_density + ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 63.7188 Mbytes +Step CPU TotEng KinEng + 0 0 35.202587 65.819079 + 100 0.24399519 36.014336 73.434063 + 200 0.48565197 40.073896 87.17957 + 300 0.72934318 47.116113 101.60024 + 400 1.039428 56.306233 113.20696 + 500 1.2882581 67.3682 120.18094 + 600 1.5421622 79.678922 137.95847 + 700 1.8119881 93.406523 150.38695 + 800 2.0993671 107.30758 169.35003 +Loop time of 2.0994 on 4 procs for 800 steps with 192 atoms + +Pair time (%) = 0.0760665 (3.62325) +Bond time (%) = 0.000117838 (0.00561295) +Neigh time (%) = 0.0679175 (3.23509) +Comm time (%) = 0.0478712 (2.28023) +Outpt time (%) = 0.00402987 (0.191953) +Other time (%) = 1.9034 (90.6639) + +Nlocal: 48 ave 76 max 34 min +Histogram: 2 0 1 0 0 0 0 0 0 1 +Nghost: 515 ave 660 max 337 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Neighs: 1680.25 ave 3128 max 827 min +Histogram: 1 0 2 0 0 0 0 0 0 1 +FullNghs: 3360.5 ave 6244 max 1660 min +Histogram: 1 0 2 0 0 0 0 0 0 1 + +Total # of neighbors = 13442 +Ave neighs/atom = 70.0104 +Ave special neighs/atom = 0 +Neighbor list builds = 80 +Dangerous builds = 0 diff --git a/examples/USER/atc/fluids/opp_force.screen b/examples/USER/atc/fluids/opp_force.screen new file mode 100644 index 0000000000..dee47ac731 --- /dev/null +++ b/examples/USER/atc/fluids/opp_force.screen @@ -0,0 +1,145 @@ +LAMMPS (14 Aug 2013) +units metal +variable E equal 20.0 +variable nx equal 16 +# allow charges +atom_style full +dielectric 1. +dimension 3 +boundary p p p +lattice fcc 4.08 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 4.08 4.08 4.08 +region BOX block -8 8 0 3 0 3 +create_box 3 BOX +Created orthogonal box = (-32.64 0 0) to (32.64 12.24 12.24) + 4 by 1 by 1 MPI processor grid +create_atoms 1 region BOX +Created 576 atoms +pair_style lj/cut 10. +#pair_style lj/cut/coul/long 10. +#kspace_style pppm 1.e-4 +#kspace_style ewald 1.e-4 +pair_coeff * * 0.2381 3.405 +mass * 39.948 +group real region BOX +576 atoms in group real +region LEFT block -5 -2 INF INF INF INF +region RIGHT block 2 5 INF INF INF INF +set region LEFT type 2 +Setting atom values ... + 108 settings made for type +set region RIGHT type 3 +Setting atom values ... + 108 settings made for type +set region LEFT charge -1. +Setting atom values ... + 108 settings made for charge +set region RIGHT charge 1. +Setting atom values ... + 108 settings made for charge +group NION region LEFT +108 atoms in group NION +group PION region RIGHT +108 atoms in group PION +neighbor 2. bin +########################################################################### +#fix EFIELD all efield $E 0.0 0.0 +########################################################################### +fix ATC real atc species_electrostatic Ar_species.mat +ATC: constructing electrostatic species coupling with parameter file Ar_species.mat + ATC: peratom PE compute created with ID: 3 + ATC: WARNING: material units real do not match lammps + ATC: 1 materials defined from Ar_species.mat + ATC: creating fem_efield extrinsic model + ATC: WARNING: material units real do not match lammps + ATC: 1 materials defined from Ar_species.mat +fix_modify ATC add_species N group NION +fix_modify ATC add_species P group PION +fix_modify ATC include atomic_charge +fix_modify ATC internal_quadrature off +fix_modify ATC extrinsic short_range off +fix_modify ATC mesh create ${nx} 1 1 BOX p p p +fix_modify ATC mesh create 16 1 1 BOX p p p + ATC: created uniform mesh with 68 nodes, 16 unique nodes, and 16 elements +fix_modify ATC atom_element_map eulerian 1 +fix_modify ATC atom_weight multiscale +fix_modify ATC initial mass_density all 0. +#fix_modify ATC initial charge_density all 0. +fix_modify ATC initial electric_potential all 0. +fix_modify ATC mesh create_nodeset left_end -8.01 -7.99 -.1 .1 -.1 .1 + ATC: created nodeset left_end with 1 nodes +fix_modify ATC fix electric_potential left_end 0. +#fix_modify ATC mesh create_nodeset right_end 7.99 8.01 -.1 .1 -.1 .1 +#fix_modify ATC fix electric_potential right_end 0. +# quick test for charged surfaces +#fix_modify ATC mesh create_faceset left_end box -8 10 -10 10 -10 10 outward +#fix_modify ATC extrinsic fix_charge left_end 0. +fix_modify ATC add_species NION type 2 +fix_modify ATC add_species PION type 3 +########################################################################### +variable n equal count(real) +print "number of atoms: $n" +number of atoms: 576 +timestep 0.0005 +thermo 100 +compute Fn NION reduce sum fx +compute Fp PION reduce sum fx +thermo_style custom step etotal temp press pe c_Fn c_Fp +# initial thermo line should be: +#0 13699.992 0 12453927 13699.992 880.49388 -880.49388 +fix_modify ATC output opp_forceFE 100 text binary + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: +NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationNION +NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationPION +NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationN +NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationP +species_concentration : species_concentrationNION +species_concentration : species_concentrationPION +species_concentration : species_concentrationN +species_concentration : species_concentrationP + +run 1000 +Setting up run ... + ATC: WARNING: material: [ar] cannot find mass_density + ATC: WARNING: physics model: [species], material: [ar] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: all initial conditions for charge_density have not been defined and the undefined are assumed zero + ATC: WARNING: all initial conditions for species_concentration have not been defined and the undefined are assumed zero + ATC: WARNING: material: [ar] cannot find mass_density + ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 50.4595 Mbytes +Step TotEng Temp Press PotEng Fn Fp + 0 13699.992 0 12453927 13699.992 880.49388 -880.49388 + 100 20040.817 16252.426 16202859 18832.862 423.97919 -423.97919 + 200 20169.984 13829.994 16359769 19142.076 -1134.6292 1134.6292 + 300 15287.67 9016.4656 13166399 14617.525 468.63207 -468.63207 + 400 20617.507 12729.152 16757508 19671.418 -1247.489 1247.489 + 500 17500.547 14981.89 14448672 16387.025 -214.58965 214.58965 + 600 16365.011 13836.901 13712389 15336.589 933.06997 -933.06997 + 700 21830.838 6644.0674 17834210 21337.021 -591.66886 591.66886 + 800 16617.582 10242.991 14041573 15856.276 203.78451 -203.78451 + 900 17427.331 10454.594 14592379 16650.298 -1704.6656 1704.6656 + 1000 19974.392 10682.026 16367773 19180.455 -1384.2794 1384.2794 +Loop time of 34.9835 on 4 procs for 1000 steps with 576 atoms + +Pair time (%) = 2.17131 (6.20667) +Bond time (%) = 0.0027945 (0.00798806) +Neigh time (%) = 0.0782308 (0.223622) +Comm time (%) = 3.05527 (8.73344) +Outpt time (%) = 0.0930898 (0.266096) +Other time (%) = 29.5828 (84.5622) + +Nlocal: 144 ave 144 max 144 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 3177 ave 3258 max 3096 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 30681 ave 31973 max 29028 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +FullNghs: 61362 ave 63684 max 59040 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 245448 +Ave neighs/atom = 426.125 +Ave special neighs/atom = 0 +Neighbor list builds = 12 +Dangerous builds = 0 diff --git a/examples/USER/atc/fluids/poisson.screen b/examples/USER/atc/fluids/poisson.screen new file mode 100644 index 0000000000..d3e3247197 --- /dev/null +++ b/examples/USER/atc/fluids/poisson.screen @@ -0,0 +1,259 @@ +LAMMPS (14 Aug 2013) +units metal +variable E equal 20.0 +variable nx equal 32 +# allow charges +atom_style full +dielectric 1. +dimension 3 +boundary f p p +lattice fcc 4.08 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 4.08 4.08 4.08 +region BOX block 0 16 0 3 0 3 +create_box 1 BOX +Created orthogonal box = (0 0 0) to (65.28 12.24 12.24) + 4 by 1 by 1 MPI processor grid +create_atoms 1 region BOX +Created 576 atoms +pair_style lj/cut 13. +pair_coeff * * 0.2381 3.405 +mass * 39.948 +group real region BOX +576 atoms in group real +set group real charge 1 +Setting atom values ... + 576 settings made for charge +########################################################################### +#fix EFIELD all efield $E 0.0 0.0 +########################################################################### +fix ATC real atc species_electrostatic Ar_species.mat +ATC: constructing electrostatic species coupling with parameter file Ar_species.mat + ATC: peratom PE compute created with ID: 3 + ATC: WARNING: material units real do not match lammps + ATC: 1 materials defined from Ar_species.mat + ATC: creating fem_efield extrinsic model + ATC: WARNING: material units real do not match lammps + ATC: 1 materials defined from Ar_species.mat +fix_modify ATC add_species ion type 1 ### <<<<< +#fix_modify ATC add_species REAL group real +fix_modify ATC include atomic_charge +fix_modify ATC internal_quadrature off +fix_modify ATC extrinsic short_range off +fix_modify ATC mesh create ${nx} 1 1 BOX f p p +fix_modify ATC mesh create 32 1 1 BOX f p p + ATC: created uniform mesh with 132 nodes, 33 unique nodes, and 32 elements +fix_modify ATC atom_element_map eulerian 1 +fix_modify ATC atom_weight multiscale +fix_modify ATC initial mass_density all 0. +#fix_modify ATC initial charge_density all 0. +########################################################################### +variable n equal count(real) +print "number of atoms: $n" +number of atoms: 576 +timestep 0.0 +thermo 1 +compute Fx real reduce sum fx +compute Fy real reduce sum fy +thermo_style custom step etotal temp press pe c_Fx c_Fy +fix_modify ATC output poissonFE 1 text binary + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: +NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationion +species_concentration : species_concentrationion + +# (1) all fixed +fix_modify ATC fix electric_potential all linear 0 0 0 $E 0 0 0 0 +fix_modify ATC fix electric_potential all linear 0 0 0 20 0 0 0 0 + ATC: created function : 0 + 20(x-0)+0(y-0)+0(z-0) +run 1 +Setting up run ... + ATC: WARNING: material: [ar] cannot find mass_density + ATC: WARNING: physics model: [species], material: [ar] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: all initial conditions for charge_density have not been defined and the undefined are assumed zero + ATC: WARNING: all initial conditions for species_concentration have not been defined and the undefined are assumed zero + ATC: WARNING: material: [ar] cannot find mass_density + ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 48.9866 Mbytes +Step TotEng Temp Press PotEng Fx Fy + 0 13388.811 0 12185513 13388.811 -11520 -5.4091662e-13 + 1 13388.811 0 12185513 13388.811 -11520 -5.4091662e-13 +Loop time of 0.260963 on 4 procs for 1 steps with 576 atoms + +Pair time (%) = 0.0105038 (4.025) +Bond time (%) = 1.07288e-06 (0.000411124) +Neigh time (%) = 0 (0) +Comm time (%) = 0.00655341 (2.51124) +Outpt time (%) = 0.0322342 (12.352) +Other time (%) = 0.211671 (81.1114) + +Nlocal: 144 ave 144 max 144 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 3556 ave 4256 max 2856 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 58212 ave 63792 max 52524 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 116424 ave 127584 max 105264 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 465696 +Ave neighs/atom = 808.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +# (2) Dirichlet +# NOTE with correct density solution is very close +#fix_modify ATC fix charge_density all 0.0588951459091903 +fix_modify ATC unfix electric_potential all +fix_modify ATC mesh create_nodeset lbc 0.0 0.0 -INF INF -INF INF + ATC: created nodeset lbc with 1 nodes +fix_modify ATC mesh create_faceset lbc 0.0 INF -INF INF -INF INF + ATC: created faceset lbc with 1 faces +fix_modify ATC mesh create_faceset rbc -INF 16.0 -INF INF -INF INF + ATC: created faceset rbc with 1 faces +fix_modify ATC fix electric_potential lbc 100.0 +run 1 +Setting up run ... + ATC: WARNING: material: [ar] cannot find mass_density + ATC: WARNING: physics model: [species], material: [ar] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [ar] cannot find mass_density + ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 48.9866 Mbytes +Step TotEng Temp Press PotEng Fx Fy + 1 13388.811 0 12185513 13388.811 -200361.27 6.719863e-13 + 2 13388.811 0 12185513 13388.811 -200361.27 6.719863e-13 +Loop time of 0.254081 on 4 procs for 1 steps with 576 atoms + +Pair time (%) = 0.0104072 (4.09602) +Bond time (%) = 1.07288e-06 (0.00042226) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0206404 (8.12356) +Outpt time (%) = 0.0137355 (5.40596) +Other time (%) = 0.209297 (82.374) + +Nlocal: 144 ave 144 max 144 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 3556 ave 4256 max 2856 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 58212 ave 63792 max 52524 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 116424 ave 127584 max 105264 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 465696 +Ave neighs/atom = 808.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +# (3) Neumann +fix_modify ATC fix_flux electric_potential rbc 0.5 +run 1 +Setting up run ... + ATC: WARNING: material: [ar] cannot find mass_density + ATC: WARNING: physics model: [species], material: [ar] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [ar] cannot find mass_density + ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 48.9866 Mbytes +Step TotEng Temp Press PotEng Fx Fy + 2 13388.811 0 12185513 13388.811 -252475.24 1.1650611e-12 + 3 13388.811 0 12185513 13388.811 -252475.24 1.1650611e-12 +Loop time of 0.0918587 on 4 procs for 1 steps with 576 atoms + +Pair time (%) = 0.013284 (14.4614) +Bond time (%) = 1.01328e-06 (0.00110308) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000460505 (0.501319) +Outpt time (%) = 0.017328 (18.8638) +Other time (%) = 0.0607851 (66.1724) + +Nlocal: 144 ave 144 max 144 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 3556 ave 4256 max 2856 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 58212 ave 63792 max 52524 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 116424 ave 127584 max 105264 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 465696 +Ave neighs/atom = 808.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +# (4) Robin eps_1 phi'_1 = eps_2/L_2 (phi_{L_2} - phi) +fix_modify ATC unfix_flux electric_potential rbc +fix_modify ATC fix_robin electric_potential rbc 0.5 -0.00001 + ATC: created function : 0.5 + -1e-05*u +run 1 +Setting up run ... + ATC: WARNING: material: [ar] cannot find mass_density + ATC: WARNING: physics model: [species], material: [ar] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [ar] cannot find mass_density + ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 48.9866 Mbytes +Step TotEng Temp Press PotEng Fx Fy + 3 13388.811 0 12185513 13388.811 -225709.12 9.1181426e-13 + 4 13388.811 0 12185513 13388.811 -225709.12 9.1181426e-13 +Loop time of 0.0331933 on 4 procs for 1 steps with 576 atoms + +Pair time (%) = 0.0132439 (39.8992) +Bond time (%) = 7.15256e-07 (0.00215482) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000455439 (1.37208) +Outpt time (%) = 0.00104851 (3.15879) +Other time (%) = 0.0184448 (55.5678) + +Nlocal: 144 ave 144 max 144 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 3556 ave 4256 max 2856 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 58212 ave 63792 max 52524 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 116424 ave 127584 max 105264 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 465696 +Ave neighs/atom = 808.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +# (5) Robins on the left and Robins on the right +fix_modify ATC unfix electric_potential lbc +fix_modify ATC fix_robin electric_potential rbc 0.01 -0.0001 + ATC: created function : 0.01 + -0.0001*u +fix_modify ATC fix_robin electric_potential lbc 0.01 -0.0001 + ATC: created function : 0.01 + -0.0001*u +run 1 +Setting up run ... + ATC: WARNING: material: [ar] cannot find mass_density + ATC: WARNING: physics model: [species], material: [ar] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: material: [ar] cannot find mass_density + ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 48.9866 Mbytes +Step TotEng Temp Press PotEng Fx Fy + 4 13388.811 0 12185513 13388.811 4.3291948e-09 -1.4571568e-12 + 5 13388.811 0 12185513 13388.811 4.3364707e-09 -1.4571568e-12 +Loop time of 0.158969 on 4 procs for 1 steps with 576 atoms + +Pair time (%) = 0.00292653 (1.84094) +Bond time (%) = 2.98023e-07 (0.000187472) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000340283 (0.214056) +Outpt time (%) = 0.012237 (7.69773) +Other time (%) = 0.143465 (90.2471) + +Nlocal: 144 ave 144 max 144 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 3556 ave 4256 max 2856 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 58212 ave 63792 max 52524 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 116424 ave 127584 max 105264 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 465696 +Ave neighs/atom = 808.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +#fix_modify ATC fix charge_density all 0.0 +#run 1 diff --git a/examples/USER/atc/fluids/shear_flow.screen b/examples/USER/atc/fluids/shear_flow.screen new file mode 100644 index 0000000000..b944fb2bba --- /dev/null +++ b/examples/USER/atc/fluids/shear_flow.screen @@ -0,0 +1,64 @@ +LAMMPS (14 Aug 2013) +Reading data file ... + orthogonal box = (-37.835 -16.215 -16.215) to (37.835 16.215 16.215) + 4 by 1 by 1 MPI processor grid + 1288 atoms + 1288 velocities +Lattice spacing in x,y,z = 5.405 5.405 5.405 +1000 atoms in group internal +288 atoms in group ghost +Lattice spacing in x,y,z = 5.405 5.405 5.405 +ATC: constructing viscous/shear coupling with parameter file Ar_viscosity.mat + ATC: peratom PE compute created with ID: 3 + ATC: 1 materials defined from Ar_viscosity.mat + ATC: created uniform mesh with 28 nodes, 7 unique nodes, and 6 elements + ATC: created elementset rbc with 1 elements + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +Setting up run ... + ATC: WARNING: all initial conditions for velocity have not been defined and the undefined are assumed zero +Memory usage per processor = 52.4731 Mbytes +Step CPU TotEng PotEng Temp + 0 0 -1119.8507 -1407.9617 96.655262 + 100 3.7 -1119.8301 -1407.8272 96.617051 + 200 11 -1119.8009 -1400.4751 94.160366 + 300 16 -1119.7239 -1410.8865 97.679021 + 400 24 -1119.6576 -1408.2534 96.817907 + 500 28 -1119.6516 -1408.5682 96.925527 + 600 38 -1119.6329 -1408.6306 96.95274 + 700 39 -1119.5365 -1418.9199 100.43692 + 800 41 -1119.4382 -1415.3432 99.270023 + 900 51 -1119.2739 -1417.3965 100.01394 + 1000 58 -1119.1165 -1413.6775 98.8191 + 1100 62 -1118.9778 -1411.4417 98.115594 + 1200 64 -1118.8576 -1421.8226 101.63848 + 1300 68 -1118.7582 -1420.5024 101.22893 + 1400 75 -1118.6322 -1425.0437 102.7947 + 1500 77 -1118.5021 -1425.0965 102.85606 + 1600 86 -1118.4008 -1423.1023 102.22105 + 1700 88 -1118.2811 -1423.5625 102.41555 + 1800 98 -1118.1439 -1423.4533 102.42497 + 1900 99 -1118.0284 -1426.7201 103.55967 + 2000 1.1e+02 -1117.8763 -1428.701 104.27524 +Loop time of 107.637 on 4 procs for 2000 steps with 1288 atoms + +Pair time (%) = 6.68767 (6.21315) +Neigh time (%) = 4.49477 (4.17585) +Comm time (%) = 24.6344 (22.8864) +Outpt time (%) = 0.123942 (0.115148) +Other time (%) = 71.6966 (66.6094) + +Nlocal: 322 ave 346 max 306 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Nghost: 3368.25 ave 4149 max 2571 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 60300.2 ave 74700 max 48490 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +FullNghs: 120600 ave 149448 max 96908 min +Histogram: 2 0 0 0 0 0 0 1 0 1 + +Total # of neighbors = 482402 +Ave neighs/atom = 374.536 +Neighbor list builds = 200 +Dangerous builds = 0 diff --git a/examples/USER/atc/fluids/shear_no_atoms.screen b/examples/USER/atc/fluids/shear_no_atoms.screen new file mode 100644 index 0000000000..a07fe9f02e --- /dev/null +++ b/examples/USER/atc/fluids/shear_no_atoms.screen @@ -0,0 +1,90 @@ +LAMMPS (14 Aug 2013) +Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 +Created orthogonal box = (-79.3701 0 0) to (79.3701 1.5874 1.5874) + 4 by 1 by 1 MPI processor grid +Lattice spacing in x,y,z = 0.904527 0.904527 0.904527 +ATC: constructing viscous/shear coupling with parameter file Ar_visc_no_atoms.mat + ATC: peratom PE compute created with ID: 3 + ATC: computed mass density : 215.93 + ATC: WARNING: material units real do not match lammps + ATC: 1 materials defined from Ar_visc_no_atoms.mat + ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements + ATC: created nodeset rbc with 1 nodes + ATC: created nodeset lbc with 1 nodes + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +Setting up run ... +Memory usage per processor = 0.432259 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 0 0 0 0 + 100 0 0 0 0 0 + 200 0 0 0 0 0 + 300 0 0 0 0 0 + 400 0 0 0 0 0 + 500 0 0 0 0 0 + 600 0 0 0 0 0 + 700 0 0 0 0 0 + 800 0 0 0 0 0 + 900 0 0 0 0 0 + 1000 0 0 0 0 0 + 1100 0 0 0 0 0 + 1200 0 0 0 0 0 + 1300 0 0 0 0 0 + 1400 0 0 0 0 0 + 1500 0 0 0 0 0 + 1600 0 0 0 0 0 + 1700 0 0 0 0 0 + 1800 0 0 0 0 0 + 1900 0 0 0 0 0 + 2000 0 0 0 0 0 + 2100 0 0 0 0 0 + 2200 0 0 0 0 0 + 2300 0 0 0 0 0 + 2400 0 0 0 0 0 + 2500 0 0 0 0 0 + 2600 0 0 0 0 0 + 2700 0 0 0 0 0 + 2800 0 0 0 0 0 + 2900 0 0 0 0 0 + 3000 0 0 0 0 0 + 3100 0 0 0 0 0 + 3200 0 0 0 0 0 + 3300 0 0 0 0 0 + 3400 0 0 0 0 0 + 3500 0 0 0 0 0 + 3600 0 0 0 0 0 + 3700 0 0 0 0 0 + 3800 0 0 0 0 0 + 3900 0 0 0 0 0 + 4000 0 0 0 0 0 + 4100 0 0 0 0 0 + 4200 0 0 0 0 0 + 4300 0 0 0 0 0 + 4400 0 0 0 0 0 + 4500 0 0 0 0 0 + 4600 0 0 0 0 0 + 4700 0 0 0 0 0 + 4800 0 0 0 0 0 + 4900 0 0 0 0 0 + 5000 0 0 0 0 0 +Loop time of 37.3637 on 4 procs for 5000 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0146993 (0.039341) +Outpt time (%) = 0.24752 (0.662459) +Other time (%) = 37.1015 (99.2982) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/hardy/consistency.screen b/examples/USER/atc/hardy/consistency.screen index 58986fe285..01d3fd0b45 100644 --- a/examples/USER/atc/hardy/consistency.screen +++ b/examples/USER/atc/hardy/consistency.screen @@ -1,12 +1,8 @@ -LAMMPS (12 Jan 2013) -log consistency.log - +LAMMPS (14 Aug 2013) units metal atom_style atomic -atom_modify sort 0 1 variable L equal 16 variable E equal 8 - # create domain lattice fcc 3.615 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 3.615 3.615 3.615 @@ -15,82 +11,74 @@ region mdRegion block 0 16 -3 3 -3 3 boundary p p p create_box 1 mdRegion Created orthogonal box = (0 -10.845 -10.845) to (57.84 10.845 10.845) - 1 by 1 by 1 MPI processor grid - + 4 by 1 by 1 MPI processor grid # create atoms create_atoms 1 region mdRegion Created 2304 atoms mass 1 63.550 - group internal region mdRegion 2304 atoms in group internal - # specify inter-atomic potential pair_style eam pair_coeff * * ../../../../potentials/Cu_u3.eam - # specify neighbor/re-neighboring parameters neighbor 0.3 bin #neigh_modify every 10 delay 0 check no neigh_modify delay 10000 check no - min_modify line quadratic minimize 1.e-10 1.e-10 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 2.9579 Mbytes +Memory usage per processor = 2.95316 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8156.16 0 -8156.16 -0.027860375 1 0 -8156.16 0 -8156.16 -0.027860375 -Loop time of 0.0263638 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.0612388 on 4 procs for 1 steps with 2304 atoms Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = - -8156.16000525 -8156.16000525 -8156.16000525 - Force two-norm initial, final = 8.49262e-13 8.39871e-13 - Force max component initial, final = 3.22242e-14 3.00038e-14 - Final line search alpha, max atom move = 1 3.00038e-14 + -8156.16000524 -8156.16000524 -8156.16000524 + Force two-norm initial, final = 8.48911e-13 8.39584e-13 + Force max component initial, final = 3.2252e-14 3.01703e-14 + Final line search alpha, max atom move = 1 3.01703e-14 Iterations, force evaluations = 1 2 -Pair time (%) = 0.0255749 (97.0075) +Pair time (%) = 0.0362611 (59.2127) Neigh time (%) = 0 (0) -Comm time (%) = 0.000288963 (1.09606) +Comm time (%) = 0.00659382 (10.7674) Outpt time (%) = 0 (0) -Other time (%) = 0.000499964 (1.8964) +Other time (%) = 0.0183838 (30.0199) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15600 max 15504 min +Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 62208 Ave neighs/atom = 27 Neighbor list builds = 0 Dangerous builds = 0 - # ID group atc PhysicsType ParameterFile -fix AtC all atc hardy -Constructing ATC transfer (hardy) -atomPE compute created with ID: 3 -fix_modify AtC transfer internal type internal -fix_modify AtC fem create mesh $E 1 1 mdRegion f p p -fix_modify AtC fem create mesh 8 1 1 mdRegion f p p - ATC:: created FEM Mesh with 36 Global Nodes, 9 Unique Nodes, and 8 Elements -fix_modify AtC transfer fields none -fix_modify AtC transfer fields add density displacement stress energy eshelby_stress temperature -fix_modify AtC transfer gradients add displacement -fix_modify AtC transfer set reference_potential_energy -#fix_modify AtC transfer hardy_reset 1 - +fix AtC internal atc field +ATC: constructing shape function field estimate + ATC: peratom PE compute created with ID: 3 +fix_modify AtC mesh create $E 1 1 mdRegion f p p +fix_modify AtC mesh create 8 1 1 mdRegion f p p + ATC: created uniform mesh with 36 nodes, 9 unique nodes, and 8 elements +fix_modify AtC fields none +fix_modify AtC fields add mass_density displacement stress internal_energy eshelby_stress temperature +fix_modify AtC gradients add displacement +fix_modify AtC set reference_potential_energy +#fix_modify AtC hardy_reset 1 # output thermo 10 thermo_style custom step pe ke press lx ly lz -fix_modify AtC transfer output consistencyFE 1 text tensor_components - ATC:: Warning : text output can create _LARGE_ files -fix_modify AtC transfer atomic_output consistencyMD 1 +fix_modify AtC output consistencyFE 1 text tensor_components + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: # displace atoms # NOTE we need to figure out how to output post minimize w/o a "run" @@ -100,29 +88,27 @@ timestep 0.0 # initial before minimization? run 1 Setting up run ... - ATC:: computing bond matrix ...........done - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 4.78897 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 22.7915 Mbytes Step PotEng KinEng Press Lx Ly Lz 1 -8156.16 0 -0.027860375 57.84 21.69 21.69 2 -8156.16 0 -0.027860375 57.84 21.69 21.69 -Loop time of 0.197476 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.036861 on 4 procs for 1 steps with 2304 atoms -Pair time (%) = 0.0089829 (4.54886) +Pair time (%) = 0.00230974 (6.26608) Neigh time (%) = 0 (0) -Comm time (%) = 0.00012517 (0.0633848) -Outpt time (%) = 4.29153e-05 (0.0217319) -Other time (%) = 0.188325 (95.366) +Comm time (%) = 0.000133157 (0.36124) +Outpt time (%) = 0.000100911 (0.27376) +Other time (%) = 0.0343172 (93.0989) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15678 max 15411 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -134,43 +120,42 @@ variable i loop $n variable i loop 10 # NOTE this does not generate KE label loop_i - #variable s equal 0.02*$i/$n*$L - #print ">>> step $i, displacement $s" change_box all x scale 1.001 remap Changing box ... orthogonal box = (-0.02892 -10.845 -10.845) to (57.8689 10.845 10.845) minimize 1.e-10 1.e-10 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 5.85709 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7835 Mbytes Step PotEng KinEng Press Lx Ly Lz 2 -8156.1458 0 -1381.2949 57.89784 21.69 21.69 3 -8156.1458 0 -1381.2949 57.89784 21.69 21.69 -Loop time of 0.02723 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.587526 on 4 procs for 1 steps with 2304 atoms Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = - -8156.14582166 -8156.14582166 -8156.14582166 - Force two-norm initial, final = 1.20102e-12 8.09841e-13 - Force max component initial, final = 5.46594e-14 3.00922e-14 - Final line search alpha, max atom move = 1 3.00922e-14 + -8156.14582163 -8156.14582163 -8156.14582163 + Force two-norm initial, final = 1.20171e-12 7.98441e-13 + Force max component initial, final = 5.47843e-14 2.98234e-14 + Final line search alpha, max atom move = 1 2.98234e-14 Iterations, force evaluations = 1 2 -Pair time (%) = 0.0264421 (97.1062) +Pair time (%) = 0.113327 (19.2888) Neigh time (%) = 0 (0) -Comm time (%) = 0.000286102 (1.05069) +Comm time (%) = 0.244407 (41.5993) Outpt time (%) = 0 (0) -Other time (%) = 0.000501871 (1.84308) +Other time (%) = 0.229793 (39.1119) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15597 max 15508 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -179,28 +164,27 @@ Dangerous builds = 0 velocity all set 0 0 0 run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 4.86526 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 22.7915 Mbytes Step PotEng KinEng Press Lx Ly Lz 3 -8156.1458 0 -1381.2949 57.89784 21.69 21.69 4 -8156.1458 0 -1381.2949 57.89784 21.69 21.69 -Loop time of 0.112819 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.500844 on 4 procs for 1 steps with 2304 atoms -Pair time (%) = 0.00889111 (7.88086) +Pair time (%) = 0.0300949 (6.00884) Neigh time (%) = 0 (0) -Comm time (%) = 0.000100136 (0.088758) -Outpt time (%) = 4.22001e-05 (0.0374051) -Other time (%) = 0.103786 (91.993) +Comm time (%) = 0.0840541 (16.7825) +Outpt time (%) = 0.06286 (12.5508) +Other time (%) = 0.323835 (64.6579) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15623 max 15488 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -208,43 +192,42 @@ Neighbor list builds = 0 Dangerous builds = 0 next i jump in.consistency loop_i - #variable s equal 0.02*$i/$n*$L - #print ">>> step $i, displacement $s" change_box all x scale 1.001 remap Changing box ... orthogonal box = (-0.0578689 -10.845 -10.845) to (57.8979 10.845 10.845) minimize 1.e-10 1.e-10 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 5.85709 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7835 Mbytes Step PotEng KinEng Press Lx Ly Lz 4 -8156.1033 0 -2755.9958 57.955738 21.69 21.69 5 -8156.1033 0 -2755.9958 57.955738 21.69 21.69 -Loop time of 0.027204 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.402513 on 4 procs for 1 steps with 2304 atoms Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = - -8156.10329877 -8156.10329877 -8156.10329877 - Force two-norm initial, final = 1.40241e-12 8.94576e-13 - Force max component initial, final = 1.06387e-13 5.59414e-14 - Final line search alpha, max atom move = 1 5.59414e-14 + -8156.10329875 -8156.10329875 -8156.10329875 + Force two-norm initial, final = 1.39476e-12 8.93933e-13 + Force max component initial, final = 1.06757e-13 5.59136e-14 + Final line search alpha, max atom move = 1 5.59136e-14 Iterations, force evaluations = 1 2 -Pair time (%) = 0.0264099 (97.0807) +Pair time (%) = 0.0815714 (20.2655) Neigh time (%) = 0 (0) -Comm time (%) = 0.000291824 (1.07272) +Comm time (%) = 0.140636 (34.9394) Outpt time (%) = 0 (0) -Other time (%) = 0.000502348 (1.84659) +Other time (%) = 0.180306 (44.7951) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15563 max 15540 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -253,28 +236,27 @@ Dangerous builds = 0 velocity all set 0 0 0 run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 4.86526 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 22.7915 Mbytes Step PotEng KinEng Press Lx Ly Lz 5 -8156.1033 0 -2755.9958 57.955738 21.69 21.69 6 -8156.1033 0 -2755.9958 57.955738 21.69 21.69 -Loop time of 0.112333 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.375042 on 4 procs for 1 steps with 2304 atoms -Pair time (%) = 0.00886989 (7.89608) +Pair time (%) = 0.0312517 (8.33286) Neigh time (%) = 0 (0) -Comm time (%) = 0.000102043 (0.09084) -Outpt time (%) = 4.19617e-05 (0.0373548) -Other time (%) = 0.103319 (91.9757) +Comm time (%) = 0.0539653 (14.3892) +Outpt time (%) = 0.0545159 (14.536) +Other time (%) = 0.235309 (62.742) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15650 max 15466 min +Histogram: 1 0 0 0 2 0 0 0 0 1 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -282,43 +264,42 @@ Neighbor list builds = 0 Dangerous builds = 0 next i jump in.consistency loop_i - #variable s equal 0.02*$i/$n*$L - #print ">>> step $i, displacement $s" change_box all x scale 1.001 remap Changing box ... orthogonal box = (-0.0868468 -10.845 -10.845) to (57.9268 10.845 10.845) minimize 1.e-10 1.e-10 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 5.85709 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7835 Mbytes Step PotEng KinEng Press Lx Ly Lz 6 -8156.0325 0 -4124.1199 58.013694 21.69 21.69 7 -8156.0325 0 -4124.1199 58.013694 21.69 21.69 -Loop time of 0.027216 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.017836 on 4 procs for 1 steps with 2304 atoms Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = - -8156.03247786 -8156.03247786 -8156.03247786 - Force two-norm initial, final = 2.13063e-12 8.13549e-13 - Force max component initial, final = 1.57216e-13 5.40783e-14 - Final line search alpha, max atom move = 1 5.40783e-14 + -8156.03247785 -8156.03247785 -8156.03247785 + Force two-norm initial, final = 2.13199e-12 8.14844e-13 + Force max component initial, final = 1.57712e-13 5.37209e-14 + Final line search alpha, max atom move = 1 5.37209e-14 Iterations, force evaluations = 1 2 -Pair time (%) = 0.0264249 (97.0933) +Pair time (%) = 0.0168754 (94.614) Neigh time (%) = 0 (0) -Comm time (%) = 0.000289202 (1.06262) +Comm time (%) = 0.000489414 (2.74396) Outpt time (%) = 0 (0) -Other time (%) = 0.000501871 (1.84403) +Other time (%) = 0.000471234 (2.64204) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15567 max 15532 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -327,28 +308,27 @@ Dangerous builds = 0 velocity all set 0 0 0 run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 4.86526 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 22.7915 Mbytes Step PotEng KinEng Press Lx Ly Lz 7 -8156.0325 0 -4124.1199 58.013694 21.69 21.69 8 -8156.0325 0 -4124.1199 58.013694 21.69 21.69 -Loop time of 0.112513 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.359948 on 4 procs for 1 steps with 2304 atoms -Pair time (%) = 0.00891304 (7.9218) +Pair time (%) = 0.023981 (6.66237) Neigh time (%) = 0 (0) -Comm time (%) = 9.799e-05 (0.0870923) -Outpt time (%) = 4.19617e-05 (0.037295) -Other time (%) = 0.10346 (91.9538) +Comm time (%) = 0.0458988 (12.7515) +Outpt time (%) = 0.0396805 (11.024) +Other time (%) = 0.250387 (69.5621) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15659 max 15491 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -356,43 +336,42 @@ Neighbor list builds = 0 Dangerous builds = 0 next i jump in.consistency loop_i - #variable s equal 0.02*$i/$n*$L - #print ">>> step $i, displacement $s" change_box all x scale 1.001 remap Changing box ... orthogonal box = (-0.115854 -10.845 -10.845) to (57.9559 10.845 10.845) minimize 1.e-10 1.e-10 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 5.85709 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7835 Mbytes Step PotEng KinEng Press Lx Ly Lz 8 -8155.9334 0 -5485.7179 58.071707 21.69 21.69 9 -8155.9334 0 -5485.7179 58.071707 21.69 21.69 -Loop time of 0.0272419 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.0175145 on 4 procs for 1 steps with 2304 atoms Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = - -8155.93340043 -8155.93340043 -8155.93340043 - Force two-norm initial, final = 1.09237e-12 6.34198e-13 - Force max component initial, final = 5.6663e-14 3.73182e-14 - Final line search alpha, max atom move = 1 3.73182e-14 + -8155.93340042 -8155.93340042 -8155.93340042 + Force two-norm initial, final = 1.09341e-12 6.35419e-13 + Force max component initial, final = 5.68295e-14 3.66235e-14 + Final line search alpha, max atom move = 1 3.66235e-14 Iterations, force evaluations = 1 2 -Pair time (%) = 0.0264537 (97.1066) +Pair time (%) = 0.0141963 (81.0543) Neigh time (%) = 0 (0) -Comm time (%) = 0.000288963 (1.06073) +Comm time (%) = 0.000411749 (2.3509) Outpt time (%) = 0 (0) -Other time (%) = 0.000499249 (1.83265) +Other time (%) = 0.0029065 (16.5948) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15569 max 15539 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -401,28 +380,27 @@ Dangerous builds = 0 velocity all set 0 0 0 run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 4.86526 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 22.7915 Mbytes Step PotEng KinEng Press Lx Ly Lz 9 -8155.9334 0 -5485.7179 58.071707 21.69 21.69 10 -8155.9334 0 -5485.7179 58.071707 21.69 21.69 -Loop time of 0.11246 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.450115 on 4 procs for 1 steps with 2304 atoms -Pair time (%) = 0.00886917 (7.8865) +Pair time (%) = 0.0389773 (8.65942) Neigh time (%) = 0 (0) -Comm time (%) = 9.799e-05 (0.0871331) -Outpt time (%) = 4.31538e-05 (0.0383725) -Other time (%) = 0.10345 (91.988) +Comm time (%) = 0.0733666 (16.2995) +Outpt time (%) = 0.057173 (12.7019) +Other time (%) = 0.280598 (62.3392) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15643 max 15487 min +Histogram: 1 0 0 2 0 0 0 0 0 1 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -430,43 +408,42 @@ Neighbor list builds = 0 Dangerous builds = 0 next i jump in.consistency loop_i - #variable s equal 0.02*$i/$n*$L - #print ">>> step $i, displacement $s" change_box all x scale 1.001 remap Changing box ... orthogonal box = (-0.144889 -10.845 -10.845) to (57.9849 10.845 10.845) minimize 1.e-10 1.e-10 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 5.85709 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7835 Mbytes Step PotEng KinEng Press Lx Ly Lz 10 -8155.8061 0 -6840.8461 58.129779 21.69 21.69 11 -8155.8061 0 -6840.8461 58.129779 21.69 21.69 -Loop time of 0.027277 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.449937 on 4 procs for 1 steps with 2304 atoms Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = - -8155.80610649 -8155.80610649 -8155.80610649 - Force two-norm initial, final = 1.05419e-12 6.87292e-13 - Force max component initial, final = 5.43445e-14 3.41394e-14 - Final line search alpha, max atom move = 1 3.41394e-14 + -8155.80610648 -8155.80610648 -8155.80610648 + Force two-norm initial, final = 1.05408e-12 6.84939e-13 + Force max component initial, final = 5.43732e-14 3.31436e-14 + Final line search alpha, max atom move = 1 3.31436e-14 Iterations, force evaluations = 1 2 -Pair time (%) = 0.0264866 (97.1025) +Pair time (%) = 0.104361 (23.1945) Neigh time (%) = 0 (0) -Comm time (%) = 0.000291109 (1.06723) +Comm time (%) = 0.188499 (41.8945) Outpt time (%) = 0 (0) -Other time (%) = 0.000499249 (1.83029) +Other time (%) = 0.157078 (34.911) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15561 max 15539 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -475,28 +452,27 @@ Dangerous builds = 0 velocity all set 0 0 0 run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 4.86526 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 22.7915 Mbytes Step PotEng KinEng Press Lx Ly Lz 11 -8155.8061 0 -6840.8461 58.129779 21.69 21.69 12 -8155.8061 0 -6840.8461 58.129779 21.69 21.69 -Loop time of 0.112385 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.307091 on 4 procs for 1 steps with 2304 atoms -Pair time (%) = 0.00889611 (7.91574) +Pair time (%) = 0.0184542 (6.00937) Neigh time (%) = 0 (0) -Comm time (%) = 9.70364e-05 (0.0863428) -Outpt time (%) = 4.31538e-05 (0.0383981) -Other time (%) = 0.103349 (91.9595) +Comm time (%) = 0.0285818 (9.30729) +Outpt time (%) = 0.039631 (12.9053) +Other time (%) = 0.220424 (71.778) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15606 max 15482 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -504,43 +480,42 @@ Neighbor list builds = 0 Dangerous builds = 0 next i jump in.consistency loop_i - #variable s equal 0.02*$i/$n*$L - #print ">>> step $i, displacement $s" change_box all x scale 1.001 remap Changing box ... orthogonal box = (-0.173954 -10.845 -10.845) to (58.014 10.845 10.845) minimize 1.e-10 1.e-10 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 5.85709 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7835 Mbytes Step PotEng KinEng Press Lx Ly Lz 12 -8155.6506 0 -8189.4905 58.187909 21.69 21.69 13 -8155.6506 0 -8189.4905 58.187909 21.69 21.69 -Loop time of 0.0274398 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.00754917 on 4 procs for 1 steps with 2304 atoms Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = - -8155.65063643 -8155.65063643 -8155.65063643 - Force two-norm initial, final = 1.14301e-12 6.31459e-13 - Force max component initial, final = 7.85908e-14 4.51722e-14 - Final line search alpha, max atom move = 1 4.51722e-14 + -8155.65063641 -8155.65063641 -8155.65063641 + Force two-norm initial, final = 1.14329e-12 6.31554e-13 + Force max component initial, final = 7.85249e-14 4.52208e-14 + Final line search alpha, max atom move = 1 4.52208e-14 Iterations, force evaluations = 1 2 -Pair time (%) = 0.026654 (97.1362) +Pair time (%) = 0.00676924 (89.6687) Neigh time (%) = 0 (0) -Comm time (%) = 0.000284195 (1.0357) +Comm time (%) = 0.00040102 (5.31211) Outpt time (%) = 0 (0) -Other time (%) = 0.000501633 (1.82812) +Other time (%) = 0.000378907 (5.01919) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15560 max 15537 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -549,28 +524,27 @@ Dangerous builds = 0 velocity all set 0 0 0 run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 4.86526 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 22.7915 Mbytes Step PotEng KinEng Press Lx Ly Lz 13 -8155.6506 0 -8189.4905 58.187909 21.69 21.69 14 -8155.6506 0 -8189.4905 58.187909 21.69 21.69 -Loop time of 0.112741 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.280009 on 4 procs for 1 steps with 2304 atoms -Pair time (%) = 0.00890708 (7.90048) +Pair time (%) = 0.0315212 (11.2572) Neigh time (%) = 0 (0) -Comm time (%) = 9.60827e-05 (0.0852243) -Outpt time (%) = 4.19617e-05 (0.0372195) -Other time (%) = 0.103696 (91.9771) +Comm time (%) = 0.0258814 (9.24305) +Outpt time (%) = 0.0120553 (4.30532) +Other time (%) = 0.210551 (75.1944) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15642 max 15467 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -578,43 +552,42 @@ Neighbor list builds = 0 Dangerous builds = 0 next i jump in.consistency loop_i - #variable s equal 0.02*$i/$n*$L - #print ">>> step $i, displacement $s" change_box all x scale 1.001 remap Changing box ... orthogonal box = (-0.203048 -10.845 -10.845) to (58.043 10.845 10.845) minimize 1.e-10 1.e-10 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 5.85709 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7835 Mbytes Step PotEng KinEng Press Lx Ly Lz 14 -8155.467 0 -9531.6689 58.246097 21.69 21.69 15 -8155.467 0 -9531.6689 58.246097 21.69 21.69 -Loop time of 0.0274611 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.20262 on 4 procs for 1 steps with 2304 atoms Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8155.46703122 -8155.46703122 -8155.46703122 - Force two-norm initial, final = 1.00962e-12 7.12727e-13 - Force max component initial, final = 5.63612e-14 4.59164e-14 - Final line search alpha, max atom move = 1 4.59164e-14 + Force two-norm initial, final = 1.009e-12 7.09731e-13 + Force max component initial, final = 5.45874e-14 4.54584e-14 + Final line search alpha, max atom move = 1 4.54584e-14 Iterations, force evaluations = 1 2 -Pair time (%) = 0.02668 (97.1558) +Pair time (%) = 0.0793063 (39.1404) Neigh time (%) = 0 (0) -Comm time (%) = 0.000283003 (1.03056) +Comm time (%) = 0.062916 (31.0512) Outpt time (%) = 0 (0) -Other time (%) = 0.000498056 (1.81368) +Other time (%) = 0.0603979 (29.8084) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15572 max 15532 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -623,28 +596,27 @@ Dangerous builds = 0 velocity all set 0 0 0 run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 4.86526 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 22.7915 Mbytes Step PotEng KinEng Press Lx Ly Lz 15 -8155.467 0 -9531.6689 58.246097 21.69 21.69 16 -8155.467 0 -9531.6689 58.246097 21.69 21.69 -Loop time of 0.112602 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.163192 on 4 procs for 1 steps with 2304 atoms -Pair time (%) = 0.00888014 (7.88631) +Pair time (%) = 0.0239644 (14.6848) Neigh time (%) = 0 (0) -Comm time (%) = 9.67979e-05 (0.0859647) -Outpt time (%) = 4.19617e-05 (0.0372655) -Other time (%) = 0.103583 (91.9905) +Comm time (%) = 0.0332344 (20.3652) +Outpt time (%) = 0.000598073 (0.366484) +Other time (%) = 0.105395 (64.5835) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15669 max 15428 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -652,43 +624,42 @@ Neighbor list builds = 0 Dangerous builds = 0 next i jump in.consistency loop_i - #variable s equal 0.02*$i/$n*$L - #print ">>> step $i, displacement $s" change_box all x scale 1.001 remap Changing box ... orthogonal box = (-0.232171 -10.845 -10.845) to (58.0722 10.845 10.845) minimize 1.e-10 1.e-10 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 5.85709 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7835 Mbytes Step PotEng KinEng Press Lx Ly Lz 16 -8155.2553 0 -10867.404 58.304343 21.69 21.69 17 -8155.2553 0 -10867.404 58.304343 21.69 21.69 -Loop time of 0.0274651 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.250275 on 4 procs for 1 steps with 2304 atoms Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8155.25533188 -8155.25533188 -8155.25533188 - Force two-norm initial, final = 1.43478e-12 7.938e-13 - Force max component initial, final = 8.71334e-14 3.40752e-14 - Final line search alpha, max atom move = 1 3.40752e-14 + Force two-norm initial, final = 1.43358e-12 7.91452e-13 + Force max component initial, final = 8.69461e-14 3.39728e-14 + Final line search alpha, max atom move = 1 3.39728e-14 Iterations, force evaluations = 1 2 -Pair time (%) = 0.0266731 (97.1162) +Pair time (%) = 0.089587 (35.7955) Neigh time (%) = 0 (0) -Comm time (%) = 0.000295162 (1.07468) +Comm time (%) = 0.111741 (44.6472) Outpt time (%) = 0 (0) -Other time (%) = 0.000496864 (1.80907) +Other time (%) = 0.0489472 (19.5574) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15577 max 15529 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -697,28 +668,27 @@ Dangerous builds = 0 velocity all set 0 0 0 run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 4.86526 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 22.7915 Mbytes Step PotEng KinEng Press Lx Ly Lz 17 -8155.2553 0 -10867.404 58.304343 21.69 21.69 18 -8155.2553 0 -10867.404 58.304343 21.69 21.69 -Loop time of 0.112447 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.283027 on 4 procs for 1 steps with 2304 atoms -Pair time (%) = 0.00889087 (7.90672) +Pair time (%) = 0.0023123 (0.816991) Neigh time (%) = 0 (0) -Comm time (%) = 0.000101805 (0.0905357) -Outpt time (%) = 4.19617e-05 (0.0373168) -Other time (%) = 0.103412 (91.9654) +Comm time (%) = 0.000139952 (0.0494482) +Outpt time (%) = 0.039601 (13.992) +Other time (%) = 0.240974 (85.1416) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15638 max 15446 min +Histogram: 1 0 0 0 1 0 0 1 0 1 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -726,43 +696,42 @@ Neighbor list builds = 0 Dangerous builds = 0 next i jump in.consistency loop_i - #variable s equal 0.02*$i/$n*$L - #print ">>> step $i, displacement $s" change_box all x scale 1.001 remap Changing box ... orthogonal box = (-0.261324 -10.845 -10.845) to (58.1013 10.845 10.845) minimize 1.e-10 1.e-10 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 5.85709 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7835 Mbytes Step PotEng KinEng Press Lx Ly Lz 18 -8155.0156 0 -12196.682 58.362647 21.69 21.69 19 -8155.0156 0 -12196.682 58.362647 21.69 21.69 -Loop time of 0.027447 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.437147 on 4 procs for 1 steps with 2304 atoms Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8155.01558008 -8155.01558008 -8155.01558008 - Force two-norm initial, final = 1.28885e-12 5.67844e-13 - Force max component initial, final = 7.82412e-14 4.01363e-14 - Final line search alpha, max atom move = 1 4.01363e-14 + Force two-norm initial, final = 1.28582e-12 5.73333e-13 + Force max component initial, final = 7.8125e-14 4.13116e-14 + Final line search alpha, max atom move = 1 4.13116e-14 Iterations, force evaluations = 1 2 -Pair time (%) = 0.0266609 (97.1361) +Pair time (%) = 0.0894799 (20.4691) Neigh time (%) = 0 (0) -Comm time (%) = 0.000284195 (1.03543) +Comm time (%) = 0.162141 (37.0906) Outpt time (%) = 0 (0) -Other time (%) = 0.000501871 (1.82851) +Other time (%) = 0.185526 (42.4403) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15592 max 15514 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -771,28 +740,27 @@ Dangerous builds = 0 velocity all set 0 0 0 run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 4.86526 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 22.7915 Mbytes Step PotEng KinEng Press Lx Ly Lz 19 -8155.0156 0 -12196.682 58.362647 21.69 21.69 20 -8155.0156 0 -12196.682 58.362647 21.69 21.69 -Loop time of 0.112461 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.0860269 on 4 procs for 1 steps with 2304 atoms -Pair time (%) = 0.00890493 (7.91825) +Pair time (%) = 0.00462395 (5.375) Neigh time (%) = 0 (0) -Comm time (%) = 9.799e-05 (0.0871326) -Outpt time (%) = 4.00543e-05 (0.0356162) -Other time (%) = 0.103418 (91.959) +Comm time (%) = 0.0131851 (15.3268) +Outpt time (%) = 0.0006001 (0.697572) +Other time (%) = 0.0676177 (78.6007) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15677 max 15419 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -800,43 +768,42 @@ Neighbor list builds = 0 Dangerous builds = 0 next i jump in.consistency loop_i - #variable s equal 0.02*$i/$n*$L - #print ">>> step $i, displacement $s" change_box all x scale 1.001 remap Changing box ... orthogonal box = (-0.290505 -10.845 -10.845) to (58.1305 10.845 10.845) minimize 1.e-10 1.e-10 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 5.85709 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7835 Mbytes Step PotEng KinEng Press Lx Ly Lz 20 -8154.7478 0 -13519.498 58.42101 21.69 21.69 21 -8154.7478 0 -13519.498 58.42101 21.69 21.69 -Loop time of 0.0275021 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.00747728 on 4 procs for 1 steps with 2304 atoms Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = - -8154.7478183 -8154.7478183 -8154.7478183 - Force two-norm initial, final = 1.24003e-12 7.60434e-13 - Force max component initial, final = 5.33219e-14 4.33395e-14 - Final line search alpha, max atom move = 1 4.33395e-14 + -8154.74781829 -8154.74781829 -8154.74781829 + Force two-norm initial, final = 1.23916e-12 7.54091e-13 + Force max component initial, final = 6.14256e-14 4.77318e-14 + Final line search alpha, max atom move = 1 4.77318e-14 Iterations, force evaluations = 1 2 -Pair time (%) = 0.02672 (97.1565) +Pair time (%) = 0.00672746 (89.9719) Neigh time (%) = 0 (0) -Comm time (%) = 0.000285149 (1.03683) +Comm time (%) = 0.000367939 (4.92076) Outpt time (%) = 0 (0) -Other time (%) = 0.000496864 (1.80664) +Other time (%) = 0.000381887 (5.1073) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15601 max 15502 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 @@ -845,28 +812,27 @@ Dangerous builds = 0 velocity all set 0 0 0 run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 4.86526 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 22.7915 Mbytes Step PotEng KinEng Press Lx Ly Lz 21 -8154.7478 0 -13519.498 58.42101 21.69 21.69 22 -8154.7478 0 -13519.498 58.42101 21.69 21.69 -Loop time of 0.11249 on 1 procs for 1 steps with 2304 atoms +Loop time of 0.407448 on 4 procs for 1 steps with 2304 atoms -Pair time (%) = 0.00891304 (7.92341) +Pair time (%) = 0.0466059 (11.4385) Neigh time (%) = 0 (0) -Comm time (%) = 9.799e-05 (0.08711) -Outpt time (%) = 4.19617e-05 (0.0373026) -Other time (%) = 0.103437 (91.9522) +Comm time (%) = 0.0559623 (13.7348) +Outpt time (%) = 0.0544453 (13.3625) +Other time (%) = 0.250434 (61.4641) -Nlocal: 2304 ave 2304 max 2304 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3852 ave 3852 max 3852 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 62208 ave 62208 max 62208 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 124416 ave 124416 max 124416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1692 ave 1692 max 1692 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 15552 ave 15703 max 15408 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +FullNghs: 31104 ave 31104 max 31104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124416 Ave neighs/atom = 54 diff --git a/examples/USER/atc/hardy/eam_kernel_convergence.screen b/examples/USER/atc/hardy/eam_kernel_convergence.screen index 5f051ebdae..4c68988399 100644 --- a/examples/USER/atc/hardy/eam_kernel_convergence.screen +++ b/examples/USER/atc/hardy/eam_kernel_convergence.screen @@ -1,11 +1,9 @@ -LAMMPS (12 Jan 2013) -log eam_kernel_convergence.log -units metal -dimension 3 -boundary p p p -atom_style atomic -atom_modify sort 0 1 - +LAMMPS (14 Aug 2013) +log eam_kernel_convergence.log +units metal +dimension 3 +boundary p p p +atom_style atomic # create system variable a equal 4.08 lattice fcc $a @@ -14,49 +12,39 @@ Lattice spacing in x,y,z = 4.08 4.08 4.08 region SYSTEM block -6 6 -6 6 -6 6 create_box 1 SYSTEM Created orthogonal box = (-24.48 -24.48 -24.48) to (24.48 24.48 24.48) - 1 by 1 by 1 MPI processor grid + 1 by 2 by 2 MPI processor grid create_atoms 1 region SYSTEM Created 6912 atoms mass 1 196.97 group internal region SYSTEM 6912 atoms in group internal - # n-th shell at sqrt(n/2) * a for FCC # distances 1:2.9 2:4.1 3:5.1 4:5.8 5:6.5 # counts 1:12:12 2:6:18 3:24:42 4:12:54 5:24:78 -#pair_style lj/cut/smooth 5.456108274435118 -#pair_coeff * * 0.7242785984051078 2.598146797350056 pair_style eam pair_coeff * * ../../../../potentials/Au_u3.eam - - # specify neighbor/re-neighboring parameters neighbor 0.3 bin neigh_modify delay 1000000 - thermo 10 thermo_style custom step ke pe pxx pyy pzz pxy - timestep 0.0 reset_timestep 0 - velocity all set 0.0 0.0 0.0 sum no units box - fix ATC internal atc hardy -Constructing ATC transfer (hardy) -atomPE compute created with ID: 3 -fix_modify ATC fem create mesh 1 1 1 SYSTEM p p p - ATC:: created FEM Mesh with 8 Global Nodes, 1 Unique Nodes, and 1 Elements -#fix_modify ATC fem create mesh 2 2 2 SYSTEM p p p -#fix_modify ATC fem create mesh 4 4 4 SYSTEM p p p -fix_modify ATC transfer fields none -fix_modify ATC transfer fields add density stress number_density -fix_modify ATC transfer set reference_potential_energy -fix_modify ATC transfer output eam_kernel_convergenceFE 1 text tensor_components - ATC:: Warning : text output can create _LARGE_ files -fix_modify ATC transfer atomic_output eam_kernel_convergenceMD 1 tensor_components -fix_modify ATC transfer on_the_fly kernel on -fix_modify ATC transfer on_the_fly bond on +ATC: constructing kernel field estimate + ATC: peratom PE compute created with ID: 3 +fix_modify ATC mesh create 1 1 1 SYSTEM p p p + ATC: created uniform mesh with 8 nodes, 1 unique nodes, and 1 elements +fix_modify ATC fields none +fix_modify ATC fields add mass_density stress number_density +##fix_modify ATC set reference_potential_energy +fix_modify ATC output eam_kernel_convergenceFE 1 text tensor_components + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +##fix_modify ATC on_the_fly kernel on ## NOTE HACK REJ 8Jan13 temporary +##fix_modify ATC on_the_fly bond on # relative to a variable d equal 0.1 @@ -70,38 +58,33 @@ label loop_i variable Ra equal $R*$a variable Ra equal 0.10000000000000000555*$a variable Ra equal 0.10000000000000000555*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 0.40800000000000002931 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 0.40800000000000002931 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.45303 Mbytes + ATC: computing bond matrix .done + ATC: kernel matrix bandwidth 0 +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 0 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done -ATC:: computing potential stress: .done - 1 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.792487 on 1 procs for 1 steps with 6912 atoms + 0 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + 1 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.300242 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026895 (3.39375) +Pair time (%) = 0.0241128 (8.03112) Neigh time (%) = 0 (0) -Comm time (%) = 0.000197887 (0.0249704) -Outpt time (%) = 0.00019002 (0.0239776) -Other time (%) = 0.765204 (96.5573) +Comm time (%) = 0.0410731 (13.68) +Outpt time (%) = 0.0514653 (17.1413) +Other time (%) = 0.183591 (61.1476) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -116,37 +99,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 0.2000000000000000111*$a variable Ra equal 0.2000000000000000111*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 0.81600000000000005862 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 0.81600000000000005862 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 0 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 1 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 2 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.415175 on 1 procs for 1 steps with 6912 atoms + 1 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 0 + 2 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.48248 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026638 (6.4161) +Pair time (%) = 0.084024 (17.415) Neigh time (%) = 0 (0) -Comm time (%) = 0.000150919 (0.0363507) -Outpt time (%) = 0.00018096 (0.0435864) -Other time (%) = 0.388205 (93.504) +Comm time (%) = 0.118364 (24.5323) +Outpt time (%) = 0.0659893 (13.6771) +Other time (%) = 0.214103 (44.3755) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -161,37 +141,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 0.30000000000000004441*$a variable Ra equal 0.30000000000000004441*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 1.224000000000000199 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 1.224000000000000199 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 0 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 2 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 3 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.415644 on 1 procs for 1 steps with 6912 atoms + 2 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 0 + 3 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.545094 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266631 (6.41488) +Pair time (%) = 0.104079 (19.0937) Neigh time (%) = 0 (0) -Comm time (%) = 0.000150681 (0.0362523) -Outpt time (%) = 0.00018096 (0.0435372) -Other time (%) = 0.388649 (93.5053) +Comm time (%) = 0.12345 (22.6474) +Outpt time (%) = 0.0724639 (13.2938) +Other time (%) = 0.245102 (44.9651) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -206,37 +183,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 0.4000000000000000222*$a variable Ra equal 0.4000000000000000222*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 1.6320000000000001172 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 1.6320000000000001172 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 0 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 3 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 4 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.414101 on 1 procs for 1 steps with 6912 atoms + 3 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 0 + 4 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.386178 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026639 (6.43297) +Pair time (%) = 0.0569655 (14.7511) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152826 (0.0369056) -Outpt time (%) = 0.000185966 (0.0449085) -Other time (%) = 0.387123 (93.4852) +Comm time (%) = 0.0992606 (25.7033) +Outpt time (%) = 0.0438565 (11.3566) +Other time (%) = 0.186095 (48.189) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -251,37 +225,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 0.5*$a variable Ra equal 0.5*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 2.0400000000000000355 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 2.0400000000000000355 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 0 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 4 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 5 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.412699 on 1 procs for 1 steps with 6912 atoms + 4 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 0 + 5 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.535095 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026638 (6.45459) +Pair time (%) = 0.0920835 (17.2088) Neigh time (%) = 0 (0) -Comm time (%) = 0.000151634 (0.0367421) -Outpt time (%) = 0.00018096 (0.0438479) -Other time (%) = 0.385728 (93.4648) +Comm time (%) = 0.173024 (32.3351) +Outpt time (%) = 0.0531778 (9.938) +Other time (%) = 0.21681 (40.5181) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -296,37 +267,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 0.60000000000000008882*$a variable Ra equal 0.60000000000000008882*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 2.4480000000000003979 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 2.4480000000000003979 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 0 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 5 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 6 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.414185 on 1 procs for 1 steps with 6912 atoms + 5 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 0 + 6 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.201573 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266511 (6.4346) +Pair time (%) = 0.0382269 (18.9643) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0367254) -Outpt time (%) = 0.000188112 (0.0454174) -Other time (%) = 0.387194 (93.4833) +Comm time (%) = 0.000640154 (0.317579) +Outpt time (%) = 0.000263035 (0.130491) +Other time (%) = 0.162443 (80.5877) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -341,37 +309,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 0.70000000000000006661*$a variable Ra equal 0.70000000000000006661*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 2.8560000000000003162 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 2.8560000000000003162 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 0 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 6 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 7 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.415117 on 1 procs for 1 steps with 6912 atoms + 6 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 0 + 7 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.429407 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266759 (6.42613) +Pair time (%) = 0.109139 (25.4161) Neigh time (%) = 0 (0) -Comm time (%) = 0.000150919 (0.0363558) -Outpt time (%) = 0.00018096 (0.0435925) -Other time (%) = 0.388109 (93.4939) +Comm time (%) = 0.155901 (36.3062) +Outpt time (%) = 0.000292003 (0.0680015) +Other time (%) = 0.164075 (38.2097) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -386,37 +351,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 0.80000000000000004441*$a variable Ra equal 0.80000000000000004441*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 3.2640000000000002345 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 3.2640000000000002345 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 47 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 7 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 8 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.421207 on 1 procs for 1 steps with 6912 atoms + 7 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 47 + 8 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.147352 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026685 (6.33537) +Pair time (%) = 0.00983864 (6.67697) Neigh time (%) = 0 (0) -Comm time (%) = 0.000153065 (0.0363396) -Outpt time (%) = 0.000180006 (0.0427358) -Other time (%) = 0.394189 (93.5856) +Comm time (%) = 0.00774616 (5.25691) +Outpt time (%) = 0.000296652 (0.201322) +Other time (%) = 0.129471 (87.8648) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -431,37 +393,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 0.9000000000000000222*$a variable Ra equal 0.9000000000000000222*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 3.6720000000000001528 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 3.6720000000000001528 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 47 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 8 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 9 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.419127 on 1 procs for 1 steps with 6912 atoms + 8 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 47 + 9 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.118696 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266428 (6.35674) +Pair time (%) = 0.00697953 (5.88018) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0362924) -Outpt time (%) = 0.00018096 (0.0431754) -Other time (%) = 0.392151 (93.5638) +Comm time (%) = 0.000497282 (0.418955) +Outpt time (%) = 0.000273347 (0.230292) +Other time (%) = 0.110946 (93.4706) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -476,37 +435,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 1*$a variable Ra equal 1*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 4.0800000000000000711 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 4.0800000000000000711 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 47 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 9 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 10 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.420732 on 1 procs for 1 steps with 6912 atoms + 9 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 47 + 10 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.402689 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266609 (6.33679) +Pair time (%) = 0.0666595 (16.5536) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0361539) -Outpt time (%) = 0.000181198 (0.0430673) -Other time (%) = 0.393738 (93.584) +Comm time (%) = 0.0105869 (2.62905) +Outpt time (%) = 0.0670815 (16.6584) +Other time (%) = 0.258361 (64.159) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -521,37 +477,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 1.1000000000000000888*$a variable Ra equal 1.1000000000000000888*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 4.4880000000000004334 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 4.4880000000000004334 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 288 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 10 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 11 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.424354 on 1 procs for 1 steps with 6912 atoms + 10 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 288 + 11 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.307537 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026649 (6.2799) +Pair time (%) = 0.0362225 (11.7783) Neigh time (%) = 0 (0) -Comm time (%) = 0.000164747 (0.0388231) -Outpt time (%) = 0.000180006 (0.0424188) -Other time (%) = 0.39736 (93.6389) +Comm time (%) = 0.0385796 (12.5447) +Outpt time (%) = 0.000294566 (0.0957824) +Other time (%) = 0.23244 (75.5813) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -566,37 +519,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 1.2000000000000001776*$a variable Ra equal 1.2000000000000001776*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 4.8960000000000007958 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 4.8960000000000007958 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 288 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 11 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 12 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.427058 on 1 procs for 1 steps with 6912 atoms + 11 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 288 + 12 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.3476 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026686 (6.24879) +Pair time (%) = 0.0432398 (12.4395) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0356184) -Outpt time (%) = 0.000179052 (0.0419269) -Other time (%) = 0.400041 (93.6737) +Comm time (%) = 0.0443696 (12.7646) +Outpt time (%) = 0.047818 (13.7566) +Other time (%) = 0.212172 (61.0393) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -611,37 +561,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 1.3000000000000000444*$a variable Ra equal 1.3000000000000000444*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 5.30400000000000027 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 5.30400000000000027 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 311 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 12 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 13 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.435981 on 1 procs for 1 steps with 6912 atoms + 12 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 311 + 13 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.430106 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026649 (6.11242) +Pair time (%) = 0.075536 (17.5622) Neigh time (%) = 0 (0) -Comm time (%) = 0.000151873 (0.0348347) -Outpt time (%) = 0.000179052 (0.0410688) -Other time (%) = 0.409001 (93.8117) +Comm time (%) = 0.0911922 (21.2023) +Outpt time (%) = 0.048534 (11.2842) +Other time (%) = 0.214844 (49.9513) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -656,37 +603,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 1.4000000000000001332*$a variable Ra equal 1.4000000000000001332*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 5.7120000000000006324 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 5.7120000000000006324 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 311 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 13 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 14 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.4356 on 1 procs for 1 steps with 6912 atoms + 13 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 311 + 14 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.284159 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026623 (6.1118) +Pair time (%) = 0.0467392 (16.4483) Neigh time (%) = 0 (0) -Comm time (%) = 0.000167131 (0.0383681) -Outpt time (%) = 0.000179052 (0.0411048) -Other time (%) = 0.408631 (93.8087) +Comm time (%) = 0.0432881 (15.2337) +Outpt time (%) = 0.000284493 (0.100118) +Other time (%) = 0.193847 (68.2179) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -701,37 +645,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 1.5*$a variable Ra equal 1.5*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 6.1200000000000001066 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 6.1200000000000001066 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 312 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 14 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 15 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.437444 on 1 procs for 1 steps with 6912 atoms + 14 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 312 + 15 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.352391 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266461 (6.09133) +Pair time (%) = 0.0567713 (16.1103) Neigh time (%) = 0 (0) -Comm time (%) = 0.000158072 (0.0361353) -Outpt time (%) = 0.000178814 (0.040877) -Other time (%) = 0.410461 (93.8317) +Comm time (%) = 0.055818 (15.8398) +Outpt time (%) = 0.0249187 (7.07134) +Other time (%) = 0.214883 (60.9785) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -746,37 +687,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 1.6000000000000000888*$a variable Ra equal 1.6000000000000000888*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 6.528000000000000469 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 6.528000000000000469 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 478 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 15 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 16 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.447661 on 1 procs for 1 steps with 6912 atoms + 15 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 478 + 16 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.332613 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0267229 (5.96945) +Pair time (%) = 0.0567642 (17.0661) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0339791) -Outpt time (%) = 0.000180006 (0.0402103) -Other time (%) = 0.420606 (93.9564) +Comm time (%) = 0.0283655 (8.52808) +Outpt time (%) = 0.026697 (8.02646) +Other time (%) = 0.220786 (66.3793) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -791,37 +729,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 1.7000000000000001776*$a variable Ra equal 1.7000000000000001776*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 6.9360000000000008313 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 6.9360000000000008313 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 478 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 16 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 17 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.447114 on 1 procs for 1 steps with 6912 atoms + 16 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 478 + 17 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.400051 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026649 (5.96022) +Pair time (%) = 0.0440897 (11.021) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0340206) -Outpt time (%) = 0.000179052 (0.0400462) -Other time (%) = 0.420134 (93.9657) +Comm time (%) = 0.0782601 (19.5625) +Outpt time (%) = 0.0452949 (11.3223) +Other time (%) = 0.232406 (58.0941) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -836,37 +771,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 1.8000000000000000444*$a variable Ra equal 1.8000000000000000444*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 7.3440000000000003055 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 7.3440000000000003055 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 478 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 17 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 18 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.452778 on 1 procs for 1 steps with 6912 atoms + 17 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 478 + 18 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.259991 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266571 (5.88745) +Pair time (%) = 0.00655723 (2.5221) Neigh time (%) = 0 (0) -Comm time (%) = 0.000150919 (0.0333318) -Outpt time (%) = 0.000179052 (0.0395453) -Other time (%) = 0.425791 (94.0397) +Comm time (%) = 0.0127867 (4.91813) +Outpt time (%) = 0.0437278 (16.819) +Other time (%) = 0.196919 (75.7408) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -881,37 +813,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 1.9000000000000001332*$a variable Ra equal 1.9000000000000001332*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 7.7520000000000006679 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 7.7520000000000006679 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 503 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 18 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 19 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.469546 on 1 procs for 1 steps with 6912 atoms + 18 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 503 + 19 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.310079 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266399 (5.67355) +Pair time (%) = 0.0415583 (13.4025) Neigh time (%) = 0 (0) -Comm time (%) = 0.000151873 (0.0323446) -Outpt time (%) = 0.000180006 (0.0383362) -Other time (%) = 0.442574 (94.2558) +Comm time (%) = 0.0384805 (12.4099) +Outpt time (%) = 0.0133858 (4.31692) +Other time (%) = 0.216654 (69.8707) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -926,37 +855,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 2*$a variable Ra equal 2*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 8.1600000000000001421 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 8.1600000000000001421 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 503 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 19 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 20 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.469246 on 1 procs for 1 steps with 6912 atoms + 19 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 503 + 20 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.19849 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026655 (5.68038) +Pair time (%) = 0.00919574 (4.63284) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.032416) -Outpt time (%) = 0.000179052 (0.0381574) -Other time (%) = 0.44226 (94.249) +Comm time (%) = 0.011555 (5.82142) +Outpt time (%) = 0.000275791 (0.138944) +Other time (%) = 0.177464 (89.4068) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -971,37 +897,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 2.1000000000000000888*$a variable Ra equal 2.1000000000000000888*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 8.5680000000000013927 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 8.5680000000000013927 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 503 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 20 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 21 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.473302 on 1 procs for 1 steps with 6912 atoms + 20 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 503 + 21 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.13786 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026655 (5.6317) +Pair time (%) = 0.00668496 (4.84911) Neigh time (%) = 0 (0) -Comm time (%) = 0.000151157 (0.0319368) -Outpt time (%) = 0.000180006 (0.0380319) -Other time (%) = 0.446316 (94.2983) +Comm time (%) = 0.000468671 (0.339963) +Outpt time (%) = 0.00025773 (0.186951) +Other time (%) = 0.130448 (94.624) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1016,37 +939,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 2.2000000000000001776*$a variable Ra equal 2.2000000000000001776*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 8.9760000000000008669 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 8.9760000000000008669 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 504 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 21 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 22 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.484476 on 1 procs for 1 steps with 6912 atoms + 21 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 504 + 22 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.107814 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266452 (5.4998) +Pair time (%) = 0.00661451 (6.13514) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.031397) -Outpt time (%) = 0.000180006 (0.0371548) -Other time (%) = 0.457499 (94.4317) +Comm time (%) = 0.000394523 (0.365931) +Outpt time (%) = 0.000290513 (0.269459) +Other time (%) = 0.100514 (93.2295) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1061,37 +981,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 2.3000000000000002665*$a variable Ra equal 2.3000000000000002665*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 9.3840000000000021174 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 9.3840000000000021174 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 504 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 22 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 23 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.491662 on 1 procs for 1 steps with 6912 atoms + 22 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 504 + 23 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.108355 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266612 (5.42266) +Pair time (%) = 0.00665593 (6.14269) Neigh time (%) = 0 (0) -Comm time (%) = 0.000150919 (0.0306957) -Outpt time (%) = 0.00018692 (0.038018) -Other time (%) = 0.464663 (94.5086) +Comm time (%) = 0.000427246 (0.394301) +Outpt time (%) = 0.000290215 (0.267837) +Other time (%) = 0.100982 (93.1952) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1106,37 +1023,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 2.4000000000000003553*$a variable Ra equal 2.4000000000000003553*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 9.7920000000000015916 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 9.7920000000000015916 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 546 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 23 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 24 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.502151 on 1 procs for 1 steps with 6912 atoms + 23 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 546 + 24 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.108156 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026655 (5.30816) +Pair time (%) = 0.00659281 (6.09565) Neigh time (%) = 0 (0) -Comm time (%) = 0.000150919 (0.0300545) -Outpt time (%) = 0.000180006 (0.035847) -Other time (%) = 0.475165 (94.6259) +Comm time (%) = 0.000379384 (0.350774) +Outpt time (%) = 0.000281692 (0.260449) +Other time (%) = 0.100902 (93.2931) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1151,37 +1065,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 2.5*$a variable Ra equal 2.5*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 10.199999999999999289 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 10.199999999999999289 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 546 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 24 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 25 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.512156 on 1 procs for 1 steps with 6912 atoms + 24 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 546 + 25 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.340118 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026499 (5.17402) +Pair time (%) = 0.047267 (13.8972) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0297001) -Outpt time (%) = 0.00017786 (0.0347278) -Other time (%) = 0.485327 (94.7616) +Comm time (%) = 0.0213372 (6.27346) +Outpt time (%) = 0.0179818 (5.28692) +Other time (%) = 0.253532 (74.5424) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1196,37 +1107,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 2.6000000000000000888*$a variable Ra equal 2.6000000000000000888*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 10.60800000000000054 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 10.60800000000000054 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 743 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 25 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 26 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.533657 on 1 procs for 1 steps with 6912 atoms + 25 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 743 + 26 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.28821 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266299 (4.99008) +Pair time (%) = 0.019009 (6.59554) Neigh time (%) = 0 (0) -Comm time (%) = 0.000158072 (0.0296204) -Outpt time (%) = 0.000178814 (0.0335073) -Other time (%) = 0.50669 (94.9468) +Comm time (%) = 0.000516176 (0.179097) +Outpt time (%) = 0.0522387 (18.1252) +Other time (%) = 0.216446 (75.1001) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1241,37 +1149,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 2.7000000000000001776*$a variable Ra equal 2.7000000000000001776*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 11.016000000000001791 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 11.016000000000001791 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 743 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 26 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 27 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.531399 on 1 procs for 1 steps with 6912 atoms + 26 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 743 + 27 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.295394 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266781 (5.02035) +Pair time (%) = 0.0570537 (19.3145) Neigh time (%) = 0 (0) -Comm time (%) = 0.000151873 (0.0285798) -Outpt time (%) = 0.000178099 (0.0335151) -Other time (%) = 0.504391 (94.9176) +Comm time (%) = 0.0329895 (11.168) +Outpt time (%) = 0.000254452 (0.0861399) +Other time (%) = 0.205096 (69.4314) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1286,37 +1191,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 2.8000000000000002665*$a variable Ra equal 2.8000000000000002665*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 11.424000000000001265 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 11.424000000000001265 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 755 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 27 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 28 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.551485 on 1 procs for 1 steps with 6912 atoms + 27 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 755 + 28 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.394992 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026638 (4.83024) +Pair time (%) = 0.0525671 (13.3084) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0275821) -Outpt time (%) = 0.00018096 (0.0328132) -Other time (%) = 0.524514 (95.1094) +Comm time (%) = 0.042494 (10.7582) +Outpt time (%) = 0.0442644 (11.2064) +Other time (%) = 0.255667 (64.727) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1331,37 +1233,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 2.9000000000000003553*$a variable Ra equal 2.9000000000000003553*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 11.832000000000002515 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 11.832000000000002515 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 755 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 28 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 29 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.558076 on 1 procs for 1 steps with 6912 atoms + 28 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 755 + 29 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.32978 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266459 (4.7746) +Pair time (%) = 0.0278023 (8.43057) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152826 (0.0273845) -Outpt time (%) = 0.000179052 (0.0320839) -Other time (%) = 0.531098 (95.1659) +Comm time (%) = 0.0396687 (12.0288) +Outpt time (%) = 0.0126302 (3.82989) +Other time (%) = 0.249679 (75.7107) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1376,37 +1275,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 3*$a variable Ra equal 3*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 12.240000000000000213 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 12.240000000000000213 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 864 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 29 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 30 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.576373 on 1 procs for 1 steps with 6912 atoms + 29 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 864 + 30 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.353342 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026655 (4.6246) +Pair time (%) = 0.0475768 (13.4648) Neigh time (%) = 0 (0) -Comm time (%) = 0.000153065 (0.0265565) -Outpt time (%) = 0.000180006 (0.0312308) -Other time (%) = 0.549385 (95.3176) +Comm time (%) = 0.023629 (6.68727) +Outpt time (%) = 0.000285506 (0.0808016) +Other time (%) = 0.281851 (79.7672) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1421,37 +1317,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 3.1000000000000000888*$a variable Ra equal 3.1000000000000000888*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 12.648000000000001464 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 12.648000000000001464 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 910 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 30 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 31 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.608049 on 1 procs for 1 steps with 6912 atoms + 30 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 910 + 31 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.278774 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026648 (4.38255) +Pair time (%) = 0.0142775 (5.12152) Neigh time (%) = 0 (0) -Comm time (%) = 0.000158072 (0.0259965) -Outpt time (%) = 0.00018692 (0.030741) -Other time (%) = 0.581056 (95.5607) +Comm time (%) = 0.00300127 (1.0766) +Outpt time (%) = 0.051642 (18.5247) +Other time (%) = 0.209853 (75.2772) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1466,37 +1359,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 3.2000000000000001776*$a variable Ra equal 3.2000000000000001776*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 13.056000000000000938 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 13.056000000000000938 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 912 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 31 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 32 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.618226 on 1 procs for 1 steps with 6912 atoms + 31 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 912 + 32 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.222321 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266511 (4.31091) +Pair time (%) = 0.0169145 (7.60813) Neigh time (%) = 0 (0) -Comm time (%) = 0.000153065 (0.0247587) -Outpt time (%) = 0.00017786 (0.0287695) -Other time (%) = 0.591244 (95.6356) +Comm time (%) = 0.000565529 (0.254375) +Outpt time (%) = 0.000303566 (0.136544) +Other time (%) = 0.204538 (92.001) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1511,37 +1401,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 3.3000000000000002665*$a variable Ra equal 3.3000000000000002665*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 13.464000000000002188 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 13.464000000000002188 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 912 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 32 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 33 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.632357 on 1 procs for 1 steps with 6912 atoms + 32 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 912 + 33 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.271986 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266988 (4.22211) +Pair time (%) = 0.0168534 (6.19641) Neigh time (%) = 0 (0) -Comm time (%) = 0.000153065 (0.0242054) -Outpt time (%) = 0.00018096 (0.0286167) -Other time (%) = 0.605324 (95.7251) +Comm time (%) = 0.000433564 (0.159407) +Outpt time (%) = 0.0317252 (11.6643) +Other time (%) = 0.222974 (81.9799) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1556,37 +1443,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 3.4000000000000003553*$a variable Ra equal 3.4000000000000003553*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 13.872000000000001663 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 13.872000000000001663 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 982 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 33 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 34 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.657665 on 1 procs for 1 steps with 6912 atoms + 33 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 982 + 34 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.343778 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266671 (4.05482) +Pair time (%) = 0.061799 (17.9764) Neigh time (%) = 0 (0) -Comm time (%) = 0.000153065 (0.023274) -Outpt time (%) = 0.00018692 (0.0284218) -Other time (%) = 0.630658 (95.8935) +Comm time (%) = 0.078127 (22.726) +Outpt time (%) = 0.000294745 (0.085737) +Other time (%) = 0.203557 (59.2119) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1601,37 +1485,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 3.5*$a variable Ra equal 3.5*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 14.280000000000001137 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 14.280000000000001137 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 982 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 34 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 35 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.658028 on 1 procs for 1 steps with 6912 atoms + 34 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 982 + 35 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.171309 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266662 (4.05244) +Pair time (%) = 0.00657851 (3.84013) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0231162) -Outpt time (%) = 0.000179052 (0.0272105) -Other time (%) = 0.631031 (95.8972) +Comm time (%) = 0.000591993 (0.34557) +Outpt time (%) = 0.000343978 (0.200794) +Other time (%) = 0.163795 (95.6135) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1646,37 +1527,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 3.6000000000000000888*$a variable Ra equal 3.6000000000000000888*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 14.688000000000000611 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 14.688000000000000611 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 982 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 35 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 36 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.687164 on 1 procs for 1 steps with 6912 atoms + 35 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 982 + 36 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.15479 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026665 (3.88044) +Pair time (%) = 0.0169563 (10.9544) Neigh time (%) = 0 (0) -Comm time (%) = 0.000158072 (0.0230035) -Outpt time (%) = 0.000185013 (0.0269241) -Other time (%) = 0.660156 (96.0696) +Comm time (%) = 0.000479996 (0.310095) +Outpt time (%) = 0.00029999 (0.193804) +Other time (%) = 0.137054 (88.5418) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1691,37 +1569,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 3.7000000000000001776*$a variable Ra equal 3.7000000000000001776*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 15.096000000000001862 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 15.096000000000001862 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 982 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 36 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 37 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.719914 on 1 procs for 1 steps with 6912 atoms + 36 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 982 + 37 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.108144 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026644 (3.701) +Pair time (%) = 0.0065847 (6.08884) Neigh time (%) = 0 (0) -Comm time (%) = 0.000151873 (0.0210959) -Outpt time (%) = 0.00018096 (0.0251363) -Other time (%) = 0.692937 (96.2528) +Comm time (%) = 0.000512004 (0.473447) +Outpt time (%) = 0.000298738 (0.276242) +Other time (%) = 0.100748 (93.1615) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1736,37 +1611,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 3.8000000000000002665*$a variable Ra equal 3.8000000000000002665*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 15.504000000000001336 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 15.504000000000001336 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 982 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 37 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 38 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.736854 on 1 procs for 1 steps with 6912 atoms + 37 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 982 + 38 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.365101 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266581 (3.61782) +Pair time (%) = 0.0161821 (4.43222) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0206433) -Outpt time (%) = 0.000179052 (0.0242996) -Other time (%) = 0.709865 (96.3372) +Comm time (%) = 0.0784575 (21.4893) +Outpt time (%) = 0.0112433 (3.0795) +Other time (%) = 0.259218 (70.999) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1781,37 +1653,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 3.9000000000000003553*$a variable Ra equal 3.9000000000000003553*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 15.912000000000002586 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 15.912000000000002586 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 982 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 38 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 39 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.745193 on 1 procs for 1 steps with 6912 atoms + 38 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 982 + 39 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.430036 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026649 (3.57612) +Pair time (%) = 0.0818088 (19.0237) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0204123) -Outpt time (%) = 0.000178099 (0.0238997) -Other time (%) = 0.718214 (96.3796) +Comm time (%) = 0.0706595 (16.431) +Outpt time (%) = 0.0469042 (10.907) +Other time (%) = 0.230664 (53.6382) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1826,37 +1695,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 4*$a variable Ra equal 4*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 16.320000000000000284 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 16.320000000000000284 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1152 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 39 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 40 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.775498 on 1 procs for 1 steps with 6912 atoms + 39 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1152 + 40 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.207975 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026664 (3.43831) +Pair time (%) = 0.00668073 (3.21227) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0196146) -Outpt time (%) = 0.000178099 (0.0229657) -Other time (%) = 0.748504 (96.5191) +Comm time (%) = 0.00038588 (0.185542) +Outpt time (%) = 0.000258744 (0.124411) +Other time (%) = 0.20065 (96.4778) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1871,37 +1737,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 4.1000000000000005329*$a variable Ra equal 4.1000000000000005329*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 16.728000000000001535 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 16.728000000000001535 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1175 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 40 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 41 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.808638 on 1 procs for 1 steps with 6912 atoms + 40 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1175 + 41 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.410035 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266709 (3.29825) +Pair time (%) = 0.07674 (18.7155) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0188108) -Outpt time (%) = 0.000185966 (0.0229975) -Other time (%) = 0.781629 (96.6599) +Comm time (%) = 0.0558463 (13.6199) +Outpt time (%) = 0.0472893 (11.533) +Other time (%) = 0.230159 (56.1316) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1916,37 +1779,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 4.2000000000000001776*$a variable Ra equal 4.2000000000000001776*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 17.136000000000002785 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 17.136000000000002785 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1176 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 41 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 42 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.83779 on 1 procs for 1 steps with 6912 atoms + 41 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1176 + 42 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.569466 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0264981 (3.16285) +Pair time (%) = 0.0682225 (11.9801) Neigh time (%) = 0 (0) -Comm time (%) = 0.000151157 (0.0180424) -Outpt time (%) = 0.000180006 (0.0214858) -Other time (%) = 0.810961 (96.7976) +Comm time (%) = 0.0417059 (7.32369) +Outpt time (%) = 0.0824587 (14.48) +Other time (%) = 0.377079 (66.2162) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -1961,37 +1821,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 4.2999999999999998224*$a variable Ra equal 4.2999999999999998224*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 17.544000000000000483 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 17.544000000000000483 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1187 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 42 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 43 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.852486 on 1 procs for 1 steps with 6912 atoms + 42 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1187 + 43 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.349966 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266502 (3.12617) +Pair time (%) = 0.0566317 (16.1821) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152826 (0.0179271) -Outpt time (%) = 0.000180006 (0.0211154) -Other time (%) = 0.825503 (96.8348) +Comm time (%) = 0.0434393 (12.4124) +Outpt time (%) = 0.0316042 (9.03066) +Other time (%) = 0.218291 (62.3749) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -2006,37 +1863,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 4.4000000000000003553*$a variable Ra equal 4.4000000000000003553*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 17.952000000000001734 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 17.952000000000001734 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1211 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 43 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 44 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.897979 on 1 procs for 1 steps with 6912 atoms + 43 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1211 + 44 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.392429 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026685 (2.97167) +Pair time (%) = 0.0517555 (13.1885) Neigh time (%) = 0 (0) -Comm time (%) = 0.000153065 (0.0170455) -Outpt time (%) = 0.000185966 (0.0207094) -Other time (%) = 0.870955 (96.9906) +Comm time (%) = 0.0731887 (18.6502) +Outpt time (%) = 0.045777 (11.665) +Other time (%) = 0.221708 (56.4963) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -2051,37 +1905,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 4.5*$a variable Ra equal 4.5*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 18.359999999999999432 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 18.359999999999999432 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1211 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 44 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 45 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.920067 on 1 procs for 1 steps with 6912 atoms + 44 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1211 + 45 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.288743 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266621 (2.89784) +Pair time (%) = 0.0428154 (14.8282) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0165326) -Outpt time (%) = 0.00018096 (0.0196681) -Other time (%) = 0.893072 (97.066) +Comm time (%) = 0.0185749 (6.43302) +Outpt time (%) = 0.0170892 (5.91848) +Other time (%) = 0.210263 (72.8203) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -2096,37 +1947,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 4.6000000000000005329*$a variable Ra equal 4.6000000000000005329*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 18.768000000000004235 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 18.768000000000004235 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1342 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 45 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 46 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.948939 on 1 procs for 1 steps with 6912 atoms + 45 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1342 + 46 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.476904 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266368 (2.80701) +Pair time (%) = 0.0492818 (10.3337) Neigh time (%) = 0 (0) -Comm time (%) = 0.000156164 (0.0164567) -Outpt time (%) = 0.000185966 (0.0195973) -Other time (%) = 0.92196 (97.1569) +Comm time (%) = 0.0432622 (9.07147) +Outpt time (%) = 0.040977 (8.5923) +Other time (%) = 0.343383 (72.0025) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -2141,37 +1989,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 4.7000000000000001776*$a variable Ra equal 4.7000000000000001776*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 19.176000000000001933 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 19.176000000000001933 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1367 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 46 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 47 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 0.999157 on 1 procs for 1 steps with 6912 atoms + 46 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1367 + 47 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.131054 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266631 (2.66856) +Pair time (%) = 0.0091778 (7.00306) Neigh time (%) = 0 (0) -Comm time (%) = 0.000150681 (0.0150808) -Outpt time (%) = 0.000181913 (0.0182067) -Other time (%) = 0.972161 (97.2982) +Comm time (%) = 0.00810724 (6.18618) +Outpt time (%) = 0.000286102 (0.218308) +Other time (%) = 0.113483 (86.5925) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -2186,37 +2031,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 4.8000000000000007105*$a variable Ra equal 4.8000000000000007105*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 19.584000000000003183 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 19.584000000000003183 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1368 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 47 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 48 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 1.04 on 1 procs for 1 steps with 6912 atoms + 47 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1368 + 48 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.324749 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.02665 (2.5625) +Pair time (%) = 0.036183 (11.1418) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0146261) -Outpt time (%) = 0.000180006 (0.0173083) -Other time (%) = 1.01302 (97.4056) +Comm time (%) = 0.0234717 (7.22765) +Outpt time (%) = 0.0480435 (14.7941) +Other time (%) = 0.217051 (66.8365) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -2231,37 +2073,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 4.9000000000000003553*$a variable Ra equal 4.9000000000000003553*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 19.992000000000000881 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 19.992000000000000881 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1410 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 48 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 49 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 1.07027 on 1 procs for 1 steps with 6912 atoms + 48 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1410 + 49 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.36251 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266371 (2.48882) +Pair time (%) = 0.0491887 (13.5689) Neigh time (%) = 0 (0) -Comm time (%) = 0.000158072 (0.0147693) -Outpt time (%) = 0.000179052 (0.0167296) -Other time (%) = 1.0433 (97.4797) +Comm time (%) = 0.0482228 (13.3025) +Outpt time (%) = 0.0454938 (12.5497) +Other time (%) = 0.219605 (60.5789) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -2276,37 +2115,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 5*$a variable Ra equal 5*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 20.399999999999998579 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 20.399999999999998579 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1414 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 49 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 50 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 1.11255 on 1 procs for 1 steps with 6912 atoms + 49 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1414 + 50 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.377475 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.02666 (2.39629) +Pair time (%) = 0.056691 (15.0185) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0136723) -Outpt time (%) = 0.000186205 (0.0167368) -Other time (%) = 1.08555 (97.5733) +Comm time (%) = 0.0432966 (11.4701) +Outpt time (%) = 0.0455235 (12.06) +Other time (%) = 0.231963 (61.4514) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -2321,37 +2157,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 5.1000000000000005329*$a variable Ra equal 5.1000000000000005329*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 20.808000000000003382 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 20.808000000000003382 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1414 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 50 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 51 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 1.14368 on 1 procs for 1 steps with 6912 atoms + 50 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1414 + 51 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.342563 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266519 (2.33037) +Pair time (%) = 0.0467207 (13.6386) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0133002) -Outpt time (%) = 0.000178099 (0.0155725) -Other time (%) = 1.11669 (97.6408) +Comm time (%) = 0.0359398 (10.4914) +Outpt time (%) = 0.0465243 (13.5812) +Other time (%) = 0.213379 (62.2888) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -2366,37 +2199,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 5.2000000000000001776*$a variable Ra equal 5.2000000000000001776*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 21.21600000000000108 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 21.21600000000000108 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1416 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 51 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 52 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 1.17359 on 1 procs for 1 steps with 6912 atoms + 51 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1416 + 52 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.360143 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266399 (2.26996) +Pair time (%) = 0.0467206 (12.9728) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0129612) -Outpt time (%) = 0.00018096 (0.0154194) -Other time (%) = 1.14661 (97.7017) +Comm time (%) = 0.0333865 (9.27036) +Outpt time (%) = 0.046984 (13.0459) +Other time (%) = 0.233052 (64.7109) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -2411,37 +2241,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 5.3000000000000007105*$a variable Ra equal 5.3000000000000007105*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 21.624000000000002331 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 21.624000000000002331 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1437 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 52 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 53 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 1.22523 on 1 procs for 1 steps with 6912 atoms + 52 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1437 + 53 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.342496 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026648 (2.17494) +Pair time (%) = 0.0341545 (9.97222) Neigh time (%) = 0 (0) -Comm time (%) = 0.000160933 (0.0131349) -Outpt time (%) = 0.000180006 (0.0146916) -Other time (%) = 1.19824 (97.7972) +Comm time (%) = 0.0283093 (8.26558) +Outpt time (%) = 0.0456939 (13.3414) +Other time (%) = 0.234339 (68.4208) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -2456,37 +2283,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 5.4000000000000003553*$a variable Ra equal 5.4000000000000003553*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 22.032000000000003581 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 22.032000000000003581 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1437 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 53 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 54 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 1.27852 on 1 procs for 1 steps with 6912 atoms + 53 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1437 + 54 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.350093 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266609 (2.08529) +Pair time (%) = 0.0466567 (13.3269) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0118974) -Outpt time (%) = 0.00018096 (0.0141538) -Other time (%) = 1.25153 (97.8887) +Comm time (%) = 0.0359852 (10.2788) +Outpt time (%) = 0.0534886 (15.2784) +Other time (%) = 0.213963 (61.1159) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -2501,37 +2325,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 5.5*$a variable Ra equal 5.5*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 22.440000000000001279 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 22.440000000000001279 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1486 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 54 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 55 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 1.30572 on 1 procs for 1 steps with 6912 atoms + 54 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1486 + 55 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.283023 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026638 (2.0401) +Pair time (%) = 0.0466025 (16.466) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152111 (0.0116496) -Outpt time (%) = 0.000178814 (0.0136946) -Other time (%) = 1.27875 (97.9346) +Comm time (%) = 0.0382988 (13.5321) +Outpt time (%) = 0.0156633 (5.53429) +Other time (%) = 0.182458 (64.4677) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -2546,37 +2367,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 5.6000000000000005329*$a variable Ra equal 5.6000000000000005329*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 22.84800000000000253 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 22.84800000000000253 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1607 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 55 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 56 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 1.33993 on 1 procs for 1 steps with 6912 atoms + 55 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1607 + 56 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.200101 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266552 (1.9893) +Pair time (%) = 0.00681722 (3.40689) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152826 (0.0114056) -Outpt time (%) = 0.000180006 (0.013434) -Other time (%) = 1.31294 (97.9859) +Comm time (%) = 0.010536 (5.26532) +Outpt time (%) = 0.0104398 (5.21724) +Other time (%) = 0.172308 (86.1106) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -2591,37 +2409,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 5.7000000000000001776*$a variable Ra equal 5.7000000000000001776*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 23.256000000000000227 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 23.256000000000000227 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1619 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 56 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 57 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 1.37967 on 1 procs for 1 steps with 6912 atoms + 56 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1619 + 57 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.34729 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266459 (1.93133) +Pair time (%) = 0.0140542 (4.04683) Neigh time (%) = 0 (0) -Comm time (%) = 0.000150919 (0.0109388) -Outpt time (%) = 0.000180006 (0.0130471) -Other time (%) = 1.35269 (98.0447) +Comm time (%) = 0.00326961 (0.941463) +Outpt time (%) = 0.0595106 (17.1357) +Other time (%) = 0.270456 (77.876) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -2636,37 +2451,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 5.8000000000000007105*$a variable Ra equal 5.8000000000000007105*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 23.664000000000005031 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 23.664000000000005031 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1641 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 57 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 58 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 1.45956 on 1 procs for 1 steps with 6912 atoms + 57 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1641 + 58 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.38494 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266299 (1.82452) +Pair time (%) = 0.05675 (14.7426) Neigh time (%) = 0 (0) -Comm time (%) = 0.000151873 (0.0104054) -Outpt time (%) = 0.000180006 (0.0123329) -Other time (%) = 1.4326 (98.1527) +Comm time (%) = 0.0333247 (8.6571) +Outpt time (%) = 0.0447482 (11.6247) +Other time (%) = 0.250117 (64.9756) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -2681,37 +2493,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 5.9000000000000003553*$a variable Ra equal 5.9000000000000003553*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 24.072000000000002728 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 24.072000000000002728 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1643 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 58 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 59 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 1.49204 on 1 procs for 1 steps with 6912 atoms + 58 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1643 + 59 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.412444 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.0266409 (1.78553) +Pair time (%) = 0.0535668 (12.9876) Neigh time (%) = 0 (0) -Comm time (%) = 0.000156164 (0.0104665) -Outpt time (%) = 0.000180006 (0.0120644) -Other time (%) = 1.46507 (98.1919) +Comm time (%) = 0.0633941 (15.3703) +Outpt time (%) = 0.0569338 (13.804) +Other time (%) = 0.23855 (57.838) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -2726,37 +2535,34 @@ jump in.eam_kernel_convergence loop_i variable Ra equal $R*$a variable Ra equal 6*$a variable Ra equal 6*4.0800000000000000711 - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - fix_modify ATC transfer kernel quartic_sphere 24.480000000000000426 - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} + fix_modify ATC kernel quartic_sphere 24.480000000000000426 # initial (1) run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.55 -Memory usage per processor = 9.91079 Mbytes + ATC: kernel matrix bandwidth 1643 + ATC: computing bond matrix .done +Memory usage per processor = 18.2282 Mbytes Step KinEng PotEng Pxx Pyy Pzz Pxy - 59 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -ATC:: computing potential stress: .done - 60 0 -27164.16 0.0224632 0.0224632 0.0224632 1.3034513e-12 -Loop time of 1.53112 on 1 procs for 1 steps with 6912 atoms + 59 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 + ATC: kernel matrix bandwidth 1643 + 60 0 -27164.16 0.0224632 0.0224632 0.0224632 -3.0464385e-13 +Loop time of 0.247306 on 4 procs for 1 steps with 6912 atoms -Pair time (%) = 0.026649 (1.74049) +Pair time (%) = 0.0260277 (10.5245) Neigh time (%) = 0 (0) -Comm time (%) = 0.000151157 (0.00987232) -Outpt time (%) = 0.000180006 (0.0117565) -Other time (%) = 1.50414 (98.2379) +Comm time (%) = 0.000401855 (0.162493) +Outpt time (%) = 0.00262171 (1.06011) +Other time (%) = 0.218255 (88.2529) -Nlocal: 6912 ave 6912 max 6912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5283 ave 5283 max 5283 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186624 ave 186624 max 186624 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 373248 ave 373248 max 373248 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1728 ave 1728 max 1728 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2463 ave 2463 max 2463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46656 ave 46656 max 46656 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 93312 ave 93312 max 93312 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 54 @@ -2765,4 +2571,3 @@ Dangerous builds = 0 # increment (2) next i jump in.eam_kernel_convergence loop_i - diff --git a/examples/USER/atc/hardy/eam_unistrain_cell.screen b/examples/USER/atc/hardy/eam_unistrain_cell.screen index 8012dd1c42..fed2279a38 100644 --- a/examples/USER/atc/hardy/eam_unistrain_cell.screen +++ b/examples/USER/atc/hardy/eam_unistrain_cell.screen @@ -1,67 +1,70 @@ -LAMMPS (12 Jan 2013) +LAMMPS (14 Aug 2013) Lattice spacing in x,y,z = 3.615 3.615 3.615 Created orthogonal box = (-65.07 -10.845 -10.845) to (65.07 10.845 10.845) - 1 by 1 by 1 MPI processor grid + 4 by 1 by 1 MPI processor grid Created 4896 atoms 4608 atoms in group internal -Constructing ATC transfer (hardy) -atomPE compute created with ID: 3 - ATC:: created FEM Mesh with 40 Global Nodes, 10 Unique Nodes, and 9 Elements +ATC: constructing kernel field estimate + ATC: peratom PE compute created with ID: 3 + ATC: created uniform mesh with 40 nodes, 10 unique nodes, and 9 elements Setting up run ... - ATC:: computing bond matrix ..........done -ATC:: computing kernel matrix ..........done - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 8.83292 Mbytes + ATC: Warning: Using native lammps partitioning + ATC: computing bond matrix ..........done +Memory usage per processor = 34.3603 Mbytes Step PotEng KinEng Press Lx Ly Lz 0 -17256.022 0 -2117.8338 130.14 21.69 21.69 1 -17256.022 0 -2117.8338 130.14 21.69 21.69 -Loop time of 0.062633 on 1 procs for 1 steps with 4896 atoms +Loop time of 0.210032 on 4 procs for 1 steps with 4896 atoms -Pair time (%) = 0.020469 (32.6808) +Pair time (%) = 0.0401667 (19.1241) Neigh time (%) = 0 (0) -Comm time (%) = 0.00018692 (0.298437) -Outpt time (%) = 8.70228e-05 (0.138941) -Other time (%) = 0.0418901 (66.8819) +Comm time (%) = 0.099825 (47.5285) +Outpt time (%) = 0.0599867 (28.5608) +Other time (%) = 0.0100535 (4.78663) -Nlocal: 4896 ave 4896 max 4896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 6120 ave 6120 max 6120 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 130032 ave 130032 max 130032 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 260064 ave 260064 max 260064 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1224 ave 1296 max 1152 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 2259 ave 2592 max 1926 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 32508 ave 34992 max 29952 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 65016 ave 69984 max 60048 min +Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 260064 Ave neighs/atom = 53.1176 Neighbor list builds = 0 Dangerous builds = 0 Displacing atoms ... - ATC:: Warning : text output can create _LARGE_ files + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 9.13809 Mbytes + ATC: kernel matrix bandwidth 1005 + ATC: Warning: Using native lammps partitioning + ATC: computing bond matrix ..........done +Memory usage per processor = 34.3603 Mbytes Step PotEng KinEng Press Lx Ly Lz 1 -17252.771 0 -14787.592 130.14 21.69 21.69 + ATC: kernel matrix bandwidth 1005 + ATC: Warning: Using native lammps partitioning 2 -17252.771 0 -14787.592 130.14 21.69 21.69 -Loop time of 0.182935 on 1 procs for 1 steps with 4896 atoms +Loop time of 0.306944 on 4 procs for 1 steps with 4896 atoms -Pair time (%) = 0.0202942 (11.0937) +Pair time (%) = 0.0369428 (12.0357) Neigh time (%) = 0 (0) -Comm time (%) = 0.000153065 (0.0836716) -Outpt time (%) = 6.50883e-05 (0.03558) -Other time (%) = 0.162423 (88.7871) +Comm time (%) = 0.0419495 (13.6668) +Outpt time (%) = 0.000748515 (0.243861) +Other time (%) = 0.227303 (74.0536) -Nlocal: 4896 ave 4896 max 4896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 6120 ave 6120 max 6120 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 130032 ave 130032 max 130032 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 260064 ave 260064 max 260064 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1224 ave 1296 max 1152 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 2259 ave 2592 max 1926 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 32508 ave 34992 max 29952 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 65016 ave 69984 max 60048 min +Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 260064 Ave neighs/atom = 53.1176 diff --git a/examples/USER/atc/hardy/eam_unistrain_mesh.screen b/examples/USER/atc/hardy/eam_unistrain_mesh.screen index 65792eaa3a..08b2d5fc27 100644 --- a/examples/USER/atc/hardy/eam_unistrain_mesh.screen +++ b/examples/USER/atc/hardy/eam_unistrain_mesh.screen @@ -1,66 +1,108 @@ -LAMMPS (12 Jan 2013) +LAMMPS (14 Aug 2013) +log eam_unistrain_mesh +units metal +atom_style atomic +# create domain +lattice fcc 3.615 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 3.615 3.615 3.615 +region simRegion block -18 18 -3 3 -3 3 +region feRegion block -18 18 -3 3 -3 3 +boundary f p p +create_box 1 simRegion Created orthogonal box = (-65.07 -10.845 -10.845) to (65.07 10.845 10.845) - 1 by 1 by 1 MPI processor grid + 4 by 1 by 1 MPI processor grid +# create atoms +region mdRegion block -17 17 -3 3 -3 3 +create_atoms 1 region mdRegion Created 4896 atoms +mass 1 63.550 +atom_modify sort 0 1 +# specify interal atoms +region mdInternal block -16 16 -3 3 -3 3 +group internal region mdInternal 4608 atoms in group internal -Constructing ATC transfer (hardy) -atomPE compute created with ID: 3 - ATC:: created FEM Mesh with 40 Global Nodes, 10 Unique Nodes, and 9 Elements +# specify inter-atomic potential +pair_style eam +pair_coeff * * ../../../../potentials/Cu_u3.eam +# specify neighbor/re-neighboring parameters +neighbor 0.3 bin +neigh_modify every 10 delay 0 check no +# setup thermal output +thermo 10 +thermo_style custom step pe ke press lx ly lz +# ID group atc PhysicsType ParameterFile +fix AtC internal atc field +ATC: constructing shape function field estimate + ATC: peratom PE compute created with ID: 3 +# fix_modify AtC atom_element_map eulerian 1 +fix_modify AtC fields none +fix_modify AtC fields add mass_density displacement stress internal_energy +fix_modify AtC gradients add displacement +fix_modify AtC fields add rotation stretch +# fix_modify AtC on_the_fly kernel on +# ID part keywords nx ny nz region +fix_modify AtC mesh create 9 1 1 feRegion f p p + ATC: created uniform mesh with 40 nodes, 10 unique nodes, and 9 elements +#fix_modify AtC mesh data_decomposition +timestep 0.001 +reset_timestep 0 +run 1 Setting up run ... - ATC:: computing bond matrix ...........done - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 8.83292 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 22.0758 Mbytes Step PotEng KinEng Press Lx Ly Lz 0 -17256.022 0 -2117.8338 130.14 21.69 21.69 1 -17256.022 0 -2117.8338 130.14 21.69 21.69 -Loop time of 0.0626969 on 1 procs for 1 steps with 4896 atoms +Loop time of 0.00487894 on 4 procs for 1 steps with 4896 atoms -Pair time (%) = 0.0204611 (32.6349) +Pair time (%) = 0.00441378 (90.4661) Neigh time (%) = 0 (0) -Comm time (%) = 0.000186682 (0.297753) -Outpt time (%) = 8.2016e-05 (0.130813) -Other time (%) = 0.0419672 (66.9365) +Comm time (%) = 0.000346899 (7.11013) +Outpt time (%) = 5.80549e-05 (1.18991) +Other time (%) = 6.02007e-05 (1.23389) -Nlocal: 4896 ave 4896 max 4896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 6120 ave 6120 max 6120 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 130032 ave 130032 max 130032 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 260064 ave 260064 max 260064 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1224 ave 1296 max 1152 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 2259 ave 2592 max 1926 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 32508 ave 34992 max 29952 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 65016 ave 69984 max 60048 min +Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 260064 Ave neighs/atom = 53.1176 Neighbor list builds = 0 Dangerous builds = 0 +displace_atoms all ramp x -0.6507 0.6507 x -65.07 65.07 Displacing atoms ... - ATC:: Warning : text output can create _LARGE_ files +fix_modify AtC output eam_unistrain_meshFE 1 text tensor_components + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 9.13809 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 22.0758 Mbytes Step PotEng KinEng Press Lx Ly Lz 1 -17252.771 0 -14787.592 130.14 21.69 21.69 2 -17252.771 0 -14787.592 130.14 21.69 21.69 -Loop time of 0.23357 on 1 procs for 1 steps with 4896 atoms +Loop time of 0.382469 on 4 procs for 1 steps with 4896 atoms -Pair time (%) = 0.020292 (8.68778) +Pair time (%) = 0.0254062 (6.64269) Neigh time (%) = 0 (0) -Comm time (%) = 0.000166893 (0.0714531) -Outpt time (%) = 6.38962e-05 (0.0273563) -Other time (%) = 0.213047 (91.2134) +Comm time (%) = 0.0194529 (5.08613) +Outpt time (%) = 0.0317523 (8.30192) +Other time (%) = 0.305858 (79.9693) -Nlocal: 4896 ave 4896 max 4896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 6120 ave 6120 max 6120 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 130032 ave 130032 max 130032 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 260064 ave 260064 max 260064 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1224 ave 1296 max 1152 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 2259 ave 2592 max 1926 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 32508 ave 34992 max 29952 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 65016 ave 69984 max 60048 min +Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 260064 Ave neighs/atom = 53.1176 diff --git a/examples/USER/atc/hardy/eam_unistrain_qcylinder.screen b/examples/USER/atc/hardy/eam_unistrain_qcylinder.screen index 20e2b8325e..d95189d5a8 100644 --- a/examples/USER/atc/hardy/eam_unistrain_qcylinder.screen +++ b/examples/USER/atc/hardy/eam_unistrain_qcylinder.screen @@ -1,67 +1,67 @@ -LAMMPS (12 Jan 2013) +LAMMPS (14 Aug 2013) Lattice spacing in x,y,z = 3.615 3.615 3.615 Created orthogonal box = (-65.07 -10.845 -10.845) to (65.07 10.845 10.845) - 1 by 1 by 1 MPI processor grid + 4 by 1 by 1 MPI processor grid Created 4896 atoms 4608 atoms in group internal -Constructing ATC transfer (hardy) -atomPE compute created with ID: 3 - ATC:: created FEM Mesh with 40 Global Nodes, 10 Unique Nodes, and 9 Elements +ATC: constructing kernel field estimate + ATC: peratom PE compute created with ID: 3 + ATC: created uniform mesh with 40 nodes, 10 unique nodes, and 9 elements Setting up run ... - ATC:: computing bond matrix ..........done -ATC:: computing kernel matrix ..........done - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 8.83292 Mbytes + ATC: computing bond matrix ..........done +Memory usage per processor = 34.3603 Mbytes Step PotEng KinEng Press Lx Ly Lz 0 -17256.022 0 -2117.8338 130.14 21.69 21.69 1 -17256.022 0 -2117.8338 130.14 21.69 21.69 -Loop time of 0.0626462 on 1 procs for 1 steps with 4896 atoms +Loop time of 0.22 on 4 procs for 1 steps with 4896 atoms -Pair time (%) = 0.020498 (32.7203) +Pair time (%) = 0.0452225 (20.5557) Neigh time (%) = 0 (0) -Comm time (%) = 0.000189066 (0.3018) -Outpt time (%) = 8.41618e-05 (0.134345) -Other time (%) = 0.0418749 (66.8435) +Comm time (%) = 0.107069 (48.6676) +Outpt time (%) = 0.0576439 (26.2018) +Other time (%) = 0.0100647 (4.57488) -Nlocal: 4896 ave 4896 max 4896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 6120 ave 6120 max 6120 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 130032 ave 130032 max 130032 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 260064 ave 260064 max 260064 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1224 ave 1296 max 1152 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 2259 ave 2592 max 1926 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 32508 ave 34992 max 29952 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 65016 ave 69984 max 60048 min +Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 260064 Ave neighs/atom = 53.1176 Neighbor list builds = 0 Dangerous builds = 0 Displacing atoms ... - ATC:: Warning : text output can create _LARGE_ files + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 9.13809 Mbytes + ATC: kernel matrix bandwidth 1005 + ATC: computing bond matrix ..........done +Memory usage per processor = 34.3603 Mbytes Step PotEng KinEng Press Lx Ly Lz 1 -17252.771 0 -14787.592 130.14 21.69 21.69 + ATC: kernel matrix bandwidth 1005 2 -17252.771 0 -14787.592 130.14 21.69 21.69 -Loop time of 0.195493 on 1 procs for 1 steps with 4896 atoms +Loop time of 0.224722 on 4 procs for 1 steps with 4896 atoms -Pair time (%) = 0.020318 (10.3932) +Pair time (%) = 0.00557947 (2.48283) Neigh time (%) = 0 (0) -Comm time (%) = 0.00015378 (0.0786626) -Outpt time (%) = 6.48499e-05 (0.0331724) -Other time (%) = 0.174957 (89.4949) +Comm time (%) = 0.00455528 (2.02708) +Outpt time (%) = 0.000734568 (0.326878) +Other time (%) = 0.213853 (95.1632) -Nlocal: 4896 ave 4896 max 4896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 6120 ave 6120 max 6120 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 130032 ave 130032 max 130032 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 260064 ave 260064 max 260064 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1224 ave 1296 max 1152 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 2259 ave 2592 max 1926 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 32508 ave 34992 max 29952 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 65016 ave 69984 max 60048 min +Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 260064 Ave neighs/atom = 53.1176 diff --git a/examples/USER/atc/hardy/eam_unistrain_qsphere.screen b/examples/USER/atc/hardy/eam_unistrain_qsphere.screen index aab6553c30..f8befbecf9 100644 --- a/examples/USER/atc/hardy/eam_unistrain_qsphere.screen +++ b/examples/USER/atc/hardy/eam_unistrain_qsphere.screen @@ -1,67 +1,65 @@ -LAMMPS (12 Jan 2013) +LAMMPS (14 Aug 2013) Lattice spacing in x,y,z = 3.615 3.615 3.615 Created orthogonal box = (-65.07 -10.845 -10.845) to (65.07 10.845 10.845) - 1 by 1 by 1 MPI processor grid + 4 by 1 by 1 MPI processor grid Created 4896 atoms 4608 atoms in group internal -Constructing ATC transfer (hardy) -atomPE compute created with ID: 3 - ATC:: created FEM Mesh with 40 Global Nodes, 10 Unique Nodes, and 9 Elements +ATC: constructing kernel field estimate + ATC: peratom PE compute created with ID: 3 + ATC: created uniform mesh with 40 nodes, 10 unique nodes, and 9 elements Setting up run ... - ATC:: computing bond matrix ..........done -ATC:: computing kernel matrix ..........done - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 8.83292 Mbytes + ATC: computing bond matrix ..........done +Memory usage per processor = 12.3855 Mbytes Step PotEng KinEng Press Lx Ly Lz 0 -17256.022 0 -2117.8338 130.14 21.69 21.69 1 -17256.022 0 -2117.8338 130.14 21.69 21.69 -Loop time of 0.0626481 on 1 procs for 1 steps with 4896 atoms +Loop time of 0.13748 on 4 procs for 1 steps with 4896 atoms -Pair time (%) = 0.020453 (32.6474) +Pair time (%) = 0.0405408 (29.4885) Neigh time (%) = 0 (0) -Comm time (%) = 0.000185966 (0.296843) -Outpt time (%) = 8.2016e-05 (0.130915) -Other time (%) = 0.0419271 (66.9248) +Comm time (%) = 0.0661281 (48.1002) +Outpt time (%) = 0.0133058 (9.67834) +Other time (%) = 0.0175053 (12.733) -Nlocal: 4896 ave 4896 max 4896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 6120 ave 6120 max 6120 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 130032 ave 130032 max 130032 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 260064 ave 260064 max 260064 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1224 ave 1296 max 1152 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 2259 ave 2592 max 1926 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 32508 ave 34992 max 29952 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 65016 ave 69984 max 60048 min +Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 260064 Ave neighs/atom = 53.1176 Neighbor list builds = 0 Dangerous builds = 0 Displacing atoms ... - ATC:: Warning : text output can create _LARGE_ files + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 9.13809 Mbytes + ATC: computing bond matrix ..........done +Memory usage per processor = 12.3855 Mbytes Step PotEng KinEng Press Lx Ly Lz 1 -17252.771 0 -14787.592 130.14 21.69 21.69 2 -17252.771 0 -14787.592 130.14 21.69 21.69 -Loop time of 0.182941 on 1 procs for 1 steps with 4896 atoms +Loop time of 0.444931 on 4 procs for 1 steps with 4896 atoms -Pair time (%) = 0.0202801 (11.0856) +Pair time (%) = 0.0429311 (9.64893) Neigh time (%) = 0 (0) -Comm time (%) = 0.000152826 (0.0835386) -Outpt time (%) = 6.50883e-05 (0.0355788) -Other time (%) = 0.162443 (88.7953) +Comm time (%) = 0.0753596 (16.9374) +Outpt time (%) = 0.0446068 (10.0256) +Other time (%) = 0.282034 (63.3881) -Nlocal: 4896 ave 4896 max 4896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 6120 ave 6120 max 6120 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 130032 ave 130032 max 130032 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 260064 ave 260064 max 260064 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1224 ave 1296 max 1152 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 2259 ave 2592 max 1926 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 32508 ave 34992 max 29952 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 65016 ave 69984 max 60048 min +Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 260064 Ave neighs/atom = 53.1176 diff --git a/examples/USER/atc/hardy/eam_unistrain_step.screen b/examples/USER/atc/hardy/eam_unistrain_step.screen index 5196ceb69d..8f922fd5d5 100644 --- a/examples/USER/atc/hardy/eam_unistrain_step.screen +++ b/examples/USER/atc/hardy/eam_unistrain_step.screen @@ -1,67 +1,109 @@ -LAMMPS (12 Jan 2013) +LAMMPS (14 Aug 2013) +units metal +atom_style atomic +# create domain +lattice fcc 3.615 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 3.615 3.615 3.615 +region simRegion block -18 18 -3 3 -3 3 +region feRegion block -18 18 -3 3 -3 3 +boundary f p p +create_box 1 simRegion Created orthogonal box = (-65.07 -10.845 -10.845) to (65.07 10.845 10.845) - 1 by 1 by 1 MPI processor grid + 4 by 1 by 1 MPI processor grid +# create atoms +region mdRegion block -17 17 -3 3 -3 3 +create_atoms 1 region mdRegion Created 4896 atoms +mass 1 63.550 +# specify interal atoms +region mdInternal block -16 16 -3 3 -3 3 +group internal region mdInternal 4608 atoms in group internal -Constructing ATC transfer (hardy) -atomPE compute created with ID: 3 - ATC:: created FEM Mesh with 40 Global Nodes, 10 Unique Nodes, and 9 Elements +# specify inter-atomic potential +pair_style eam +pair_coeff * * ../../../../potentials/Cu_u3.eam +# specify neighbor/re-neighboring parameters +neighbor 0.3 bin +neigh_modify every 10 delay 0 check no +# setup thermal output +thermo 10 +thermo_style custom step pe ke press lx ly lz +# ID group atc PhysicsType ParameterFile +fix AtC internal atc hardy +ATC: constructing kernel field estimate + ATC: peratom PE compute created with ID: 3 +fix_modify AtC kernel step 9.0375 +# fix_modify AtC atom_element_map eulerian 1 +fix_modify AtC fields none +fix_modify AtC fields add mass_density displacement stress internal_energy +fix_modify AtC gradients add displacement +# fix_modify AtC on_the_fly kernel on +# fix_modify AtC on_the_fly bond on +# ID part keywords nx ny nz region +fix_modify AtC mesh create 9 1 1 feRegion f p p + ATC: created uniform mesh with 40 nodes, 10 unique nodes, and 9 elements +# equilibrate MD field +timestep 0.001 +reset_timestep 0 +run 1 Setting up run ... - ATC:: computing bond matrix ..........done -ATC:: computing kernel matrix ..........done - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 8.83292 Mbytes + ATC: computing bond matrix ..........done +Memory usage per processor = 34.3603 Mbytes Step PotEng KinEng Press Lx Ly Lz 0 -17256.022 0 -2117.8338 130.14 21.69 21.69 1 -17256.022 0 -2117.8338 130.14 21.69 21.69 -Loop time of 0.062566 on 1 procs for 1 steps with 4896 atoms +Loop time of 0.172684 on 4 procs for 1 steps with 4896 atoms -Pair time (%) = 0.020539 (32.8278) +Pair time (%) = 0.026729 (15.4786) Neigh time (%) = 0 (0) -Comm time (%) = 0.000174761 (0.279322) -Outpt time (%) = 8.58307e-05 (0.137184) -Other time (%) = 0.0417664 (66.7557) +Comm time (%) = 0.082336 (47.6802) +Outpt time (%) = 0.045118 (26.1275) +Other time (%) = 0.018501 (10.7138) -Nlocal: 4896 ave 4896 max 4896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 6120 ave 6120 max 6120 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 130032 ave 130032 max 130032 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 260064 ave 260064 max 260064 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1224 ave 1296 max 1152 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 2259 ave 2592 max 1926 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 32508 ave 34992 max 29952 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 65016 ave 69984 max 60048 min +Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 260064 Ave neighs/atom = 53.1176 Neighbor list builds = 0 Dangerous builds = 0 +displace_atoms all ramp x -0.6507 0.6507 x -65.07 65.07 Displacing atoms ... - ATC:: Warning : text output can create _LARGE_ files +fix_modify AtC output eam_unistrain_stepFE 1 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 9.13809 Mbytes + ATC: kernel matrix bandwidth 1005 + ATC: computing bond matrix ..........done +Memory usage per processor = 34.3603 Mbytes Step PotEng KinEng Press Lx Ly Lz 1 -17252.771 0 -14787.592 130.14 21.69 21.69 + ATC: kernel matrix bandwidth 1005 2 -17252.771 0 -14787.592 130.14 21.69 21.69 -Loop time of 0.180487 on 1 procs for 1 steps with 4896 atoms +Loop time of 0.30425 on 4 procs for 1 steps with 4896 atoms -Pair time (%) = 0.0203531 (11.2767) +Pair time (%) = 0.0258307 (8.48995) Neigh time (%) = 0 (0) -Comm time (%) = 0.000156879 (0.08692) -Outpt time (%) = 6.48499e-05 (0.0359305) -Other time (%) = 0.159912 (88.6004) +Comm time (%) = 0.0273772 (8.99826) +Outpt time (%) = 0.000741243 (0.243629) +Other time (%) = 0.250301 (82.2682) -Nlocal: 4896 ave 4896 max 4896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 6120 ave 6120 max 6120 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 130032 ave 130032 max 130032 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 260064 ave 260064 max 260064 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1224 ave 1296 max 1152 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 2259 ave 2592 max 1926 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 32508 ave 34992 max 29952 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 65016 ave 69984 max 60048 min +Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 260064 Ave neighs/atom = 53.1176 diff --git a/examples/USER/atc/hardy/eam_volume_stretch.screen b/examples/USER/atc/hardy/eam_volume_stretch.screen index 49e349604f..d3d36b0239 100644 --- a/examples/USER/atc/hardy/eam_volume_stretch.screen +++ b/examples/USER/atc/hardy/eam_volume_stretch.screen @@ -1,9 +1,6 @@ -LAMMPS (12 Jan 2013) - +LAMMPS (14 Aug 2013) units metal atom_style atomic -atom_modify sort 0 1 - # create domain lattice fcc 3.615 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 3.615 3.615 3.615 @@ -14,123 +11,103 @@ region mdInternal block -3 3 -3 3 -3 3 boundary p p p create_box 1 simRegion Created orthogonal box = (-10.845 -10.845 -10.845) to (10.845 10.845 10.845) - 1 by 1 by 1 MPI processor grid - + 1 by 2 by 2 MPI processor grid # create atoms create_atoms 1 region mdRegion Created 864 atoms mass 1 63.550 - -# specify interal/ghost atoms +# specify interal atoms group internal region mdInternal 864 atoms in group internal -#group ghost subtract all internal - # specify inter-atomic potential pair_style eam pair_coeff * * ../../../../potentials/Cu_u3.eam - # specify neighbor/re-neighboring parameters neighbor 0.3 bin neigh_modify every 10 delay 0 check no - # setup thermal output thermo 10 thermo_style custom step pe ke press lx ly lz - - # time integrator -fix NVE all nve - +# fix NVE all nve # ID group atc PhysicsType ParameterFile -fix AtC internal atc hardy -Constructing ATC transfer (hardy) -atomPE compute created with ID: 3 -fix_modify AtC transfer fields none -fix_modify AtC transfer fields add density -fix_modify AtC transfer fields add energy -fix_modify AtC transfer fields add stress -fix_modify AtC neighbor_reset_frequency 100000 - +fix AtC internal atc field +ATC: constructing shape function field estimate + ATC: peratom PE compute created with ID: 3 +fix_modify AtC fields none +fix_modify AtC fields add mass_density +fix_modify AtC fields add internal_energy +fix_modify AtC fields add stress # ID part keywords nx ny nz region -fix_modify AtC fem create mesh 2 2 2 feRegion p p p - ATC:: created FEM Mesh with 27 Global Nodes, 8 Unique Nodes, and 8 Elements - +fix_modify AtC mesh create 2 2 2 feRegion p p p + ATC: created uniform mesh with 27 nodes, 8 unique nodes, and 8 elements log eam_volume_stretch.log - # equilibrate MD field - -timestep 0.001 +timestep 0.0 # 0.001 reset_timestep 0 run 1 Setting up run ... - ATC:: computing bond matrix ...........done - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 4.34254 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 20.2625 Mbytes Step PotEng KinEng Press Lx Ly Lz 0 -3058.56 0 -0.027860375 21.69 21.69 21.69 - 1 -3058.56 1.8391755e-30 -0.027860375 21.69 21.69 21.69 -Loop time of 0.0108039 on 1 procs for 1 steps with 864 atoms + 1 -3058.56 0 -0.027860375 21.69 21.69 21.69 +Loop time of 0.0294803 on 4 procs for 1 steps with 864 atoms -Pair time (%) = 0.00339484 (31.4223) +Pair time (%) = 0.0104292 (35.3769) Neigh time (%) = 0 (0) -Comm time (%) = 5.6982e-05 (0.527419) -Outpt time (%) = 2.88486e-05 (0.26702) -Other time (%) = 0.00732327 (67.7833) +Comm time (%) = 0.0189348 (64.2289) +Outpt time (%) = 6.9201e-05 (0.234737) +Other time (%) = 4.70281e-05 (0.159524) -Nlocal: 864 ave 864 max 864 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2052 ave 2052 max 2052 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 23328 ave 23328 max 23328 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 46656 ave 46656 max 46656 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 216 ave 216 max 216 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1080 ave 1080 max 1080 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 5832 ave 5832 max 5832 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 11664 ave 11664 max 11664 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46656 Ave neighs/atom = 54 Neighbor list builds = 0 Dangerous builds = 0 - # stretch system change_box all x scale 1.001 y scale 1.001 z scale 1.001 remap Changing box ... orthogonal box = (-10.8558 -10.845 -10.845) to (10.8558 10.845 10.845) orthogonal box = (-10.8558 -10.8558 -10.845) to (10.8558 10.8558 10.845) orthogonal box = (-10.8558 -10.8558 -10.8558) to (10.8558 10.8558 10.8558) - -fix_modify AtC transfer output eam_volume_stretchFE 1 text tensor_components - ATC:: Warning : text output can create _LARGE_ files -# fix_modify AtC transfer atomic_output eam_volume_stretchMD 1 text +fix_modify AtC output eam_volume_stretchFE 1 text tensor_components + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 4.95 -Memory usage per processor = 4.34254 Mbytes + ATC: computing bond matrix ...........done +Memory usage per processor = 20.2625 Mbytes Step PotEng KinEng Press Lx Ly Lz - 1 -3058.5204 1.8391755e-30 -4126.8763 21.71169 21.71169 21.71169 - 2 -3058.5204 2.3402676e-29 -4126.8763 21.71169 21.71169 21.71169 -Loop time of 0.0757251 on 1 procs for 1 steps with 864 atoms + 1 -3058.5204 0 -4126.8763 21.71169 21.71169 21.71169 + 2 -3058.5204 0 -4126.8763 21.71169 21.71169 21.71169 +Loop time of 0.0434771 on 4 procs for 1 steps with 864 atoms -Pair time (%) = 0.00336003 (4.43715) +Pair time (%) = 0.000937521 (2.15636) Neigh time (%) = 0 (0) -Comm time (%) = 4.91142e-05 (0.0648586) -Outpt time (%) = 2.88486e-05 (0.0380966) -Other time (%) = 0.0722871 (95.4599) +Comm time (%) = 0.000136197 (0.313261) +Outpt time (%) = 0.000539005 (1.23975) +Other time (%) = 0.0418643 (96.2906) -Nlocal: 864 ave 864 max 864 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2052 ave 2052 max 2052 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 23328 ave 23328 max 23328 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 46656 ave 46656 max 46656 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 216 ave 216 max 216 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1080 ave 1080 max 1080 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 5832 ave 5832 max 5832 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 11664 ave 11664 max 11664 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46656 Ave neighs/atom = 54 Neighbor list builds = 0 Dangerous builds = 0 - diff --git a/examples/USER/atc/hardy/eshelby_static.screen b/examples/USER/atc/hardy/eshelby_static.screen index 456007409c..ae81ed2a1c 100644 --- a/examples/USER/atc/hardy/eshelby_static.screen +++ b/examples/USER/atc/hardy/eshelby_static.screen @@ -1,12 +1,12 @@ -LAMMPS (12 Jan 2013) -log eshelby_static.log -units metal -atom_style atomic -dimension 3 -boundary p p p -atom_modify sort 0 1 - -# create domain +LAMMPS (14 Aug 2013) +log eshelby_static.log +units metal +dimension 3 +boundary p p p +atom_style atomic +# create system +#lattice fcc 3.615 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 +#lattice fcc 3.615 origin 0.2 0.2 0.2 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 lattice fcc 4.08 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 4.08 4.08 4.08 region SYSTEM block -10 10 -10 10 0 3 @@ -14,99 +14,98 @@ region UPPER block -10 10 0 10 0 3 region LOWER block -10 0 -10 10 0 3 create_box 1 SYSTEM Created orthogonal box = (-40.8 -40.8 0) to (40.8 40.8 12.24) - 1 by 1 by 1 MPI processor grid - -# create atoms + 2 by 2 by 1 MPI processor grid create_atoms 1 region SYSTEM Created 4800 atoms mass 1 63.55 - -# group atoms by region group internal region SYSTEM 4800 atoms in group internal group upper region UPPER 2400 atoms in group upper group lower region LOWER 2400 atoms in group lower - -# specify inter-atomic potential +#pair_style eam +#pair_coeff * * ../../../../potentials/Cu_u3.eam +#pair_style lj/smooth 8.0 10.0 +#pair_coeff * * 10.0 1.5 pair_style lj/smooth/linear 5.456108274435118 pair_coeff * * 0.7242785984051078 2.598146797350056 - -# define region above/below crack +# define region region abovecrack block -2.01 2.01 0 8 INF INF units lattice group abovecrack region abovecrack 384 atoms in group abovecrack region belowcrack block -2.01 2.01 -8 0 INF INF units lattice group belowcrack region belowcrack 384 atoms in group belowcrack - -# specify neighbor/re-neighboring parameters neighbor 1.0 bin neigh_modify delay 1000000 neigh_modify exclude group abovecrack belowcrack - -# setup thermal output thermo 10 compute_modify thermo_temp extra 0 -thermo_style custom step ke pe press +region FORCECHECK block -6 0 6 10 0 3 +group FORCECHECK region FORCECHECK +288 atoms in group FORCECHECK +compute fxsum FORCECHECK reduce sum fx +compute fysum FORCECHECK reduce sum fy +compute fzsum FORCECHECK reduce sum fz +thermo_style custom step ke pe press c_fxsum c_fysum c_fzsum +thermo_modify format 1 %4i format 2 %3.1g format 3 %20.16g timestep 0.0 - # (1) minimize the system to get a relaxed configuration min_modify line quadratic variable tol equal 1.e-11 minimize 0.0 ${tol} 100000 1000000 minimize 0.0 9.999999999999999395e-12 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 5.32453 Mbytes -Step KinEng PotEng Press - 0 0 -18803.885 157.04581 - 10 0 -18804.051 -167.23257 - 20 0 -18804.054 -154.10675 - 30 0 -18804.055 -133.48818 - 40 0 -18804.055 -129.97657 - 50 0 -18804.055 -130.96286 - 60 0 -18804.055 -130.04134 - 70 0 -18804.055 -129.72642 - 80 0 -18804.055 -129.64952 - 90 0 -18804.055 -129.62765 - 100 0 -18804.055 -129.61925 - 110 0 -18804.055 -129.61875 - 120 0 -18804.055 -129.61941 - 130 0 -18804.055 -129.61928 - 140 0 -18804.055 -129.61924 - 150 0 -18804.055 -129.61922 - 160 0 -18804.055 -129.61922 - 170 0 -18804.055 -129.61922 - 180 0 -18804.055 -129.61922 - 190 0 -18804.055 -129.61922 - 200 0 -18804.055 -129.61922 - 210 0 -18804.055 -129.61922 - 218 0 -18804.055 -129.61922 -Loop time of 5.53898 on 1 procs for 218 steps with 4800 atoms +Memory usage per processor = 2.89514 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum + 0 0 -18803.88531507588 157.04581 3.4067194e-13 7.5394552e-14 -1.1171619e-15 + 10 0 -18804.05078386973 -167.23257 0.0038622644 -0.02973841 -2.7822961e-14 + 20 0 -18804.05398912934 -154.10675 -0.02209957 -0.079098411 -7.7483013e-14 + 30 0 -18804.05486888189 -133.48818 -0.013415553 0.039069634 1.3330819e-13 + 40 0 -18804.05508909051 -129.97657 -0.025714944 -0.00039124981 2.825702e-14 + 50 0 -18804.05511094083 -130.96286 0.00017302887 -0.00041936437 2.8474273e-14 + 60 0 -18804.05511286108 -130.04134 -8.0562031e-06 0.00040854586 1.4817637e-13 + 70 0 -18804.05511296557 -129.72642 2.4196188e-05 -8.3754634e-05 -8.2968141e-14 + 80 0 -18804.05511297355 -129.64952 -2.8214304e-05 0.00016439854 -1.7192415e-13 + 90 0 -18804.05511297455 -129.62765 -2.763398e-05 -1.3852197e-05 -1.0552489e-13 + 100 0 -18804.05511297478 -129.61925 -5.0791248e-06 -1.5172318e-05 -1.473598e-13 + 110 0 -18804.05511297482 -129.61875 -2.3891669e-07 4.3035847e-06 -8.2480275e-14 + 120 0 -18804.05511297477 -129.61941 4.1478414e-07 -2.9139069e-07 2.8750763e-14 + 130 0 -18804.05511297506 -129.61928 -8.2070128e-08 -1.155778e-08 1.8408353e-14 + 140 0 -18804.05511297482 -129.61924 -4.4570566e-08 2.6123951e-08 1.3097633e-13 + 150 0 -18804.05511297488 -129.61922 -2.699227e-08 2.1606944e-08 -1.1053083e-13 + 160 0 -18804.055112975 -129.61922 6.8667407e-09 9.0120222e-09 -7.0315769e-14 + 170 0 -18804.05511297498 -129.61922 3.88537e-09 3.1573261e-09 -1.5273464e-13 + 180 0 -18804.0551129748 -129.61922 3.7525026e-10 -2.6212562e-10 9.9078408e-14 + 190 0 -18804.05511297483 -129.61922 5.6720697e-12 8.8140874e-12 -4.9151834e-14 + 200 0 -18804.05511297479 -129.61922 -5.3396542e-11 3.7182177e-11 1.0315588e-13 + 210 0 -18804.05511297483 -129.61922 -7.4321343e-12 3.6389846e-12 1.5270715e-13 + 217 0 -18804.05511297483 -129.61922 -8.7495582e-13 -9.0918848e-13 -1.5813771e-13 +Loop time of 10.6219 on 4 procs for 217 steps with 4800 atoms Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -18803.8853151 -18804.055113 -18804.055113 - Force two-norm initial, final = 2.91621 9.56326e-12 - Force max component initial, final = 0.331329 5.12474e-13 - Final line search alpha, max atom move = 1 5.12474e-13 - Iterations, force evaluations = 218 436 + Force two-norm initial, final = 2.91621 9.94487e-12 + Force max component initial, final = 0.331329 4.98176e-13 + Final line search alpha, max atom move = 1 4.98176e-13 + Iterations, force evaluations = 217 434 -Pair time (%) = 5.22886 (94.4012) +Pair time (%) = 1.4734 (13.8714) Neigh time (%) = 0 (0) -Comm time (%) = 0.0854142 (1.54206) -Outpt time (%) = 0.00108838 (0.0196495) -Other time (%) = 0.223614 (4.03711) +Comm time (%) = 6.48505 (61.0536) +Outpt time (%) = 0.137212 (1.29179) +Other time (%) = 2.52624 (23.7833) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 186222 ave 186222 max 186222 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2856 ave 2856 max 2856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46555.5 ave 46908 max 46203 min +Histogram: 1 1 0 0 0 0 0 0 1 1 Total # of neighbors = 186222 Ave neighs/atom = 38.7963 @@ -114,89 +113,95 @@ Neighbor list builds = 0 Dangerous builds = 0 write_restart eshelby.restart System init for write_restart ... - -# setup ATC fix +# (2) pull crack apart reset_timestep 0 -fix PK1 internal atc hardy -Constructing ATC transfer (hardy) -atomPE compute created with ID: 3 -fix_modify PK1 fem create mesh 10 10 1 SYSTEM p f p - ATC:: created FEM Mesh with 242 Global Nodes, 110 Unique Nodes, and 100 Elements -fix_modify PK1 transfer fields none -fix_modify PK1 transfer fields add density energy temperature stress displacement -fix_modify PK1 transfer fields add eshelby_stress transformed_stress -fix_modify PK1 transfer gradients add displacement -fix_modify PK1 transfer set reference_potential_energy -fix_modify PK1 transfer output eshelby_staticFE 1 text tensor_components - ATC:: Warning : text output can create _LARGE_ files -fix_modify PK1 transfer atomic_output eshelby_staticMD 1 +fix PK1 internal atc field +ATC: constructing shape function field estimate + ATC: peratom PE compute created with ID: 6 +# NOTE tune this relative to lattice size +fix_modify PK1 mesh create 10 10 1 SYSTEM p f p + ATC: created uniform mesh with 242 nodes, 110 unique nodes, and 100 elements +fix_modify PK1 fields none +fix_modify PK1 fields add mass_density internal_energy temperature stress displacement +fix_modify PK1 fields add eshelby_stress transformed_stress +fix_modify PK1 gradients add displacement +fix_modify PK1 set reference_potential_energy +fix_modify PK1 output eshelby_staticFE 1 text binary tensor_components + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: +#fix_modify PK1 on_the_fly #-- make concentric loops around one/both of the crack tips #-- & another around undefected material (loop0) fix_modify PK1 mesh create_faceset loop0 box -6 0 6 10 -INF INF outward - ATC:: created faceset loop0 with 10 faces -fix_modify PK1 transfer boundary_integral eshelby_stress faceset loop0 -fix_modify PK1 transfer boundary_integral stress faceset loop0 -fix_modify PK1 transfer boundary_integral energy faceset loop0 -#fix_modify PK1 transfer boundary_integral displacement_gradient faceset loop0 + ATC: created faceset loop0 with 10 faces +fix_modify PK1 output boundary_integral eshelby_stress faceset loop0 +fix_modify PK1 output boundary_integral stress faceset loop0 +fix_modify PK1 output boundary_integral internal_energy faceset loop0 +#fix_modify PK1 output boundary_integral displacement_gradient faceset loop0 fix_modify PK1 mesh create_faceset loop1 box -6 0 -2 2 -INF INF outward - ATC:: created faceset loop1 with 10 faces -fix_modify PK1 transfer boundary_integral eshelby_stress faceset loop1 -fix_modify PK1 transfer boundary_integral stress faceset loop1 -fix_modify PK1 transfer boundary_integral energy faceset loop1 -#fix_modify PK1 transfer boundary_integral displacement_gradient faceset loop1 + ATC: created faceset loop1 with 10 faces +fix_modify PK1 output boundary_integral eshelby_stress faceset loop1 +fix_modify PK1 output boundary_integral stress faceset loop1 +fix_modify PK1 output boundary_integral internal_energy faceset loop1 +#fix_modify PK1 output boundary_integral displacement_gradient faceset loop1 fix_modify PK1 mesh create_faceset loop2 box -8 0 -4 4 -INF INF outward - ATC:: created faceset loop2 with 16 faces -fix_modify PK1 transfer boundary_integral eshelby_stress faceset loop2 -fix_modify PK1 transfer boundary_integral stress faceset loop2 -fix_modify PK1 transfer boundary_integral energy faceset loop2 -#fix_modify PK1 transfer boundary_integral displacement_gradient faceset loop2 + ATC: created faceset loop2 with 16 faces +fix_modify PK1 output boundary_integral eshelby_stress faceset loop2 +fix_modify PK1 output boundary_integral stress faceset loop2 +fix_modify PK1 output boundary_integral internal_energy faceset loop2 +#fix_modify PK1 output boundary_integral displacement_gradient faceset loop2 fix_modify PK1 mesh create_faceset loop3 box -10 0 -6 6 -INF INF outward - ATC:: created faceset loop3 with 22 faces -fix_modify PK1 transfer boundary_integral eshelby_stress faceset loop3 -fix_modify PK1 transfer boundary_integral stress faceset loop3 -fix_modify PK1 transfer boundary_integral energy faceset loop3 -#fix_modify PK1 transfer boundary_integral displacement_gradient faceset loop3 + ATC: created faceset loop3 with 22 faces +fix_modify PK1 output boundary_integral eshelby_stress faceset loop3 +fix_modify PK1 output boundary_integral stress faceset loop3 +fix_modify PK1 output boundary_integral internal_energy faceset loop3 +#fix_modify PK1 output boundary_integral displacement_gradient faceset loop3 fix_modify PK1 mesh create_faceset loop4 box 0 8 -6 6 -INF INF outward - ATC:: created faceset loop4 with 20 faces -fix_modify PK1 transfer boundary_integral eshelby_stress faceset loop4 -fix_modify PK1 transfer boundary_integral stress faceset loop4 -fix_modify PK1 transfer boundary_integral energy faceset loop4 -#fix_modify PK1 transfer boundary_integral displacement_gradient faceset loop4 - -# initial ATC step to designate reference state + ATC: created faceset loop4 with 20 faces +fix_modify PK1 output boundary_integral eshelby_stress faceset loop4 +fix_modify PK1 output boundary_integral stress faceset loop4 +fix_modify PK1 output boundary_integral internal_energy faceset loop4 +#fix_modify PK1 output boundary_integral displacement_gradient faceset loop4 +#-- compute across crack jumps in displacement +#fix PK1upper internal atc hardy +#fix_modify PK1upper mesh create 10 5 1 UPPER p f p +#fix_modify PK1upper fields none +#fix_modify PK1upper fields add displacement +#fix PK1lower lower atc hardy +#fix_modify PK1lower mesh create 10 5 1 LOWER p f p +#fix_modify PK1lower fields none +#fix_modify PK1lower fields add displacement +# initial (1) run 1 Setting up run ... - ATC:: computing bond matrix ...........done - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.45611 -Memory usage per processor = 9.74961 Mbytes -Step KinEng PotEng Press - 0 0 -18804.055 -129.61922 - 1 0 -18804.055 -129.61922 -Loop time of 0.913711 on 1 procs for 1 steps with 4800 atoms + ATC: computing bond matrix ...........done +Memory usage per processor = 23.0387 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum + 0 0 -18804.05511297483 -129.61922 -8.7410388e-13 -9.0953256e-13 -1.5920078e-13 + 1 0 -18804.05511297483 -129.61922 -8.7410388e-13 -9.0953256e-13 -1.5920078e-13 +Loop time of 0.317934 on 4 procs for 1 steps with 4800 atoms -Pair time (%) = 0.012948 (1.41708) +Pair time (%) = 0.00576746 (1.81405) Neigh time (%) = 0 (0) -Comm time (%) = 0.000232935 (0.0254933) -Outpt time (%) = 5.79357e-05 (0.0063407) -Other time (%) = 0.900472 (98.5511) +Comm time (%) = 0.00962543 (3.0275) +Outpt time (%) = 0.000138164 (0.0434567) +Other time (%) = 0.302403 (95.115) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 185718 ave 185718 max 185718 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 371436 ave 371436 max 371436 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2856 ave 2856 max 2856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46429.5 ave 46491 max 46397 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +FullNghs: 92859 ave 92859 max 92859 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 371436 Ave neighs/atom = 77.3825 Neighbor list builds = 0 Dangerous builds = 0 - -# pull crack apart +# increment (2) variable L equal 20 variable n equal 10 variable i loop $n @@ -218,61 +223,62 @@ Changing box ... orthogonal box = (-40.8 -40.8 0) to (40.8 41.4528 12.24) minimize 0.0 ${tol} 100000 1000000 minimize 0.0 9.999999999999999395e-12 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 11.2755 Mbytes -Step KinEng PotEng Press - 1 0 -18796.247 -27029.118 - 10 0 -18796.593 -25837.901 - 20 0 -18796.667 -25563.184 - 30 0 -18796.681 -25530.748 - 40 0 -18796.684 -25532.787 - 50 0 -18796.685 -25530.1 - 60 0 -18796.685 -25529.455 - 70 0 -18796.685 -25529.029 - 80 0 -18796.685 -25528.794 - 90 0 -18796.685 -25528.665 - 100 0 -18796.685 -25528.714 - 110 0 -18796.685 -25528.743 - 120 0 -18796.685 -25528.748 - 130 0 -18796.685 -25528.748 - 140 0 -18796.685 -25528.747 - 150 0 -18796.685 -25528.746 - 160 0 -18796.685 -25528.746 - 170 0 -18796.685 -25528.746 - 180 0 -18796.685 -25528.746 - 190 0 -18796.685 -25528.746 - 200 0 -18796.685 -25528.746 - 210 0 -18796.685 -25528.746 - 220 0 -18796.685 -25528.746 - 230 0 -18796.685 -25528.746 - 240 0 -18796.685 -25528.746 - 249 0 -18796.685 -25528.746 -Loop time of 6.04356 on 1 procs for 248 steps with 4800 atoms + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7254 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum + 1 0 -18796.24699487574 -27029.118 0.0043960333 -0.0014055346 -2.1929333e-13 + 10 0 -18796.59340724873 -25837.901 0.003228698 -0.0079514347 2.0472166e-13 + 20 0 -18796.6674229111 -25563.184 -0.41208254 0.60939356 -2.0133201e-14 + 30 0 -18796.68137488175 -25530.748 -0.10427399 0.046278834 1.8345742e-13 + 40 0 -18796.68416289275 -25532.787 0.037932219 6.742707e-05 -8.1854662e-14 + 50 0 -18796.68482000328 -25530.1 -0.017743055 -0.022407353 1.3725132e-13 + 60 0 -18796.68490342712 -25529.455 -0.0020694891 -0.00021194339 8.87658e-15 + 70 0 -18796.68490563928 -25529.029 -0.00025956468 0.00076638248 6.737666e-15 + 80 0 -18796.68490592246 -25528.794 0.00018670711 0.00010345638 2.3358052e-14 + 90 0 -18796.68490596423 -25528.665 5.7402299e-05 -0.00011112274 3.9048625e-14 + 100 0 -18796.68490596863 -25528.714 4.3186467e-05 -1.5316686e-05 -1.7127619e-13 + 110 0 -18796.68490597046 -25528.743 -1.6546701e-05 2.5136036e-06 4.4969237e-14 + 120 0 -18796.68490597065 -25528.748 -7.9352058e-06 1.4659191e-06 4.516873e-14 + 130 0 -18796.68490597036 -25528.748 4.8463939e-07 -6.647491e-07 -8.9565508e-14 + 140 0 -18796.68490597038 -25528.747 1.4258574e-07 2.4166009e-07 -1.0210062e-13 + 150 0 -18796.6849059704 -25528.746 -1.5186279e-07 3.3560936e-07 4.9280025e-14 + 160 0 -18796.68490597036 -25528.746 -1.3274959e-07 -7.2180252e-08 -7.3246964e-14 + 170 0 -18796.6849059705 -25528.746 -2.2715599e-08 -5.7380609e-09 3.1984831e-14 + 180 0 -18796.68490597034 -25528.746 9.6442526e-09 6.3084056e-09 1.0609569e-14 + 190 0 -18796.68490597043 -25528.746 -3.5484652e-11 2.9988142e-09 -2.1633736e-14 + 200 0 -18796.68490597063 -25528.746 -5.2937969e-10 -7.7295492e-10 -5.912458e-14 + 210 0 -18796.68490597045 -25528.746 3.0338545e-10 4.6398359e-10 3.7685133e-14 + 220 0 -18796.68490597037 -25528.746 1.5461683e-10 -8.041256e-11 -4.610895e-15 + 230 0 -18796.6849059705 -25528.746 -9.2570447e-12 -6.5234379e-11 -5.6801785e-14 + 240 0 -18796.68490597055 -25528.746 -1.9896646e-11 3.3817194e-11 9.6343072e-14 + 249 0 -18796.68490597057 -25528.746 3.4677051e-13 6.539951e-12 -8.5036145e-15 +Loop time of 8.79155 on 4 procs for 248 steps with 4800 atoms Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -18796.2469949 -18796.684906 -18796.684906 - Force two-norm initial, final = 1.3176 9.96134e-12 - Force max component initial, final = 0.199684 3.64944e-13 - Final line search alpha, max atom move = 1 3.64944e-13 + Force two-norm initial, final = 1.3176 9.93035e-12 + Force max component initial, final = 0.199684 4.01235e-13 + Final line search alpha, max atom move = 1 4.01235e-13 Iterations, force evaluations = 248 496 -Pair time (%) = 5.69356 (94.2086) +Pair time (%) = 2.0681 (23.5237) Neigh time (%) = 0 (0) -Comm time (%) = 0.0970294 (1.6055) -Outpt time (%) = 0.0012455 (0.0206087) -Other time (%) = 0.25173 (4.16526) +Comm time (%) = 4.54814 (51.7331) +Outpt time (%) = 0.220124 (2.50382) +Other time (%) = 1.95519 (22.2394) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 154452 ave 154452 max 154452 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 308904 ave 308904 max 308904 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2856 ave 2856 max 2856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 38613 ave 38650 max 38593 min +Histogram: 1 1 1 0 0 0 0 0 0 1 +FullNghs: 77226 ave 77226 max 77226 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 308904 Ave neighs/atom = 64.355 @@ -281,30 +287,27 @@ Dangerous builds = 0 # reset_timestep $i run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.45611 -Memory usage per processor = 9.90219 Mbytes -Step KinEng PotEng Press - 249 0 -18796.685 -25528.746 -ATC::check_pair_map has found that pair map and bond table need to be recomputed - ATC:: computing bond matrix ...........done - 250 0 -18796.685 -25528.746 -Loop time of 12.3214 on 1 procs for 1 steps with 4800 atoms + ATC: computing bond matrix ...........done +Memory usage per processor = 23.0387 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum + 249 0 -18796.68490597057 -25528.746 3.4668762e-13 6.5399934e-12 -9.027501e-15 + 250 0 -18796.68490597057 -25528.746 3.4668762e-13 6.5399934e-12 -9.027501e-15 +Loop time of 0.807379 on 4 procs for 1 steps with 4800 atoms -Pair time (%) = 0.0122342 (0.0992921) +Pair time (%) = 0.00261557 (0.323958) Neigh time (%) = 0 (0) -Comm time (%) = 0.000203848 (0.00165442) -Outpt time (%) = 5.79357e-05 (0.000470203) -Other time (%) = 12.3089 (99.8986) +Comm time (%) = 0.0248603 (3.07913) +Outpt time (%) = 0.0667176 (8.26348) +Other time (%) = 0.713185 (88.3334) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 156936 ave 156936 max 156936 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 313872 ave 313872 max 313872 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2856 ave 2856 max 2856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 39234 ave 39251 max 39210 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +FullNghs: 78468 ave 78468 max 78468 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 313872 Ave neighs/atom = 65.39 @@ -323,62 +326,63 @@ Changing box ... orthogonal box = (-40.8 -40.8 0) to (40.8 42.1056 12.24) minimize 0.0 ${tol} 100000 1000000 minimize 0.0 9.999999999999999395e-12 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 11.2755 Mbytes -Step KinEng PotEng Press - 250 0 -18774.761 -50163.01 - 260 0 -18775.118 -48920.946 - 270 0 -18775.183 -48678.889 - 280 0 -18775.195 -48656.554 - 290 0 -18775.197 -48656.927 - 300 0 -18775.197 -48656.203 - 310 0 -18775.198 -48655.78 - 320 0 -18775.198 -48655.465 - 330 0 -18775.198 -48655.282 - 340 0 -18775.198 -48655.198 - 350 0 -18775.198 -48655.259 - 360 0 -18775.198 -48655.294 - 370 0 -18775.198 -48655.307 - 380 0 -18775.198 -48655.306 - 390 0 -18775.198 -48655.305 - 400 0 -18775.198 -48655.305 - 410 0 -18775.198 -48655.305 - 420 0 -18775.198 -48655.305 - 430 0 -18775.198 -48655.305 - 440 0 -18775.198 -48655.305 - 450 0 -18775.198 -48655.305 - 460 0 -18775.198 -48655.305 - 470 0 -18775.198 -48655.305 - 480 0 -18775.198 -48655.305 - 490 0 -18775.198 -48655.305 - 500 0 -18775.198 -48655.305 - 502 0 -18775.198 -48655.305 -Loop time of 6.1296 on 1 procs for 252 steps with 4800 atoms + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7254 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum + 250 0 -18774.7608425896 -50163.01 0.022793727 -0.0011966205 -6.9763639e-14 + 260 0 -18775.11815298796 -48920.946 -0.0020464819 0.054982281 -1.2962201e-13 + 270 0 -18775.18252080679 -48678.889 -0.34679638 0.69588603 -1.2788208e-13 + 280 0 -18775.19462114314 -48656.554 -0.076015057 0.089569497 -1.744941e-13 + 290 0 -18775.19691196808 -48656.927 0.035624013 0.00032299188 7.0958864e-14 + 300 0 -18775.19746441122 -48656.203 -0.017029282 -0.019207942 -1.6668958e-13 + 310 0 -18775.19753012962 -48655.78 -0.00092746818 -0.00063117528 -4.9509008e-14 + 320 0 -18775.1975322318 -48655.465 -0.00035233821 0.00035846818 1.1448481e-13 + 330 0 -18775.19753254089 -48655.282 0.00031000783 4.2978579e-05 4.7592139e-14 + 340 0 -18775.19753260198 -48655.198 0.00012092645 -0.0001956234 -6.6075617e-14 + 350 0 -18775.19753260996 -48655.259 8.355958e-05 -6.1522389e-05 -2.3907959e-14 + 360 0 -18775.19753261247 -48655.294 -3.6272959e-05 -3.2757726e-05 6.0155006e-14 + 370 0 -18775.19753261278 -48655.307 -1.201859e-06 1.8229791e-06 7.0894679e-14 + 380 0 -18775.19753261278 -48655.306 3.3337492e-07 -1.4066916e-06 6.4266301e-14 + 390 0 -18775.19753261297 -48655.305 -1.9304843e-07 3.1853504e-07 -7.5422307e-14 + 400 0 -18775.1975326128 -48655.305 -4.3810387e-07 3.5975388e-07 -2.9199212e-13 + 410 0 -18775.19753261264 -48655.305 -7.4599947e-08 -2.1594499e-08 1.7863662e-13 + 420 0 -18775.19753261279 -48655.305 -9.5193689e-08 -3.6461161e-08 -2.0470257e-13 + 430 0 -18775.19753261263 -48655.305 4.6607151e-08 8.6445473e-09 9.6754202e-14 + 440 0 -18775.1975326129 -48655.305 2.4237351e-09 -1.2429845e-09 1.0966575e-13 + 450 0 -18775.19753261285 -48655.305 8.1342633e-10 -5.063303e-10 -7.5980888e-15 + 460 0 -18775.19753261275 -48655.305 -1.1228805e-10 1.0966651e-09 -1.9831879e-13 + 470 0 -18775.1975326128 -48655.305 3.6006653e-10 -4.1751033e-10 7.1487954e-14 + 480 0 -18775.1975326128 -48655.305 -7.0608855e-11 -7.7232654e-11 1.1836886e-13 + 490 0 -18775.19753261282 -48655.305 -2.1050048e-11 2.8067392e-11 6.9531186e-14 + 500 0 -18775.19753261291 -48655.305 -1.3303657e-12 1.0812714e-11 -3.0850322e-14 + 502 0 -18775.19753261292 -48655.305 -2.2029077e-12 8.0001559e-12 7.7080703e-14 +Loop time of 7.09933 on 4 procs for 252 steps with 4800 atoms Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -18774.7608426 -18775.1975326 -18775.1975326 - Force two-norm initial, final = 1.30136 8.58975e-12 - Force max component initial, final = 0.197635 3.80418e-13 - Final line search alpha, max atom move = 1 3.80418e-13 + Force two-norm initial, final = 1.30136 8.69208e-12 + Force max component initial, final = 0.197635 3.90715e-13 + Final line search alpha, max atom move = 1 3.90715e-13 Iterations, force evaluations = 252 504 -Pair time (%) = 5.77374 (94.1945) +Pair time (%) = 1.53346 (21.6001) Neigh time (%) = 0 (0) -Comm time (%) = 0.0985744 (1.60817) -Outpt time (%) = 0.00129032 (0.0210507) -Other time (%) = 0.255989 (4.17628) +Comm time (%) = 2.79308 (39.3428) +Outpt time (%) = 0.210507 (2.96517) +Other time (%) = 2.56228 (36.0919) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 147846 ave 147846 max 147846 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 295692 ave 295692 max 295692 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2856 ave 2856 max 2856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 36961.5 ave 36975 max 36946 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +FullNghs: 73923 ave 73923 max 73923 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 295692 Ave neighs/atom = 61.6025 @@ -387,28 +391,27 @@ Dangerous builds = 0 # reset_timestep $i run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.45611 -Memory usage per processor = 9.90219 Mbytes -Step KinEng PotEng Press - 502 0 -18775.198 -48655.305 - 503 0 -18775.198 -48655.305 -Loop time of 0.417698 on 1 procs for 1 steps with 4800 atoms + ATC: computing bond matrix ...........done +Memory usage per processor = 23.0387 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum + 502 0 -18775.19753261291 -48655.305 -2.2034903e-12 7.9996871e-12 7.6945395e-14 + 503 0 -18775.19753261291 -48655.305 -2.2034903e-12 7.9996871e-12 7.6945395e-14 +Loop time of 0.487686 on 4 procs for 1 steps with 4800 atoms -Pair time (%) = 0.0120342 (2.88107) +Pair time (%) = 0.00259829 (0.532778) Neigh time (%) = 0 (0) -Comm time (%) = 0.000202894 (0.0485744) -Outpt time (%) = 5.81741e-05 (0.0139273) -Other time (%) = 0.405403 (97.0564) +Comm time (%) = 0.0105814 (2.16971) +Outpt time (%) = 0.00929224 (1.90537) +Other time (%) = 0.465214 (95.3921) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 148392 ave 148392 max 148392 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 296784 ave 296784 max 296784 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2856 ave 2856 max 2856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 37098 ave 37123 max 37065 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +FullNghs: 74196 ave 74196 max 74196 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296784 Ave neighs/atom = 61.83 @@ -427,64 +430,65 @@ Changing box ... orthogonal box = (-40.8 -40.8 0) to (40.8 42.7584 12.24) minimize 0.0 ${tol} 100000 1000000 minimize 0.0 9.999999999999999395e-12 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 10.894 Mbytes -Step KinEng PotEng Press - 503 0 -18740.221 -71179.578 - 510 0 -18740.526 -70113.846 - 520 0 -18740.639 -69700.828 - 530 0 -18740.663 -69635.147 - 540 0 -18740.666 -69628.118 - 550 0 -18740.667 -69631.698 - 560 0 -18740.667 -69632.27 - 570 0 -18740.667 -69632.317 - 580 0 -18740.667 -69632.193 - 590 0 -18740.667 -69632.144 - 600 0 -18740.667 -69632.2 - 610 0 -18740.667 -69632.272 - 620 0 -18740.667 -69632.291 - 630 0 -18740.667 -69632.299 - 640 0 -18740.667 -69632.297 - 650 0 -18740.667 -69632.296 - 660 0 -18740.667 -69632.296 - 670 0 -18740.667 -69632.296 - 680 0 -18740.667 -69632.296 - 690 0 -18740.667 -69632.296 - 700 0 -18740.667 -69632.296 - 710 0 -18740.667 -69632.296 - 720 0 -18740.667 -69632.296 - 730 0 -18740.667 -69632.296 - 740 0 -18740.667 -69632.296 - 750 0 -18740.667 -69632.296 - 760 0 -18740.667 -69632.296 - 770 0 -18740.667 -69632.296 - 772 0 -18740.667 -69632.296 -Loop time of 6.41119 on 1 procs for 269 steps with 4800 atoms + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7254 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum + 503 0 -18740.22094539338 -71179.578 0.042436929 -0.00058766122 5.4461644e-14 + 510 0 -18740.52574537834 -70113.846 0.019892443 -0.0066976455 -1.2749177e-13 + 520 0 -18740.63866698476 -69700.828 -0.43415456 0.62751438 1.5471131e-13 + 530 0 -18740.66253797384 -69635.147 -0.14858913 -0.043191718 4.748632e-14 + 540 0 -18740.6660230413 -69628.118 0.033003494 0.010684797 4.9816054e-14 + 550 0 -18740.66684194138 -69631.698 -0.012343376 -0.022846192 -5.7769761e-14 + 560 0 -18740.66695998782 -69632.27 -0.0038103507 -0.006758347 1.8627461e-14 + 570 0 -18740.66696771383 -69632.317 0.0010108722 0.00038579232 -3.6953079e-14 + 580 0 -18740.66696843877 -69632.193 0.00032732592 -0.00057715667 6.4896005e-14 + 590 0 -18740.66696862285 -69632.144 0.0004393829 -0.00015285667 -1.511534e-13 + 600 0 -18740.66696865366 -69632.2 0.0002718906 8.0751254e-05 -1.3815338e-14 + 610 0 -18740.66696866142 -69632.272 -3.6811401e-05 -6.1493862e-05 -4.1636833e-14 + 620 0 -18740.66696866208 -69632.291 -1.1155812e-05 6.5073211e-06 -5.2661001e-14 + 630 0 -18740.66696866224 -69632.299 -2.8684447e-06 5.8543601e-07 -3.9829251e-14 + 640 0 -18740.66696866222 -69632.297 -7.6240734e-07 -7.3536712e-07 6.2965258e-14 + 650 0 -18740.66696866228 -69632.296 -7.7940189e-07 2.5064706e-06 -1.4706986e-13 + 660 0 -18740.6669686622 -69632.296 3.8750053e-07 1.4372821e-07 -3.1100122e-14 + 670 0 -18740.66696866235 -69632.296 -1.8890263e-07 -1.7245331e-07 -7.3170636e-15 + 680 0 -18740.66696866209 -69632.296 5.9915857e-08 -2.9041318e-08 -7.703907e-14 + 690 0 -18740.66696866221 -69632.296 1.2799751e-08 -1.6205375e-08 -6.2477801e-14 + 700 0 -18740.66696866215 -69632.296 5.0774321e-09 2.1777722e-09 -9.9720579e-14 + 710 0 -18740.66696866214 -69632.296 -1.6058649e-09 4.0847939e-10 1.1093557e-14 + 720 0 -18740.66696866211 -69632.296 2.5047088e-10 -9.5276707e-10 5.3210908e-14 + 730 0 -18740.66696866212 -69632.296 1.5784225e-10 -5.5112915e-11 9.522938e-14 + 740 0 -18740.66696866219 -69632.296 -1.1518922e-10 -2.0835743e-11 1.9975341e-14 + 750 0 -18740.6669686621 -69632.296 -3.8143832e-11 4.6393645e-11 -6.0802058e-14 + 760 0 -18740.66696866212 -69632.296 -9.0617494e-12 1.2776108e-11 1.2775718e-13 + 770 0 -18740.66696866213 -69632.296 -2.5180353e-12 -1.8959756e-12 2.3569688e-14 + 772 0 -18740.66696866214 -69632.296 -5.2109265e-12 -1.9328798e-12 -1.1258355e-14 +Loop time of 10.4509 on 4 procs for 269 steps with 4800 atoms Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -18740.2209454 -18740.6669687 -18740.6669687 - Force two-norm initial, final = 1.28947 9.87336e-12 - Force max component initial, final = 0.19586 4.55941e-13 - Final line search alpha, max atom move = 1 4.55941e-13 + Force two-norm initial, final = 1.28947 9.88499e-12 + Force max component initial, final = 0.19586 3.96302e-13 + Final line search alpha, max atom move = 1 3.96302e-13 Iterations, force evaluations = 269 538 -Pair time (%) = 6.03183 (94.0829) +Pair time (%) = 1.78253 (17.0562) Neigh time (%) = 0 (0) -Comm time (%) = 0.105233 (1.6414) -Outpt time (%) = 0.00138688 (0.0216322) -Other time (%) = 0.272739 (4.2541) +Comm time (%) = 6.04586 (57.8501) +Outpt time (%) = 0.103009 (0.985649) +Other time (%) = 2.51951 (24.1081) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 146190 ave 146190 max 146190 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 292380 ave 292380 max 292380 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2856 ave 2856 max 2856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 36547.5 ave 36589 max 36503 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +FullNghs: 73095 ave 73095 max 73095 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292380 Ave neighs/atom = 60.9125 @@ -493,28 +497,27 @@ Dangerous builds = 0 # reset_timestep $i run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.45611 -Memory usage per processor = 9.52072 Mbytes -Step KinEng PotEng Press - 772 0 -18740.667 -69632.296 - 773 0 -18740.667 -69632.296 -Loop time of 0.417181 on 1 procs for 1 steps with 4800 atoms + ATC: computing bond matrix ...........done +Memory usage per processor = 23.0387 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum + 772 0 -18740.66696866215 -69632.296 -5.2107068e-12 -1.9333735e-12 -1.0859369e-14 + 773 0 -18740.66696866215 -69632.296 -5.2107068e-12 -1.9333735e-12 -1.0859369e-14 +Loop time of 1.37249 on 4 procs for 1 steps with 4800 atoms -Pair time (%) = 0.0119832 (2.87241) +Pair time (%) = 0.0025475 (0.185612) Neigh time (%) = 0 (0) -Comm time (%) = 0.000199795 (0.0478916) -Outpt time (%) = 5.79357e-05 (0.0138874) -Other time (%) = 0.40494 (97.0658) +Comm time (%) = 0.160218 (11.6735) +Outpt time (%) = 0.0743265 (5.41545) +Other time (%) = 1.1354 (82.7255) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 146616 ave 146616 max 146616 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 293232 ave 293232 max 293232 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2856 ave 2856 max 2856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 36654 ave 36717 max 36596 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +FullNghs: 73308 ave 73308 max 73308 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293232 Ave neighs/atom = 61.09 @@ -533,63 +536,64 @@ Changing box ... orthogonal box = (-40.8 -40.8 0) to (40.8 43.4112 12.24) minimize 0.0 ${tol} 100000 1000000 minimize 0.0 9.999999999999999395e-12 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 10.8951 Mbytes -Step KinEng PotEng Press - 773 0 -18693.666 -90194.671 - 780 0 -18693.977 -89108.484 - 790 0 -18694.102 -88649.429 - 800 0 -18694.13 -88567.278 - 810 0 -18694.134 -88559.997 - 820 0 -18694.135 -88563.347 - 830 0 -18694.135 -88564.139 - 840 0 -18694.135 -88564.237 - 850 0 -18694.135 -88564.177 - 860 0 -18694.135 -88564.103 - 870 0 -18694.135 -88564.126 - 880 0 -18694.135 -88564.176 - 890 0 -18694.135 -88564.19 - 900 0 -18694.135 -88564.203 - 910 0 -18694.135 -88564.204 - 920 0 -18694.135 -88564.203 - 930 0 -18694.135 -88564.203 - 940 0 -18694.135 -88564.203 - 950 0 -18694.135 -88564.203 - 960 0 -18694.135 -88564.203 - 970 0 -18694.135 -88564.203 - 980 0 -18694.135 -88564.203 - 990 0 -18694.135 -88564.203 - 1000 0 -18694.135 -88564.203 - 1010 0 -18694.135 -88564.203 - 1020 0 -18694.135 -88564.203 - 1030 0 -18694.135 -88564.203 - 1032 0 -18694.135 -88564.203 -Loop time of 6.16549 on 1 procs for 259 steps with 4800 atoms + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7254 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum + 773 0 -18693.66587952461 -90194.671 0.063702858 0.00034764707 3.1089714e-14 + 780 0 -18693.97673971806 -89108.484 0.031180803 -0.0072593906 -1.0696131e-13 + 790 0 -18694.10178196363 -88649.429 -0.45437346 0.6792836 -5.3984595e-15 + 800 0 -18694.13014771662 -88567.278 -0.15697662 -0.013106095 -7.2589504e-14 + 810 0 -18694.13402657088 -88559.997 0.02596227 0.044720917 -5.2988863e-14 + 820 0 -18694.13485964635 -88563.347 -0.011123094 -0.022007456 -9.397344e-14 + 830 0 -18694.13498855082 -88564.139 -0.0034872424 -0.0069926492 1.9340432e-14 + 840 0 -18694.13499960769 -88564.237 0.00071682697 -0.00052543471 -1.3546456e-14 + 850 0 -18694.13500022692 -88564.177 -0.00018710267 8.8516819e-05 -8.5794219e-14 + 860 0 -18694.13500035583 -88564.103 0.00030396893 -0.00024100413 -2.134265e-13 + 870 0 -18694.13500038065 -88564.126 0.00024126745 4.592756e-05 -5.439052e-13 + 880 0 -18694.13500038689 -88564.176 -1.5490579e-05 -6.8952995e-05 -6.6298703e-13 + 890 0 -18694.13500038718 -88564.19 -4.6769486e-06 2.1421428e-05 -2.0346971e-12 + 900 0 -18694.13500038748 -88564.203 -1.9113332e-06 -1.5885822e-07 -2.1443611e-12 + 910 0 -18694.13500038753 -88564.204 -1.809664e-07 -1.6506767e-06 -3.6864192e-12 + 920 0 -18694.13500038753 -88564.203 -3.6953839e-07 6.4809133e-07 -5.7557188e-12 + 930 0 -18694.13500038745 -88564.203 1.5219849e-07 3.1170517e-07 -2.1760104e-11 + 940 0 -18694.13500038737 -88564.203 -2.2003925e-07 -3.0377181e-08 -1.9391159e-11 + 950 0 -18694.13500038737 -88564.203 -2.1937908e-09 -6.6808879e-09 -6.9718068e-12 + 960 0 -18694.13500038756 -88564.203 5.6044285e-09 -1.8903536e-08 -4.7082997e-13 + 970 0 -18694.1350003873 -88564.203 1.7243584e-09 -3.0105237e-09 -8.1476492e-14 + 980 0 -18694.13500038745 -88564.203 1.4689015e-09 3.1015348e-10 2.3777855e-14 + 990 0 -18694.13500038741 -88564.203 -1.966375e-10 -2.0503779e-10 -3.0092248e-14 +1000 0 -18694.13500038748 -88564.203 1.3654005e-10 -3.1843256e-10 -6.6578687e-14 +1010 0 -18694.13500038744 -88564.203 -3.0276585e-11 1.1110089e-11 -1.2101604e-13 +1020 0 -18694.13500038753 -88564.203 -3.0206456e-11 -1.5138533e-11 -1.6674162e-14 +1030 0 -18694.13500038753 -88564.203 1.507389e-12 1.1376859e-11 -6.9095771e-14 +1032 0 -18694.13500038751 -88564.203 1.2597073e-12 1.0879965e-11 3.8890766e-14 +Loop time of 8.72546 on 4 procs for 259 steps with 4800 atoms Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -18693.6658795 -18694.1350004 -18694.1350004 - Force two-norm initial, final = 1.28204 9.40092e-12 - Force max component initial, final = 0.194164 3.81528e-13 - Final line search alpha, max atom move = 1 3.81528e-13 + Force two-norm initial, final = 1.28204 9.41219e-12 + Force max component initial, final = 0.194164 4.11711e-13 + Final line search alpha, max atom move = 1 4.11711e-13 Iterations, force evaluations = 259 518 -Pair time (%) = 5.79697 (94.0228) +Pair time (%) = 1.68795 (19.3452) Neigh time (%) = 0 (0) -Comm time (%) = 0.101371 (1.64417) -Outpt time (%) = 0.00133944 (0.0217247) -Other time (%) = 0.26581 (4.31126) +Comm time (%) = 4.65341 (53.3315) +Outpt time (%) = 0.0229532 (0.26306) +Other time (%) = 2.36114 (27.0603) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 145314 ave 145314 max 145314 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 290628 ave 290628 max 290628 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2856 ave 2856 max 2856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 36328.5 ave 36381 max 36265 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +FullNghs: 72657 ave 72657 max 72657 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 290628 Ave neighs/atom = 60.5475 @@ -598,28 +602,27 @@ Dangerous builds = 0 # reset_timestep $i run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.45611 -Memory usage per processor = 9.52178 Mbytes -Step KinEng PotEng Press - 1032 0 -18694.135 -88564.203 - 1033 0 -18694.135 -88564.203 -Loop time of 0.417548 on 1 procs for 1 steps with 4800 atoms + ATC: computing bond matrix ...........done +Memory usage per processor = 23.0387 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum +1032 0 -18694.13500038751 -88564.203 1.2597022e-12 1.0880291e-11 3.8668721e-14 +1033 0 -18694.13500038751 -88564.203 1.2597022e-12 1.0880291e-11 3.8668721e-14 +Loop time of 1.2401 on 4 procs for 1 steps with 4800 atoms -Pair time (%) = 0.011971 (2.86697) +Pair time (%) = 0.00509548 (0.410893) Neigh time (%) = 0 (0) -Comm time (%) = 0.000208855 (0.0500193) -Outpt time (%) = 5.88894e-05 (0.0141036) -Other time (%) = 0.405309 (97.0689) +Comm time (%) = 0.0248823 (2.00648) +Outpt time (%) = 0.0769173 (6.20251) +Other time (%) = 1.1332 (91.3801) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 145476 ave 145476 max 145476 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 290952 ave 290952 max 290952 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2856 ave 2856 max 2856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 36369 ave 36391 max 36349 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +FullNghs: 72738 ave 72738 max 72738 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 290952 Ave neighs/atom = 60.615 @@ -638,64 +641,65 @@ Changing box ... orthogonal box = (-40.8 -40.8 0) to (40.8 44.064 12.24) minimize 0.0 ${tol} 100000 1000000 minimize 0.0 9.999999999999999395e-12 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 10.8951 Mbytes -Step KinEng PotEng Press - 1033 0 -18636.11 -107306.84 - 1040 0 -18636.431 -106192.36 - 1050 0 -18636.573 -105676.48 - 1060 0 -18636.608 -105569.62 - 1070 0 -18636.612 -105559.38 - 1080 0 -18636.613 -105561.67 - 1090 0 -18636.613 -105564.55 - 1100 0 -18636.613 -105565.01 - 1110 0 -18636.613 -105565.22 - 1120 0 -18636.613 -105565.3 - 1130 0 -18636.613 -105565.4 - 1140 0 -18636.613 -105565.47 - 1150 0 -18636.613 -105565.48 - 1160 0 -18636.613 -105565.49 - 1170 0 -18636.613 -105565.49 - 1180 0 -18636.613 -105565.49 - 1190 0 -18636.613 -105565.49 - 1200 0 -18636.613 -105565.49 - 1210 0 -18636.613 -105565.49 - 1220 0 -18636.613 -105565.49 - 1230 0 -18636.613 -105565.49 - 1240 0 -18636.613 -105565.49 - 1250 0 -18636.613 -105565.49 - 1260 0 -18636.613 -105565.49 - 1270 0 -18636.613 -105565.49 - 1280 0 -18636.613 -105565.49 - 1290 0 -18636.613 -105565.49 - 1300 0 -18636.613 -105565.49 - 1305 0 -18636.613 -105565.49 -Loop time of 6.52942 on 1 procs for 272 steps with 4800 atoms + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7254 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum +1033 0 -18636.11013032917 -107306.84 0.087179197 0.0015874207 5.9226929e-14 +1040 0 -18636.43103673087 -106192.36 0.044337741 -0.0066832041 -2.711581e-13 +1050 0 -18636.57280297759 -105676.48 -0.48638084 0.8314865 -7.1536527e-14 +1060 0 -18636.60771660457 -105569.62 -0.16511159 -0.030767882 5.0612552e-13 +1070 0 -18636.61229428169 -105559.38 0.021430043 0.030969805 6.5606374e-14 +1080 0 -18636.6131951782 -105561.67 -0.0062332338 -0.016535145 -1.4061989e-12 +1090 0 -18636.61336187003 -105564.55 -0.0033479828 -0.0098903018 -2.3661307e-12 +1100 0 -18636.61337988257 -105565.01 0.00082221778 -0.0023605315 -7.5842631e-12 +1110 0 -18636.61338086593 -105565.22 -0.00041685633 0.00079578125 -1.8850539e-11 +1120 0 -18636.61338113123 -105565.3 0.0005607417 -0.00034040033 -1.6063452e-10 +1130 0 -18636.61338119124 -105565.4 0.00025131709 1.3912646e-05 -2.1913269e-10 +1140 0 -18636.61338120433 -105565.47 -1.6069476e-05 -8.4841428e-06 -1.807068e-09 +1150 0 -18636.61338120511 -105565.48 -2.0354865e-05 -9.6508247e-06 -1.6113042e-09 +1160 0 -18636.6133812051 -105565.49 -8.4560077e-06 6.3269038e-07 -1.6308327e-10 +1170 0 -18636.61338120514 -105565.49 -2.6432899e-07 -1.3205451e-06 -1.4417877e-11 +1180 0 -18636.61338120505 -105565.49 -5.2221108e-07 6.0279457e-07 -6.2287736e-12 +1190 0 -18636.61338120524 -105565.49 1.2160526e-07 1.4909178e-06 -3.4658057e-11 +1200 0 -18636.61338120506 -105565.49 -2.610876e-07 -1.0438531e-07 -5.191389e-12 +1210 0 -18636.61338120499 -105565.49 -2.7802297e-08 -3.8082618e-08 -6.6586493e-14 +1220 0 -18636.61338120526 -105565.49 1.7558125e-08 -1.2699266e-08 2.385505e-14 +1230 0 -18636.61338120508 -105565.49 3.2094906e-10 -2.7796004e-09 1.0958595e-13 +1240 0 -18636.61338120509 -105565.49 3.6676946e-09 -7.792043e-10 1.1116975e-13 +1250 0 -18636.61338120498 -105565.49 1.3566517e-09 9.0741524e-10 3.6538654e-13 +1260 0 -18636.61338120516 -105565.49 1.7336501e-10 -5.0765115e-10 -3.5913113e-14 +1270 0 -18636.61338120517 -105565.49 -4.7390856e-11 -8.8615663e-11 -3.1520793e-14 +1280 0 -18636.61338120521 -105565.49 -6.1333239e-11 6.4489745e-11 -7.3884475e-14 +1290 0 -18636.61338120518 -105565.49 -2.2122047e-11 -7.9136919e-12 -9.8118562e-14 +1300 0 -18636.61338120521 -105565.49 1.081791e-11 1.3057743e-11 1.0332013e-14 +1305 0 -18636.61338120521 -105565.49 5.0637371e-12 8.1071121e-12 -3.3531337e-14 +Loop time of 6.73875 on 4 procs for 272 steps with 4800 atoms Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -18636.1101303 -18636.6133812 -18636.6133812 - Force two-norm initial, final = 1.27885 8.63114e-12 - Force max component initial, final = 0.192559 5.33628e-13 - Final line search alpha, max atom move = 1 5.33628e-13 + Force two-norm initial, final = 1.27885 8.7139e-12 + Force max component initial, final = 0.192559 3.94851e-13 + Final line search alpha, max atom move = 1 3.94851e-13 Iterations, force evaluations = 272 544 -Pair time (%) = 6.14393 (94.0961) +Pair time (%) = 2.0734 (30.7683) Neigh time (%) = 0 (0) -Comm time (%) = 0.106229 (1.62693) -Outpt time (%) = 0.00140095 (0.0214559) -Other time (%) = 0.277863 (4.25556) +Comm time (%) = 3.07345 (45.6086) +Outpt time (%) = 0.112664 (1.67188) +Other time (%) = 1.47924 (21.9513) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 144822 ave 144822 max 144822 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 289644 ave 289644 max 289644 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2856 ave 2856 max 2856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 36205.5 ave 36236 max 36183 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +FullNghs: 72411 ave 72411 max 72411 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289644 Ave neighs/atom = 60.3425 @@ -704,30 +708,27 @@ Dangerous builds = 0 # reset_timestep $i run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.45611 -Memory usage per processor = 9.52178 Mbytes -Step KinEng PotEng Press - 1305 0 -18636.613 -105565.49 -ATC::check_pair_map has found that pair map and bond table need to be recomputed - ATC:: computing bond matrix ..........done - 1306 0 -18636.613 -105565.49 -Loop time of 11.3451 on 1 procs for 1 steps with 4800 atoms + ATC: computing bond matrix ...........done +Memory usage per processor = 23.0387 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum +1305 0 -18636.61338120522 -105565.49 5.0642547e-12 8.1072881e-12 -3.333011e-14 +1306 0 -18636.61338120522 -105565.49 5.0642547e-12 8.1072881e-12 -3.333011e-14 +Loop time of 0.64154 on 4 procs for 1 steps with 4800 atoms -Pair time (%) = 0.012018 (0.105931) +Pair time (%) = 0.002563 (0.399507) Neigh time (%) = 0 (0) -Comm time (%) = 0.000200987 (0.00177157) -Outpt time (%) = 5.81741e-05 (0.000512768) -Other time (%) = 11.3328 (99.8918) +Comm time (%) = 0.0348787 (5.43672) +Outpt time (%) = 0.014325 (2.23291) +Other time (%) = 0.589773 (91.9309) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 145110 ave 145110 max 145110 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 290220 ave 290220 max 290220 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2856 ave 2856 max 2856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 36277.5 ave 36294 max 36263 min +Histogram: 1 0 1 0 0 1 0 0 0 1 +FullNghs: 72555 ave 72555 max 72555 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 290220 Ave neighs/atom = 60.4625 @@ -746,64 +747,65 @@ Changing box ... orthogonal box = (-40.8 -40.8 0) to (40.8 44.7168 12.24) minimize 0.0 ${tol} 100000 1000000 minimize 0.0 9.999999999999999395e-12 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 10.8951 Mbytes -Step KinEng PotEng Press - 1306 0 -18568.529 -122625.13 - 1310 0 -18568.749 -121901.81 - 1320 0 -18569.005 -120950.18 - 1330 0 -18569.073 -120727.11 - 1340 0 -18569.086 -120691.34 - 1350 0 -18569.087 -120692.66 - 1360 0 -18569.088 -120694.96 - 1370 0 -18569.088 -120695.45 - 1380 0 -18569.088 -120695.76 - 1390 0 -18569.088 -120695.97 - 1400 0 -18569.088 -120696.04 - 1410 0 -18569.088 -120696.15 - 1420 0 -18569.088 -120696.18 - 1430 0 -18569.088 -120696.19 - 1440 0 -18569.088 -120696.2 - 1450 0 -18569.088 -120696.2 - 1460 0 -18569.088 -120696.2 - 1470 0 -18569.088 -120696.2 - 1480 0 -18569.088 -120696.2 - 1490 0 -18569.088 -120696.2 - 1500 0 -18569.088 -120696.2 - 1510 0 -18569.088 -120696.2 - 1520 0 -18569.088 -120696.2 - 1530 0 -18569.088 -120696.2 - 1540 0 -18569.088 -120696.2 - 1550 0 -18569.088 -120696.2 - 1560 0 -18569.088 -120696.2 - 1570 0 -18569.088 -120696.2 - 1575 0 -18569.088 -120696.2 -Loop time of 6.3752 on 1 procs for 269 steps with 4800 atoms + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7254 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum +1306 0 -18568.52876784999 -122625.13 0.11327516 0.0031492485 -6.8263971e-14 +1310 0 -18568.74882073336 -121901.81 0.095186133 -0.0011416444 -8.7660781e-14 +1320 0 -18569.00454251567 -120950.18 -0.2410968 0.95855071 2.5853018e-13 +1330 0 -18569.07349706784 -120727.11 -0.24319965 -0.2912924 2.5074474e-13 +1340 0 -18569.08574491055 -120691.34 -0.012980899 0.14967506 -3.1190935e-13 +1350 0 -18569.08742093104 -120692.66 0.020268874 -0.022779739 -7.7562089e-14 +1360 0 -18569.08784344275 -120694.96 -0.017030722 -0.011207164 -1.9529864e-13 +1370 0 -18569.08790197284 -120695.45 -0.00055562662 -0.0042723235 -1.835242e-13 +1380 0 -18569.08790491389 -120695.76 -0.0010121555 0.00048878622 -5.4929325e-13 +1390 0 -18569.0879053711 -120695.97 0.00033781243 -0.00022074882 -1.9400809e-12 +1400 0 -18569.08790544242 -120696.04 0.00023923846 -0.00026303293 -7.7404767e-12 +1410 0 -18569.08790546677 -120696.15 0.00020998502 0.0001546831 -1.9456521e-11 +1420 0 -18569.08790547033 -120696.18 -1.9687675e-06 -1.5683061e-05 -2.6463075e-11 +1430 0 -18569.08790547062 -120696.19 -6.2370159e-06 1.6065939e-06 -5.4179854e-11 +1440 0 -18569.08790547075 -120696.2 -4.190645e-06 -4.6222325e-07 -6.4106238e-12 +1450 0 -18569.08790547073 -120696.2 5.0919634e-07 -1.0856681e-06 -8.6963423e-14 +1460 0 -18569.08790547067 -120696.2 -2.9904815e-07 9.091392e-08 6.2362268e-13 +1470 0 -18569.08790547063 -120696.2 2.0150636e-08 6.7285708e-07 2.618978e-12 +1480 0 -18569.08790547054 -120696.2 -3.083908e-07 -6.9259129e-08 3.8106879e-12 +1490 0 -18569.08790547073 -120696.2 2.6034682e-09 -1.2826672e-08 3.4164425e-13 +1500 0 -18569.08790547059 -120696.2 6.7729363e-10 -4.2930907e-09 9.8204431e-14 +1510 0 -18569.08790547062 -120696.2 -9.5846333e-10 -1.9455995e-09 4.7516678e-14 +1520 0 -18569.08790547062 -120696.2 1.5667016e-09 -6.459461e-11 -1.4132272e-13 +1530 0 -18569.08790547058 -120696.2 1.0396352e-09 1.4696064e-10 -3.2439329e-14 +1540 0 -18569.08790547059 -120696.2 -1.3541683e-12 -4.5800821e-10 3.0200668e-14 +1550 0 -18569.0879054705 -120696.2 -3.8374448e-11 -1.6138199e-11 -4.7493259e-14 +1560 0 -18569.08790547055 -120696.2 -3.19902e-11 9.1507895e-12 1.8244087e-14 +1570 0 -18569.08790547052 -120696.2 -1.7156297e-11 4.6740893e-12 3.5214887e-16 +1575 0 -18569.08790547054 -120696.2 -5.0504343e-12 -3.9081775e-13 6.7177167e-14 +Loop time of 9.25103 on 4 procs for 269 steps with 4800 atoms Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -18568.5287678 -18569.0879055 -18569.0879055 - Force two-norm initial, final = 1.27524 9.18981e-12 - Force max component initial, final = 0.191046 4.0907e-13 - Final line search alpha, max atom move = 1 4.0907e-13 + Force two-norm initial, final = 1.27524 9.29525e-12 + Force max component initial, final = 0.191046 5.2689e-13 + Final line search alpha, max atom move = 1 5.2689e-13 Iterations, force evaluations = 269 538 -Pair time (%) = 5.99356 (94.0136) +Pair time (%) = 1.47668 (15.9624) Neigh time (%) = 0 (0) -Comm time (%) = 0.105349 (1.65248) -Outpt time (%) = 0.00140333 (0.0220123) -Other time (%) = 0.274894 (4.31192) +Comm time (%) = 3.84872 (41.6032) +Outpt time (%) = 0.228203 (2.46679) +Other time (%) = 3.69742 (39.9677) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 144642 ave 144642 max 144642 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 289284 ave 289284 max 289284 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2856 ave 2856 max 2856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 36160.5 ave 36177 max 36150 min +Histogram: 1 1 0 0 1 0 0 0 0 1 +FullNghs: 72321 ave 72321 max 72321 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289284 Ave neighs/atom = 60.2675 @@ -812,30 +814,27 @@ Dangerous builds = 0 # reset_timestep $i run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.45611 -Memory usage per processor = 9.52178 Mbytes -Step KinEng PotEng Press - 1575 0 -18569.088 -120696.2 -ATC::check_pair_map has found that pair map and bond table need to be recomputed - ATC:: computing bond matrix ...........done - 1576 0 -18569.088 -120696.2 -Loop time of 11.3507 on 1 procs for 1 steps with 4800 atoms + ATC: computing bond matrix ...........done +Memory usage per processor = 23.0387 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum +1575 0 -18569.08790547054 -120696.2 -5.0503339e-12 -3.9139805e-13 6.7683706e-14 +1576 0 -18569.08790547054 -120696.2 -5.0503339e-12 -3.9139805e-13 6.7683706e-14 +Loop time of 0.539415 on 4 procs for 1 steps with 4800 atoms -Pair time (%) = 0.011955 (0.105324) +Pair time (%) = 0.00513172 (0.951349) Neigh time (%) = 0 (0) -Comm time (%) = 0.000200987 (0.0017707) -Outpt time (%) = 5.91278e-05 (0.000520918) -Other time (%) = 11.3385 (99.8924) +Comm time (%) = 0.0307288 (5.69668) +Outpt time (%) = 0.0395864 (7.33877) +Other time (%) = 0.463968 (86.0132) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 144702 ave 144702 max 144702 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 289404 ave 289404 max 289404 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2856 ave 2856 max 2856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 36175.5 ave 36206 max 36147 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +FullNghs: 72351 ave 72351 max 72351 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289404 Ave neighs/atom = 60.2925 @@ -854,66 +853,67 @@ Changing box ... orthogonal box = (-40.8 -40.8 0) to (40.8 45.3696 12.24) minimize 0.0 ${tol} 100000 1000000 minimize 0.0 9.999999999999999395e-12 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 10.8951 Mbytes -Step KinEng PotEng Press - 1576 0 -18491.902 -136205.45 - 1580 0 -18492.131 -135456.73 - 1590 0 -18492.431 -134349.55 - 1600 0 -18492.527 -134029.75 - 1610 0 -18492.545 -133963.95 - 1620 0 -18492.547 -133959.78 - 1630 0 -18492.548 -133962.99 - 1640 0 -18492.548 -133964.99 - 1650 0 -18492.548 -133965.77 - 1660 0 -18492.548 -133966.51 - 1670 0 -18492.548 -133966.85 - 1680 0 -18492.548 -133967.17 - 1690 0 -18492.548 -133967.22 - 1700 0 -18492.548 -133967.22 - 1710 0 -18492.548 -133967.22 - 1720 0 -18492.548 -133967.22 - 1730 0 -18492.548 -133967.22 - 1740 0 -18492.548 -133967.22 - 1750 0 -18492.548 -133967.22 - 1760 0 -18492.548 -133967.22 - 1770 0 -18492.548 -133967.22 - 1780 0 -18492.548 -133967.22 - 1790 0 -18492.548 -133967.22 - 1800 0 -18492.548 -133967.22 - 1810 0 -18492.548 -133967.22 - 1820 0 -18492.548 -133967.22 - 1830 0 -18492.548 -133967.22 - 1840 0 -18492.548 -133967.22 - 1850 0 -18492.548 -133967.22 - 1860 0 -18492.548 -133967.22 - 1867 0 -18492.548 -133967.22 -Loop time of 6.90634 on 1 procs for 291 steps with 4800 atoms + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7254 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum +1576 0 -18491.90169921529 -136205.45 0.14307644 0.0051325969 1.0172852e-13 +1580 0 -18492.1310576982 -135456.73 0.12095202 0.0011746767 1.4052995e-13 +1590 0 -18492.43123925865 -134349.55 -0.24024543 0.9903784 -1.7584198e-13 +1600 0 -18492.52677637159 -134029.75 -0.27750893 -0.14147964 -8.1081843e-14 +1610 0 -18492.54487664072 -133963.95 -0.026440274 0.078470791 1.7319913e-13 +1620 0 -18492.54726511076 -133959.78 0.033197488 -0.011966987 1.1562539e-13 +1630 0 -18492.54782232645 -133962.99 -0.022229907 -0.0082739991 1.1270845e-13 +1640 0 -18492.54790581508 -133964.99 0.0004273738 -0.0098225601 1.9093147e-13 +1650 0 -18492.54791271241 -133965.77 -0.00039139543 0.0001276143 8.4582688e-13 +1660 0 -18492.5479137973 -133966.51 0.00060980725 -0.0001052093 1.9350329e-12 +1670 0 -18492.54791403718 -133966.85 0.00023817137 -0.00052460153 2.0599427e-11 +1680 0 -18492.54791412406 -133967.17 0.00012036401 0.00016590705 3.1029334e-11 +1690 0 -18492.54791413136 -133967.22 4.3077888e-05 3.7995289e-05 2.1927101e-10 +1700 0 -18492.54791413183 -133967.22 -2.1812294e-05 -2.2334739e-06 5.7539537e-11 +1710 0 -18492.54791413153 -133967.22 -6.6937911e-07 2.7960399e-06 1.9197604e-12 +1720 0 -18492.5479141317 -133967.22 2.699247e-06 2.5072053e-07 2.4410942e-13 +1730 0 -18492.54791413172 -133967.22 5.4986594e-07 -2.6582947e-07 -8.9572447e-15 +1740 0 -18492.54791413186 -133967.22 -3.0716408e-07 1.3843207e-06 4.2735693e-13 +1750 0 -18492.54791413182 -133967.22 -2.7601617e-07 -9.7796011e-09 2.7825147e-12 +1760 0 -18492.54791413178 -133967.22 -7.9591846e-08 -1.0148109e-07 8.6370928e-13 +1770 0 -18492.54791413184 -133967.22 1.8878696e-08 -9.8577802e-09 3.5801223e-14 +1780 0 -18492.54791413205 -133967.22 -6.1481142e-09 -4.2156327e-09 2.3894775e-13 +1790 0 -18492.54791413176 -133967.22 -6.7764872e-10 2.9868985e-10 3.3884354e-14 +1800 0 -18492.54791413182 -133967.22 1.4509676e-09 1.2334929e-09 -5.65702e-14 +1810 0 -18492.5479141318 -133967.22 8.4658451e-10 -1.3259555e-10 -2.8058285e-14 +1820 0 -18492.5479141317 -133967.22 -1.0651127e-10 -8.8667524e-11 6.1565336e-15 +1830 0 -18492.54791413185 -133967.22 -4.1737809e-11 8.9127831e-11 -1.167573e-13 +1840 0 -18492.54791413181 -133967.22 -5.2870488e-11 1.9493503e-11 -4.1844132e-14 +1850 0 -18492.54791413184 -133967.22 -5.6782406e-12 1.2649759e-13 -1.0939426e-13 +1860 0 -18492.54791413187 -133967.22 -1.9471408e-12 3.263459e-12 1.1285244e-14 +1867 0 -18492.54791413186 -133967.22 6.9845188e-13 6.5521008e-12 -1.1701317e-13 +Loop time of 9.30006 on 4 procs for 291 steps with 4800 atoms Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -18491.9016992 -18492.5479141 -18492.5479141 - Force two-norm initial, final = 1.27584 9.84184e-12 - Force max component initial, final = 0.189643 4.49668e-13 - Final line search alpha, max atom move = 1 4.49668e-13 + Force two-norm initial, final = 1.27584 9.73889e-12 + Force max component initial, final = 0.189643 4.5029e-13 + Final line search alpha, max atom move = 1 4.5029e-13 Iterations, force evaluations = 291 582 -Pair time (%) = 6.49384 (94.0273) +Pair time (%) = 1.95602 (21.0323) Neigh time (%) = 0 (0) -Comm time (%) = 0.11403 (1.65109) -Outpt time (%) = 0.00149918 (0.0217072) -Other time (%) = 0.296967 (4.29992) +Comm time (%) = 4.05937 (43.6488) +Outpt time (%) = 0.0457499 (0.491931) +Other time (%) = 3.23893 (34.8269) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 144318 ave 144318 max 144318 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 288636 ave 288636 max 288636 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2856 ave 2856 max 2856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 36079.5 ave 36110 max 36044 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +FullNghs: 72159 ave 72159 max 72159 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288636 Ave neighs/atom = 60.1325 @@ -922,30 +922,27 @@ Dangerous builds = 0 # reset_timestep $i run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.45611 -Memory usage per processor = 9.52178 Mbytes -Step KinEng PotEng Press - 1867 0 -18492.548 -133967.22 -ATC::check_pair_map has found that pair map and bond table need to be recomputed - ATC:: computing bond matrix ...........done - 1868 0 -18492.548 -133967.22 -Loop time of 11.3592 on 1 procs for 1 steps with 4800 atoms + ATC: computing bond matrix ...........done +Memory usage per processor = 23.0387 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum +1867 0 -18492.54791413186 -133967.22 6.9777732e-13 6.551863e-12 -1.1686745e-13 +1868 0 -18492.54791413186 -133967.22 6.9777732e-13 6.551863e-12 -1.1686745e-13 +Loop time of 0.296894 on 4 procs for 1 steps with 4800 atoms -Pair time (%) = 0.01196 (0.10529) +Pair time (%) = 0.00758874 (2.55605) Neigh time (%) = 0 (0) -Comm time (%) = 0.000200987 (0.00176938) -Outpt time (%) = 5.79357e-05 (0.000510035) -Other time (%) = 11.3469 (99.8924) +Comm time (%) = 0.00534135 (1.79908) +Outpt time (%) = 0.00306052 (1.03085) +Other time (%) = 0.280903 (94.614) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 144378 ave 144378 max 144378 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 288756 ave 288756 max 288756 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2856 ave 2856 max 2856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 36094.5 ave 36117 max 36051 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +FullNghs: 72189 ave 72189 max 72189 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288756 Ave neighs/atom = 60.1575 @@ -964,123 +961,124 @@ Changing box ... orthogonal box = (-40.8 -40.8 0) to (40.8 46.0224 12.24) minimize 0.0 ${tol} 100000 1000000 minimize 0.0 9.999999999999999395e-12 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 10.8951 Mbytes -Step KinEng PotEng Press - 1868 0 -18407.238 -148059.35 - 1870 0 -18407.358 -147753.08 - 1880 0 -18407.836 -145851.12 - 1890 0 -18408.202 -144020.77 - 1900 0 -18408.593 -141218.96 - 1910 0 -18409.477 -134179.79 - 1920 0 -18413.661 -125476.69 - 1930 0 -18416.454 -120852.21 - 1940 0 -18421.54 -112486.78 - 1950 0 -18427.383 -104240.11 - 1960 0 -18435.072 -93444.302 - 1970 0 -18441.731 -83874.071 - 1980 0 -18449.283 -71174.26 - 1990 0 -18456.102 -63370.417 - 2000 0 -18464.965 -54276.273 - 2010 0 -18480.843 -45585.245 - 2020 0 -18499.97 -40168.543 - 2030 0 -18524.078 -27767.284 - 2040 0 -18537.082 -17260.136 - 2050 0 -18543.454 -8525.7544 - 2060 0 -18544.263 -4763.9914 - 2070 0 -18544.518 -2931.8791 - 2080 0 -18544.564 -2064.91 - 2090 0 -18544.581 -1446.8095 - 2100 0 -18544.584 -1255.1845 - 2110 0 -18544.585 -1134.1523 - 2120 0 -18544.585 -1063.9481 - 2130 0 -18544.585 -1036.832 - 2140 0 -18544.585 -1027.9973 - 2150 0 -18544.585 -1020.1185 - 2160 0 -18544.585 -1018.1787 - 2170 0 -18544.585 -1016.96 - 2180 0 -18544.585 -1016.5672 - 2190 0 -18544.585 -1016.2308 - 2200 0 -18544.585 -1016.1502 - 2210 0 -18544.585 -1016.092 - 2220 0 -18544.585 -1016.0547 - 2230 0 -18544.585 -1016.0418 - 2240 0 -18544.585 -1016.0334 - 2250 0 -18544.585 -1016.0286 - 2260 0 -18544.585 -1016.0263 - 2270 0 -18544.585 -1016.0256 - 2280 0 -18544.585 -1016.025 - 2290 0 -18544.585 -1016.0248 - 2300 0 -18544.585 -1016.0247 - 2310 0 -18544.585 -1016.0246 - 2320 0 -18544.585 -1016.0246 - 2330 0 -18544.585 -1016.0246 - 2340 0 -18544.585 -1016.0246 - 2350 0 -18544.585 -1016.0246 - 2360 0 -18544.585 -1016.0246 - 2370 0 -18544.585 -1016.0246 - 2380 0 -18544.585 -1016.0246 - 2390 0 -18544.585 -1016.0246 - 2400 0 -18544.585 -1016.0246 - 2410 0 -18544.585 -1016.0246 - 2413 0 -18544.585 -1016.0246 -Loop time of 13.5093 on 1 procs for 545 steps with 4800 atoms + ATC: computing bond matrix ...........done +Memory usage per processor = 23.7254 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum +1868 0 -18407.23836455257 -148059.35 0.17824806 0.0077631243 -1.6145679e-13 +1870 0 -18407.35825930425 -147753.08 0.17162524 0.0068226839 5.1991397e-14 +1880 0 -18407.83559382475 -145851.12 -0.021096249 -0.13180348 2.8685387e-13 +1890 0 -18408.2015011047 -144020.77 -0.64909152 1.2116413 1.6853186e-13 +1900 0 -18408.59292951682 -141218.96 -0.08302438 -0.47582143 -1.4403756e-13 +1910 0 -18409.4765396664 -134179.79 0.81588279 0.52187663 -1.4081618e-14 +1920 0 -18413.66102681115 -125476.69 -0.75246577 0.63898014 2.3906745e-13 +1930 0 -18416.45369771184 -120852.21 0.62028044 -0.10465531 9.6651246e-13 +1940 0 -18421.53975460122 -112486.78 -0.65003602 1.5468217 9.6126319e-13 +1950 0 -18427.38266756838 -104240.11 -0.84329602 1.5646833 1.841461e-12 +1960 0 -18435.07175167299 -93444.303 -0.37984669 2.2664338 3.4765593e-14 +1970 0 -18441.73057718596 -83874.061 0.058480218 1.3986995 1.3299761e-12 +1980 0 -18449.28291594671 -71174.024 0.063935535 1.163249 -1.3587948e-13 +1990 0 -18456.10248218176 -63369.916 1.0177229 0.74671187 -1.6969395e-12 +2000 0 -18464.9998740891 -54232.856 0.75646448 -0.26067276 -6.1633641e-12 +2010 0 -18480.88491289675 -45481.647 0.78433604 2.2535262 1.5989705e-12 +2020 0 -18500.1431770592 -40030.074 1.0452221 0.88528823 1.7144593e-12 +2030 0 -18521.50155145743 -30200.138 2.2932883 2.6095268 4.6325582e-12 +2040 0 -18537.85209559528 -16777.734 3.3443628 0.21170446 -1.5426219e-12 +2050 0 -18542.89363908397 -9535.43 0.21119377 -0.23199164 -2.3318361e-12 +2060 0 -18544.16187127086 -5630.8493 0.27761823 0.17400597 1.1770047e-12 +2070 0 -18544.47853257111 -3453.3272 0.0052400191 0.56277282 -5.3569822e-13 +2080 0 -18544.55460189864 -2361.9773 -0.034319823 0.11396983 8.0015682e-13 +2090 0 -18544.57775090135 -1652.5596 0.063904673 0.020843455 6.1015602e-13 +2100 0 -18544.58333280036 -1325.0949 0.0088898695 0.05436218 -3.1974944e-13 +2110 0 -18544.58449704061 -1189.9357 -0.0081196536 0.023093202 1.3144347e-13 +2120 0 -18544.58489130795 -1090.6528 -0.013334939 -0.00083308441 7.5689455e-14 +2130 0 -18544.58499173266 -1051.4974 -0.007217772 0.0061402811 -3.8091058e-14 +2140 0 -18544.58501317528 -1033.4783 0.00055171322 0.0007881195 -4.2004594e-14 +2150 0 -18544.58501921195 -1024.1479 0.00064646979 0.0012980319 3.2533004e-14 +2160 0 -18544.58502058311 -1019.8368 -0.00090273924 0.00044863611 -1.0888686e-13 +2170 0 -18544.58502098134 -1017.7954 -0.00056580161 0.0005662624 -6.8519843e-14 +2180 0 -18544.58502106684 -1016.9371 -0.00015623361 3.9990029e-05 1.5700288e-13 +2190 0 -18544.58502108469 -1016.4696 -2.0813878e-05 8.8730455e-05 1.7381756e-13 +2200 0 -18544.5850210904 -1016.2354 8.6129055e-06 -1.7118006e-05 -4.039824e-14 +2210 0 -18544.58502109143 -1016.1477 -4.8479759e-06 8.8410543e-06 4.5199955e-14 +2220 0 -18544.58502109175 -1016.0882 -1.5290276e-05 1.2769498e-05 1.7888468e-14 +2230 0 -18544.58502109184 -1016.0561 -3.3543653e-06 5.4823802e-06 8.233865e-14 +2240 0 -18544.58502109185 -1016.0425 -3.2853651e-07 1.3036026e-06 1.2482376e-13 +2250 0 -18544.58502109189 -1016.0335 4.7657222e-07 6.1102889e-07 -7.725591e-14 +2260 0 -18544.58502109182 -1016.0292 -2.5962662e-07 2.1173209e-07 -3.1006447e-14 +2270 0 -18544.58502109182 -1016.0269 -2.5168543e-07 2.1347313e-07 -2.4950528e-14 +2280 0 -18544.58502109193 -1016.0257 6.8141159e-08 3.3618215e-08 5.1035565e-14 +2290 0 -18544.58502109191 -1016.0252 1.8988043e-08 6.7251267e-08 -1.104429e-13 +2300 0 -18544.58502109201 -1016.0248 6.4237605e-08 1.3866362e-10 -1.1696547e-13 +2310 0 -18544.58502109178 -1016.0247 1.3031489e-08 5.416356e-09 -9.1763402e-14 +2320 0 -18544.58502109178 -1016.0246 -2.0349924e-10 1.2570585e-08 -1.196352e-13 +2330 0 -18544.58502109163 -1016.0246 5.7314652e-10 -1.9545557e-09 -1.7981623e-13 +2340 0 -18544.58502109184 -1016.0246 2.8219654e-09 4.0619579e-10 -2.5039346e-13 +2350 0 -18544.58502109179 -1016.0246 1.2039679e-09 3.8910008e-10 1.2338047e-13 +2360 0 -18544.58502109167 -1016.0246 4.8857533e-10 8.2124555e-12 -1.3082417e-13 +2370 0 -18544.58502109163 -1016.0246 5.7344183e-11 1.4028061e-11 -7.1036926e-15 +2380 0 -18544.58502109162 -1016.0246 6.9331788e-11 1.5899597e-10 1.4037903e-13 +2390 0 -18544.58502109099 -1016.0246 1.7919444e-11 3.2794189e-12 1.1836018e-13 +2400 0 -18544.58502109086 -1016.0246 4.7017882e-11 2.5658087e-12 -1.9249706e-13 +2410 0 -18544.58502109079 -1016.0246 9.0523535e-12 -5.1709692e-12 -8.4116741e-14 +2420 0 -18544.58502109054 -1016.0246 2.8651381e-12 8.1466436e-12 1.5645645e-13 +2430 0 -18544.58502109047 -1016.0246 9.2212618e-13 -1.7898741e-13 9.6594607e-14 +2432 0 -18544.58502109047 -1016.0246 -2.5384753e-13 1.381581e-12 7.1834899e-15 +Loop time of 5.84244 on 4 procs for 564 steps with 4800 atoms Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -18407.2383646 -18544.5850211 -18544.5850211 - Force two-norm initial, final = 1.27905 9.903e-12 - Force max component initial, final = 0.188373 5.21611e-13 - Final line search alpha, max atom move = 1 5.21611e-13 - Iterations, force evaluations = 545 1041 + Force two-norm initial, final = 1.27905 9.63484e-12 + Force max component initial, final = 0.188373 4.51583e-13 + Final line search alpha, max atom move = 1 4.51583e-13 + Iterations, force evaluations = 564 1082 -Pair time (%) = 11.7872 (87.2523) -Neigh time (%) = 0.958884 (7.09795) -Comm time (%) = 0.210124 (1.5554) -Outpt time (%) = 0.00291777 (0.0215982) -Other time (%) = 0.550201 (4.07275) +Pair time (%) = 2.87584 (49.2232) +Neigh time (%) = 0.265235 (4.53979) +Comm time (%) = 1.7622 (30.162) +Outpt time (%) = 0.027319 (0.467596) +Other time (%) = 0.911857 (15.6075) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 155220 ave 155220 max 155220 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 310440 ave 310440 max 310440 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2700 ave 2700 max 2700 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 38596.5 ave 38637 max 38540 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +FullNghs: 77193 ave 77193 max 77193 min +Histogram: 4 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 310440 -Ave neighs/atom = 64.675 +Total # of neighbors = 308772 +Ave neighs/atom = 64.3275 Neighbor list builds = 19 Dangerous builds = 0 # reset_timestep $i run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.45611 -Memory usage per processor = 9.90326 Mbytes -Step KinEng PotEng Press - 2413 0 -18544.585 -1016.0246 - ATC:: computing bond matrix ..........done - 2414 0 -18544.585 -1016.0246 -Loop time of 14.2344 on 1 procs for 1 steps with 4800 atoms + ATC: computing bond matrix ..........done +Memory usage per processor = 23.0387 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum +2432 0 -18544.58502109047 -1016.0246 -2.5329791e-13 1.381277e-12 7.3534928e-15 +2433 0 -18544.58502109047 -1016.0246 -2.5329791e-13 1.381277e-12 7.3534928e-15 +Loop time of 0.1929 on 4 procs for 1 steps with 4800 atoms -Pair time (%) = 0.012403 (0.087134) +Pair time (%) = 0.0026933 (1.39621) Neigh time (%) = 0 (0) -Comm time (%) = 0.000200033 (0.00140528) -Outpt time (%) = 5.60284e-05 (0.000393612) -Other time (%) = 14.2217 (99.9111) +Comm time (%) = 0.000305772 (0.158513) +Outpt time (%) = 0.00638688 (3.31097) +Other time (%) = 0.183514 (95.1343) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 179760 ave 179760 max 179760 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 359520 ave 359520 max 359520 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2700 ave 2700 max 2700 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 44940 ave 45026 max 44838 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +FullNghs: 89880 ave 89880 max 89880 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 359520 Ave neighs/atom = 74.9 @@ -1099,51 +1097,52 @@ Changing box ... orthogonal box = (-40.8 -40.8 0) to (40.8 46.6752 12.24) minimize 0.0 ${tol} 100000 1000000 minimize 0.0 9.999999999999999395e-12 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 11.2776 Mbytes -Step KinEng PotEng Press - 2414 0 -18537.769 -24298.948 - 2420 0 -18539.681 -17588.839 - 2430 0 -18542.788 -6765.5295 - 2440 0 -18544.584 -979.67322 - 2450 0 -18544.585 -939.15405 - 2460 0 -18544.585 -995.52306 - 2470 0 -18544.585 -1008.3857 - 2480 0 -18544.585 -1008.5135 - 2490 0 -18544.585 -1008.4454 - 2500 0 -18544.585 -1008.4422 - 2510 0 -18544.585 -1008.4422 - 2520 0 -18544.585 -1008.4423 - 2530 0 -18544.585 -1008.4423 - 2540 0 -18544.585 -1008.4423 - 2550 0 -18544.585 -1008.4423 - 2556 0 -18544.585 -1008.4423 -Loop time of 3.4201 on 1 procs for 142 steps with 4800 atoms + ATC: computing bond matrix ..........done +Memory usage per processor = 23.7261 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum +2433 0 -18537.76901415941 -24298.948 3.8747523e-13 5.2831402e-12 -6.6347969e-14 +2440 0 -18540.01318499379 -16519.475 -3.2208582e-12 -2.7180729e-05 -4.0105939e-13 +2450 0 -18543.0953686088 -5752.9757 8.4202206e-12 7.0443093 7.1120193e-14 +2460 0 -18544.58421511342 -984.24581 4.48884e-13 0.11138675 -7.4289533e-14 +2470 0 -18544.58494424724 -937.76995 -1.4907155e-12 -0.029415925 -1.4615392e-13 +2480 0 -18544.58501777505 -1005.2306 -2.5313443e-12 -0.0028072577 4.4010802e-13 +2490 0 -18544.58502108903 -1008.4303 -1.2945912e-12 0.00023653818 1.8944256e-12 +2500 0 -18544.58502109101 -1008.5152 3.1169104e-13 1.8192203e-05 -3.9932814e-13 +2510 0 -18544.58502109143 -1008.4451 -1.4675192e-12 -2.074999e-06 -1.7850652e-13 +2520 0 -18544.58502109134 -1008.4422 3.9145238e-13 -1.3068582e-07 6.0760945e-13 +2530 0 -18544.58502109258 -1008.4422 6.2648817e-12 -5.3016e-10 4.406718e-14 +2540 0 -18544.58502109214 -1008.4423 -1.8432447e-11 2.1091244e-09 2.1755358e-12 +2550 0 -18544.58502109095 -1008.4423 -1.588503e-13 3.5010943e-11 1.1601831e-14 +2560 0 -18544.58502109056 -1008.4423 1.7819469e-13 1.3868038e-11 6.517703e-14 +2570 0 -18544.58502109044 -1008.4423 1.4870776e-12 -1.2270293e-11 9.0609811e-14 +2575 0 -18544.58502109047 -1008.4423 -2.3857825e-13 1.0195675e-11 6.0073474e-15 +Loop time of 0.756386 on 4 procs for 142 steps with 4800 atoms Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -18537.7690142 -18544.5850211 -18544.5850211 - Force two-norm initial, final = 2.90351 8.54501e-12 - Force max component initial, final = 0.18742 4.67085e-13 - Final line search alpha, max atom move = 1 4.67085e-13 + Force two-norm initial, final = 2.90351 8.35114e-12 + Force max component initial, final = 0.18742 4.36984e-13 + Final line search alpha, max atom move = 1 4.36984e-13 Iterations, force evaluations = 142 284 -Pair time (%) = 3.2194 (94.1317) +Pair time (%) = 0.661463 (87.4504) Neigh time (%) = 0 (0) -Comm time (%) = 0.0554338 (1.62082) -Outpt time (%) = 0.000701666 (0.0205159) -Other time (%) = 0.144568 (4.227) +Comm time (%) = 0.066303 (8.76576) +Outpt time (%) = 0.00166374 (0.21996) +Other time (%) = 0.0269565 (3.56385) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 162000 ave 162000 max 162000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 324000 ave 324000 max 324000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2700 ave 2700 max 2700 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 40500 ave 40568 max 40427 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +FullNghs: 81000 ave 81000 max 81000 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 324000 Ave neighs/atom = 67.5 @@ -1152,29 +1151,27 @@ Dangerous builds = 0 # reset_timestep $i run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.45611 -Memory usage per processor = 9.90432 Mbytes -Step KinEng PotEng Press - 2556 0 -18544.585 -1008.4423 - ATC:: computing bond matrix ..........done - 2557 0 -18544.585 -1008.4423 -Loop time of 14.152 on 1 procs for 1 steps with 4800 atoms + ATC: computing bond matrix ..........done +Memory usage per processor = 23.0394 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum +2575 0 -18544.58502109042 -1008.4423 -2.3877189e-13 1.0195595e-11 6.0385724e-15 +2576 0 -18544.58502109042 -1008.4423 -2.3877189e-13 1.0195595e-11 6.0385724e-15 +Loop time of 0.201727 on 4 procs for 1 steps with 4800 atoms -Pair time (%) = 0.0124421 (0.087918) +Pair time (%) = 0.00267446 (1.32578) Neigh time (%) = 0 (0) -Comm time (%) = 0.000203848 (0.00144042) -Outpt time (%) = 5.6982e-05 (0.000402644) -Other time (%) = 14.1393 (99.9102) +Comm time (%) = 0.000333369 (0.165258) +Outpt time (%) = 0.00615078 (3.04907) +Other time (%) = 0.192568 (95.4599) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 179760 ave 179760 max 179760 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 359520 ave 359520 max 359520 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2700 ave 2700 max 2700 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 44940 ave 45033 max 44832 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +FullNghs: 89880 ave 89880 max 89880 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 359520 Ave neighs/atom = 74.9 @@ -1193,50 +1190,50 @@ Changing box ... orthogonal box = (-40.8 -40.8 0) to (40.8 47.328 12.24) minimize 0.0 ${tol} 100000 1000000 minimize 0.0 9.999999999999999395e-12 100000 1000000 -WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173) Setting up minimization ... -Memory usage per processor = 11.2776 Mbytes -Step KinEng PotEng Press - 2557 0 -18537.869 -23952.428 - 2560 0 -18538.805 -21218.074 - 2570 0 -18541.911 -9564.4516 - 2580 0 -18544.567 -914.96139 - 2590 0 -18544.585 -942.89805 - 2600 0 -18544.585 -940.14174 - 2610 0 -18544.585 -1000.7428 - 2620 0 -18544.585 -1001.0309 - 2630 0 -18544.585 -1000.9981 - 2640 0 -18544.585 -1000.9727 - 2650 0 -18544.585 -1000.9723 - 2660 0 -18544.585 -1000.9723 - 2670 0 -18544.585 -1000.9724 - 2680 0 -18544.585 -1000.9724 - 2681 0 -18544.585 -1000.9724 -Loop time of 2.99289 on 1 procs for 124 steps with 4800 atoms + ATC: computing bond matrix ..........done +Memory usage per processor = 23.7261 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum +2576 0 -18537.86919514 -23952.428 -6.3755067e-13 1.8610839e-11 -6.2221062e-14 +2580 0 -18539.14079053524 -19773.613 -6.9875621e-12 -2.1231065e-12 -7.5061485e-15 +2590 0 -18542.20234735839 -8563.5634 3.3833963e-12 5.0447263 -9.290832e-14 +2600 0 -18544.58003335739 -936.09475 -3.8256923e-12 0.15421118 -2.7653921e-13 +2610 0 -18544.58488125377 -936.26337 -4.1992287e-13 -0.061485489 -9.5439281e-14 +2620 0 -18544.58498734563 -969.47152 -2.7277214e-11 -0.0023912698 -1.5980862e-12 +2630 0 -18544.5850210808 -1000.7463 3.2661308e-13 0.0004509302 -9.8292902e-14 +2640 0 -18544.58502109149 -1001.032 -7.2744767e-13 -1.2247845e-05 -1.2311333e-14 +2650 0 -18544.58502109259 -1000.9825 2.2260383e-12 1.1703007e-05 6.7454722e-13 +2660 0 -18544.58502109259 -1000.9724 -5.3904045e-12 9.5787661e-08 1.8519162e-12 +2670 0 -18544.58502109156 -1000.9723 -1.0012351e-12 -1.132507e-08 -4.9276555e-14 +2680 0 -18544.58502109152 -1000.9723 -4.3052271e-13 9.7475523e-09 -5.7240497e-13 +2690 0 -18544.58502109055 -1000.9724 3.8952735e-14 2.8103179e-10 1.3394841e-12 +2700 0 -18544.58502109041 -1000.9724 3.6211563e-13 6.3288004e-12 3.3577308e-14 +Loop time of 0.771028 on 4 procs for 124 steps with 4800 atoms Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -18537.8691951 -18544.5850211 -18544.5850211 - Force two-norm initial, final = 2.8826 9.40264e-12 - Force max component initial, final = 0.18607 3.77032e-13 - Final line search alpha, max atom move = 1 3.77032e-13 + Force two-norm initial, final = 2.8826 9.42071e-12 + Force max component initial, final = 0.18607 4.28359e-13 + Final line search alpha, max atom move = 1 4.28359e-13 Iterations, force evaluations = 124 248 -Pair time (%) = 2.81757 (94.142) +Pair time (%) = 0.602882 (78.192) Neigh time (%) = 0 (0) -Comm time (%) = 0.0484951 (1.62034) -Outpt time (%) = 0.000660896 (0.0220822) -Other time (%) = 0.126166 (4.21554) +Comm time (%) = 0.13337 (17.2977) +Outpt time (%) = 0.00144494 (0.187404) +Other time (%) = 0.0333309 (4.32291) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 162000 ave 162000 max 162000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 324000 ave 324000 max 324000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2700 ave 2700 max 2700 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 40500 ave 40577 max 40425 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 81000 ave 81000 max 81000 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 324000 Ave neighs/atom = 67.5 @@ -1245,29 +1242,27 @@ Dangerous builds = 0 # reset_timestep $i run 1 Setting up run ... - ATC:: conversion factor for energy/vol -> stress 1.60218e+06 - ATC:: cutoff radius 5.45611 -Memory usage per processor = 9.90432 Mbytes -Step KinEng PotEng Press - 2681 0 -18544.585 -1000.9724 - ATC:: computing bond matrix ..........done - 2682 0 -18544.585 -1000.9724 -Loop time of 14.1548 on 1 procs for 1 steps with 4800 atoms + ATC: computing bond matrix ..........done +Memory usage per processor = 23.0394 Mbytes +Step KinEng PotEng Press fxsum fysum fzsum +2700 0 -18544.5850210904 -1000.9724 3.6220691e-13 6.3290068e-12 3.3001379e-14 +2701 0 -18544.5850210904 -1000.9724 3.6220691e-13 6.3290068e-12 3.3001379e-14 +Loop time of 0.844953 on 4 procs for 1 steps with 4800 atoms -Pair time (%) = 0.012419 (0.0877368) +Pair time (%) = 0.00514245 (0.608608) Neigh time (%) = 0 (0) -Comm time (%) = 0.000208139 (0.00147045) -Outpt time (%) = 5.72205e-05 (0.000404247) -Other time (%) = 14.1421 (99.9104) +Comm time (%) = 0.114826 (13.5896) +Outpt time (%) = 0.0676661 (8.00826) +Other time (%) = 0.657319 (77.7935) -Nlocal: 4800 ave 4800 max 4800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7896 ave 7896 max 7896 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 179760 ave 179760 max 179760 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 359520 ave 359520 max 359520 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2700 ave 2700 max 2700 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 44940 ave 45075 max 44784 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +FullNghs: 89880 ave 89880 max 89880 min +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 359520 Ave neighs/atom = 74.9 diff --git a/examples/USER/atc/hardy/in.consistency b/examples/USER/atc/hardy/in.consistency index ef115471f5..75ceeef286 100644 --- a/examples/USER/atc/hardy/in.consistency +++ b/examples/USER/atc/hardy/in.consistency @@ -1,56 +1,45 @@ +# This test compares the thermodynamic consistency of the stress, displacement_gradient +# and internal energy density as calculated with the Hardy/field method. +# # we should see: # * H = Grad u exact except at the free boundaries where we get u at CM != node # * \Delta W / \Delta F = P converging with smaller load step / dt # since W and P are consistent via the balance laws thanks to Hard echo both -log consistency.log - units metal atom_style atomic -atom_modify sort 0 1 variable L equal 16 variable E equal 8 - # create domain lattice fcc 3.615 origin 0.25 0.25 0.25 region mdRegion block 0 $L -3 3 -3 3 boundary p p p create_box 1 mdRegion - # create atoms create_atoms 1 region mdRegion mass 1 63.550 - group internal region mdRegion - # specify inter-atomic potential pair_style eam pair_coeff * * ../../../../potentials/Cu_u3.eam - # specify neighbor/re-neighboring parameters neighbor 0.3 bin #neigh_modify every 10 delay 0 check no neigh_modify delay 10000 check no - min_modify line quadratic minimize 1.e-10 1.e-10 100000 1000000 - # ID group atc PhysicsType ParameterFile -fix AtC all atc hardy -fix_modify AtC transfer internal type internal -fix_modify AtC fem create mesh $E 1 1 mdRegion f p p -fix_modify AtC transfer fields none -fix_modify AtC transfer fields add density displacement stress energy eshelby_stress temperature -fix_modify AtC transfer gradients add displacement -fix_modify AtC transfer set reference_potential_energy -#fix_modify AtC transfer hardy_reset 1 - +fix AtC internal atc field +fix_modify AtC mesh create $E 1 1 mdRegion f p p +fix_modify AtC fields none +fix_modify AtC fields add mass_density displacement stress internal_energy eshelby_stress temperature +fix_modify AtC gradients add displacement +fix_modify AtC set reference_potential_energy +#fix_modify AtC hardy_reset 1 # output thermo 10 thermo_style custom step pe ke press lx ly lz -fix_modify AtC transfer output consistencyFE 1 text tensor_components -fix_modify AtC transfer atomic_output consistencyMD 1 - +fix_modify AtC output consistencyFE 1 text tensor_components # displace atoms # NOTE we need to figure out how to output post minimize w/o a "run" # or try to interface with "dump" @@ -63,8 +52,6 @@ variable n equal 10 variable i loop $n # NOTE this does not generate KE label loop_i - #variable s equal 0.02*$i/$n*$L - #print ">>> step $i, displacement $s" change_box all x scale 1.001 remap minimize 1.e-10 1.e-10 100000 1000000 velocity all set 0 0 0 diff --git a/examples/USER/atc/hardy/in.eam_kernel_convergence b/examples/USER/atc/hardy/in.eam_kernel_convergence index 982f9dde52..5961f768a8 100644 --- a/examples/USER/atc/hardy/in.eam_kernel_convergence +++ b/examples/USER/atc/hardy/in.eam_kernel_convergence @@ -1,11 +1,11 @@ +# This test examines the convergence of the Hardy localization (kernel) function +# with respect to its range for the calculation of stress. echo both -log eam_kernel_convergence.log -units metal -dimension 3 -boundary p p p -atom_style atomic -atom_modify sort 0 1 - +log eam_kernel_convergence.log +units metal +dimension 3 +boundary p p p +atom_style atomic # create system variable a equal 4.08 lattice fcc $a @@ -14,39 +14,27 @@ create_box 1 SYSTEM create_atoms 1 region SYSTEM mass 1 196.97 group internal region SYSTEM - # n-th shell at sqrt(n/2) * a for FCC # distances 1:2.9 2:4.1 3:5.1 4:5.8 5:6.5 # counts 1:12:12 2:6:18 3:24:42 4:12:54 5:24:78 -#pair_style lj/cut/smooth 5.456108274435118 -#pair_coeff * * 0.7242785984051078 2.598146797350056 pair_style eam pair_coeff * * ../../../../potentials/Au_u3.eam - - # specify neighbor/re-neighboring parameters neighbor 0.3 bin neigh_modify delay 1000000 - thermo 10 thermo_style custom step ke pe pxx pyy pzz pxy - timestep 0.0 reset_timestep 0 - velocity all set 0.0 0.0 0.0 sum no units box - fix ATC internal atc hardy -fix_modify ATC fem create mesh 1 1 1 SYSTEM p p p -#fix_modify ATC fem create mesh 2 2 2 SYSTEM p p p -#fix_modify ATC fem create mesh 4 4 4 SYSTEM p p p -fix_modify ATC transfer fields none -fix_modify ATC transfer fields add density stress number_density -fix_modify ATC transfer set reference_potential_energy -fix_modify ATC transfer output eam_kernel_convergenceFE 1 text tensor_components -fix_modify ATC transfer atomic_output eam_kernel_convergenceMD 1 tensor_components -fix_modify ATC transfer on_the_fly kernel on -fix_modify ATC transfer on_the_fly bond on +fix_modify ATC mesh create 1 1 1 SYSTEM p p p +fix_modify ATC fields none +fix_modify ATC fields add mass_density stress number_density +##fix_modify ATC set reference_potential_energy +fix_modify ATC output eam_kernel_convergenceFE 1 text tensor_components +##fix_modify ATC on_the_fly kernel on ## NOTE HACK REJ 8Jan13 temporary +##fix_modify ATC on_the_fly bond on # relative to a variable d equal 0.1 @@ -55,13 +43,9 @@ variable i loop $n label loop_i variable R equal $i*$d variable Ra equal $R*$a - #fix_modify ATC transfer kernel step ${Ra} - #fix_modify ATC transfer kernel quartic_cylinder ${Ra} - fix_modify ATC transfer kernel quartic_sphere ${Ra} - #fix_modify ATC transfer kernel cell ${Ra} + fix_modify ATC kernel quartic_sphere ${Ra} # initial (1) run 1 # increment (2) next i jump in.eam_kernel_convergence loop_i - diff --git a/examples/USER/atc/hardy/in.eam_unistrain_cell b/examples/USER/atc/hardy/in.eam_unistrain_cell index 1463a116bd..e250551da9 100644 --- a/examples/USER/atc/hardy/in.eam_unistrain_cell +++ b/examples/USER/atc/hardy/in.eam_unistrain_cell @@ -1,65 +1,45 @@ -#AtC Thermal Coupling -log eam_unistrain_cell.log - +# This test calculates several Hardy fields for a system subjected to +# unaxial strain using the "cell" Hardy localization function. units metal atom_style atomic -atom_modify sort 0 1 - # create domain lattice fcc 3.615 origin 0.25 0.25 0.25 -#lattice fcc 3.615 origin 0.117 0.117 0.117 -#lattice fcc 3.615 origin 0.12 0.12 0.12 region simRegion block -18 18 -3 3 -3 3 region feRegion block -18 18 -3 3 -3 3 boundary f p p create_box 1 simRegion - # create atoms region mdRegion block -17 17 -3 3 -3 3 create_atoms 1 region mdRegion mass 1 63.550 - -# specify interal/ghost atoms +# specify interal atoms region mdInternal block -16 16 -3 3 -3 3 group internal region mdInternal -#group ghost subtract all internal - # specify inter-atomic potential pair_style eam pair_coeff * * ../../../../potentials/Cu_u3.eam - # specify neighbor/re-neighboring parameters neighbor 0.3 bin neigh_modify every 10 delay 0 check no - # setup thermal output thermo 10 thermo_style custom step pe ke press lx ly lz - # ID group atc PhysicsType ParameterFile fix AtC internal atc hardy -fix_modify AtC transfer kernel cell 7.23 7.23 7.23 -# fix_modify AtC transfer kernel cell 14.46 10.845 10.845 +fix_modify AtC kernel cell 7.23 7.23 7.23 # fix_modify AtC atom_element_map eulerian 1 -fix_modify AtC transfer fields none -fix_modify AtC transfer fields add density displacement stress energy -fix_modify AtC transfer gradients add displacement -fix_modify AtC neighbor_reset_frequency 1 -# fix_modify AtC transfer on_the_fly kernel on -# fix_modify AtC transfer on_the_fly bond on +fix_modify AtC fields none +fix_modify AtC fields add mass_density displacement stress internal_energy +fix_modify AtC gradients add displacement +# fix_modify AtC on_the_fly kernel on +# fix_modify AtC on_the_fly bond on # ID part keywords nx ny nz region -fix_modify AtC fem create mesh 9 1 1 feRegion f p p - +fix_modify AtC mesh create 9 1 1 feRegion f p p +fix_modify AtC mesh lammps_partition # equilibrate MD field - timestep 0.001 reset_timestep 0 run 1 - displace_atoms all ramp x -0.6507 0.6507 x -65.07 65.07 - -fix_modify AtC transfer output eam_unistrain_cellFE 1 text tensor_components -fix_modify AtC transfer atomic_output eam_unistrain_cellMD 1 - +fix_modify AtC output eam_unistrain_cellFE 1 text tensor_components run 1 - diff --git a/examples/USER/atc/hardy/in.eam_unistrain_mesh b/examples/USER/atc/hardy/in.eam_unistrain_mesh index 11a0d5cc50..baf3e6e4b3 100644 --- a/examples/USER/atc/hardy/in.eam_unistrain_mesh +++ b/examples/USER/atc/hardy/in.eam_unistrain_mesh @@ -1,61 +1,47 @@ -#AtC Thermal Coupling -log eam_unistrain_mesh.log - - +# This test calculates several Hardy fields for a system subjected to +# unaxial strain for the "field" option of using the mesh's shape functions +# as the Hardy localization function. +echo both +log eam_unistrain_mesh units metal atom_style atomic -atom_modify sort 0 1 - # create domain lattice fcc 3.615 origin 0.25 0.25 0.25 region simRegion block -18 18 -3 3 -3 3 region feRegion block -18 18 -3 3 -3 3 boundary f p p create_box 1 simRegion - # create atoms region mdRegion block -17 17 -3 3 -3 3 create_atoms 1 region mdRegion mass 1 63.550 - -# specify interal/ghost atoms +atom_modify sort 0 1 +# specify interal atoms region mdInternal block -16 16 -3 3 -3 3 group internal region mdInternal -#group ghost subtract all internal - # specify inter-atomic potential pair_style eam pair_coeff * * ../../../../potentials/Cu_u3.eam - # specify neighbor/re-neighboring parameters neighbor 0.3 bin neigh_modify every 10 delay 0 check no - # setup thermal output thermo 10 thermo_style custom step pe ke press lx ly lz - # ID group atc PhysicsType ParameterFile -fix AtC internal atc hardy +fix AtC internal atc field # fix_modify AtC atom_element_map eulerian 1 -fix_modify AtC transfer fields none -fix_modify AtC transfer fields add density displacement stress energy -fix_modify AtC transfer gradients add displacement -fix_modify AtC neighbor_reset_frequency 1 - +fix_modify AtC fields none +fix_modify AtC fields add mass_density displacement stress internal_energy +fix_modify AtC gradients add displacement +fix_modify AtC fields add rotation stretch +# fix_modify AtC on_the_fly kernel on # ID part keywords nx ny nz region -fix_modify AtC fem create mesh 9 1 1 feRegion f p p - -# equilibrate MD field - +fix_modify AtC mesh create 9 1 1 feRegion f p p +#fix_modify AtC mesh data_decomposition timestep 0.001 reset_timestep 0 run 1 - displace_atoms all ramp x -0.6507 0.6507 x -65.07 65.07 - -fix_modify AtC transfer output eam_unistrain_meshFE 1 text tensor_components -fix_modify AtC transfer atomic_output eam_unistrain_meshMD 1 - +fix_modify AtC output eam_unistrain_meshFE 1 text tensor_components run 1 - diff --git a/examples/USER/atc/hardy/in.eam_unistrain_qcylinder b/examples/USER/atc/hardy/in.eam_unistrain_qcylinder index 5ea042dfe1..83be292477 100644 --- a/examples/USER/atc/hardy/in.eam_unistrain_qcylinder +++ b/examples/USER/atc/hardy/in.eam_unistrain_qcylinder @@ -1,67 +1,44 @@ -#AtC Thermal Coupling -log eam_unistrain_qcylinder.log - +# This test calculates several Hardy fields for a system subjected to +# unaxial strain using the "quartic_cylinder" Hardy localization function. units metal atom_style atomic -atom_modify sort 0 1 - # create domain lattice fcc 3.615 origin 0.25 0.25 0.25 region simRegion block -18 18 -3 3 -3 3 region feRegion block -18 18 -3 3 -3 3 boundary f p p create_box 1 simRegion - # create atoms region mdRegion block -17 17 -3 3 -3 3 create_atoms 1 region mdRegion mass 1 63.550 - -# specify interal/ghost atoms +# specify interal atoms region mdInternal block -16 16 -3 3 -3 3 group internal region mdInternal -#group ghost subtract all internal - # specify inter-atomic potential pair_style eam pair_coeff * * ../../../../potentials/Cu_u3.eam - # specify neighbor/re-neighboring parameters neighbor 0.3 bin neigh_modify every 10 delay 0 check no - # setup thermal output thermo 10 thermo_style custom step pe ke press lx ly lz - # ID group atc PhysicsType ParameterFile fix AtC internal atc hardy -fix_modify AtC transfer kernel quartic_cylinder 9.0375 +fix_modify AtC kernel quartic_cylinder 9.0375 # fix_modify AtC atom_element_map eulerian 1 -fix_modify AtC transfer fields none -fix_modify AtC transfer fields add density displacement stress energy -fix_modify AtC transfer gradients add displacement -fix_modify AtC neighbor_reset_frequency 1 -# fix_modify AtC transfer on_the_fly kernel on -# fix_modify AtC transfer on_the_fly bond on - +fix_modify AtC fields none +fix_modify AtC fields add mass_density displacement stress internal_energy +fix_modify AtC gradients add displacement +# fix_modify AtC on_the_fly kernel on +# fix_modify AtC on_the_fly bond on # ID part keywords nx ny nz region -fix_modify AtC fem create mesh 9 1 1 feRegion f p p - -# specify atom types -fix_modify AtC transfer internal type internal -fix_modify AtC transfer boundary type ghost - +fix_modify AtC mesh create 9 1 1 feRegion f p p # equilibrate MD field - timestep 0.001 reset_timestep 0 run 1 - displace_atoms all ramp x -0.6507 0.6507 x -65.07 65.07 - -fix_modify AtC transfer output eam_unistrain_qcylinderFE 1 text -fix_modify AtC transfer atomic_output eam_unistrain_qcylinderMD 1 - +fix_modify AtC output eam_unistrain_qcylinderFE 1 text run 1 - diff --git a/examples/USER/atc/hardy/in.eam_unistrain_qsphere b/examples/USER/atc/hardy/in.eam_unistrain_qsphere index 8807eb9fb2..6d0e5ceff8 100644 --- a/examples/USER/atc/hardy/in.eam_unistrain_qsphere +++ b/examples/USER/atc/hardy/in.eam_unistrain_qsphere @@ -1,68 +1,44 @@ -#AtC Thermal Coupling -log eam_unistrain_qsphere.log - - +# This test calculates several Hardy fields for a system subjected to +# unaxial strain using the "quartic_sphere" Hardy localization function. units metal atom_style atomic -atom_modify sort 0 1 - # create domain lattice fcc 3.615 origin 0.25 0.25 0.25 region simRegion block -18 18 -3 3 -3 3 region feRegion block -18 18 -3 3 -3 3 boundary f p p create_box 1 simRegion - # create atoms region mdRegion block -17 17 -3 3 -3 3 create_atoms 1 region mdRegion mass 1 63.550 - -# specify interal/ghost atoms +# specify interal atoms region mdInternal block -16 16 -3 3 -3 3 group internal region mdInternal -#group ghost subtract all internal - # specify inter-atomic potential pair_style eam pair_coeff * * ../../../../potentials/Cu_u3.eam - # specify neighbor/re-neighboring parameters neighbor 0.3 bin neigh_modify every 10 delay 0 check no - # setup thermal output thermo 10 thermo_style custom step pe ke press lx ly lz - # ID group atc PhysicsType ParameterFile fix AtC internal atc hardy -fix_modify AtC transfer kernel quartic_sphere 9.0375 +fix_modify AtC kernel quartic_sphere 9.0375 # fix_modify AtC atom_element_map eulerian 1 -fix_modify AtC transfer fields none -fix_modify AtC transfer fields add density displacement stress energy -fix_modify AtC transfer gradients add displacement -fix_modify AtC neighbor_reset_frequency 1 -# fix_modify AtC transfer on_the_fly kernel on -# fix_modify AtC transfer on_the_fly bond on - +fix_modify AtC fields none +fix_modify AtC fields add mass_density displacement stress internal_energy +fix_modify AtC gradients add displacement +fix_modify AtC on_the_fly kernel on +# fix_modify AtC on_the_fly bond on # ID part keywords nx ny nz region -fix_modify AtC fem create mesh 9 1 1 feRegion f p p - -# specify atom types -fix_modify AtC transfer internal type internal -fix_modify AtC transfer boundary type ghost - +fix_modify AtC mesh create 9 1 1 feRegion f p p # equilibrate MD field - timestep 0.001 reset_timestep 0 run 1 - displace_atoms all ramp x -0.6507 0.6507 x -65.07 65.07 - -fix_modify AtC transfer output eam_unistrain_qsphereFE 1 text -fix_modify AtC transfer atomic_output eam_unistrain_qsphereMD 1 - +fix_modify AtC output eam_unistrain_qsphereFE 1 text run 1 - diff --git a/examples/USER/atc/hardy/in.eam_unistrain_step b/examples/USER/atc/hardy/in.eam_unistrain_step index 979cfaf624..70014b0c9c 100644 --- a/examples/USER/atc/hardy/in.eam_unistrain_step +++ b/examples/USER/atc/hardy/in.eam_unistrain_step @@ -1,67 +1,45 @@ -#AtC Thermal Coupling -log eam_unistrain_step.log - +# This test calculates several Hardy fields for a system subjected to +# unaxial strain using the "step" Hardy localization function. +echo both units metal atom_style atomic -atom_modify sort 0 1 - # create domain lattice fcc 3.615 origin 0.25 0.25 0.25 region simRegion block -18 18 -3 3 -3 3 region feRegion block -18 18 -3 3 -3 3 boundary f p p create_box 1 simRegion - # create atoms region mdRegion block -17 17 -3 3 -3 3 create_atoms 1 region mdRegion mass 1 63.550 - -# specify interal/ghost atoms +# specify interal atoms region mdInternal block -16 16 -3 3 -3 3 group internal region mdInternal -#group ghost subtract all internal - # specify inter-atomic potential pair_style eam pair_coeff * * ../../../../potentials/Cu_u3.eam - # specify neighbor/re-neighboring parameters neighbor 0.3 bin neigh_modify every 10 delay 0 check no - # setup thermal output thermo 10 thermo_style custom step pe ke press lx ly lz - # ID group atc PhysicsType ParameterFile fix AtC internal atc hardy -fix_modify AtC transfer kernel step 9.0375 +fix_modify AtC kernel step 9.0375 # fix_modify AtC atom_element_map eulerian 1 -fix_modify AtC transfer fields none -fix_modify AtC transfer fields add density displacement stress energy -fix_modify AtC transfer gradients add displacement -fix_modify AtC neighbor_reset_frequency 1 -# fix_modify AtC transfer on_the_fly kernel on -# fix_modify AtC transfer on_the_fly bond on - +fix_modify AtC fields none +fix_modify AtC fields add mass_density displacement stress internal_energy +fix_modify AtC gradients add displacement +# fix_modify AtC on_the_fly kernel on +# fix_modify AtC on_the_fly bond on # ID part keywords nx ny nz region -fix_modify AtC fem create mesh 9 1 1 feRegion f p p - -# specify atom types -fix_modify AtC transfer internal type internal -fix_modify AtC transfer boundary type ghost - +fix_modify AtC mesh create 9 1 1 feRegion f p p # equilibrate MD field - timestep 0.001 reset_timestep 0 run 1 - displace_atoms all ramp x -0.6507 0.6507 x -65.07 65.07 - -fix_modify AtC transfer output eam_unistrain_stepFE 1 text -fix_modify AtC transfer atomic_output eam_unistrain_stepMD 1 - +fix_modify AtC output eam_unistrain_stepFE 1 text run 1 - diff --git a/examples/USER/atc/hardy/in.eam_volume_stretch b/examples/USER/atc/hardy/in.eam_volume_stretch index 60c4df86a8..53d95b8830 100644 --- a/examples/USER/atc/hardy/in.eam_volume_stretch +++ b/examples/USER/atc/hardy/in.eam_volume_stretch @@ -1,10 +1,8 @@ -#AtC Thermal Coupling +# This test calculates Hardy fields for a system subjected +# to a volumetric stretch. echo both - units metal atom_style atomic -atom_modify sort 0 1 - # create domain lattice fcc 3.615 origin 0.25 0.25 0.25 region simRegion block -3 3 -3 3 -3 3 @@ -13,55 +11,36 @@ region mdRegion block -3 3 -3 3 -3 3 region mdInternal block -3 3 -3 3 -3 3 boundary p p p create_box 1 simRegion - # create atoms create_atoms 1 region mdRegion mass 1 63.550 - -# specify interal/ghost atoms +# specify interal atoms group internal region mdInternal -#group ghost subtract all internal - # specify inter-atomic potential pair_style eam pair_coeff * * ../../../../potentials/Cu_u3.eam - # specify neighbor/re-neighboring parameters neighbor 0.3 bin neigh_modify every 10 delay 0 check no - # setup thermal output thermo 10 thermo_style custom step pe ke press lx ly lz - - # time integrator -fix NVE all nve - +# fix NVE all nve # ID group atc PhysicsType ParameterFile -fix AtC internal atc hardy -fix_modify AtC transfer fields none -fix_modify AtC transfer fields add density -fix_modify AtC transfer fields add energy -fix_modify AtC transfer fields add stress -fix_modify AtC neighbor_reset_frequency 100000 - +fix AtC internal atc field +fix_modify AtC fields none +fix_modify AtC fields add mass_density +fix_modify AtC fields add internal_energy +fix_modify AtC fields add stress # ID part keywords nx ny nz region -fix_modify AtC fem create mesh 2 2 2 feRegion p p p - +fix_modify AtC mesh create 2 2 2 feRegion p p p log eam_volume_stretch.log - # equilibrate MD field - -timestep 0.001 +timestep 0.0 # 0.001 reset_timestep 0 run 1 - # stretch system change_box all x scale 1.001 y scale 1.001 z scale 1.001 remap - -fix_modify AtC transfer output eam_volume_stretchFE 1 text tensor_components -# fix_modify AtC transfer atomic_output eam_volume_stretchMD 1 text - +fix_modify AtC output eam_volume_stretchFE 1 text tensor_components run 1 - diff --git a/examples/USER/atc/hardy/in.eshelby_static b/examples/USER/atc/hardy/in.eshelby_static index d09a5e628c..b0ccc94af5 100644 --- a/examples/USER/atc/hardy/in.eshelby_static +++ b/examples/USER/atc/hardy/in.eshelby_static @@ -16,101 +16,105 @@ # boundary surface area rather than a periphery). If we multiply the 2*gamma # quantity times the thickness t = 3*4.08 = 12.24 Å, we obtain 2*gamma*t = # 3.914352 eV/Å, which agrees with the mesh calculation. -echo both -log eshelby_static.log -units metal -atom_style atomic -dimension 3 -boundary p p p -atom_modify sort 0 1 - -# create domain +echo both +log eshelby_static.log +units metal +dimension 3 +boundary p p p +atom_style atomic +# create system +#lattice fcc 3.615 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 +#lattice fcc 3.615 origin 0.2 0.2 0.2 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 lattice fcc 4.08 origin 0.25 0.25 0.25 region SYSTEM block -10 10 -10 10 0 3 region UPPER block -10 10 0 10 0 3 region LOWER block -10 0 -10 10 0 3 create_box 1 SYSTEM - -# create atoms create_atoms 1 region SYSTEM mass 1 63.55 - -# group atoms by region group internal region SYSTEM group upper region UPPER group lower region LOWER - -# specify inter-atomic potential +#pair_style eam +#pair_coeff * * ../../../../potentials/Cu_u3.eam +#pair_style lj/smooth 8.0 10.0 +#pair_coeff * * 10.0 1.5 pair_style lj/smooth/linear 5.456108274435118 pair_coeff * * 0.7242785984051078 2.598146797350056 - -# define region above/below crack +# define region region abovecrack block -2.01 2.01 0 8 INF INF units lattice group abovecrack region abovecrack region belowcrack block -2.01 2.01 -8 0 INF INF units lattice group belowcrack region belowcrack - -# specify neighbor/re-neighboring parameters neighbor 1.0 bin neigh_modify delay 1000000 neigh_modify exclude group abovecrack belowcrack - -# setup thermal output thermo 10 compute_modify thermo_temp extra 0 -thermo_style custom step ke pe press +region FORCECHECK block -6 0 6 10 0 3 +group FORCECHECK region FORCECHECK +compute fxsum FORCECHECK reduce sum fx +compute fysum FORCECHECK reduce sum fy +compute fzsum FORCECHECK reduce sum fz +thermo_style custom step ke pe press c_fxsum c_fysum c_fzsum +thermo_modify format 1 %4i format 2 %3.1g format 3 %20.16g timestep 0.0 - # (1) minimize the system to get a relaxed configuration min_modify line quadratic variable tol equal 1.e-11 minimize 0.0 ${tol} 100000 1000000 write_restart eshelby.restart - -# setup ATC fix +# (2) pull crack apart reset_timestep 0 -fix PK1 internal atc hardy -fix_modify PK1 fem create mesh 10 10 1 SYSTEM p f p -fix_modify PK1 transfer fields none -fix_modify PK1 transfer fields add density energy temperature stress displacement -fix_modify PK1 transfer fields add eshelby_stress transformed_stress -fix_modify PK1 transfer gradients add displacement -fix_modify PK1 transfer set reference_potential_energy -fix_modify PK1 transfer output eshelby_staticFE 1 text tensor_components -fix_modify PK1 transfer atomic_output eshelby_staticMD 1 - +fix PK1 internal atc field +# NOTE tune this relative to lattice size +fix_modify PK1 mesh create 10 10 1 SYSTEM p f p +fix_modify PK1 fields none +fix_modify PK1 fields add mass_density internal_energy temperature stress displacement +fix_modify PK1 fields add eshelby_stress transformed_stress +fix_modify PK1 gradients add displacement +fix_modify PK1 set reference_potential_energy +fix_modify PK1 output eshelby_staticFE 1 text binary tensor_components +#fix_modify PK1 on_the_fly #-- make concentric loops around one/both of the crack tips #-- & another around undefected material (loop0) fix_modify PK1 mesh create_faceset loop0 box -6 0 6 10 -INF INF outward -fix_modify PK1 transfer boundary_integral eshelby_stress faceset loop0 -fix_modify PK1 transfer boundary_integral stress faceset loop0 -fix_modify PK1 transfer boundary_integral energy faceset loop0 -#fix_modify PK1 transfer boundary_integral displacement_gradient faceset loop0 +fix_modify PK1 output boundary_integral eshelby_stress faceset loop0 +fix_modify PK1 output boundary_integral stress faceset loop0 +fix_modify PK1 output boundary_integral internal_energy faceset loop0 +#fix_modify PK1 output boundary_integral displacement_gradient faceset loop0 fix_modify PK1 mesh create_faceset loop1 box -6 0 -2 2 -INF INF outward -fix_modify PK1 transfer boundary_integral eshelby_stress faceset loop1 -fix_modify PK1 transfer boundary_integral stress faceset loop1 -fix_modify PK1 transfer boundary_integral energy faceset loop1 -#fix_modify PK1 transfer boundary_integral displacement_gradient faceset loop1 +fix_modify PK1 output boundary_integral eshelby_stress faceset loop1 +fix_modify PK1 output boundary_integral stress faceset loop1 +fix_modify PK1 output boundary_integral internal_energy faceset loop1 +#fix_modify PK1 output boundary_integral displacement_gradient faceset loop1 fix_modify PK1 mesh create_faceset loop2 box -8 0 -4 4 -INF INF outward -fix_modify PK1 transfer boundary_integral eshelby_stress faceset loop2 -fix_modify PK1 transfer boundary_integral stress faceset loop2 -fix_modify PK1 transfer boundary_integral energy faceset loop2 -#fix_modify PK1 transfer boundary_integral displacement_gradient faceset loop2 +fix_modify PK1 output boundary_integral eshelby_stress faceset loop2 +fix_modify PK1 output boundary_integral stress faceset loop2 +fix_modify PK1 output boundary_integral internal_energy faceset loop2 +#fix_modify PK1 output boundary_integral displacement_gradient faceset loop2 fix_modify PK1 mesh create_faceset loop3 box -10 0 -6 6 -INF INF outward -fix_modify PK1 transfer boundary_integral eshelby_stress faceset loop3 -fix_modify PK1 transfer boundary_integral stress faceset loop3 -fix_modify PK1 transfer boundary_integral energy faceset loop3 -#fix_modify PK1 transfer boundary_integral displacement_gradient faceset loop3 +fix_modify PK1 output boundary_integral eshelby_stress faceset loop3 +fix_modify PK1 output boundary_integral stress faceset loop3 +fix_modify PK1 output boundary_integral internal_energy faceset loop3 +#fix_modify PK1 output boundary_integral displacement_gradient faceset loop3 fix_modify PK1 mesh create_faceset loop4 box 0 8 -6 6 -INF INF outward -fix_modify PK1 transfer boundary_integral eshelby_stress faceset loop4 -fix_modify PK1 transfer boundary_integral stress faceset loop4 -fix_modify PK1 transfer boundary_integral energy faceset loop4 -#fix_modify PK1 transfer boundary_integral displacement_gradient faceset loop4 - -# initial ATC step to designate reference state +fix_modify PK1 output boundary_integral eshelby_stress faceset loop4 +fix_modify PK1 output boundary_integral stress faceset loop4 +fix_modify PK1 output boundary_integral internal_energy faceset loop4 +#fix_modify PK1 output boundary_integral displacement_gradient faceset loop4 +#-- compute across crack jumps in displacement +#fix PK1upper internal atc hardy +#fix_modify PK1upper mesh create 10 5 1 UPPER p f p +#fix_modify PK1upper fields none +#fix_modify PK1upper fields add displacement +#fix PK1lower lower atc hardy +#fix_modify PK1lower mesh create 10 5 1 LOWER p f p +#fix_modify PK1lower fields none +#fix_modify PK1lower fields add displacement +# initial (1) run 1 - -# pull crack apart +# increment (2) variable L equal 20 variable n equal 10 variable i loop $n diff --git a/examples/USER/atc/hardy/in.nvt b/examples/USER/atc/hardy/in.nvt index 4aa7cad7a4..6fca4b7325 100644 --- a/examples/USER/atc/hardy/in.nvt +++ b/examples/USER/atc/hardy/in.nvt @@ -1,31 +1,36 @@ -units real -atom_style atomic -echo both -dimension 3 -boundary p p p -lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 -region box block 0 5 0 5 0 5 -read_data nvt.data - -pair_style lj/cut 13.0 +# This test calculates Hardy fields for a system +# underdoing dynamics at a finite temperature. +units real +atom_style atomic +echo both +dimension 3 +boundary p p p +lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 +region box block 0 5 0 5 0 5 +read_data nvt.data +pair_style lj/cut 13.0 pair_coeff 1 1 0.2381 3.405 - group internal region box - -fix ATC internal atc hardy -fix_modify ATC fem create mesh 1 1 1 box p p p -fix_modify ATC atom_element_map eulerian 100 -fix_modify ATC transfer fields none -fix_modify ATC transfer fields add density energy stress temperature -fix_modify ATC transfer output nvtFE 100 text - +fix ATC internal atc field +fix_modify ATC mesh create 1 1 1 box p p p +fix_modify ATC atom_element_map eulerian 100 +fix_modify ATC fields none +fix_modify ATC fields add mass_density energy stress temperature kinetic_temperature +fix_modify ATC fields add velocity thermal_energy kinetic_energy +fix_modify ATC output nvtFE 100 text +fix PP internal atc field +fix_modify PP filter type step # defaults to running +fix_modify PP filter on +fix_modify PP mesh create 1 1 1 box p p p +fix_modify PP atom_element_map eulerian 100 +fix_modify PP fields add mass_density energy stress temperature kinetic_temperature +fix_modify PP fields add velocity thermal_energy kinetic_energy +fix_modify PP output nvtPP 100 text thermo 100 compute_modify thermo_temp extra 0 -thermo_style custom step temp etotal ke pe press -log nvt.log - +thermo_style custom step temp etotal ke pe press vol timestep 4.0 reset_timestep 0 -fix NVT all nvt temp 30 30 10 drag 0.2 tchain 1 +fix NVT all nvt temp 30 30 10.0 drag 0.2 tchain 1 +log nvt.log run 1000 - diff --git a/examples/USER/atc/hardy/nvt.screen b/examples/USER/atc/hardy/nvt.screen index 5f13794635..cdf62c72e4 100644 --- a/examples/USER/atc/hardy/nvt.screen +++ b/examples/USER/atc/hardy/nvt.screen @@ -1,88 +1,88 @@ -LAMMPS (12 Jan 2013) -dimension 3 -boundary p p p -lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 +LAMMPS (14 Aug 2013) +dimension 3 +boundary p p p +lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.376 5.376 5.376 -region box block 0 5 0 5 0 5 -read_data nvt.data +region box block 0 5 0 5 0 5 +read_data nvt.data Reading data file ... orthogonal box = (0 0 0) to (26.88 26.88 26.88) - 1 by 1 by 1 MPI processor grid + 1 by 2 by 2 MPI processor grid 500 atoms 500 velocities - -pair_style lj/cut 13.0 +pair_style lj/cut 13.0 pair_coeff 1 1 0.2381 3.405 - group internal region box 500 atoms in group internal +fix ATC internal atc field +ATC: constructing shape function field estimate + ATC: peratom PE compute created with ID: 3 +fix_modify ATC mesh create 1 1 1 box p p p + ATC: created uniform mesh with 8 nodes, 1 unique nodes, and 1 elements +fix_modify ATC atom_element_map eulerian 100 +fix_modify ATC fields none +fix_modify ATC fields add mass_density energy stress temperature kinetic_temperature +fix_modify ATC fields add velocity thermal_energy kinetic_energy +fix_modify ATC output nvtFE 100 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: -fix ATC internal atc hardy -Constructing ATC transfer (hardy) -atomPE compute created with ID: 3 -fix_modify ATC fem create mesh 1 1 1 box p p p - ATC:: created FEM Mesh with 8 Global Nodes, 1 Unique Nodes, and 1 Elements -fix_modify ATC atom_element_map eulerian 100 -fix_modify ATC transfer fields none -fix_modify ATC transfer fields add density energy stress temperature -fix_modify ATC transfer output nvtFE 100 text - ATC:: Warning : text output can create _LARGE_ files +fix PP internal atc field +ATC: constructing shape function field estimate + ATC: peratom PE compute created with ID: 3 +fix_modify PP filter type step # defaults to running +fix_modify PP filter on +fix_modify PP mesh create 1 1 1 box p p p + ATC: created uniform mesh with 8 nodes, 1 unique nodes, and 1 elements +fix_modify PP atom_element_map eulerian 100 +fix_modify PP fields add mass_density energy stress temperature kinetic_temperature +fix_modify PP fields add velocity thermal_energy kinetic_energy +fix_modify PP output nvtPP 100 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: thermo 100 compute_modify thermo_temp extra 0 -thermo_style custom step temp etotal ke pe press -log nvt.log - +thermo_style custom step temp etotal ke pe press vol timestep 4.0 reset_timestep 0 -fix NVT all nvt temp 30 30 10 drag 0.2 tchain 1 +fix NVT all nvt temp 30 30 10.0 drag 0.2 tchain 1 +log nvt.log run 1000 Setting up run ... - ATC:: computing bond matrix ...........done - ATC:: conversion factor for energy/vol -> stress 68568.4 - ATC:: cutoff radius 13 -Memory usage per processor = 4.5546 Mbytes -Step Temp TotEng KinEng PotEng Press - 0 31.104176 -898.55796 46.35782 -944.91578 -584.20571 - ATC:: computing bond matrix ...........done - 100 29.954062 -903.43223 44.643685 -948.07591 -646.45662 - ATC:: computing bond matrix ...........done - 200 29.952147 -900.39726 44.640831 -945.03809 -583.44492 - ATC:: computing bond matrix ...........done - 300 29.91148 -902.38105 44.58022 -946.96127 -626.6874 - ATC:: computing bond matrix ...........done - 400 29.936718 -900.07678 44.617835 -944.69461 -580.74144 - ATC:: computing bond matrix ...........done - 500 29.952289 -899.58418 44.641042 -944.22522 -570.0108 - ATC:: computing bond matrix ...........done - 600 29.980195 -901.64307 44.682633 -946.3257 -614.13849 - ATC:: computing bond matrix ...........done - 700 29.88447 -901.31686 44.539965 -945.85683 -604.74508 - ATC:: computing bond matrix ...........done - 800 29.876839 -900.32866 44.528592 -944.85725 -587.67852 - ATC:: computing bond matrix ...........done - 900 29.966977 -899.86769 44.662933 -944.53062 -581.80498 - ATC:: computing bond matrix ...........done - 1000 29.907621 -901.57887 44.574469 -946.15334 -613.00908 -Loop time of 65.0846 on 1 procs for 1000 steps with 500 atoms + ATC: computing bond matrix ...........done + ATC: computing bond matrix ...........done +Memory usage per processor = 40.9608 Mbytes +Step Temp TotEng KinEng PotEng Press Volume + 0 31.104176 -898.55796 46.35782 -944.91578 -584.20571 19421.725 + 100 29.954062 -903.43223 44.643685 -948.07591 -646.45662 19421.725 + 200 29.952147 -900.39726 44.640831 -945.03809 -583.44492 19421.725 + 300 29.91148 -902.38105 44.58022 -946.96127 -626.6874 19421.725 + 400 29.936718 -900.07678 44.617835 -944.69461 -580.74144 19421.725 + 500 29.952289 -899.58418 44.641042 -944.22522 -570.0108 19421.725 + 600 29.980195 -901.64307 44.682633 -946.3257 -614.13849 19421.725 + 700 29.88447 -901.31686 44.539965 -945.85683 -604.74508 19421.725 + 800 29.876839 -900.32866 44.528592 -944.85725 -587.67852 19421.725 + 900 29.966977 -899.86769 44.662933 -944.53062 -581.80498 19421.725 + 1000 29.907621 -901.57887 44.574469 -946.15334 -613.00908 19421.725 +Loop time of 6.81743 on 4 procs for 1000 steps with 500 atoms -Pair time (%) = 4.38716 (6.7407) +Pair time (%) = 0.99375 (14.5766) Neigh time (%) = 0 (0) -Comm time (%) = 0.0962148 (0.14783) -Outpt time (%) = 0.000242472 (0.000372548) -Other time (%) = 60.601 (93.1111) +Comm time (%) = 2.8781 (42.2167) +Outpt time (%) = 0.115153 (1.6891) +Other time (%) = 2.83043 (41.5175) -Nlocal: 500 ave 500 max 500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 4130 ave 4130 max 4130 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 91149 ave 91149 max 91149 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 182298 ave 182298 max 182298 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 125 ave 129 max 121 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 2563 ave 2567 max 2559 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 22787.2 ave 23476 max 22083 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +FullNghs: 45574.5 ave 47047 max 44066 min +Histogram: 1 0 0 0 0 2 0 0 0 1 Total # of neighbors = 182298 Ave neighs/atom = 364.596 Neighbor list builds = 0 Dangerous builds = 0 - diff --git a/examples/USER/atc/mesh/Ar_ttm.mat b/examples/USER/atc/mesh/Ar_ttm.mat new file mode 100644 index 0000000000..9f80303cda --- /dev/null +++ b/examples/USER/atc/mesh/Ar_ttm.mat @@ -0,0 +1,35 @@ +material Ar real +heat_capacity constant +capacity 0.000000063363 +end +electron_heat_capacity constant +capacity 0.000000063363 +end +heat_flux linear +conductivity 0.0000000030111 +end +electron_heat_flux linear +conductivity 0.0000000030111 +end +electron_phonon_exchange linear +coefficient 0.00000000001 +end +end + +material Null real +heat_capacity constant +capacity 1.0 +end +electron_heat_capacity constant +capacity 1.0 +end +heat_flux linear +conductivity 0.0 +end +electron_heat_flux linear +conductivity 0.0 +end +electron_phonon_exchange linear +coefficient 0.0 +end +end diff --git a/examples/USER/atc/mesh/Si.mat b/examples/USER/atc/mesh/Si.mat new file mode 100644 index 0000000000..adaaa607dd --- /dev/null +++ b/examples/USER/atc/mesh/Si.mat @@ -0,0 +1,9 @@ +material Si metal +#### two temperature #################### +#heat_capacity constant +#capacity 0.124578126430817 # E / L^3 +#end +heat_flux linear +conductivity 722.65698 # E / t / L / T +end +end diff --git a/examples/USER/atc/mesh/gaussianIC1d_hex.screen b/examples/USER/atc/mesh/gaussianIC1d_hex.screen new file mode 100644 index 0000000000..da11d82c50 --- /dev/null +++ b/examples/USER/atc/mesh/gaussianIC1d_hex.screen @@ -0,0 +1,107 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic + +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region mdRegion block -12 12 -3 3 -3 3 +region mdInternal block -10 10 -3 3 -3 3 + +# create atoms +boundary f p p +create_box 1 mdRegion +Created orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215) + 4 by 1 by 1 MPI processor grid +create_atoms 1 region mdRegion +Created 3456 atoms +mass 1 39.95 +pair_style lj/cut 13.5 +pair_coeff 1 1 .238 3.405 13.5 + +# specify interal/ghost atoms +group internal region mdInternal +2880 atoms in group internal +velocity internal create 40 87287 mom yes loop geom # <<< NOTE + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# ID group atc PhysicsType ParameterFile +fix AtC internal atc two_temperature Ar_ttm.mat +ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat + ATC: peratom PE compute created with ID: 3 + ATC: 2 materials defined from Ar_ttm.mat + ATC: creating two_temperature extrinsic model + ATC: 2 materials defined from Ar_ttm.mat + +fix_modify AtC mesh read gaussianIC1d_hex.mesh + ATC: read 44 nodes + ATC: read 10 HEX8 elements + ATC: WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive + +# fix a temperature +fix_modify AtC fix temperature all 20.0 +fix_modify AtC initial temperature all 20.0 +fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 +fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 + +# turn on thermostat +fix_modify AtC extrinsic exchange off +fix_modify AtC control thermal rescale 10 + +# equilibrate MD field +timestep 5.0 +thermo 10 + +#output +fix_modify AtC output gaussianIC1d_hexFE 10 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + + +# change thermostat +fix_modify AtC unfix temperature all +fix_modify AtC unfix electron_temperature all +fix_modify AtC control thermal flux +fix_modify AtC extrinsic exchange on +fix_modify AtC extrinsic electron_integration explicit 10 + +# run with FE +thermo_style custom step temp pe f_AtC[2] f_AtC[4] +reset_timestep 0 +run 100 # 400 +Setting up run ... +Memory usage per processor = 52.9302 Mbytes +Step Temp PotEng AtC[2] AtC[4] + 0 33.331404 -6667.7177 20 21.852118 + 10 29.605914 -6628.8617 15.526061 21.823928 + 20 20.144352 -6529.8249 4.1452637 21.728037 + 30 10.661516 -6429.3908 -7.2917185 21.537517 + 40 7.6716875 -6394.7484 -10.961235 21.28913 + 50 11.012891 -6425.2214 -7.0020953 21.050343 + 60 15.276591 -6465.7767 -1.8390571 20.85387 + 70 17.15209 -6482.1581 0.55215503 20.688207 + 80 17.028137 -6478.0796 0.55504167 20.530699 + 90 16.865355 -6473.5664 0.41999569 20.372106 + 100 17.920474 -6481.673 1.6267665 20.219157 +Loop time of 5.05638 on 4 procs for 100 steps with 3456 atoms + +Pair time (%) = 0.947014 (18.7291) +Neigh time (%) = 0.418835 (8.2833) +Comm time (%) = 0.338576 (6.69601) +Outpt time (%) = 0.024951 (0.493455) +Other time (%) = 3.327 (65.7981) + +Nlocal: 864 ave 864 max 864 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 6741 ave 7924 max 5558 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 272828 ave 288265 max 257696 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 545657 ave 575527 max 515800 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 2182628 +Ave neighs/atom = 631.547 +Neighbor list builds = 10 +Dangerous builds = 0 diff --git a/examples/USER/atc/mesh/gaussianIC2d_hex.screen b/examples/USER/atc/mesh/gaussianIC2d_hex.screen new file mode 100644 index 0000000000..65c3ef8073 --- /dev/null +++ b/examples/USER/atc/mesh/gaussianIC2d_hex.screen @@ -0,0 +1,286 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic + +variable L equal 12 +variable l2 equal 6 +variable l equal 4 +variable w equal 2 + +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region mdRegion cylinder z 0. 0. ${l2} -$w $w +region mdRegion cylinder z 0. 0. 6 -$w $w +region mdRegion cylinder z 0. 0. 6 -2 $w +region mdRegion cylinder z 0. 0. 6 -2 2 +region mdInternal cylinder z 0. 0. $l -$w $w +region mdInternal cylinder z 0. 0. 4 -$w $w +region mdInternal cylinder z 0. 0. 4 -2 $w +region mdInternal cylinder z 0. 0. 4 -2 2 + +boundary f f f +pair_style lj/cut 13.5 +read_data circle_temp.init +Reading data file ... + orthogonal box = (-64.86 -64.86 -10.81) to (64.86 64.86 10.81) + 2 by 2 by 1 MPI processor grid + 1792 atoms + 1792 velocities +fix ZWALLS all wall/reflect zlo EDGE zhi EDGE +mass 1 39.95 +pair_coeff 1 1 .238 3.405 13.5 +group internal region mdInternal +832 atoms in group internal +group ghost subtract all internal +960 atoms in group ghost + +fix AtC internal atc two_temperature Ar_ttm.mat +ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat + ATC: peratom PE compute created with ID: 3 + ATC: 2 materials defined from Ar_ttm.mat + ATC: creating two_temperature extrinsic model + ATC: 2 materials defined from Ar_ttm.mat +# computational geometry +fix_modify AtC mesh read gaussianIC2d_hex.mesh + ATC: read 388 nodes + ATC: read 173 HEX8 elements + ATC: created nodeset 11 with 22 nodes + ATC: created nodeset 12 with 22 nodes + ATC: WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive +#fix_modify AtC mesh read gaussianIC2d_hex.exo +#fix_modify AtC mesh read gaussianIC2d_hex2.exo +#fix_modify AtC mesh read gaussianIC2d_hex2.mesh +fix_modify AtC mesh write parsed_gaussianIC2d_hex.mesh +fix_modify AtC mesh output gaussianIC2d_hexMESH +fix_modify AtC boundary ghost +# numerical parameters +fix_modify AtC time_integration fractional_step +fix_modify AtC internal_quadrature off + +# initial conditions +fix_modify AtC fix temperature all 20.0 +# NOTE this is only gaussian in x +fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 + +# thermostat +fix_modify AtC control thermal rescale 10 +fix_modify AtC extrinsic exchange off + +# run to equilibrate +thermo_style custom step temp pe f_AtC[2] f_AtC[4] +timestep 1.0 +thermo 10 +run 400 +Setting up run ... +Memory usage per processor = 91.5244 Mbytes +Step Temp PotEng AtC[2] AtC[4] + 0 18.559464 -2927.2438 20 22.619065 + 10 9.2908989 -2926.8636 20 22.619065 + 20 9.2908989 -2926.1076 20 22.619065 + 30 9.2908989 -2924.9455 20 22.619065 + 40 9.2908989 -2923.3809 20 22.619065 + 50 9.2908989 -2921.4179 20 22.619065 + 60 9.2908989 -2919.0624 20 22.619065 + 70 9.2908989 -2916.3227 20 22.619065 + 80 9.2908989 -2913.2105 20 22.619065 + 90 9.2908989 -2909.7421 20 22.619065 + 100 9.2908989 -2905.9396 20 22.619065 + 110 9.2908989 -2901.8364 20 22.619065 + 120 9.2908989 -2897.474 20 22.619065 + 130 9.2908989 -2892.8985 20 22.619065 + 140 9.2908989 -2888.1815 20 22.619065 + 150 9.2908989 -2883.3945 20 22.619065 + 160 9.2908989 -2878.6283 20 22.619065 + 170 9.2908989 -2873.9874 20 22.619065 + 180 9.2908989 -2869.5705 20 22.619065 + 190 9.2908989 -2865.4802 20 22.619065 + 200 9.2908989 -2861.8004 20 22.619065 + 210 9.2908989 -2858.6064 20 22.619065 + 220 9.2908989 -2855.9338 20 22.619065 + 230 9.2908989 -2853.7842 20 22.619065 + 240 9.2908989 -2852.155 20 22.619065 + 250 9.2908989 -2850.9801 20 22.619065 + 260 9.2908989 -2850.2014 20 22.619065 + 270 9.2908989 -2849.745 20 22.619065 + 280 9.2908989 -2849.5468 20 22.619065 + 290 9.2908989 -2849.5383 20 22.619065 + 300 9.2908989 -2849.6571 20 22.619065 + 310 9.2908989 -2849.8648 20 22.619065 + 320 9.2908989 -2850.1261 20 22.619065 + 330 9.2908989 -2850.4068 20 22.619065 + 340 9.2908989 -2850.6989 20 22.619065 + 350 9.2908989 -2850.9948 20 22.619065 + 360 9.2908989 -2851.2898 20 22.619065 + 370 9.2908989 -2851.5911 20 22.619065 + 380 9.2908989 -2851.9001 20 22.619065 + 390 9.2908989 -2852.2299 20 22.619065 + 400 9.2908989 -2852.6005 20 22.619065 +Loop time of 26.8725 on 4 procs for 400 steps with 1792 atoms + +Pair time (%) = 1.1555 (4.29993) +Neigh time (%) = 0 (0) +Comm time (%) = 3.3023 (12.2888) +Outpt time (%) = 0.070357 (0.261817) +Other time (%) = 22.3444 (83.1495) + +Nlocal: 448 ave 448 max 448 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 696 ave 696 max 696 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 51280 ave 52662 max 49886 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +FullNghs: 102560 ave 102560 max 102560 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 410240 +Ave neighs/atom = 228.929 +Neighbor list builds = 0 +Dangerous builds = 0 + +# boundary conditions +fix_modify AtC unfix temperature all +fix_modify AtC unfix electron_temperature all +fix_modify AtC fix temperature 11 20.0 +fix_modify AtC fix temperature 12 20.0 + +# numerical parameters +fix_modify AtC extrinsic electron_integration explicit 10 + +# thermostat +fix_modify AtC control thermal flux +fix_modify AtC extrinsic exchange on + +# output +fix_modify AtC output gaussianIC2d_hexFE 10 full_text binary + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +dump D1 all atom 10 gaussianIC2d_hex.dmp + +# relax the system +run 1000 +Setting up run ... +Memory usage per processor = 96.3294 Mbytes +Step Temp PotEng AtC[2] AtC[4] + 400 9.2908989 -2852.6005 20 22.619065 + 410 9.3739709 -2853.0186 20.040932 22.611409 + 420 9.4777325 -2853.5491 20.093686 22.603893 + 430 9.603939 -2854.2014 20.159312 22.596534 + 440 9.7542127 -2854.9791 20.238859 22.589353 + 450 9.9295278 -2855.9033 20.332984 22.582373 + 460 10.130063 -2856.9771 20.441869 22.575614 + 470 10.35505 -2858.1731 20.565152 22.569098 + 480 10.602677 -2859.5024 20.701879 22.562845 + 490 10.870017 -2860.9396 20.85048 22.556874 + 500 11.153033 -2862.4773 21.008778 22.551199 + 510 11.446646 -2864.0797 21.174034 22.545832 + 520 11.744908 -2865.7188 21.343051 22.540779 + 530 12.041263 -2867.364 21.512313 22.53604 + 540 12.328877 -2868.9829 21.678162 22.531611 + 550 12.600994 -2870.5197 21.836981 22.527482 + 560 12.851303 -2871.9663 21.985384 22.523636 + 570 13.074293 -2873.2785 22.120399 22.520052 + 580 13.265513 -2874.4253 22.239594 22.516705 + 590 13.421751 -2875.3914 22.341174 22.513566 + 600 13.541109 -2876.1789 22.424015 22.510605 + 610 13.623016 -2876.7775 22.487675 22.507788 + 620 13.668152 -2877.1854 22.532362 22.505085 + 630 13.678331 -2877.4076 22.558874 22.502464 + 640 13.656332 -2877.4627 22.568531 22.499895 + 650 13.605722 -2877.3683 22.563078 22.497353 + 660 13.530708 -2877.1524 22.544625 22.494813 + 670 13.435942 -2876.8175 22.515544 22.492256 + 680 13.326383 -2876.406 22.478395 22.489667 + 690 13.207157 -2875.947 22.435845 22.487033 + 700 13.083403 -2875.4566 22.390572 22.484348 + 710 12.960144 -2874.9651 22.345189 22.48161 + 720 12.842152 -2874.501 22.302149 22.478818 + 730 12.73379 -2874.0887 22.263653 22.47598 + 740 12.638847 -2873.7524 22.231544 22.473103 + 750 12.560388 -2873.4976 22.207229 22.470197 + 760 12.500634 -2873.3389 22.191608 22.467277 + 770 12.46088 -2873.2928 22.185044 22.464357 + 780 12.441476 -2873.3551 22.187384 22.46145 + 790 12.441898 -2873.5323 22.198021 22.458571 + 800 12.46082 -2873.805 22.215988 22.455733 + 810 12.49627 -2874.168 22.240082 22.452947 + 820 12.545761 -2874.6084 22.268974 22.450223 + 830 12.606442 -2875.1154 22.30132 22.447568 + 840 12.675209 -2875.662 22.335827 22.444987 + 850 12.748831 -2876.2487 22.37131 22.442482 + 860 12.82405 -2876.8458 22.406711 22.440055 + 870 12.897672 -2877.4308 22.441104 22.437705 + 880 12.966664 -2877.9918 22.473679 22.435429 + 890 13.028239 -2878.5162 22.503727 22.433223 + 900 13.079989 -2878.9972 22.530647 22.431081 + 910 13.120007 -2879.4076 22.553961 22.428997 + 920 13.147015 -2879.7527 22.573337 22.426963 + 930 13.16047 -2880.0242 22.58862 22.424972 + 940 13.160646 -2880.2274 22.59987 22.423016 + 950 13.148646 -2880.3654 22.607373 22.421086 + 960 13.126349 -2880.4343 22.611652 22.419177 + 970 13.096257 -2880.4731 22.613422 22.417282 + 980 13.061264 -2880.4808 22.61352 22.415397 + 990 13.024335 -2880.4734 22.612794 22.413521 + 1000 12.988154 -2880.4712 22.611974 22.411652 + 1010 12.954832 -2880.4752 22.61156 22.409791 + 1020 12.925706 -2880.5039 22.611782 22.407939 + 1030 12.901268 -2880.5535 22.612583 22.406098 + 1040 12.88122 -2880.6284 22.613671 22.404269 + 1050 12.864638 -2880.7185 22.614595 22.402454 + 1060 12.850161 -2880.8186 22.614818 22.400653 + 1070 12.836182 -2880.9229 22.613762 22.398864 + 1080 12.820975 -2881.0195 22.610813 22.397087 + 1090 12.802812 -2881.1106 22.605315 22.395317 + 1100 12.780035 -2881.173 22.596564 22.39355 + 1110 12.751178 -2881.197 22.583861 22.391781 + 1120 12.715144 -2881.1906 22.566647 22.390003 + 1130 12.671396 -2881.1397 22.544644 22.388208 + 1140 12.620084 -2881.0462 22.517962 22.386389 + 1150 12.562182 -2880.9131 22.487201 22.384538 + 1160 12.499543 -2880.7564 22.453506 22.382651 + 1170 12.434887 -2880.5794 22.418573 22.380722 + 1180 12.371719 -2880.4084 22.384601 22.378752 + 1190 12.314101 -2880.2706 22.354147 22.376742 + 1200 12.266306 -2880.174 22.329904 22.374701 + 1210 12.232344 -2880.154 22.31439 22.372639 + 1220 12.215387 -2880.2186 22.309572 22.370571 + 1230 12.217218 -2880.3818 22.316512 22.368514 + 1240 12.237824 -2880.6446 22.335104 22.366485 + 1250 12.275283 -2880.9982 22.36402 22.364503 + 1260 12.325989 -2881.4247 22.400878 22.362581 + 1270 12.385157 -2881.8965 22.442588 22.360729 + 1280 12.447441 -2882.39 22.485773 22.358953 + 1290 12.507528 -2882.8684 22.527171 22.357252 + 1300 12.560627 -2883.3106 22.563936 22.355622 + 1310 12.602763 -2883.7013 22.59382 22.354054 + 1320 12.630896 -2884.014 22.615213 22.352535 + 1330 12.642918 -2884.2415 22.627102 22.351052 + 1340 12.63759 -2884.376 22.628986 22.349588 + 1350 12.614465 -2884.4144 22.620781 22.348128 + 1360 12.573824 -2884.3577 22.602735 22.346656 + 1370 12.516666 -2884.2059 22.575396 22.345156 + 1380 12.444674 -2883.9691 22.539592 22.343613 + 1390 12.360208 -2883.6693 22.496432 22.342016 + 1400 12.266237 -2883.307 22.447301 22.340354 +Loop time of 294.852 on 4 procs for 1000 steps with 1792 atoms + +Pair time (%) = 3.79985 (1.28873) +Neigh time (%) = 0.0335855 (0.0113906) +Comm time (%) = 18.051 (6.12205) +Outpt time (%) = 3.2335 (1.09665) +Other time (%) = 269.734 (91.4812) + +Nlocal: 448 ave 448 max 448 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 696 ave 696 max 696 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 52292.2 ave 52503 max 52099 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +FullNghs: 104584 ave 104823 max 104416 min +Histogram: 1 1 0 0 1 0 0 0 0 1 + +Total # of neighbors = 418338 +Ave neighs/atom = 233.448 +Neighbor list builds = 2 +Dangerous builds = 0 diff --git a/examples/USER/atc/mesh/gaussianIC2d_hex20_uniform.screen b/examples/USER/atc/mesh/gaussianIC2d_hex20_uniform.screen new file mode 100644 index 0000000000..65ddc19241 --- /dev/null +++ b/examples/USER/atc/mesh/gaussianIC2d_hex20_uniform.screen @@ -0,0 +1,106 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic + +variable L equal 12 +variable l2 equal 6 +variable l equal 4 +variable w equal 2 + +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region mdInternal block -$l $l -$l $l -$w $w +region mdInternal block -4 $l -$l $l -$w $w +region mdInternal block -4 4 -$l $l -$w $w +region mdInternal block -4 4 -4 $l -$w $w +region mdInternal block -4 4 -4 4 -$w $w +region mdInternal block -4 4 -4 4 -2 $w +region mdInternal block -4 4 -4 4 -2 2 + +boundary f f f # p +pair_style lj/cut 13.5 +read_data temp.init +Reading data file ... + orthogonal box = (-64.86 -64.86 -10.81) to (64.86 64.86 10.81) + 2 by 2 by 1 MPI processor grid + 2304 atoms + 2304 velocities +fix ZWALLS all wall/reflect zlo EDGE zhi EDGE +mass 1 39.95 +pair_coeff 1 1 .238 3.405 13.5 +group internal region mdInternal +1024 atoms in group internal + +fix AtC internal atc two_temperature Ar_ttm.mat +ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat + ATC: peratom PE compute created with ID: 3 + ATC: 2 materials defined from Ar_ttm.mat + ATC: creating two_temperature extrinsic model + ATC: 2 materials defined from Ar_ttm.mat +fix_modify AtC mesh read gaussianIC2d_hex20_uniform.mesh + ATC: read 803 nodes + ATC: read 100 HEX20 elements + ATC: created nodeset 11 with 53 nodes + ATC: created nodeset 12 with 53 nodes + ATC: WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive +fix_modify AtC output gaussianIC2d_hex20_uniformFE 10 full_text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + + +fix_modify AtC initial temperature all 20.0 +# NOTE this is only gaussian in x +fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 +fix_modify AtC fix temperature 11 20.0 +fix_modify AtC fix temperature 12 20.0 +fix_modify AtC control thermal flux +fix_modify AtC extrinsic exchange on +fix_modify AtC extrinsic electron_integration explicit 10 + +thermo_style custom step temp pe f_AtC[2] f_AtC[4] +timestep 1.0 +thermo 10 +run 100 +Setting up run ... +DiagonalMatrix::inv(): Warning: Matrix is badly scaled. RCOND = -0.1875 +DiagonalMatrix::inv(): Warning: Matrix is badly scaled. RCOND = -0.1875 +DiagonalMatrix::inv(): Warning: Matrix is badly scaled. RCOND = -0.1875 +DiagonalMatrix::inv(): Warning: Matrix is badly scaled. RCOND = -0.1875 +DiagonalMatrix::inv(): Warning: Matrix is badly scaled. RCOND = -0.1875 +DiagonalMatrix::inv(): Warning: Matrix is badly scaled. RCOND = -0.1875 +DiagonalMatrix::inv(): Warning: Matrix is badly scaled. RCOND = -0.1875 +DiagonalMatrix::inv(): Warning: Matrix is badly scaled. RCOND = -0.1875 +Memory usage per processor = 115.483 Mbytes +Step Temp PotEng AtC[2] AtC[4] + 0 9.9496068 -3732.5766 20 21.685336 + 10 9.9699944 -3732.6743 20.008305 21.694995 + 20 9.9879237 -3732.7594 20.015777 21.704833 + 30 10.002475 -3732.8273 20.02158 21.714852 + 40 10.013007 -3732.8613 20.025464 21.725057 + 50 10.019238 -3732.8657 20.027325 21.735449 + 60 10.021286 -3732.8402 20.027223 21.746031 + 70 10.019648 -3732.7833 20.025372 21.756808 + 80 10.015134 -3732.7051 20.022115 21.767782 + 90 10.008795 -3732.612 20.017899 21.778957 + 100 10.001827 -3732.5177 20.013234 21.790338 +Loop time of 19.9066 on 4 procs for 100 steps with 2304 atoms + +Pair time (%) = 0.396025 (1.98942) +Neigh time (%) = 0 (0) +Comm time (%) = 0.421989 (2.11984) +Outpt time (%) = 0.125925 (0.63258) +Other time (%) = 18.9627 (95.2582) + +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 720 ave 720 max 720 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 67354.5 ave 67632 max 66958 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +FullNghs: 134709 ave 134859 max 134422 min +Histogram: 1 0 0 0 0 0 0 1 1 1 + +Total # of neighbors = 538836 +Ave neighs/atom = 233.87 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/mesh/gaussianIC2d_hex27_uniform.screen b/examples/USER/atc/mesh/gaussianIC2d_hex27_uniform.screen new file mode 100644 index 0000000000..38cd4e350e --- /dev/null +++ b/examples/USER/atc/mesh/gaussianIC2d_hex27_uniform.screen @@ -0,0 +1,98 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic + +variable L equal 12 +variable l2 equal 6 +variable l equal 4 +variable w equal 2 + +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region mdInternal block -$l $l -$l $l -$w $w +region mdInternal block -4 $l -$l $l -$w $w +region mdInternal block -4 4 -$l $l -$w $w +region mdInternal block -4 4 -4 $l -$w $w +region mdInternal block -4 4 -4 4 -$w $w +region mdInternal block -4 4 -4 4 -2 $w +region mdInternal block -4 4 -4 4 -2 2 + +boundary f f f # p +pair_style lj/cut 13.5 +read_data temp.init +Reading data file ... + orthogonal box = (-64.86 -64.86 -10.81) to (64.86 64.86 10.81) + 2 by 2 by 1 MPI processor grid + 2304 atoms + 2304 velocities +fix ZWALLS all wall/reflect zlo EDGE zhi EDGE +mass 1 39.95 +pair_coeff 1 1 .238 3.405 13.5 +group internal region mdInternal +1024 atoms in group internal + +fix AtC internal atc two_temperature Ar_ttm.mat +ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat + ATC: peratom PE compute created with ID: 3 + ATC: 2 materials defined from Ar_ttm.mat + ATC: creating two_temperature extrinsic model + ATC: 2 materials defined from Ar_ttm.mat +fix_modify AtC mesh read gaussianIC2d_hex27_uniform.mesh + ATC: read 1323 nodes + ATC: read 100 HEX27 elements + ATC: created nodeset 11 with 63 nodes + ATC: created nodeset 12 with 63 nodes + ATC: WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive +fix_modify AtC output gaussianIC2d_hex27_uniformFE 10 full_text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + + +fix_modify AtC initial temperature all 20.0 +# NOTE this is only gaussian in x +fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 +fix_modify AtC fix temperature 11 20.0 +fix_modify AtC fix temperature 12 20.0 +fix_modify AtC control thermal flux +fix_modify AtC extrinsic exchange on +fix_modify AtC extrinsic electron_integration explicit 10 + +thermo_style custom step temp pe f_AtC[2] f_AtC[4] +timestep 1.0 +thermo 10 +run 100 +Setting up run ... +Memory usage per processor = 151.827 Mbytes +Step Temp PotEng AtC[2] AtC[4] + 0 9.9496068 -3732.5766 20 21.562235 + 10 9.9699622 -3732.6743 20.007315 21.548252 + 20 9.9878746 -3732.7599 20.014881 21.535376 + 30 10.002549 -3732.8288 20.02203 21.523502 + 40 10.013448 -3732.8655 20.028514 21.512538 + 50 10.020357 -3732.8733 20.034158 21.502398 + 60 10.023429 -3732.8538 20.038874 21.493003 + 70 10.02316 -3732.8028 20.042672 21.484284 + 80 10.020335 -3732.7341 20.045647 21.476176 + 90 10.015946 -3732.6496 20.047969 21.468622 + 100 10.011086 -3732.5676 20.049857 21.461569 +Loop time of 21.8378 on 4 procs for 100 steps with 2304 atoms + +Pair time (%) = 0.387772 (1.77569) +Neigh time (%) = 0 (0) +Comm time (%) = 0.458654 (2.10028) +Outpt time (%) = 0.208197 (0.95338) +Other time (%) = 20.7831 (95.1706) + +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 720 ave 720 max 720 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 67354.5 ave 67632 max 66958 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +FullNghs: 134709 ave 134859 max 134422 min +Histogram: 1 0 0 0 0 0 0 1 1 1 + +Total # of neighbors = 538836 +Ave neighs/atom = 233.87 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/mesh/gaussianIC2d_hex_uniform.screen b/examples/USER/atc/mesh/gaussianIC2d_hex_uniform.screen new file mode 100644 index 0000000000..88a0537202 --- /dev/null +++ b/examples/USER/atc/mesh/gaussianIC2d_hex_uniform.screen @@ -0,0 +1,124 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic + +variable L equal 12 +variable l2 equal 6 +variable l equal 4 +variable w equal 2 + +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region mdInternal block -$l $l -$l $l -$w $w +region mdInternal block -4 $l -$l $l -$w $w +region mdInternal block -4 4 -$l $l -$w $w +region mdInternal block -4 4 -4 $l -$w $w +region mdInternal block -4 4 -4 4 -$w $w +region mdInternal block -4 4 -4 4 -2 $w +region mdInternal block -4 4 -4 4 -2 2 + +boundary f f f # p +pair_style lj/cut 13.5 +read_data temp.init +Reading data file ... + orthogonal box = (-64.86 -64.86 -10.81) to (64.86 64.86 10.81) + 2 by 2 by 1 MPI processor grid + 2304 atoms + 2304 velocities +fix ZWALLS all wall/reflect zlo EDGE zhi EDGE +mass 1 39.95 +pair_coeff 1 1 .238 3.405 13.5 +group internal region mdInternal +1024 atoms in group internal + +fix AtC internal atc two_temperature Ar_ttm.mat +ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat +terminate called after throwing an instance of ' ATC: peratom PE compute created with ID: 3 + ATC: 2 materials defined from Ar_ttm.mat + ATC: creating two_temperature extrinsic model + ATC: 2 materials defined from Ar_ttm.mat +#fix_modify AtC mesh read gaussianIC2d_hex_uniform.mesh f f p +fix_modify AtC mesh read gaussianIC2d_hex_uniform.exo f f p + ATC: P0, ERROR: mesh file is of unknown type. +ATC::ATC_Error' +[pharsalus:35393] *** Process received signal *** +[pharsalus:35393] Signal: Aborted (6) +[pharsalus:35393] Signal code: (-6) +[pharsalus:35393] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500] +[pharsalus:35393] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5] +[pharsalus:35393] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085] +[pharsalus:35393] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d] +[pharsalus:35393] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6] +[pharsalus:35393] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13] +[pharsalus:35393] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96] +[pharsalus:35393] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x68b090] +[pharsalus:35393] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x6b31d9] +[pharsalus:35393] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x792edb] +[pharsalus:35393] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7949bc] +[pharsalus:35393] [11] ../../../lmp_openmpi(main+0x49) [0x7a28f9] +[pharsalus:35393] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd] +[pharsalus:35393] [13] ../../../lmp_openmpi() [0x537209] +[pharsalus:35393] *** End of error message *** + ATC: P1, ERROR: mesh file is of unknown type. + ATC: P2, ERROR: mesh file is of unknown type. +terminate called after throwing an instance of 'ATC::ATC_Error' +terminate called after throwing an instance of 'ATC::ATC_Error' +[pharsalus:35404] *** Process received signal *** +[pharsalus:35404] Signal: Aborted (6) +[pharsalus:35404] Signal code: (-6) +[pharsalus:35396] *** Process received signal *** +[pharsalus:35396] Signal: Aborted (6) +[pharsalus:35396] Signal code: (-6) +[pharsalus:35404] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500] +[pharsalus:35404] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5] +[pharsalus:35404] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085] +[pharsalus:35404] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d] +[pharsalus:35404] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6] +[pharsalus:35404] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13] +[pharsalus:35404] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96] +[pharsalus:35404] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x68b090] +[pharsalus:35404] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x6b31d9] +[pharsalus:35404] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x792edb] +[pharsalus:35404] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7949bc] +[pharsalus:35404] [11] ../../../lmp_openmpi(main+0x49) [0x7a28f9] +[pharsalus:35404] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd] +[pharsalus:35404] [13] ../../../lmp_openmpi() [0x537209] +[pharsalus:35404] *** End of error message *** +[pharsalus:35396] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500] +[pharsalus:35396] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5] +[pharsalus:35396] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085] +[pharsalus:35396] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d] +[pharsalus:35396] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6] +[pharsalus:35396] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13] +[pharsalus:35396] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96] +[pharsalus:35396] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x68b090] +[pharsalus:35396] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x6b31d9] +[pharsalus:35396] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x792edb] +[pharsalus:35396] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7949bc] +[pharsalus:35396] [11] ../../../lmp_openmpi(main+0x49) [0x7a28f9] +[pharsalus:35396] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd] +[pharsalus:35396] [13] ../../../lmp_openmpi() [0x537209] +[pharsalus:35396] *** End of error message *** + ATC: P3, ERROR: mesh file is of unknown type. +terminate called after throwing an instance of 'ATC::ATC_Error' +[pharsalus:35408] *** Process received signal *** +[pharsalus:35408] Signal: Aborted (6) +[pharsalus:35408] Signal code: (-6) +[pharsalus:35408] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500] +[pharsalus:35408] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5] +[pharsalus:35408] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085] +[pharsalus:35408] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d] +[pharsalus:35408] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6] +[pharsalus:35408] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13] +[pharsalus:35408] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96] +[pharsalus:35408] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x70) [0x68b090] +[pharsalus:35408] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x6b31d9] +[pharsalus:35408] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x792edb] +[pharsalus:35408] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7949bc] +[pharsalus:35408] [11] ../../../lmp_openmpi(main+0x49) [0x7a28f9] +[pharsalus:35408] [12] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd] +[pharsalus:35408] [13] ../../../lmp_openmpi() [0x537209] +[pharsalus:35408] *** End of error message *** +-------------------------------------------------------------------------- +mpirun noticed that process rank 2 with PID 35404 on node pharsalus exited on signal 6 (Aborted). +-------------------------------------------------------------------------- diff --git a/examples/USER/atc/mesh/gaussianIC2d_tet.screen b/examples/USER/atc/mesh/gaussianIC2d_tet.screen new file mode 100644 index 0000000000..d63a1529e8 --- /dev/null +++ b/examples/USER/atc/mesh/gaussianIC2d_tet.screen @@ -0,0 +1,101 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic + +variable L equal 12 +variable l2 equal 6 +variable l equal 4 +variable w equal 2 + +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region mdInternal block -$l $l -$l $l -$w $w +region mdInternal block -4 $l -$l $l -$w $w +region mdInternal block -4 4 -$l $l -$w $w +region mdInternal block -4 4 -4 $l -$w $w +region mdInternal block -4 4 -4 4 -$w $w +region mdInternal block -4 4 -4 4 -2 $w +region mdInternal block -4 4 -4 4 -2 2 + +boundary f f f # p +pair_style lj/cut 13.5 +read_data temp.init +Reading data file ... + orthogonal box = (-64.86 -64.86 -10.81) to (64.86 64.86 10.81) + 2 by 2 by 1 MPI processor grid + 2304 atoms + 2304 velocities +fix ZWALLS all wall/reflect zlo EDGE zhi EDGE +mass 1 39.95 +pair_coeff 1 1 .238 3.405 13.5 +group internal region mdInternal +1024 atoms in group internal + +fix AtC internal atc two_temperature Ar_ttm.mat +ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat + ATC: peratom PE compute created with ID: 3 + ATC: 2 materials defined from Ar_ttm.mat + ATC: creating two_temperature extrinsic model + ATC: 2 materials defined from Ar_ttm.mat +fix_modify AtC mesh read gaussianIC2d_tet.mesh + ATC: read 485 nodes + ATC: read 1856 TET4 elements + ATC: created nodeset 11 with 32 nodes + ATC: created nodeset 12 with 32 nodes + ATC: WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive +#fix_modify AtC mesh read gaussianIC2d_tet.exo +fix_modify AtC mesh write parsed_gaussianIC2d_tet.mesh +fix_modify AtC mesh output parsed_gaussianIC2d_tetMESH +fix_modify AtC output gaussianIC2d_tetFE 10 full_text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + + +fix_modify AtC initial temperature all 20.0 +# NOTE this is only gaussian in x +fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 +fix_modify AtC fix temperature 11 20.0 +fix_modify AtC fix temperature 12 20.0 +fix_modify AtC control thermal flux +fix_modify AtC extrinsic exchange on +fix_modify AtC extrinsic electron_integration explicit 10 + +thermo_style custom step temp pe f_AtC[2] f_AtC[4] +timestep 1.0 +thermo 10 +run 100 +Setting up run ... +Memory usage per processor = 32.4132 Mbytes +Step Temp PotEng AtC[2] AtC[4] + 0 9.9496068 -3732.5766 20 21.692124 + 10 9.9724484 -3732.6738 20.007206 21.687471 + 20 9.9926238 -3732.757 20.013879 21.682923 + 30 10.009028 -3732.8203 20.019195 21.678475 + 40 10.02084 -3732.8482 20.022822 21.674117 + 50 10.027595 -3732.8423 20.02456 21.669843 + 60 10.029238 -3732.8013 20.024358 21.665645 + 70 10.026101 -3732.7238 20.022321 21.661517 + 80 10.018854 -3732.6191 20.018692 21.657452 + 90 10.008439 -3732.4929 20.013835 21.653444 + 100 9.995993 -3732.3576 20.008205 21.649488 +Loop time of 62.5354 on 4 procs for 100 steps with 2304 atoms + +Pair time (%) = 0.465697 (0.744692) +Neigh time (%) = 0 (0) +Comm time (%) = 1.19777 (1.91534) +Outpt time (%) = 0.132981 (0.212649) +Other time (%) = 60.739 (97.1273) + +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 720 ave 720 max 720 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 67354.5 ave 67632 max 66958 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +FullNghs: 134709 ave 134859 max 134422 min +Histogram: 1 0 0 0 0 0 0 1 1 1 + +Total # of neighbors = 538836 +Ave neighs/atom = 233.87 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/mesh/in.gaussianIC1d_hex b/examples/USER/atc/mesh/in.gaussianIC1d_hex new file mode 100644 index 0000000000..f1a4356ada --- /dev/null +++ b/examples/USER/atc/mesh/in.gaussianIC1d_hex @@ -0,0 +1,56 @@ +echo both +units real +atom_style atomic + +lattice fcc 5.405 origin 0.25 0.25 0.25 +region mdRegion block -12 12 -3 3 -3 3 +region mdInternal block -10 10 -3 3 -3 3 + +# create atoms +boundary f p p +create_box 1 mdRegion +create_atoms 1 region mdRegion +mass 1 39.95 +pair_style lj/cut 13.5 +pair_coeff 1 1 .238 3.405 13.5 + +# specify interal/ghost atoms +group internal region mdInternal +velocity internal create 40 87287 mom yes loop geom # <<< NOTE + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# ID group atc PhysicsType ParameterFile +fix AtC internal atc two_temperature Ar_ttm.mat + +fix_modify AtC mesh read gaussianIC1d_hex.mesh + +# fix a temperature +fix_modify AtC fix temperature all 20.0 +fix_modify AtC initial temperature all 20.0 +fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 +fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 + +# turn on thermostat +fix_modify AtC extrinsic exchange off +fix_modify AtC control thermal rescale 10 + +# equilibrate MD field +timestep 5.0 +thermo 10 + +#output +fix_modify AtC output gaussianIC1d_hexFE 10 text + +# change thermostat +fix_modify AtC unfix temperature all +fix_modify AtC unfix electron_temperature all +fix_modify AtC control thermal flux +fix_modify AtC extrinsic exchange on +fix_modify AtC extrinsic electron_integration explicit 10 + +# run with FE +thermo_style custom step temp pe f_AtC[2] f_AtC[4] +reset_timestep 0 +run 100 # 400 diff --git a/examples/USER/atc/mesh/in.gaussianIC2d_hex b/examples/USER/atc/mesh/in.gaussianIC2d_hex new file mode 100644 index 0000000000..2d148b1cb2 --- /dev/null +++ b/examples/USER/atc/mesh/in.gaussianIC2d_hex @@ -0,0 +1,69 @@ +echo both +units real +atom_style atomic + +variable L equal 12 +variable l2 equal 6 +variable l equal 4 +variable w equal 2 + +lattice fcc 5.405 origin 0.25 0.25 0.25 +region mdRegion cylinder z 0. 0. ${l2} -$w $w +region mdInternal cylinder z 0. 0. $l -$w $w + +boundary f f f +pair_style lj/cut 13.5 +read_data circle_temp.init +fix ZWALLS all wall/reflect zlo EDGE zhi EDGE +mass 1 39.95 +pair_coeff 1 1 .238 3.405 13.5 +group internal region mdInternal +group ghost subtract all internal + +fix AtC internal atc two_temperature Ar_ttm.mat +# computational geometry +fix_modify AtC mesh read gaussianIC2d_hex.mesh +#fix_modify AtC mesh read gaussianIC2d_hex.exo +#fix_modify AtC mesh read gaussianIC2d_hex2.exo +#fix_modify AtC mesh read gaussianIC2d_hex2.mesh +fix_modify AtC mesh write parsed_gaussianIC2d_hex.mesh +fix_modify AtC mesh output gaussianIC2d_hexMESH +fix_modify AtC boundary ghost +# numerical parameters +fix_modify AtC time_integration fractional_step +fix_modify AtC internal_quadrature off + +# initial conditions +fix_modify AtC fix temperature all 20.0 +# NOTE this is only gaussian in x +fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 + +# thermostat +fix_modify AtC control thermal rescale 10 +fix_modify AtC extrinsic exchange off + +# run to equilibrate +thermo_style custom step temp pe f_AtC[2] f_AtC[4] +timestep 1.0 +thermo 10 +run 400 + +# boundary conditions +fix_modify AtC unfix temperature all +fix_modify AtC unfix electron_temperature all +fix_modify AtC fix temperature 11 20.0 +fix_modify AtC fix temperature 12 20.0 + +# numerical parameters +fix_modify AtC extrinsic electron_integration explicit 10 + +# thermostat +fix_modify AtC control thermal flux +fix_modify AtC extrinsic exchange on + +# output +fix_modify AtC output gaussianIC2d_hexFE 10 full_text binary +dump D1 all atom 10 gaussianIC2d_hex.dmp + +# relax the system +run 1000 diff --git a/examples/USER/atc/mesh/in.gaussianIC2d_hex20_uniform b/examples/USER/atc/mesh/in.gaussianIC2d_hex20_uniform new file mode 100644 index 0000000000..49aa5c084d --- /dev/null +++ b/examples/USER/atc/mesh/in.gaussianIC2d_hex20_uniform @@ -0,0 +1,37 @@ +echo both +units real +atom_style atomic + +variable L equal 12 +variable l2 equal 6 +variable l equal 4 +variable w equal 2 + +lattice fcc 5.405 origin 0.25 0.25 0.25 +region mdInternal block -$l $l -$l $l -$w $w + +boundary f f f # p +pair_style lj/cut 13.5 +read_data temp.init +fix ZWALLS all wall/reflect zlo EDGE zhi EDGE +mass 1 39.95 +pair_coeff 1 1 .238 3.405 13.5 +group internal region mdInternal + +fix AtC internal atc two_temperature Ar_ttm.mat +fix_modify AtC mesh read gaussianIC2d_hex20_uniform.mesh +fix_modify AtC output gaussianIC2d_hex20_uniformFE 10 full_text + +fix_modify AtC initial temperature all 20.0 +# NOTE this is only gaussian in x +fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 +fix_modify AtC fix temperature 11 20.0 +fix_modify AtC fix temperature 12 20.0 +fix_modify AtC control thermal flux +fix_modify AtC extrinsic exchange on +fix_modify AtC extrinsic electron_integration explicit 10 + +thermo_style custom step temp pe f_AtC[2] f_AtC[4] +timestep 1.0 +thermo 10 +run 100 diff --git a/examples/USER/atc/mesh/in.gaussianIC2d_hex27_uniform b/examples/USER/atc/mesh/in.gaussianIC2d_hex27_uniform new file mode 100644 index 0000000000..897d420b2f --- /dev/null +++ b/examples/USER/atc/mesh/in.gaussianIC2d_hex27_uniform @@ -0,0 +1,37 @@ +echo both +units real +atom_style atomic + +variable L equal 12 +variable l2 equal 6 +variable l equal 4 +variable w equal 2 + +lattice fcc 5.405 origin 0.25 0.25 0.25 +region mdInternal block -$l $l -$l $l -$w $w + +boundary f f f # p +pair_style lj/cut 13.5 +read_data temp.init +fix ZWALLS all wall/reflect zlo EDGE zhi EDGE +mass 1 39.95 +pair_coeff 1 1 .238 3.405 13.5 +group internal region mdInternal + +fix AtC internal atc two_temperature Ar_ttm.mat +fix_modify AtC mesh read gaussianIC2d_hex27_uniform.mesh +fix_modify AtC output gaussianIC2d_hex27_uniformFE 10 full_text + +fix_modify AtC initial temperature all 20.0 +# NOTE this is only gaussian in x +fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 +fix_modify AtC fix temperature 11 20.0 +fix_modify AtC fix temperature 12 20.0 +fix_modify AtC control thermal flux +fix_modify AtC extrinsic exchange on +fix_modify AtC extrinsic electron_integration explicit 10 + +thermo_style custom step temp pe f_AtC[2] f_AtC[4] +timestep 1.0 +thermo 10 +run 100 diff --git a/examples/USER/atc/mesh/in.gaussianIC2d_tet b/examples/USER/atc/mesh/in.gaussianIC2d_tet new file mode 100644 index 0000000000..6e5c0d7dd6 --- /dev/null +++ b/examples/USER/atc/mesh/in.gaussianIC2d_tet @@ -0,0 +1,40 @@ +echo both +units real +atom_style atomic + +variable L equal 12 +variable l2 equal 6 +variable l equal 4 +variable w equal 2 + +lattice fcc 5.405 origin 0.25 0.25 0.25 +region mdInternal block -$l $l -$l $l -$w $w + +boundary f f f # p +pair_style lj/cut 13.5 +read_data temp.init +fix ZWALLS all wall/reflect zlo EDGE zhi EDGE +mass 1 39.95 +pair_coeff 1 1 .238 3.405 13.5 +group internal region mdInternal + +fix AtC internal atc two_temperature Ar_ttm.mat +fix_modify AtC mesh read gaussianIC2d_tet.mesh +#fix_modify AtC mesh read gaussianIC2d_tet.exo +fix_modify AtC mesh write parsed_gaussianIC2d_tet.mesh +fix_modify AtC mesh output parsed_gaussianIC2d_tetMESH +fix_modify AtC output gaussianIC2d_tetFE 10 full_text + +fix_modify AtC initial temperature all 20.0 +# NOTE this is only gaussian in x +fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 +fix_modify AtC fix temperature 11 20.0 +fix_modify AtC fix temperature 12 20.0 +fix_modify AtC control thermal flux +fix_modify AtC extrinsic exchange on +fix_modify AtC extrinsic electron_integration explicit 10 + +thermo_style custom step temp pe f_AtC[2] f_AtC[4] +timestep 1.0 +thermo 10 +run 100 diff --git a/examples/USER/atc/mesh/in.kernel2d_hex b/examples/USER/atc/mesh/in.kernel2d_hex new file mode 100644 index 0000000000..7b7710a816 --- /dev/null +++ b/examples/USER/atc/mesh/in.kernel2d_hex @@ -0,0 +1,32 @@ +echo both +units real +atom_style atomic + +# correct mass density = 1.0120 +# NOTE the mesh is not currently periodic, so the density estimate is off by a factor of 2 + +variable L equal 6 +variable w equal 2 + +lattice fcc 5.405 origin 0.25 0.25 0.25 +region BOX block -$L $L -$L $L -$w $w + +boundary f f p +create_box 1 BOX +create_atoms 1 region BOX +mass 1 39.95 +pair_style lj/cut 13.5 +pair_coeff 1 1 .238 3.405 13.5 +group internal region BOX + +fix AtC internal atc hardy +fix_modify AtC kernel quartic_cylinder 5.0 +fix_modify AtC mesh read gaussianIC2d_hex.mesh +fix_modify AtC fields add mass_density +fix_modify AtC output kernel2d_hexFE 1 full_text binary +#dump CONFIG all custom 1 kernel2d_hexMD.dmp id type x y z + +thermo_style custom step cpu temp +timestep 0.0 +thermo 1 +run 2 diff --git a/examples/USER/atc/mesh/in.kernel2d_tet b/examples/USER/atc/mesh/in.kernel2d_tet new file mode 100644 index 0000000000..b5bc3832a4 --- /dev/null +++ b/examples/USER/atc/mesh/in.kernel2d_tet @@ -0,0 +1,28 @@ +echo both +units real +atom_style atomic + +variable L equal 6 +variable w equal 2 + +lattice fcc 5.405 origin 0.25 0.25 0.25 +region BOX block -$L $L -$L $L -$w $w + +boundary f f p +create_box 1 BOX +create_atoms 1 region BOX +mass 1 39.95 +pair_style lj/cut 13.5 +pair_coeff 1 1 .238 3.405 13.5 +group internal region BOX + +fix AtC internal atc hardy +fix_modify AtC kernel quartic_sphere 5.0 +fix_modify AtC mesh read gaussianIC2d_tet.mesh +fix_modify AtC fields add mass_density +fix_modify AtC output kernel2d_tetFE 1 full_text binary + +thermo_style custom step cpu temp +timestep 0.0 +thermo 1 +run 2 diff --git a/examples/USER/atc/mesh/in.mesh2d_tet b/examples/USER/atc/mesh/in.mesh2d_tet new file mode 100644 index 0000000000..6bff0ef4fd --- /dev/null +++ b/examples/USER/atc/mesh/in.mesh2d_tet @@ -0,0 +1,29 @@ +echo both +units real +atom_style atomic + +variable L equal 6 +variable w equal 2 + +lattice fcc 5.405 origin 0.25 0.25 0.25 +region BOX block -$L $L -$L $L -$w $w + +boundary f f p +create_box 1 BOX +create_atoms 1 region BOX +mass 1 39.95 +pair_style lj/cut 13.5 +pair_coeff 1 1 .238 3.405 13.5 +group internal region BOX + +fix AtC internal atc field +fix_modify AtC mesh read gaussianIC2d_tet.mesh +fix_modify AtC fields add mass_density +fix_modify AtC output mesh2d_tetFE 1 full_text binary + +dump CONFIG all custom 10 mesh2d_tet.dmp id type x y z + +thermo_style custom step cpu temp +timestep 0.0 +thermo 1 +run 2 diff --git a/examples/USER/atc/mesh/in.semicircle b/examples/USER/atc/mesh/in.semicircle new file mode 100644 index 0000000000..8d0741e44a --- /dev/null +++ b/examples/USER/atc/mesh/in.semicircle @@ -0,0 +1,101 @@ +# this input can be used to generate the benchmark for in.gaussianIC2d_hex_uniform +echo both +units real +atom_style atomic + +variable l equal 8 +variable g equal 2 +variable lg equal $l+$g +variable w equal 2 + +lattice fcc 5.405 origin 0.25 0.25 0.25 +boundary f f f + +# region to create atoms +region bigCyl cylinder z 0. 0. ${lg} -$w $w +region offsetPlane block -${lg} $g -${lg} ${lg} -$w $w +region mdRegion intersect 2 bigCyl offsetPlane +#create_box 1 mdRegion +pair_style lj/cut 13.5 +read_data semicircle_init.atm + +# region for internal atoms +region mdInternalCyl cylinder z 0. 0. $l -$w $w +region leftHalfPlane block INF 0. INF INF INF INF +region mdInternal intersect 2 mdInternalCyl leftHalfPlane + +# region for coupling ghosts +region rightHalfPlane block 0. INF INF INF INF INF +region mdGhost union 2 rightHalfPlane mdInternal side out + +#create_atoms 1 region mdRegion +#create_atoms 1 region mdInternal +#create_atoms 2 region mdGhost +#region outerGhost intersect 2 rightHalfPlane mdRegion +#create_atoms 3 region outerGhost + +#pair_style lj/cut 13.5 +fix ZWALLS all wall/reflect zlo EDGE zhi EDGE +#mass 1 39.95 +#pair_coeff 1 1 .238 3.405 13.5 +group internal region mdInternal +group ghost region mdGhost +#velocity internal create 40 102486 mom yes rot yes dist gaussian +#write_restart semicircle_init.rst + +# ATC commands +fix AtC internal atc thermal Ar_ttm.mat +fix_modify AtC boundary ghost +fix_modify AtC mesh read semicircle.mesh f f p +fix_modify AtC mesh nodeset_to_elementset 2 hole min +fix_modify AtC internal_quadrature off +fix_modify AtC time_integration fractional_step + +# initial conditions +fix_modify AtC fix temperature all 20. +fix_modify AtC control thermal rescale 10 +fix_modify AtC control tolerance 1.e-14 # tolerance needed to produce consistent parallel and serial results + +# initial output +#fix_modify AtC mesh output semicircle_mesh +#fix_modify AtC output semicircle_init 100 text binary +#dump D1 all atom 100 semicircle_init.dmp + +# run +timestep 5.0 +thermo 100 +run 500 + +# boundary conditions +fix_modify AtC unfix temperature all +fix_modify AtC fix temperature 1 20. +fix_modify AtC control thermal flux +fix_modify AtC control localized_lambda on + +# NOTE appears to be a problem with the temporal ramp function +variable delta_t equal 1000*5. +fix_modify AtC source temperature hole temporal_ramp 0. 0.0000000001 ${delta_t} + +# equilibrate filter +fix_modify AtC filter type exponential +fix_modify AtC filter scale 1000. +fix_modify AtC filter on + +# equilibration output +fix_modify AtC output semicircleFE 100 full_text #binary +#undump D1 +#dump D1 all atom 100 semicircle_equil.dmp + +# run +fix_modify AtC reset_time 0. +reset_timestep 0 +thermo 100 +run 1000 + +# heat source +# NOTE second run omitted as it causes diffs in parallel execution after just one timestep, not sure why +#fix_modify AtC source temperature hole 0.0000000001 +#fix_modify AtC output semicircleFE 1 full_text #binary +#undump D1 +#dump D1 all atom 100 semicircle.dmp +#run 1#000 diff --git a/examples/USER/atc/mesh/kernel2d_hex.screen b/examples/USER/atc/mesh/kernel2d_hex.screen new file mode 100644 index 0000000000..d0d8a225a2 --- /dev/null +++ b/examples/USER/atc/mesh/kernel2d_hex.screen @@ -0,0 +1,81 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic + +# correct mass density = 1.0120 +# NOTE the mesh is not currently periodic, so the density estimate is off by a factor of 2 + +variable L equal 6 +variable w equal 2 + +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region BOX block -$L $L -$L $L -$w $w +region BOX block -6 $L -$L $L -$w $w +region BOX block -6 6 -$L $L -$w $w +region BOX block -6 6 -6 $L -$w $w +region BOX block -6 6 -6 6 -$w $w +region BOX block -6 6 -6 6 -2 $w +region BOX block -6 6 -6 6 -2 2 + +boundary f f p +create_box 1 BOX +Created orthogonal box = (-32.43 -32.43 -10.81) to (32.43 32.43 10.81) + 2 by 2 by 1 MPI processor grid +create_atoms 1 region BOX +Created 2304 atoms +mass 1 39.95 +pair_style lj/cut 13.5 +pair_coeff 1 1 .238 3.405 13.5 +group internal region BOX +2304 atoms in group internal + +fix AtC internal atc hardy +ATC: constructing kernel field estimate + ATC: peratom PE compute created with ID: 3 +fix_modify AtC kernel quartic_cylinder 5.0 +fix_modify AtC mesh read gaussianIC2d_hex.mesh + ATC: read 388 nodes + ATC: read 173 HEX8 elements + ATC: created nodeset 11 with 22 nodes + ATC: created nodeset 12 with 22 nodes + ATC: WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive +fix_modify AtC fields add mass_density +fix_modify AtC output kernel2d_hexFE 1 full_text binary + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +#dump CONFIG all custom 1 kernel2d_hexMD.dmp id type x y z + +thermo_style custom step cpu temp +timestep 0.0 +thermo 1 +run 2 +Setting up run ... + ATC: kernel matrix bandwidth 535 +Memory usage per processor = 490.313 Mbytes +Step CPU Temp + 0 0 0 + 1 0.015694857 0 + 2 0.02523303 0 +Loop time of 0.025247 on 4 procs for 2 steps with 2304 atoms + +Pair time (%) = 0.00923944 (36.5961) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000781298 (3.09461) +Outpt time (%) = 0.00327528 (12.9729) +Other time (%) = 0.011951 (47.3364) + +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2664 ave 2664 max 2664 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 91072 ave 92484 max 89660 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +FullNghs: 182144 ave 182144 max 182144 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 728576 +Ave neighs/atom = 316.222 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/mesh/kernel2d_tet.screen b/examples/USER/atc/mesh/kernel2d_tet.screen new file mode 100644 index 0000000000..d793477f07 --- /dev/null +++ b/examples/USER/atc/mesh/kernel2d_tet.screen @@ -0,0 +1,77 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic + +variable L equal 6 +variable w equal 2 + +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region BOX block -$L $L -$L $L -$w $w +region BOX block -6 $L -$L $L -$w $w +region BOX block -6 6 -$L $L -$w $w +region BOX block -6 6 -6 $L -$w $w +region BOX block -6 6 -6 6 -$w $w +region BOX block -6 6 -6 6 -2 $w +region BOX block -6 6 -6 6 -2 2 + +boundary f f p +create_box 1 BOX +Created orthogonal box = (-32.43 -32.43 -10.81) to (32.43 32.43 10.81) + 2 by 2 by 1 MPI processor grid +create_atoms 1 region BOX +Created 2304 atoms +mass 1 39.95 +pair_style lj/cut 13.5 +pair_coeff 1 1 .238 3.405 13.5 +group internal region BOX +2304 atoms in group internal + +fix AtC internal atc hardy +ATC: constructing kernel field estimate + ATC: peratom PE compute created with ID: 3 +fix_modify AtC kernel quartic_sphere 5.0 +fix_modify AtC mesh read gaussianIC2d_tet.mesh + ATC: read 485 nodes + ATC: read 1856 TET4 elements + ATC: created nodeset 11 with 32 nodes + ATC: created nodeset 12 with 32 nodes + ATC: WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive +fix_modify AtC fields add mass_density +fix_modify AtC output kernel2d_tetFE 1 full_text binary + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + + +thermo_style custom step cpu temp +timestep 0.0 +thermo 1 +run 2 +Setting up run ... + ATC: kernel matrix bandwidth 551 +Memory usage per processor = 603.85 Mbytes +Step CPU Temp + 0 0 0 + 1 0.0049650669 0 + 2 0.014286995 0 +Loop time of 0.0143003 on 4 procs for 2 steps with 2304 atoms + +Pair time (%) = 0.00910032 (63.6373) +Neigh time (%) = 0 (0) +Comm time (%) = 0.00106293 (7.43293) +Outpt time (%) = 0.00271261 (18.9689) +Other time (%) = 0.00142443 (9.96086) + +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2664 ave 2664 max 2664 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 91072 ave 92484 max 89660 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +FullNghs: 182144 ave 182144 max 182144 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 728576 +Ave neighs/atom = 316.222 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/mesh/mesh2d_tet.screen b/examples/USER/atc/mesh/mesh2d_tet.screen new file mode 100644 index 0000000000..7e5dc1d503 --- /dev/null +++ b/examples/USER/atc/mesh/mesh2d_tet.screen @@ -0,0 +1,77 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic + +variable L equal 6 +variable w equal 2 + +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region BOX block -$L $L -$L $L -$w $w +region BOX block -6 $L -$L $L -$w $w +region BOX block -6 6 -$L $L -$w $w +region BOX block -6 6 -6 $L -$w $w +region BOX block -6 6 -6 6 -$w $w +region BOX block -6 6 -6 6 -2 $w +region BOX block -6 6 -6 6 -2 2 + +boundary f f p +create_box 1 BOX +Created orthogonal box = (-32.43 -32.43 -10.81) to (32.43 32.43 10.81) + 2 by 2 by 1 MPI processor grid +create_atoms 1 region BOX +Created 2304 atoms +mass 1 39.95 +pair_style lj/cut 13.5 +pair_coeff 1 1 .238 3.405 13.5 +group internal region BOX +2304 atoms in group internal + +fix AtC internal atc field +ATC: constructing shape function field estimate + ATC: peratom PE compute created with ID: 3 +fix_modify AtC mesh read gaussianIC2d_tet.mesh + ATC: read 485 nodes + ATC: read 1856 TET4 elements + ATC: created nodeset 11 with 32 nodes + ATC: created nodeset 12 with 32 nodes + ATC: WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive +fix_modify AtC fields add mass_density +fix_modify AtC output mesh2d_tetFE 1 full_text binary + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + + +dump CONFIG all custom 10 mesh2d_tet.dmp id type x y z + +thermo_style custom step cpu temp +timestep 0.0 +thermo 1 +run 2 +Setting up run ... +Memory usage per processor = 11.9239 Mbytes +Step CPU Temp + 0 0 0 + 1 0.0050430298 0 + 2 0.015191078 0 +Loop time of 0.0152113 on 4 procs for 2 steps with 2304 atoms + +Pair time (%) = 0.00921327 (60.5684) +Neigh time (%) = 0 (0) +Comm time (%) = 0.00139874 (9.19539) +Outpt time (%) = 0.00295776 (19.4444) +Other time (%) = 0.00164157 (10.7918) + +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2664 ave 2664 max 2664 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 91072 ave 92484 max 89660 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +FullNghs: 182144 ave 182144 max 182144 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 728576 +Ave neighs/atom = 316.222 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/mesh/semicircle.screen b/examples/USER/atc/mesh/semicircle.screen new file mode 100644 index 0000000000..2437d3bad9 --- /dev/null +++ b/examples/USER/atc/mesh/semicircle.screen @@ -0,0 +1,204 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic + +variable l equal 8 +variable g equal 2 +variable lg equal $l+$g +variable lg equal 8+$g +variable lg equal 8+2 +variable w equal 2 + +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +boundary f f f + +# region to create atoms +region bigCyl cylinder z 0. 0. ${lg} -$w $w +region bigCyl cylinder z 0. 0. 10 -$w $w +region bigCyl cylinder z 0. 0. 10 -2 $w +region bigCyl cylinder z 0. 0. 10 -2 2 +region offsetPlane block -${lg} $g -${lg} ${lg} -$w $w +region offsetPlane block -10 $g -${lg} ${lg} -$w $w +region offsetPlane block -10 2 -${lg} ${lg} -$w $w +region offsetPlane block -10 2 -10 ${lg} -$w $w +region offsetPlane block -10 2 -10 10 -$w $w +region offsetPlane block -10 2 -10 10 -2 $w +region offsetPlane block -10 2 -10 10 -2 2 +region mdRegion intersect 2 bigCyl offsetPlane +#create_box 1 mdRegion +pair_style lj/cut 13.5 +read_data semicircle_init.atm +Reading data file ... + orthogonal box = (-54.05 -54.05 -10.81) to (10.81 54.05 10.81) + 2 by 2 by 1 MPI processor grid + 3168 atoms + 3168 velocities + +# region for internal atoms +region mdInternalCyl cylinder z 0. 0. $l -$w $w +region mdInternalCyl cylinder z 0. 0. 8 -$w $w +region mdInternalCyl cylinder z 0. 0. 8 -2 $w +region mdInternalCyl cylinder z 0. 0. 8 -2 2 +region leftHalfPlane block INF 0. INF INF INF INF +region mdInternal intersect 2 mdInternalCyl leftHalfPlane + +# region for coupling ghosts +region rightHalfPlane block 0. INF INF INF INF INF +region mdGhost union 2 rightHalfPlane mdInternal side out + +#create_atoms 1 region mdRegion +#create_atoms 1 region mdInternal +#create_atoms 2 region mdGhost +#region outerGhost intersect 2 rightHalfPlane mdRegion +#create_atoms 3 region outerGhost + +#pair_style lj/cut 13.5 +fix ZWALLS all wall/reflect zlo EDGE zhi EDGE +#mass 1 39.95 +#pair_coeff 1 1 .238 3.405 13.5 +group internal region mdInternal +1624 atoms in group internal +group ghost region mdGhost +904 atoms in group ghost +#velocity internal create 40 102486 mom yes rot yes dist gaussian +#write_restart semicircle_init.rst + +# ATC commands +fix AtC internal atc thermal Ar_ttm.mat +ATC: constructing thermal coupling with parameter file Ar_ttm.mat + ATC: peratom PE compute created with ID: 3 + ATC: 2 materials defined from Ar_ttm.mat +fix_modify AtC boundary ghost +fix_modify AtC mesh read semicircle.mesh f f p + ATC: P1, writing periodicity corrected mesh: periodic_semicircle.mesh + ATC: P2, writing periodicity corrected mesh: periodic_semicircle.mesh + ATC: P3, writing periodicity corrected mesh: periodic_semicircle.mesh + ATC: read 398 nodes + ATC: read 176 HEX8 elements + ATC: condensed 199 periodic nodes in the 3 direction + ATC: created nodeset 1 with 44 nodes + ATC: created nodeset 2 with 4 nodes + ATC: WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive + ATC: P0, writing periodicity corrected mesh: periodic_semicircle.mesh +fix_modify AtC mesh nodeset_to_elementset 2 hole min +fix_modify AtC internal_quadrature off +fix_modify AtC time_integration fractional_step + +# initial conditions +fix_modify AtC fix temperature all 20. +fix_modify AtC control thermal rescale 10 +fix_modify AtC control tolerance 1.e-14 # tolerance needed to produce consistent parallel and serial results + +# initial output +#fix_modify AtC mesh output semicircle_mesh +#fix_modify AtC output semicircle_init 100 text binary +#dump D1 all atom 100 semicircle_init.dmp + +# run +timestep 5.0 +thermo 100 +run 500 +Setting up run ... +Memory usage per processor = 94.811 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 20.498895 -5250.6971 0 -5057.1829 -1088.0506 + 100 10.255763 -5131.7808 0 -5034.9641 -671.92179 + 200 10.255763 -5194.8934 0 -5098.0766 -664.20614 + 300 10.255763 -5191.6455 0 -5094.8288 -564.44341 + 400 10.255763 -5185.5031 0 -5088.6864 -611.34498 + 500 10.255763 -5185.1021 0 -5088.2853 -686.81479 +Loop time of 15.2128 on 4 procs for 500 steps with 3168 atoms + +Pair time (%) = 2.78663 (18.3176) +Neigh time (%) = 0.0548139 (0.360314) +Comm time (%) = 3.63319 (23.8824) +Outpt time (%) = 0.000398099 (0.00261687) +Other time (%) = 8.73779 (57.437) + +Nlocal: 792 ave 944 max 640 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 860 ave 888 max 832 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 95743.8 ave 114417 max 76793 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 191488 ave 228943 max 153856 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 765950 +Ave neighs/atom = 241.777 +Neighbor list builds = 5 +Dangerous builds = 0 + +# boundary conditions +fix_modify AtC unfix temperature all +fix_modify AtC fix temperature 1 20. +fix_modify AtC control thermal flux +fix_modify AtC control localized_lambda on + +# NOTE appears to be a problem with the temporal ramp function +variable delta_t equal 1000*5. +fix_modify AtC source temperature hole temporal_ramp 0. 0.0000000001 ${delta_t} +fix_modify AtC source temperature hole temporal_ramp 0. 0.0000000001 5000 + +# equilibrate filter +fix_modify AtC filter type exponential +fix_modify AtC filter scale 1000. +fix_modify AtC filter on + +# equilibration output +fix_modify AtC output semicircleFE 100 full_text #binary + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +#undump D1 +#dump D1 all atom 100 semicircle_equil.dmp + +# run +fix_modify AtC reset_time 0. +reset_timestep 0 +thermo 100 +run 1000 +Setting up run ... +Memory usage per processor = 108.386 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 10.255763 -5185.1021 0 -5088.2853 -686.81479 + 100 9.9160769 -5177.6646 0 -5084.0545 -753.44628 + 200 10.215779 -5182.5539 0 -5086.1147 -721.64916 + 300 10.609664 -5183.8798 0 -5083.7222 -672.99308 + 400 10.754797 -5188.6804 0 -5087.1527 -620.77678 + 500 10.271869 -5184.1487 0 -5087.18 -643.71337 + 600 10.214975 -5184.0211 0 -5087.5894 -687.47365 + 700 10.231487 -5182.315 0 -5085.7274 -719.65308 + 800 10.245262 -5181.8268 0 -5085.1092 -707.19351 + 900 10.342331 -5183.9012 0 -5086.2673 -667.21622 + 1000 10.446039 -5184.9612 0 -5086.3482 -647.13367 +Loop time of 83.0725 on 4 procs for 1000 steps with 3168 atoms + +Pair time (%) = 6.33517 (7.62607) +Neigh time (%) = 0.152702 (0.183818) +Comm time (%) = 8.85507 (10.6595) +Outpt time (%) = 0.0723367 (0.0870767) +Other time (%) = 67.6572 (81.4436) + +Nlocal: 792 ave 944 max 640 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 860 ave 888 max 832 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 95600.8 ave 114809 max 76836 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 191202 ave 228917 max 153483 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 764806 +Ave neighs/atom = 241.416 +Neighbor list builds = 8 +Dangerous builds = 0 + +# heat source +# NOTE second run omitted as it causes diffs in parallel execution after just one timestep, not sure why +#fix_modify AtC source temperature hole 0.0000000001 +#fix_modify AtC output semicircleFE 1 full_text #binary +#undump D1 +#dump D1 all atom 100 semicircle.dmp +#run 1#000 diff --git a/examples/USER/atc/molecule/harmonic_bonds.screen b/examples/USER/atc/molecule/harmonic_bonds.screen new file mode 100644 index 0000000000..a344b0382d --- /dev/null +++ b/examples/USER/atc/molecule/harmonic_bonds.screen @@ -0,0 +1,122 @@ +LAMMPS (14 Aug 2013) +units lj +lattice sc 1.0 +Lattice spacing in x,y,z = 1 1 1 +boundary p p p +neighbor 1.0 bin +neigh_modify every 5 delay 0 check yes + +atom_style full +bond_style quartic +#angle_style harmonic +pair_style lj/cut 2.5 +pair_modify table 0 +special_bonds lj 1.0 1.0 1.0 + +read_data harmonic_bonds.data +Scanning data file ... + 6 = max bonds/atom +Reading data file ... + orthogonal box = (-6.54473 -6.54473 -6.54473) to (6.54473 6.54473 6.54473) + 1 by 2 by 2 MPI processor grid + 2100 atoms + 2600 bonds +Finding 1-2 1-3 1-4 neighbors ... + 6 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 16 = max # of 1-4 neighbors + 18 = max # of special neighbors + +# k b1 b2 rc U0 +bond_coeff 1 1434.3 -0.7589 0.00 1.5 67.2234 +pair_coeff * * 1.0 1.0 2.5 + +timestep 0.005 +fix 1 all npt temp 0.3 0.3 1.0 iso 0.1 0.1 10.0 +thermo_style custom step temp etotal evdwl ebond pxx pyy pzz lz +thermo_modify flush yes +thermo 100 +reset_timestep 0 + + +######################################################################## +variable l equal xhi +#region MESH block xlo xhi ylo yhi zlo zhi +region MESH block -$l $l -$l $l -$l $l +region MESH block -6.5447300000000003806 $l -$l $l -$l $l +region MESH block -6.5447300000000003806 6.5447300000000003806 -$l $l -$l $l +region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 $l -$l $l +region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806 -$l $l +region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 $l +region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806 +group MESH region MESH +2100 atoms in group MESH +# ID group atc PhysicsType ParameterFile +fix ATC all atc field +ATC: constructing shape function field estimate + ATC: peratom PE compute created with ID: 5 +fix_modify ATC fields add mass_density energy stress heat_flux +# ID part keywords nx ny nz region +fix_modify ATC mesh create 4 4 1 MESH p p p + ATC: created uniform mesh with 50 nodes, 16 unique nodes, and 16 elements +fix_modify ATC bond_interactions on +fix_modify ATC pair_interactions off +fix_modify ATC output nodeset all average energy +fix_modify ATC output nodeset all average stress +fix_modify ATC output harmonic_bondsFE 100 full_text binary tensor_components + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +######################################################################## + +dump d1 all custom 1000 config.dmp id type mol x y z ix iy iz +run 1000 +Setting up run ... +WARNING: Inconsistent image flags (../domain.cpp:607) + ATC: computing bond matrix ...........done +Memory usage per processor = 22.5059 Mbytes +Step Temp TotEng E_vdwl E_bond Pxx Pyy Pzz Lz + 0 0 27.418101 -4.9222297 32.340331 -6.4375188 -5.3652966 -8.8338595 13.08946 + ATC: computing bond matrix ...........done + 100 2.2145029 25.770666 -4.6618339 27.112327 1.4701161 2.16737 2.7891188 13.107872 + ATC: computing bond matrix ...........done + 200 1.6441119 24.285276 -4.6100702 26.430353 -0.2111306 0.11829479 -0.34968383 13.21971 + ATC: computing bond matrix ...........done + 300 1.2519109 23.218023 -4.7073226 26.048373 -0.90980473 -0.55453672 -1.175576 13.280803 + ATC: computing bond matrix ...........done + 400 1.0087196 22.413664 -4.8800967 25.781401 -0.94622376 -0.72705532 -0.96132435 13.209446 + ATC: computing bond matrix ...........done + 500 0.85508692 21.781946 -5.1146958 25.614623 -0.25867636 0.45882845 -1.5464988 13.067112 + ATC: computing bond matrix ...........done + 600 0.72896043 21.277404 -5.3122654 25.496749 -0.23318524 -0.79102184 -0.28592714 12.940731 + ATC: computing bond matrix ...........done + 700 0.63573201 20.877991 -5.4819279 25.406775 -0.22930105 0.17264694 -0.13977843 12.838254 + ATC: computing bond matrix ...........done + 800 0.54900117 20.560582 -5.6107452 25.348218 -0.40709766 -0.32952441 -0.39623019 12.765768 + ATC: computing bond matrix ...........done + 900 0.4864295 20.309827 -5.7089607 25.289491 0.18995702 -0.4389685 0.32204857 12.716563 + ATC: computing bond matrix ...........done + 1000 0.43059305 20.104384 -5.8079042 25.266707 -0.0082532778 0.34329484 0.20699648 12.673678 +Loop time of 3.13147 on 4 procs for 1000 steps with 2100 atoms + +Pair time (%) = 1.25995 (40.2352) +Bond time (%) = 0.115811 (3.69829) +Neigh time (%) = 0.358909 (11.4614) +Comm time (%) = 0.819216 (26.1607) +Outpt time (%) = 0.038662 (1.23463) +Other time (%) = 0.538919 (17.2098) + +Nlocal: 525 ave 530 max 523 min +Histogram: 2 1 0 0 0 0 0 0 0 1 +Nghost: 3067.75 ave 3080 max 3059 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Neighs: 48006.5 ave 48692 max 47634 min +Histogram: 1 1 1 0 0 0 0 0 0 1 +FullNghs: 96013 ave 97189 max 95320 min +Histogram: 2 0 0 1 0 0 0 0 0 1 + +Total # of neighbors = 384052 +Ave neighs/atom = 182.882 +Ave special neighs/atom = 13.3324 +Neighbor list builds = 28 +Dangerous builds = 0 diff --git a/examples/USER/atc/molecule/in.harmonic_bonds b/examples/USER/atc/molecule/in.harmonic_bonds new file mode 100644 index 0000000000..100a51ba40 --- /dev/null +++ b/examples/USER/atc/molecule/in.harmonic_bonds @@ -0,0 +1,55 @@ +# run018 <017/tolammps.py -> input.lammps +# T->0.3 harmonic->quartic +# Np=900 +# f=6 +# dens = 0.80 +# rigid wall: none + +log harmonic_bonds.log +echo both +units lj +lattice sc 1.0 +boundary p p p +neighbor 1.0 bin +neigh_modify every 5 delay 0 check yes + +atom_style full +bond_style quartic +#angle_style harmonic +pair_style lj/cut 2.5 +pair_modify table 0 +special_bonds lj 1.0 1.0 1.0 + +read_data harmonic_bonds.data + +# k b1 b2 rc U0 +bond_coeff 1 1434.3 -0.7589 0.00 1.5 67.2234 +pair_coeff * * 1.0 1.0 2.5 + +timestep 0.005 +fix 1 all npt temp 0.3 0.3 1.0 iso 0.1 0.1 10.0 +thermo_style custom step temp etotal evdwl ebond pxx pyy pzz lz +thermo_modify flush yes +thermo 100 +reset_timestep 0 + + +######################################################################## +variable l equal xhi +#region MESH block xlo xhi ylo yhi zlo zhi +region MESH block -$l $l -$l $l -$l $l +group MESH region MESH +# ID group atc PhysicsType ParameterFile +fix ATC all atc field +fix_modify ATC fields add mass_density energy stress heat_flux +# ID part keywords nx ny nz region +fix_modify ATC mesh create 4 4 1 MESH p p p +fix_modify ATC bond_interactions on +fix_modify ATC pair_interactions off +fix_modify ATC output nodeset all average energy +fix_modify ATC output nodeset all average stress +fix_modify ATC output harmonic_bondsFE 100 full_text binary tensor_components +######################################################################## + +dump d1 all custom 1000 config.dmp id type mol x y z ix iy iz +run 1000 diff --git a/examples/USER/atc/molecule/in.polarize b/examples/USER/atc/molecule/in.polarize new file mode 100755 index 0000000000..4d6e5457f0 --- /dev/null +++ b/examples/USER/atc/molecule/in.polarize @@ -0,0 +1,119 @@ +### +log log.water + +variable nstepsequil equal 1000000 +variable nsteps equal 100 +variable temp equal 300.0 +variable tdamp equal 0.100 +variable x_dim equal 50 +variable y_dim equal 50 +variable z_fluid equal 37.7919 +variable efieldz equal -0.0723725329978652551934 +variable x_max equal ${x_dim}/2 +variable y_max equal ${y_dim}/2 +variable fluid_half_thickness equal ${z_fluid}/2 +variable buffer equal 2.45 +variable zhiwall equal ${fluid_half_thickness}+${buffer} +variable zlowall equal -${fluid_half_thickness}-${buffer} +variable zmaxatc equal ${fluid_half_thickness}+10 +variable zmaxsub equal ${zmaxatc}-0.1 +variable zmaxsup equal ${zmaxatc}+0.1 + +variable cellatc equal 5 + + +units metal +atom_style full +dimension 3 +newton off +neighbor 2 bin +neigh_modify every 1 delay 1 check no +boundary p p f +kspace_style pppm 1e-5 +kspace_modify slab 3.0 +pair_style lj/cut/coul/long 13.0 13.0 +bond_style harmonic +angle_style harmonic +read_data waterequil.data + + +#velocity all create 0.0 482748 dist uniform + +lattice sc 0.05 + +#region ATC block EDGE EDGE EDGE EDGE -${zmaxatc} ${zmaxatc} units box +#variable nelemelec equal round(2*${zmaxatc}/0.05) +region ATC block EDGE EDGE EDGE EDGE EDGE EDGE units box +# region ATC block EDGE EDGE EDGE EDGE 0.0 0.05 units box +#region ATC block -${fem_atc} ${fem_atc} -${fem_atc} ${fem_atc} -${fem_atc} ${fem_atc} units box +variable nelem equal 2 +# variable nelem equal 1 + +group water type 1 2 +group hyd type 1 +group oxy type 2 + +timestep 0.0005 +dielectric 1.0 + +pair_coeff 1 * 0.0 0.0 +pair_coeff 2 2 0.006596 3.1507 + +bond_coeff 1 19.513855 0.957200 + +angle_coeff 1 2.385027 104.519997 + +special_bonds amber + +#fix 2 all nvt temp ${temp} ${temp} ${tdamp} + +fix lowall oxy wall/lj1043 zlo ${zlowall} 0.1351 3.1507 11.0275 units box +fix hiwall oxy wall/lj1043 zhi ${zhiwall} 0.1351 3.1507 11.0275 units box + +fix efield all efield 0. 0. v_efieldz + +# assign SHAKE fixes +fix 1 all shake 0.00001 500 5000 b 1 a 1 + +thermo 100 +thermo_style custom step temp ke pe etotal f_efield f_lowall f_hiwall + +variable dumpfreq equal 1 + +#dump 1 all atom 500 waterequil.dump +#dump_modify 1 image yes scale no flush yes + +#run ${nstepsequil} + +#write_restart waterequil.restart + +#unfix 2 +fix 3 all nve + +fix AtC all atc hardy +fix_modify AtC mesh create 1 1 ${nelem} ATC p p f +#fix_modify AtC_half mesh create 1 1 ${nelem} ATC p p f +fix_modify AtC kernel cell 25 25 ${cellatc} +fix_modify AtC atom_element_map eulerian ${dumpfreq} +fix_modify AtC fields none +fix_modify AtC fields add dipole_moment mass_density +fix_modify AtC add_molecule small Water water +fix_modify AtC output polarizeFE ${dumpfreq} text vector_components +run ${nsteps} + + +#fix AtCH hyd atc field +#fix_modify AtCH mesh create 1 1 ${nelemelec} ATC p p f +#fix_modify AtCH atom_element_map eulerian ${dumpfreq} +#fix_modify AtCH fields add number_density +#fix_modify AtCH output FEH ${dumpfreq} text binary + +#fix AtCO oxy atc field +#fix_modify AtCO mesh create 1 1 ${nelemelec} ATC p p f +#fix_modify AtCO atom_element_map eulerian ${dumpfreq} +#fix_modify AtCO fields add number_density +#fix_modify AtCO output FEO ${dumpfreq} text binary + +#run ${nsteps} + +#write_restart waterendpolarize.restart diff --git a/examples/USER/atc/molecule/in.quartic_bonds b/examples/USER/atc/molecule/in.quartic_bonds new file mode 100644 index 0000000000..661e72dd90 --- /dev/null +++ b/examples/USER/atc/molecule/in.quartic_bonds @@ -0,0 +1,60 @@ +# run019 <016/tolammps.py -> input.lammps +# T=0.3 harmonic +# Np=900 +# f=6 +# dens = 0.80 +# rigid wall: none + +log quartic_bonds.log +echo both +units lj +lattice sc 1.0 +boundary p p p +neighbor 1.0 bin +neigh_modify every 5 delay 0 check yes + +atom_style full +bond_style harmonic +#angle_style harmonic +pair_style lj/cut 2.5 +pair_modify table 0 +special_bonds lj 0.0 1.0 1.0 + +read_data quartic_bonds.data + +special_bonds lj 0.0 1.0 1.0 + +bond_coeff 1 100.0 1.0 + +pair_coeff * * 1.0 1.0 2.5 + +timestep 0.005 + +fix NPT all npt temp 1.0 1.0 1.0 iso 0.1 0.1 10.0 + +thermo_style custom step temp etotal evdwl ebond pxx pyy pzz lz +thermo_modify flush yes +thermo 100 + +######################################################################## +variable l equal xhi +region MESH block -$l $l -$l $l -$l $l +group MESH region MESH +# ID group atc PhysicsType ParameterFile +fix ATC MESH atc field +fix_modify ATC atom_element_map eulerian 100 +fix_modify ATC fields add mass_density energy stress +## ID part keywords nx ny nz region +fix_modify ATC mesh create 4 4 1 MESH p p p +fix_modify ATC bond_interactions on +fix_modify ATC pair_interactions on +fix_modify ATC output nodeset all average energy +fix_modify ATC output nodeset all average stress +fix_modify ATC output quartic_bondsFE 100 full_text binary tensor_components +######################################################################### + +reset_timestep 0 + +dump d1 all custom 10000 config.dmp id type mol x y z ix iy iz + +run 400 diff --git a/examples/USER/atc/molecule/in.water b/examples/USER/atc/molecule/in.water new file mode 100644 index 0000000000..775749db01 --- /dev/null +++ b/examples/USER/atc/molecule/in.water @@ -0,0 +1,96 @@ +log water.log + +variable nstepsequil equal 500000 +variable nsteps equal 1000#2500000 +variable temp equal 300.0 +variable tdamp equal 0.100 +variable x_dim equal 20 +variable y_dim equal 20 +variable z_fluid equal 30 +variable efieldz equal -5 +variable seed equal 868026 +variable x_max equal ${x_dim}/2 +variable y_max equal ${y_dim}/2 +variable fluid_half_thickness equal ${z_fluid}/2 +#variable zmaxatc equal ${fluid_half_thickness} +#variable zmaxsub equal ${zmaxatc}-0.1 +#variable zmaxsup equal ${zmaxatc}+0.1 + +units metal +atom_style full +dimension 3 +newton off +neighbor 2 bin +neigh_modify every 1 delay 3 check yes +boundary p p p +kspace_style pppm 1e-4 +pair_style lj/cut/coul/long 13.0 9.0 +bond_style harmonic +angle_style harmonic +#read_data waterbox.dat # for equilibration +read_data water.init + +lattice sc 0.05 + +region ATC block EDGE EDGE EDGE EDGE EDGE EDGE units box +#variable nelem equal round(2*${zmaxatc}/0.05) +variable nelem equal 1 + +group water type 1 2 +group hyd type 1 +group oxy type 2 + +timestep 0.0005 +thermo 100 + +thermo_style custom step temp epair emol etotal press + +dielectric 1.0 + +pair_coeff 1 * 0.0 0.0 +pair_coeff 2 2 0.006596 3.1507 +bond_coeff 1 19.513855 0.957200 + +angle_coeff 1 2.385027 104.519997 + +special_bonds amber + +# assign SHAKE fixes +##fix 1 water shake 0.01 3 0 b 1 a 1 + +#velocity all create 0.0 1 rot yes dist uniform # for equilibration + +variable dumpfreq equal 100 + +dump 1 all atom 500 waterequil.dump +dump_modify 1 image yes scale no flush yes + +fix 2 all nvt temp ${temp} ${temp} ${tdamp} + + +fix press_avetime all ave/time 10 1 10 c_thermo_press ave running file pressdata.log + +#run ${nstepsequil} + +fix efield all efield 0. 0. v_efieldz + +#run ${nstepsequil} + +unfix 2 +#fix 3 all nve + +fix AtC all atc species_electrostatic water.mat +fix_modify AtC mesh create 1 1 ${nelem} ATC p p p +fix_modify AtC atom_element_map eulerian ${dumpfreq} +fix_modify AtC internal_quadrature off +fix_modify AtC atom_weight multiscale +fix_modify AtC add_species Hyd type 1 +fix_modify AtC add_species Oxy type 2 +fix_modify AtC add_molecule small Water water +fix_modify AtC fix electric_potential all 0. +fix_modify AtC extrinsic short_range off +fix_modify AtC output waterFE ${dumpfreq} text binary + +run ${nsteps} + +#write_restart water.restart # for equilibration diff --git a/examples/USER/atc/molecule/polarize.screen b/examples/USER/atc/molecule/polarize.screen new file mode 100644 index 0000000000..6b70aef648 --- /dev/null +++ b/examples/USER/atc/molecule/polarize.screen @@ -0,0 +1,26 @@ +LAMMPS (14 Aug 2013) +Scanning data file ... + 2 = max bonds/atom + 1 = max angles/atom +Reading data file ... + orthogonal box = (-25 -25 -21.8959) to (25 25 21.8959) + 2 by 2 by 1 MPI processor grid + 9474 atoms + 9474 velocities + 6316 bonds + 3158 angles +Finding 1-2 1-3 1-4 neighbors ... + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors +Lattice spacing in x,y,z = 0.05 0.05 0.05 +9474 atoms in group water +6316 atoms in group hyd +3158 atoms in group oxy +Finding 1-2 1-3 1-4 neighbors ... + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors +ERROR: Invalid fix style (../modify.cpp:714) diff --git a/examples/USER/atc/molecule/quartic_bonds.screen b/examples/USER/atc/molecule/quartic_bonds.screen new file mode 100644 index 0000000000..d8c36c6880 --- /dev/null +++ b/examples/USER/atc/molecule/quartic_bonds.screen @@ -0,0 +1,115 @@ +LAMMPS (14 Aug 2013) +units lj +lattice sc 1.0 +Lattice spacing in x,y,z = 1 1 1 +boundary p p p +neighbor 1.0 bin +neigh_modify every 5 delay 0 check yes + +atom_style full +bond_style harmonic +#angle_style harmonic +pair_style lj/cut 2.5 +pair_modify table 0 +special_bonds lj 0.0 1.0 1.0 + +read_data quartic_bonds.data +Scanning data file ... + 6 = max bonds/atom +Reading data file ... + orthogonal box = (-6.54473 -6.54473 -6.54473) to (6.54473 6.54473 6.54473) + 1 by 2 by 2 MPI processor grid + 2100 atoms + 2600 bonds +Finding 1-2 1-3 1-4 neighbors ... + 6 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 16 = max # of 1-4 neighbors + 18 = max # of special neighbors + +special_bonds lj 0.0 1.0 1.0 + +bond_coeff 1 100.0 1.0 + +pair_coeff * * 1.0 1.0 2.5 + +timestep 0.005 + +fix NPT all npt temp 1.0 1.0 1.0 iso 0.1 0.1 10.0 + +thermo_style custom step temp etotal evdwl ebond pxx pyy pzz lz +thermo_modify flush yes +thermo 100 + +######################################################################## +variable l equal xhi +region MESH block -$l $l -$l $l -$l $l +region MESH block -6.5447300000000003806 $l -$l $l -$l $l +region MESH block -6.5447300000000003806 6.5447300000000003806 -$l $l -$l $l +region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 $l -$l $l +region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806 -$l $l +region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 $l +region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806 +group MESH region MESH +2100 atoms in group MESH +# ID group atc PhysicsType ParameterFile +fix ATC MESH atc field +ATC: constructing shape function field estimate + ATC: peratom PE compute created with ID: 5 +fix_modify ATC atom_element_map eulerian 100 +fix_modify ATC fields add mass_density energy stress +## ID part keywords nx ny nz region +fix_modify ATC mesh create 4 4 1 MESH p p p + ATC: created uniform mesh with 50 nodes, 16 unique nodes, and 16 elements +fix_modify ATC bond_interactions on +fix_modify ATC pair_interactions on +fix_modify ATC output nodeset all average energy +fix_modify ATC output nodeset all average stress +fix_modify ATC output quartic_bondsFE 100 full_text binary tensor_components + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +######################################################################### + +reset_timestep 0 + +dump d1 all custom 10000 config.dmp id type mol x y z ix iy iz + +run 400 +Setting up run ... +WARNING: Inconsistent image flags (../domain.cpp:607) + ATC: computing bond matrix ..........done +Memory usage per processor = 24.4426 Mbytes +Step Temp TotEng E_vdwl E_bond Pxx Pyy Pzz Lz + 0 0 -4.2793581 -4.9222297 0.64287162 -0.122936 -0.43455241 -0.37510432 13.08946 + ATC: computing bond matrix ..........done + 100 0.51761758 -4.2411444 -5.3350909 0.31788979 -1.8360748 -1.7957803 -1.6501347 13.061394 + ATC: computing bond matrix ..........done + 200 0.55719016 -4.194575 -5.3921735 0.36221126 -0.83902447 -1.0583266 -0.82924205 12.978287 + ATC: computing bond matrix ..........done + 300 0.60702877 -4.114999 -5.4634339 0.43832539 -0.05969492 -0.37357729 0.1227012 12.887908 + ATC: computing bond matrix ..........done + 400 0.67773634 -4.0068285 -5.5021915 0.47924261 0.5562405 0.24275905 0.4181606 12.828709 +Loop time of 27.2369 on 4 procs for 400 steps with 2100 atoms + +Pair time (%) = 0.510639 (1.87481) +Bond time (%) = 0.0195364 (0.0717276) +Neigh time (%) = 0.107538 (0.394826) +Comm time (%) = 1.0591 (3.88848) +Outpt time (%) = 0.088418 (0.324626) +Other time (%) = 25.4517 (93.4455) + +Nlocal: 525 ave 528 max 522 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 3037 ave 3052 max 3022 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Neighs: 45578.5 ave 45912 max 45191 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +FullNghs: 91157 ave 91645 max 90702 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 364628 +Ave neighs/atom = 173.632 +Ave special neighs/atom = 13.3324 +Neighbor list builds = 9 +Dangerous builds = 0 diff --git a/examples/USER/atc/molecule/water.mat b/examples/USER/atc/molecule/water.mat new file mode 100644 index 0000000000..14a37b6f1e --- /dev/null +++ b/examples/USER/atc/molecule/water.mat @@ -0,0 +1,5 @@ +material water metal + electric_field linear + permittivity + end +end diff --git a/examples/USER/atc/molecule/water.screen b/examples/USER/atc/molecule/water.screen new file mode 100644 index 0000000000..55fb7b57f4 --- /dev/null +++ b/examples/USER/atc/molecule/water.screen @@ -0,0 +1,94 @@ +LAMMPS (14 Aug 2013) +Scanning data file ... + 2 = max bonds/atom + 1 = max angles/atom +Reading data file ... + orthogonal box = (-15 -15 -15) to (15 15 15) + 1 by 2 by 2 MPI processor grid + 2709 atoms + 2709 velocities + 1806 bonds + 903 angles +Finding 1-2 1-3 1-4 neighbors ... + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors +Lattice spacing in x,y,z = 0.05 0.05 0.05 +2709 atoms in group water +1806 atoms in group hyd +903 atoms in group oxy +Finding 1-2 1-3 1-4 neighbors ... + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors +ATC: constructing electrostatic species coupling with parameter file water.mat + ATC: peratom PE compute created with ID: 3 + ATC: 1 materials defined from water.mat + ATC: creating fem_efield extrinsic model + ATC: 1 materials defined from water.mat + ATC: created uniform mesh with 8 nodes, 1 unique nodes, and 1 elements + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: +NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationHyd +NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationOxy +species_concentration : species_concentrationHyd +species_concentration : species_concentrationOxy + +PPPM initialization ... + G vector (1/distance) = 0.297171 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00115732 + estimated relative force accuracy = 8.03715e-05 + using double precision FFTs + 3d grid and FFT values/proc = 6400 1620 +Setting up run ... + ATC: WARNING: material: [water] cannot find mass_density + ATC: WARNING: physics model: [species], material: [water] does not provide all interfaces for physics and will be treated as null + ATC: WARNING: all initial conditions for mass_density have not been defined and the undefined are assumed zero + ATC: WARNING: all initial conditions for charge_density have not been defined and the undefined are assumed zero + ATC: WARNING: all initial conditions for species_concentration have not been defined and the undefined are assumed zero + ATC: WARNING: material: [water] cannot find mass_density + ATC: WARNING: physics model: [species electrostatic], material: [water] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 109.05 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 197.00275 -442.89515 0.59348399 -373.34352 21627.063 + 100 829.3047 -532.01992 298.21091 56.477887 47888.516 + 200 742.78324 -696.73237 968.19413 531.46299 -41757.145 + 300 1194.0466 -640.77501 416.31161 193.49647 -47297.597 + 400 722.14402 -655.95913 486.9587 83.776312 -117009.94 + 500 856.93093 -774.82666 955.23125 480.36167 -144380.28 + 600 614.34783 -818.49346 1205.9216 602.47228 -170076.9 + 700 738.19704 -704.05013 689.90234 244.2481 -138086.85 + 800 899.87085 -671.8463 565.65986 208.80118 -105587 + 900 906.34219 -708.2316 826.832 435.85322 -84326.935 + 1000 920.33455 -635.04398 592.63924 279.74592 -40120.926 +Loop time of 77.471 on 4 procs for 1000 steps with 2709 atoms + +Pair time (%) = 55.1982 (71.2501) +Bond time (%) = 0.153222 (0.197779) +Kspce time (%) = 15.7133 (20.2828) +Neigh time (%) = 1.59633 (2.06054) +Comm time (%) = 1.12795 (1.45597) +Outpt time (%) = 0.117281 (0.151386) +Other time (%) = 3.56472 (4.60136) + +FFT time (% of Kspce) = 2.53183 (16.1127) +FFT Gflps 3d (1d only) = 0.399473 3.27799 + +Nlocal: 677.25 ave 694 max 650 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Nghost: 11513.2 ave 11662 max 11354 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Neighs: 821091 ave 848197 max 781864 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +FullNghs: 963818 ave 999880 max 913538 min +Histogram: 1 0 0 0 1 0 0 0 1 1 + +Total # of neighbors = 3855272 +Ave neighs/atom = 1423.13 +Ave special neighs/atom = 2 +Neighbor list builds = 23 +Dangerous builds = 0 diff --git a/examples/USER/atc/svn.stdout b/examples/USER/atc/svn.stdout new file mode 100644 index 0000000000..173788e75b --- /dev/null +++ b/examples/USER/atc/svn.stdout @@ -0,0 +1,226 @@ +Adding atc/cauchy_born +Adding atc/cauchy_born/Ar_CauchyBorn.mat +Adding atc/cauchy_born/Ar_CauchyBorn_linear.mat +Adding atc/cauchy_born/Au_CauchyBorn.mat +Adding atc/cauchy_born/Au_CauchyBorn_linear.mat +Adding atc/cauchy_born/Au_eam.mat +Adding atc/cauchy_born/Au_eam_linear.mat +Adding atc/cauchy_born/Cu_CauchyBorn.mat +Adding atc/cauchy_born/cb_biaxial.screen +Adding atc/cauchy_born/cb_shear.screen +Adding atc/cauchy_born/cb_unistrain.screen +Adding atc/cauchy_born/cb_unistrain_eam.screen +Adding atc/cauchy_born/cb_unistrain_eam_linear.screen +Adding atc/cauchy_born/cb_unistrain_linear.screen +Adding atc/cauchy_born/cb_volumetric.screen +Adding atc/cauchy_born/flying_cube.screen +Adding atc/cauchy_born/ftcb_constV.screen +Adding atc/cauchy_born/in.cb_biaxial +Adding atc/cauchy_born/in.cb_shear +Adding atc/cauchy_born/in.cb_unistrain +Adding atc/cauchy_born/in.cb_unistrain_eam +Adding atc/cauchy_born/in.cb_unistrain_eam_linear +Adding atc/cauchy_born/in.cb_unistrain_linear +Adding atc/cauchy_born/in.cb_volumetric +Adding atc/cauchy_born/in.flying_cube +Adding atc/cauchy_born/in.ftcb_constV +Adding atc/cauchy_born/in.read_xref +Adding atc/cauchy_born/read_xref.screen +Adding atc/drift_diffusion +Adding atc/drift_diffusion/Ar_ddm.mat +Adding atc/drift_diffusion/CNT_ddm.mat +Adding atc/drift_diffusion/Cu_cddm.mat +Adding atc/drift_diffusion/SiGe_ddm_schrodinger.mat +Adding atc/drift_diffusion/SiVacuum_cddm_schrodinger.mat +Adding atc/drift_diffusion/SiVacuum_ddm_schrodinger.mat +Adding atc/drift_diffusion/Si_ddm.mat +Adding atc/drift_diffusion/Si_ddm_eq.mat +Adding atc/drift_diffusion/Si_ddm_schrodinger.mat +Adding atc/drift_diffusion/Si_ddm_thermopower.mat +Adding atc/drift_diffusion/convective_pulse.screen +Adding atc/drift_diffusion/ddm_schrodinger.screen +Adding atc/drift_diffusion/finite_well.screen +Adding atc/drift_diffusion/in.convective_pulse +Adding atc/drift_diffusion/in.ddm_schrodinger +Adding atc/drift_diffusion/in.finite_well +Adding atc/drift_diffusion/in.no_atoms_ddm +Adding atc/drift_diffusion/in.null_material_ddm +Adding atc/drift_diffusion/in.poisson1d_noatoms +Adding atc/drift_diffusion/in.poisson2d_noatoms +Adding atc/drift_diffusion/in.schrodinger-poisson2d_Jconstraint +Adding atc/drift_diffusion/in.schrodinger-poisson2d_convective +Adding atc/drift_diffusion/in.schrodinger-poisson2d_noatoms +Adding atc/drift_diffusion/no_atoms_ddm.screen +Adding atc/drift_diffusion/null_material_ddm.screen +Adding atc/drift_diffusion/poisson1d_noatoms.screen +Adding atc/drift_diffusion/poisson2d_noatoms.screen +Adding atc/drift_diffusion/schrodinger-poisson2d_Jconstraint.screen +Adding atc/drift_diffusion/schrodinger-poisson2d_convective.screen +Adding atc/drift_diffusion/schrodinger-poisson2d_noatoms.screen +Adding atc/dxa +Adding atc/dxa/in.eam_tension_frame +Adding atc/dxa/in.eam_tension_mesh_frame +Adding atc/elastic +Adding atc/elastic/Ar_CauchyBorn.mat +Adding atc/elastic/Ar_CauchyBornLinear.mat +Adding atc/elastic/Ar_damped.mat +Adding atc/elastic/Ar_elastic.mat +Adding atc/elastic/Ar_thermo_elastic.mat +Adding atc/elastic/Au_elastic.mat +Adding atc/elastic/CNT.mat +Adding atc/elastic/CNT_electrostatic.mat +Adding atc/elastic/CNT_electrostatic2.mat +Adding atc/elastic/CNT_id.mat +Adding atc/elastic/bar1d.screen +Adding atc/elastic/bar1d_damped.screen +Adding atc/elastic/bar1d_flux.screen +Adding atc/elastic/bar1d_frac_step.screen +Adding atc/elastic/bar1d_ghost_flux.screen +Adding atc/elastic/bar1d_thermo_elastic.screen +Adding atc/elastic/cnt_electrostatic.screen +Adding atc/elastic/cnt_electrostatic2.screen +Adding atc/elastic/cnt_fixed_charge.screen +Adding atc/elastic/eam_energy.screen +Adding atc/elastic/electron_density.screen +Adding atc/elastic/electrostatic_bending.screen +Adding atc/elastic/electrostatic_bending_dos.screen +Adding atc/elastic/in.bar1d +Adding atc/elastic/in.bar1d_damped +Adding atc/elastic/in.bar1d_flux +Adding atc/elastic/in.bar1d_frac_step +Adding atc/elastic/in.bar1d_ghost_flux +Adding atc/elastic/in.bar1d_thermo_elastic +Adding atc/elastic/in.cnt_electrostatic +Adding atc/elastic/in.cnt_electrostatic2 +Adding atc/elastic/in.cnt_fixed_charge +Adding atc/elastic/in.eam_energy +Adding atc/elastic/in.electron_density +Adding atc/elastic/in.electrostatic_bending +Adding atc/elastic/in.electrostatic_bending_dos +Adding atc/elastic/in.no_atoms +Adding atc/elastic/in.no_atoms_cb +Adding atc/elastic/in.no_atoms_cb_linear +Adding atc/elastic/no_atoms.screen +Adding atc/elastic/no_atoms_cb.screen +Adding atc/elastic/no_atoms_cb_linear.screen +Adding atc/fluids +Adding atc/fluids/Ar_elastic.mat +Adding atc/fluids/Ar_electrostatic.mat +Adding atc/fluids/Ar_liquid.mat +Adding atc/fluids/Ar_species.mat +Adding atc/fluids/Ar_species_dl.mat +Adding atc/fluids/Ar_thermal.mat +Adding atc/fluids/Ar_visc_no_atoms.mat +Adding atc/fluids/Ar_viscosity.mat +Adding atc/fluids/bar1d_fluids.screen +Adding atc/fluids/concentration.screen +Adding atc/fluids/conducting_interface.screen +Adding atc/fluids/dielectric.mat +Adding atc/fluids/dielectric_interface.screen +Adding atc/fluids/double_layer.screen +Adding atc/fluids/in.bar1d_fluids +Adding atc/fluids/in.concentration +Adding atc/fluids/in.conducting_interface +Adding atc/fluids/in.dielectric_interface +Adding atc/fluids/in.double_layer +Adding atc/fluids/in.liquid_electrostatic +Adding atc/fluids/in.opp_force +Adding atc/fluids/in.poisson +Adding atc/fluids/in.shear_flow +Adding atc/fluids/in.shear_no_atoms +Adding atc/fluids/liquid_electrostatic.screen +Adding atc/fluids/opp_force.screen +Adding atc/fluids/poisson.screen +Adding atc/fluids/shear_flow.screen +Adding atc/fluids/shear_no_atoms.screen +Sending atc/hardy/consistency.screen +Sending atc/hardy/eam_kernel_convergence.screen +Sending atc/hardy/eam_unistrain_cell.screen +Sending atc/hardy/eam_unistrain_mesh.screen +Sending atc/hardy/eam_unistrain_qcylinder.screen +Sending atc/hardy/eam_unistrain_qsphere.screen +Sending atc/hardy/eam_unistrain_step.screen +Sending atc/hardy/eam_volume_stretch.screen +Sending atc/hardy/eshelby_static.screen +Sending atc/hardy/in.consistency +Sending atc/hardy/in.eam_kernel_convergence +Sending atc/hardy/in.eam_unistrain_cell +Sending atc/hardy/in.eam_unistrain_mesh +Sending atc/hardy/in.eam_unistrain_qcylinder +Sending atc/hardy/in.eam_unistrain_qsphere +Sending atc/hardy/in.eam_unistrain_step +Sending atc/hardy/in.eam_volume_stretch +Sending atc/hardy/in.eshelby_static +Sending atc/hardy/in.nvt +Sending atc/hardy/nvt.screen +Adding atc/mesh +Adding atc/mesh/Ar_ttm.mat +Adding atc/mesh/Si.mat +Adding atc/mesh/gaussianIC1d_hex.screen +Adding atc/mesh/gaussianIC2d_hex.screen +Adding atc/mesh/gaussianIC2d_hex20_uniform.screen +Adding atc/mesh/gaussianIC2d_hex27_uniform.screen +Adding atc/mesh/gaussianIC2d_hex_uniform.screen +Adding atc/mesh/gaussianIC2d_tet.screen +Adding atc/mesh/in.gaussianIC1d_hex +Adding atc/mesh/in.gaussianIC2d_hex +Adding atc/mesh/in.gaussianIC2d_hex20_uniform +Adding atc/mesh/in.gaussianIC2d_hex27_uniform +Adding atc/mesh/in.gaussianIC2d_tet +Adding atc/mesh/in.kernel2d_hex +Adding atc/mesh/in.kernel2d_tet +Adding atc/mesh/in.mesh2d_tet +Adding atc/mesh/in.semicircle +Adding atc/mesh/kernel2d_hex.screen +Adding atc/mesh/kernel2d_tet.screen +Adding atc/mesh/mesh2d_tet.screen +Adding atc/mesh/semicircle.screen +Adding atc/molecule +Adding atc/molecule/harmonic_bonds.screen +Adding atc/molecule/in.harmonic_bonds +Adding atc/molecule/in.polarize +Adding atc/molecule/in.quartic_bonds +Adding atc/molecule/in.water +Adding atc/molecule/polarize.screen +Adding atc/molecule/quartic_bonds.screen +Adding atc/molecule/water.mat +Adding atc/molecule/water.screen +Adding atc/svn.stdout +Adding atc/thermal +Adding atc/thermal/Ar_thermal.mat +Adding atc/thermal/bar1d.screen +Adding atc/thermal/bar1d_all_atoms.screen +Adding atc/thermal/bar1d_combined.screen +Adding atc/thermal/bar1d_flux.screen +Adding atc/thermal/bar1d_frac_step.screen +Adding atc/thermal/bar1d_hoover.screen +Adding atc/thermal/bar1d_interpolate.screen +Adding atc/thermal/bar1d_lumped.screen +Adding atc/thermal/in.bar1d +Adding atc/thermal/in.bar1d_all_atoms +Adding atc/thermal/in.bar1d_combined +Adding atc/thermal/in.bar1d_flux +Adding atc/thermal/in.bar1d_frac_step +Adding atc/thermal/in.bar1d_hoover +Adding atc/thermal/in.bar1d_interpolate +Adding atc/thermal/in.bar1d_lumped +Adding atc/thermal/in.no_atoms +Adding atc/thermal/no_atoms.screen +Adding atc/two_temperature +Adding atc/two_temperature/Ar_ttm.mat +Adding atc/two_temperature/Cu_ttm.mat +Adding atc/two_temperature/bar1d_ttm.screen +Adding atc/two_temperature/cutout.screen +Adding atc/two_temperature/gaussianIC_ttm.screen +Adding atc/two_temperature/in.bar1d_ttm +Adding atc/two_temperature/in.cutout +Adding atc/two_temperature/in.gaussianIC_ttm +Adding atc/two_temperature/in.no_atoms +Adding atc/two_temperature/in.restart +Adding atc/two_temperature/in.uniform_exchange +Adding atc/two_temperature/in.uniform_heating +Adding atc/two_temperature/no_atoms.screen +Adding atc/two_temperature/restart.screen +Adding atc/two_temperature/uniform_exchange.screen +Adding atc/two_temperature/uniform_heating.screen +Transmitting file data .... \ No newline at end of file diff --git a/examples/USER/atc/thermal/Ar_thermal.mat b/examples/USER/atc/thermal/Ar_thermal.mat new file mode 100644 index 0000000000..b9e858ee9f --- /dev/null +++ b/examples/USER/atc/thermal/Ar_thermal.mat @@ -0,0 +1,14 @@ +material Ar real + heat_flux linear + conductivity .00000000168 + end +end + +material Ar2 real + heat_flux linear + conductivity .00000000316 + end +end + +material vacuum real +end diff --git a/examples/USER/atc/thermal/bar1d.screen b/examples/USER/atc/thermal/bar1d.screen new file mode 100644 index 0000000000..72363cdf1f --- /dev/null +++ b/examples/USER/atc/thermal/bar1d.screen @@ -0,0 +1,274 @@ +LAMMPS (14 Aug 2013) +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init +Reading data file ... + orthogonal box = (-27.025 -16.215 -16.215) to (27.025 16.215 16.215) + 2 by 1 by 2 MPI processor grid + 1440 atoms + 1440 velocities +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region simRegion block -12 12 -3 3 -3 3 +# create atoms, NOTE commented out for restart +#region mdRegion block -5 5 -3 3 -3 3 +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 +# specify interal/ghost atoms +region mdInternal block -4 4 -3 3 -3 3 +group internal region mdInternal +1152 atoms in group internal +group ghost subtract all internal +288 atoms in group ghost +# velocities have Vcm = 0, NOTE next four lines commented out for restart +#velocity internal create 40. 87287 mom yes loop geom +#pair_style lj/cut 13.5 +##pair_coeff 1 1 0.010323166 3.405 13.5 +#pair_coeff 1 1 .238 3.405 13.5 +neighbor 5. bin +neigh_modify every 10 delay 0 check no +# ID group atc PhysicsType ParameterFile +fix AtC internal atc thermal Ar_thermal.mat +ATC: constructing thermal coupling with parameter file Ar_thermal.mat + ATC: peratom PE compute created with ID: 3 + ATC: 3 materials defined from Ar_thermal.mat +fix_modify AtC boundary ghost +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p + ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements +fix_modify AtC internal_quadrature off +# fix a temperature +fix_modify AtC fix temperature all 20. +# turn on thermostat +fix_modify AtC control thermal rescale 10 +# equilibrate MD field +#dump D1 all atom 100 dump.bar1d +#fix_modify AtC output bar1dfe 100 +timestep 5 +variable xdof equal 3*count(ghost) +compute_modify thermo_temp extra ${xdof} +compute_modify thermo_temp extra 864 +thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] +thermo_modify format 1 %6i format 2 %7.2g +thermo 100 +run 400 +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 92.2171 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -2573.6428 -2710.8793 412.06718 39.965279 20 + 100 5.9 -2537.6764 -2606.3542 412.06718 20 20 + 200 9.7 -2584.8754 -2653.5532 412.06718 20 20 + 300 14 -2575.3126 -2643.9904 412.06718 20 20 + 400 16 -2573.4199 -2642.0977 412.06718 20 20 +Loop time of 16.4237 on 4 procs for 400 steps with 1440 atoms + +Pair time (%) = 2.1238 (12.9313) +Neigh time (%) = 1.37325 (8.36136) +Comm time (%) = 8.1983 (49.9174) +Outpt time (%) = 0.0300894 (0.183207) +Other time (%) = 4.6983 (28.6068) + +Nlocal: 360 ave 360 max 360 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4060 ave 4060 max 4060 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 104865 ave 104966 max 104653 min +Histogram: 1 0 0 0 0 0 0 1 0 2 +FullNghs: 209730 ave 209902 max 209521 min +Histogram: 1 0 0 0 1 0 0 1 0 1 + +Total # of neighbors = 838918 +Ave neighs/atom = 582.582 +Neighbor list builds = 40 +Dangerous builds = 0 +# change thermostat to hoover +fix_modify AtC unfix temperature all +fix_modify AtC control thermal hoover +#fix_modify AtC localized_lambda on +fix_modify AtC filter type exponential +fix_modify AtC filter scale 10000.0 +fix_modify AtC filter on +# add nodesets +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF + ATC: created nodeset lbc with 1 nodes +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF + ATC: created nodeset rbc with 1 nodes +fix_modify AtC fix temperature lbc 40. +fix_modify AtC fix temperature rbc 20. +# initialize filter +#thermo 1 +run 100 +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 99.502 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 400 0 -2573.4199 -2642.0977 412.06718 20 20 + 500 2.4 -2573.7738 -2643.7447 433.14294 20.376549 21.713472 +Loop time of 2.43555 on 4 procs for 100 steps with 1440 atoms + +Pair time (%) = 0.425805 (17.4829) +Neigh time (%) = 0.25075 (10.2954) +Comm time (%) = 0.707323 (29.0416) +Outpt time (%) = 0.0401273 (1.64757) +Other time (%) = 1.01154 (41.5325) + +Nlocal: 360 ave 360 max 360 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4060 ave 4060 max 4060 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 104765 ave 105086 max 104556 min +Histogram: 2 0 0 0 1 0 0 0 0 1 +FullNghs: 209530 ave 209833 max 209326 min +Histogram: 1 0 1 1 0 0 0 0 0 1 + +Total # of neighbors = 838118 +Ave neighs/atom = 582.026 +Neighbor list builds = 10 +Dangerous builds = 0 +# set up output, should be before a "run" +fix_modify AtC output bar1dFE 100 text binary + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +# ouput command +#dump D1 all atom 1000 dump.bar1d +# run with FE +reset_timestep 0 +thermo 100 +run 10000 +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 99.502 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -2573.7738 -2643.7447 433.14294 20.376549 21.713472 + 100 9.2 -2573.654 -2645.0562 436.6146 20.793359 21.86901 + 200 10 -2574.0035 -2642.057 439.70235 19.818183 22.007349 + 300 13 -2573.5186 -2646.5507 442.73301 21.268004 22.143129 + 400 19 -2573.2662 -2641.032 445.39809 19.734394 22.262531 + 500 24 -2573.5673 -2644.7553 447.93109 20.730998 22.376015 + 600 32 -2572.9368 -2641.5818 450.33706 19.990452 22.483808 + 700 34 -2573.2457 -2642.9406 452.61859 20.296182 22.586025 + 800 35 -2573.215 -2642.7311 454.75264 20.244128 22.681635 + 900 36 -2572.7227 -2643.5215 456.77865 20.617654 22.772405 + 1000 38 -2572.411 -2644.5969 458.68289 21.021605 22.857719 + 1100 42 -2571.4099 -2642.08 460.52888 20.580181 22.940424 + 1200 47 -2570.5495 -2641.7296 462.26173 20.728698 23.01806 + 1300 48 -2570.2491 -2640.8115 463.9083 20.548784 23.09183 + 1400 49 -2570.159 -2641.2853 465.40156 20.713007 23.158731 + 1500 60 -2569.5061 -2642.2055 467.00405 21.171116 23.230527 + 1600 61 -2568.7522 -2639.5247 468.45299 20.609988 23.295442 + 1700 70 -2569.1809 -2642.0975 469.79048 21.23439 23.355365 + 1800 73 -2568.7484 -2643.2103 471.10946 21.684386 23.414458 + 1900 83 -2568.2581 -2641.5017 472.49875 21.329637 23.476701 + 2000 84 -2568.192 -2641.4647 473.7794 21.338078 23.534077 + 2100 85 -2568.0746 -2639.9335 474.99711 20.926347 23.588633 + 2200 92 -2567.2717 -2642.2868 476.13779 21.845489 23.639738 + 2300 96 -2566.7209 -2639.9022 477.31159 21.311461 23.692327 + 2400 1e+02 -2566.6054 -2638.8118 478.44655 21.027558 23.743176 + 2500 1.1e+02 -2565.7629 -2639.6423 479.55196 21.514764 23.792701 + 2600 1.1e+02 -2565.9248 -2642.5794 480.54223 22.322945 23.837067 + 2700 1.1e+02 -2564.9995 -2640.0503 481.61938 21.855895 23.885326 + 2800 1.2e+02 -2565.2468 -2638.033 482.61597 21.196395 23.929975 + 2900 1.2e+02 -2565.0496 -2639.4905 483.63717 21.678286 23.975727 + 3000 1.3e+02 -2565.1382 -2637.5132 484.58683 21.076652 24.018275 + 3100 1.3e+02 -2564.4793 -2636.7861 485.5364 21.056785 24.060817 + 3200 1.3e+02 -2564.1799 -2637.5024 486.53294 21.352561 24.105465 + 3300 1.4e+02 -2564.4531 -2641.3463 487.42873 22.392434 24.145598 + 3400 1.4e+02 -2564.2323 -2641.0072 488.30292 22.357973 24.184764 + 3500 1.4e+02 -2563.378 -2635.3819 489.17087 20.968574 24.22365 + 3600 1.4e+02 -2563.5014 -2637.8324 490.1027 21.646291 24.265398 + 3700 1.4e+02 -2563.4092 -2638.0479 490.92648 21.735889 24.302305 + 3800 1.4e+02 -2563.0307 -2637.5397 491.76937 21.698123 24.340068 + 3900 1.4e+02 -2562.1415 -2637.2704 492.65132 21.878653 24.379582 + 4000 1.4e+02 -2561.9969 -2637.3928 493.4009 21.956415 24.413165 + 4100 1.5e+02 -2560.7688 -2636.0902 494.20978 21.934699 24.449405 + 4200 1.5e+02 -2561.3033 -2638.2324 494.92948 22.402886 24.481649 + 4300 1.5e+02 -2560.9897 -2637.0909 495.72929 22.161791 24.517482 + 4400 1.5e+02 -2561.1677 -2638.5004 496.4863 22.520422 24.551398 + 4500 1.5e+02 -2560.4797 -2637.3716 497.21153 22.392069 24.58389 + 4600 1.5e+02 -2560.5787 -2637.0577 497.94655 22.271795 24.61682 + 4700 1.5e+02 -2560.9645 -2639.5115 498.65048 22.874032 24.648358 + 4800 1.6e+02 -2560.4451 -2637.6681 499.40401 22.488483 24.682118 + 4900 1.6e+02 -2559.5243 -2635.9383 500.10679 22.252874 24.713604 + 5000 1.6e+02 -2559.4948 -2637.7238 500.83953 22.781444 24.746432 + 5100 1.6e+02 -2559.6822 -2636.169 501.53339 22.274071 24.777518 + 5200 1.6e+02 -2559.6398 -2637.3169 502.26381 22.620718 24.810243 + 5300 1.6e+02 -2558.6285 -2634.5293 502.8444 22.103424 24.836255 + 5400 1.6e+02 -2558.6394 -2637.9487 503.59005 23.096025 24.869662 + 5500 1.6e+02 -2558.1403 -2636.176 504.21716 22.725144 24.897757 + 5600 1.6e+02 -2558.0703 -2635.1367 504.9347 22.442865 24.929905 + 5700 1.6e+02 -2558.0656 -2636.7197 505.52087 22.905225 24.956167 + 5800 1.6e+02 -2557.3777 -2634.8266 506.20982 22.554253 24.987033 + 5900 1.7e+02 -2557.2526 -2635.9743 506.86422 22.924918 25.016352 + 6000 1.7e+02 -2557.3833 -2637.2291 507.48018 23.25228 25.043948 + 6100 1.7e+02 -2556.0263 -2633.5407 508.11625 22.573338 25.072446 + 6200 1.7e+02 -2555.7442 -2634.4379 508.74696 22.916758 25.100703 + 6300 1.7e+02 -2555.855 -2635.6232 509.35007 23.229653 25.127723 + 6400 1.7e+02 -2555.9332 -2634.2034 509.90097 22.793416 25.152405 + 6500 1.7e+02 -2555.6529 -2635.6085 510.47402 23.284242 25.178079 + 6600 1.8e+02 -2554.8702 -2633.8042 511.0317 22.986719 25.203064 + 6700 1.8e+02 -2555.4594 -2637.4199 511.60862 23.868095 25.228911 + 6800 1.8e+02 -2555.1345 -2633.0307 512.18015 22.684507 25.254517 + 6900 1.8e+02 -2555.2031 -2635.8935 512.79344 23.498217 25.281994 + 7000 1.9e+02 -2554.4149 -2634.996 513.32816 23.466386 25.305951 + 7100 1.9e+02 -2555.5655 -2636.9961 513.95657 23.713805 25.334105 + 7200 1.9e+02 -2554.6219 -2632.7377 514.567 22.748451 25.361454 + 7300 1.9e+02 -2553.7348 -2633.5176 515.135 23.233924 25.386901 + 7400 1.9e+02 -2553.6835 -2632.7483 515.7035 23.024829 25.412371 + 7500 1.9e+02 -2554.1585 -2634.2224 516.25704 23.315779 25.437171 + 7600 1.9e+02 -2553.7146 -2636.4167 516.79495 24.084074 25.461271 + 7700 1.9e+02 -2553.0976 -2633.1654 517.39991 23.316903 25.488375 + 7800 1.9e+02 -2553.7234 -2633.6408 517.98568 23.273102 25.514618 + 7900 1.9e+02 -2553.1575 -2635.2362 518.49062 23.902519 25.537241 + 8000 2e+02 -2553.0069 -2632.9282 519.06292 23.274267 25.562881 + 8100 2e+02 -2552.2172 -2632.9349 519.57824 23.506176 25.585969 + 8200 2e+02 -2552.6329 -2633.705 520.13682 23.609392 25.610994 + 8300 2e+02 -2553.0514 -2636.5364 520.66438 24.312051 25.63463 + 8400 2e+02 -2551.9158 -2634.5593 521.15401 24.066989 25.656566 + 8500 2e+02 -2551.162 -2632.582 521.69313 23.710703 25.68072 + 8600 2e+02 -2551.323 -2631.8792 522.25824 23.459141 25.706039 + 8700 2e+02 -2551.3995 -2634.1924 522.75555 24.110486 25.728319 + 8800 2e+02 -2551.5524 -2635.9593 523.28139 24.580545 25.751878 + 8900 2e+02 -2550.9859 -2634.5116 523.74996 24.3239 25.772871 + 9000 2e+02 -2550.3986 -2630.9451 524.29066 23.456323 25.797095 + 9100 2.1e+02 -2550.2258 -2632.4852 524.79409 23.955138 25.81965 + 9200 2.1e+02 -2549.7276 -2633.251 525.32924 24.323252 25.843626 + 9300 2.2e+02 -2549.2309 -2632.0111 525.82326 24.1068 25.86576 + 9400 2.2e+02 -2549.1793 -2631.7908 526.23399 24.057681 25.884161 + 9500 2.2e+02 -2549.3234 -2632.8586 526.74802 24.326659 25.907191 + 9600 2.3e+02 -2548.7761 -2630.2005 527.18774 23.711964 25.926891 + 9700 2.3e+02 -2548.5531 -2631.9225 527.62451 24.27839 25.946459 + 9800 2.3e+02 -2548.3632 -2632.4871 528.04194 24.49812 25.965161 + 9900 2.4e+02 -2548.2216 -2631.2195 528.52701 24.170186 25.986893 + 10000 2.4e+02 -2547.7787 -2631.2232 528.97935 24.300246 26.007159 +Loop time of 242.304 on 4 procs for 10000 steps with 1440 atoms + +Pair time (%) = 43.3749 (17.9011) +Neigh time (%) = 22.0746 (9.11032) +Comm time (%) = 67.2326 (27.7472) +Outpt time (%) = 0.223967 (0.0924324) +Other time (%) = 109.398 (45.1489) + +Nlocal: 360 ave 360 max 360 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4060 ave 4060 max 4060 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 104823 ave 104983 max 104416 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +FullNghs: 209646 ave 209959 max 209315 min +Histogram: 1 0 1 0 0 0 0 0 1 1 + +Total # of neighbors = 838584 +Ave neighs/atom = 582.35 +Neighbor list builds = 1000 +Dangerous builds = 0 diff --git a/examples/USER/atc/thermal/bar1d_all_atoms.screen b/examples/USER/atc/thermal/bar1d_all_atoms.screen new file mode 100644 index 0000000000..5aa0e5d6d1 --- /dev/null +++ b/examples/USER/atc/thermal/bar1d_all_atoms.screen @@ -0,0 +1,102 @@ +LAMMPS (14 Aug 2013) +Reading data file ... + orthogonal box = (-37.835 -16.215 -16.215) to (37.835 16.215 16.215) + 4 by 1 by 1 MPI processor grid + 2016 atoms + 2016 velocities +Lattice spacing in x,y,z = 5.405 5.405 5.405 +1728 atoms in group internal +288 atoms in group ghost +ATC: constructing thermal coupling with parameter file Ar_thermal.mat + ATC: peratom PE compute created with ID: 3 + ATC: 3 materials defined from Ar_thermal.mat + ATC: created uniform mesh with 28 nodes, 7 unique nodes, and 6 elements + ATC: created faceset obndy with 2 faces + ATC: created faceset lbndy with 1 faces + ATC: created faceset rbndy with 1 faces +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 51.7361 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -3635.4921 -3841.4065 206.03359 39.976852 20 + 100 2.1 -3585.2592 -3688.276 206.03359 20 20 + 200 3.4 -3649.8412 -3752.858 206.03359 20 20 + 300 4.6 -3638.7879 -3741.8047 206.03359 20 20 + 400 5.7 -3641.387 -3744.4038 206.03359 20 20 +Loop time of 5.67905 on 4 procs for 400 steps with 2016 atoms + +Pair time (%) = 2.2389 (39.4237) +Neigh time (%) = 0.928223 (16.3447) +Comm time (%) = 1.40274 (24.7002) +Outpt time (%) = 0.00123483 (0.0217436) +Other time (%) = 1.10796 (19.5096) + +Nlocal: 504 ave 504 max 504 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5411 ave 6594 max 4228 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 152906 ave 168710 max 137650 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 305812 ave 336029 max 275367 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1223248 +Ave neighs/atom = 606.77 +Neighbor list builds = 40 +Dangerous builds = 0 + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 53.9738 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -3641.387 -3744.4038 206.03359 20 20 + 200 3.7 -3641.4558 -3741.6259 200.24916 19.447339 19.248846 + 400 7.2 -3641.3526 -3743.9363 205.0775 19.915921 19.699533 + 600 19 -3641.375 -3743.2251 203.6111 19.773486 19.612208 + 800 21 -3641.3598 -3745.7684 208.72769 20.270195 20.147681 + 1000 23 -3641.3633 -3744.4804 206.14469 20.01948 20.000916 + 1200 25 -3641.3461 -3745.088 207.39643 20.140774 20.048989 + 1400 29 -3641.3142 -3744.8632 207.01063 20.103323 20.101701 + 1600 31 -3641.3156 -3742.7705 202.82111 19.69678 19.661121 + 1800 34 -3641.316 -3743.0731 203.426 19.755441 19.722221 + 2000 36 -3641.3398 -3742.3792 201.99012 19.616091 19.597215 + 2200 38 -3641.3731 -3743.0677 203.30107 19.743306 19.727173 + 2400 48 -3641.2828 -3745.8996 209.14521 20.310613 20.319088 + 2600 58 -3641.3634 -3743.8039 204.79274 19.888105 19.949094 + 2800 64 -3641.3441 -3741.4297 200.08277 19.430931 19.239953 + 3000 75 -3641.3148 -3742.6599 202.602 19.675455 19.709217 + 3200 84 -3641.2859 -3742.6672 202.6744 19.68247 19.589857 + 3400 96 -3641.3698 -3743.1191 203.41009 19.753928 19.61843 + 3600 1.1e+02 -3641.2872 -3742.8149 202.96721 19.710905 19.636161 + 3800 1.1e+02 -3641.3532 -3741.7567 200.71871 19.492661 19.553996 + 4000 1.2e+02 -3641.3678 -3740.8478 198.87111 19.313344 19.20547 + 4200 1.3e+02 -3641.3412 -3743.3077 203.84569 19.79609 19.758581 + 4400 1.4e+02 -3641.2985 -3743.926 205.16703 19.924421 19.682565 + 4600 1.5e+02 -3641.3583 -3741.5377 200.27113 19.449139 19.459934 + 4800 1.6e+02 -3641.3204 -3742.091 201.45376 19.563917 19.472208 + 5000 1.7e+02 -3641.3593 -3745.2374 207.66855 20.167216 20.028789 +Loop time of 171.652 on 4 procs for 5000 steps with 2016 atoms + +Pair time (%) = 31.6573 (18.4428) +Neigh time (%) = 15.4889 (9.02343) +Comm time (%) = 43.5228 (25.3553) +Outpt time (%) = 0.171351 (0.0998248) +Other time (%) = 80.8113 (47.0786) + +Nlocal: 504 ave 504 max 504 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5411 ave 6594 max 4228 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 152904 ave 169876 max 137279 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 305807 ave 336458 max 275593 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1223228 +Ave neighs/atom = 606.76 +Neighbor list builds = 500 +Dangerous builds = 0 diff --git a/examples/USER/atc/thermal/bar1d_combined.screen b/examples/USER/atc/thermal/bar1d_combined.screen new file mode 100644 index 0000000000..a128be2a8e --- /dev/null +++ b/examples/USER/atc/thermal/bar1d_combined.screen @@ -0,0 +1,164 @@ +LAMMPS (14 Aug 2013) +Reading data file ... + orthogonal box = (-27.025 -16.215 -16.215) to (27.025 16.215 16.215) + 2 by 1 by 2 MPI processor grid + 1440 atoms + 1440 velocities +Lattice spacing in x,y,z = 5.405 5.405 5.405 +1152 atoms in group internal +144 atoms in group ghost +ATC: constructing thermal coupling with parameter file Ar_thermal.mat + ATC: peratom PE compute created with ID: 3 + ATC: 3 materials defined from Ar_thermal.mat + ATC: created uniform mesh with 44 nodes, 11 unique nodes, and 10 elements + ATC: created faceset ibndy with 1 faces + ATC: created faceset obndy with 1 faces +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 91.5825 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -2573.6428 -2710.8793 343.38932 35.524692 20 + 10 0.79 -2626.7498 -2695.4276 343.38932 17.777778 20 + 20 1.8 -2600.7022 -2669.38 343.38932 17.777778 20 + 30 2.6 -2570.0142 -2638.6921 343.38932 17.777778 20 + 40 2.7 -2548.1494 -2616.8273 343.38932 17.777778 20 + 50 2.8 -2541.6409 -2610.3188 343.38932 17.777778 20 + 60 2.9 -2539.3355 -2608.0134 343.38932 17.777778 20 + 70 3 -2534.3684 -2603.0463 343.38932 17.777778 20 + 80 3.1 -2530.2415 -2598.9194 343.38932 17.777778 20 + 90 3.1 -2531.3411 -2600.019 343.38932 17.777778 20 + 100 3.2 -2537.6764 -2606.3542 343.38932 17.777778 20 + 110 3.3 -2546.506 -2615.1838 343.38932 17.777778 20 + 120 3.4 -2555.0937 -2623.7716 343.38932 17.777778 20 + 130 3.6 -2562.4178 -2631.0957 343.38932 17.777778 20 + 140 3.7 -2568.7827 -2637.4606 343.38932 17.777778 20 + 150 3.9 -2574.6292 -2643.307 343.38932 17.777778 20 + 160 4.1 -2579.7542 -2648.432 343.38932 17.777778 20 + 170 4.4 -2583.6629 -2652.3408 343.38932 17.777778 20 + 180 5.1 -2585.9113 -2654.5892 343.38932 17.777778 20 + 190 5.3 -2586.1786 -2654.8565 343.38932 17.777778 20 + 200 5.6 -2584.8754 -2653.5532 343.38932 17.777778 20 + 210 7.4 -2582.8956 -2651.5734 343.38932 17.777778 20 + 220 7.6 -2580.6882 -2649.366 343.38932 17.777778 20 + 230 7.7 -2578.24 -2646.9179 343.38932 17.777778 20 + 240 9.2 -2575.9058 -2644.5836 343.38932 17.777778 20 + 250 10 -2574.2875 -2642.9654 343.38932 17.777778 20 + 260 13 -2573.8273 -2642.5052 343.38932 17.777778 20 + 270 14 -2574.3017 -2642.9796 343.38932 17.777778 20 + 280 14 -2574.7059 -2643.3838 343.38932 17.777778 20 + 290 15 -2574.7745 -2643.4524 343.38932 17.777778 20 + 300 15 -2575.3126 -2643.9904 343.38932 17.777778 20 + 310 15 -2576.5002 -2645.178 343.38932 17.777778 20 + 320 15 -2577.7411 -2646.419 343.38932 17.777778 20 + 330 16 -2578.2283 -2646.9061 343.38932 17.777778 20 + 340 16 -2577.7485 -2646.4263 343.38932 17.777778 20 + 350 16 -2576.9631 -2645.6409 343.38932 17.777778 20 + 360 16 -2576.0309 -2644.7088 343.38932 17.777778 20 + 370 16 -2574.9309 -2643.6088 343.38932 17.777778 20 + 380 16 -2573.7943 -2642.4721 343.38932 17.777778 20 + 390 16 -2573.0353 -2641.7132 343.38932 17.777778 20 + 400 16 -2573.4199 -2642.0977 343.38932 17.777778 20 +Loop time of 16.4321 on 4 procs for 400 steps with 1440 atoms + +Pair time (%) = 1.87474 (11.409) +Neigh time (%) = 1.47132 (8.95394) +Comm time (%) = 7.98522 (48.5952) +Outpt time (%) = 0.265947 (1.61846) +Other time (%) = 4.83487 (29.4233) + +Nlocal: 360 ave 360 max 360 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4060 ave 4060 max 4060 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 104865 ave 104966 max 104653 min +Histogram: 1 0 0 0 0 0 0 1 0 2 +FullNghs: 209730 ave 209902 max 209521 min +Histogram: 1 0 0 0 1 0 0 1 0 1 + +Total # of neighbors = 838918 +Ave neighs/atom = 582.582 +Neighbor list builds = 40 +Dangerous builds = 0 + ATC: created nodeset lbc with 1 nodes + ATC: created nodeset rbc with 1 nodes + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 104.578 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -2573.4199 -2642.0977 343.38932 17.777778 20 + 100 11 -2574.1221 -2644.1227 366.86215 18.120179 22.151933 + 200 13 -2574.368 -2645.6588 372.76111 18.454143 22.464272 + 300 23 -2574.5571 -2642.1914 368.54473 17.507654 22.241023 + 400 24 -2573.8831 -2646.3956 381.21405 18.77039 22.91184 + 500 25 -2574.1212 -2641.3392 373.2869 17.399874 22.492112 + 600 33 -2575.6292 -2645.7049 381.45457 18.139627 22.924575 + 700 37 -2574.5398 -2642.276 379.21993 17.534018 22.806254 + 800 48 -2575.7147 -2644.4983 383.4578 17.805128 23.030642 + 900 49 -2575.9679 -2644.264 384.40144 17.678956 23.080605 + 1000 50 -2574.7257 -2644.11 388.41299 17.960637 23.293009 + 1100 59 -2574.3951 -2645.4009 393.54083 18.380392 23.564519 + 1200 62 -2573.4022 -2643.2837 393.1983 18.089328 23.546383 + 1300 73 -2573.1301 -2643.3336 395.59223 18.172701 23.673137 + 1400 75 -2573.6807 -2643.1251 395.65516 17.976194 23.676469 + 1500 85 -2573.941 -2642.7411 396.10118 17.809426 23.700085 + 1600 87 -2572.2731 -2643.4215 402.46406 18.417286 24.036987 + 1700 96 -2571.634 -2640.8286 400.21007 17.911532 23.917643 + 1800 98 -2574.22 -2645.1741 405.32422 18.367004 24.188427 + 1900 1e+02 -2572.1014 -2643.7409 408.29043 18.544436 24.345483 + 2000 1.1e+02 -2572.7805 -2643.7309 408.51237 18.366044 24.357234 + 2100 1.1e+02 -2574.4982 -2645.4058 409.91869 18.354974 24.431696 + 2200 1.2e+02 -2573.6994 -2643.2148 408.43574 17.994584 24.353177 + 2300 1.2e+02 -2572.9286 -2645.0323 414.83736 18.664591 24.69213 + 2400 1.3e+02 -2572.8631 -2643.1356 412.49463 18.190579 24.568087 + 2500 1.3e+02 -2573.1978 -2641.401 409.7314 17.654899 24.421779 + 2600 1.4e+02 -2572.5709 -2642.9318 415.39198 18.213443 24.721496 + 2700 1.5e+02 -2573.8846 -2646.8168 421.79985 18.879037 25.060781 + 2800 1.5e+02 -2572.2696 -2643.6382 419.83482 18.47431 24.956737 + 2900 1.5e+02 -2572.3981 -2641.2173 415.8328 17.814358 24.744837 + 3000 1.5e+02 -2572.0099 -2643.1283 421.40094 18.409529 25.03966 + 3100 1.5e+02 -2573.6747 -2642.5137 417.77509 17.819488 24.847677 + 3200 1.5e+02 -2572.3897 -2640.7218 417.75014 17.688295 24.846356 + 3300 1.5e+02 -2572.4622 -2641.0094 419.22189 17.74395 24.924283 + 3400 1.5e+02 -2574.397 -2645.7327 425.93117 18.465771 25.279527 + 3500 1.5e+02 -2574.1636 -2645.5142 427.08548 18.469627 25.340645 + 3600 1.5e+02 -2573.5119 -2643.5124 425.4481 18.120142 25.253949 + 3700 1.6e+02 -2574.6195 -2641.8713 420.88263 17.408634 25.012216 + 3800 1.6e+02 -2573.6828 -2642.8075 425.44497 17.893448 25.253783 + 3900 1.6e+02 -2575.0132 -2644.4186 426.83652 17.966112 25.327463 + 4000 1.6e+02 -2574.095 -2642.3458 425.44626 17.667234 25.253852 + 4100 1.6e+02 -2573.8305 -2644.7007 431.68177 18.345287 25.58401 + 4200 1.6e+02 -2571.5672 -2641.8797 431.58249 18.200917 25.578753 + 4300 1.6e+02 -2572.9189 -2643.2307 432.52704 18.20073 25.628766 + 4400 1.6e+02 -2571.8961 -2644.0122 437.07886 18.667804 25.869776 + 4500 1.7e+02 -2572.4669 -2641.0876 430.98608 17.762985 25.547174 + 4600 1.7e+02 -2572.9128 -2643.1457 434.95838 18.180311 25.7575 + 4700 1.7e+02 -2572.7779 -2644.3091 438.24406 18.516384 25.931471 + 4800 1.7e+02 -2570.0191 -2640.9336 437.72427 18.356762 25.903949 + 4900 1.7e+02 -2570.9577 -2643.6775 442.01839 18.824052 26.131315 + 5000 1.7e+02 -2570.5553 -2642.7117 441.50654 18.678228 26.104213 +Loop time of 170.264 on 4 procs for 5000 steps with 1440 atoms + +Pair time (%) = 22.2611 (13.0744) +Neigh time (%) = 11.5912 (6.80777) +Comm time (%) = 45.8903 (26.9524) +Outpt time (%) = 0.176552 (0.103693) +Other time (%) = 90.3452 (53.0617) + +Nlocal: 360 ave 360 max 360 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4060 ave 4060 max 4060 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 104894 ave 105161 max 104681 min +Histogram: 1 0 1 0 0 1 0 0 0 1 +FullNghs: 209788 ave 209864 max 209694 min +Histogram: 1 0 0 0 0 1 1 0 0 1 + +Total # of neighbors = 839152 +Ave neighs/atom = 582.744 +Neighbor list builds = 500 +Dangerous builds = 0 diff --git a/examples/USER/atc/thermal/bar1d_flux.screen b/examples/USER/atc/thermal/bar1d_flux.screen new file mode 100644 index 0000000000..b74efbd0c4 --- /dev/null +++ b/examples/USER/atc/thermal/bar1d_flux.screen @@ -0,0 +1,251 @@ +LAMMPS (14 Aug 2013) +Reading data file ... + orthogonal box = (-27.025 -16.215 -16.215) to (27.025 16.215 16.215) + 2 by 1 by 2 MPI processor grid + 1440 atoms + 1440 velocities +Lattice spacing in x,y,z = 5.405 5.405 5.405 +1152 atoms in group internal +288 atoms in group ghost +ATC: constructing thermal coupling with parameter file Ar_thermal.mat + ATC: peratom PE compute created with ID: 3 + ATC: 3 materials defined from Ar_thermal.mat + ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements + ATC: created faceset ibndy with 2 faces + ATC: created faceset obndy with 2 faces +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 91.5825 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -2573.6428 -2710.8793 412.06718 39.965279 20 + 10 1.2 -2626.7498 -2695.4276 412.06718 20 20 + 20 2.1 -2600.7022 -2669.38 412.06718 20 20 + 30 2.4 -2570.0142 -2638.6921 412.06718 20 20 + 40 2.5 -2548.1494 -2616.8273 412.06718 20 20 + 50 2.7 -2541.6409 -2610.3188 412.06718 20 20 + 60 2.8 -2539.3355 -2608.0134 412.06718 20 20 + 70 2.9 -2534.3684 -2603.0463 412.06718 20 20 + 80 3.2 -2530.2415 -2598.9194 412.06718 20 20 + 90 3.3 -2531.3411 -2600.019 412.06718 20 20 + 100 3.4 -2537.6764 -2606.3542 412.06718 20 20 + 110 3.6 -2546.506 -2615.1838 412.06718 20 20 + 120 3.7 -2555.0937 -2623.7716 412.06718 20 20 + 130 3.9 -2562.4178 -2631.0957 412.06718 20 20 + 140 6.2 -2568.7827 -2637.4606 412.06718 20 20 + 150 7.4 -2574.6292 -2643.307 412.06718 20 20 + 160 8.1 -2579.7542 -2648.432 412.06718 20 20 + 170 8.3 -2583.6629 -2652.3408 412.06718 20 20 + 180 8.4 -2585.9113 -2654.5892 412.06718 20 20 + 190 8.6 -2586.1786 -2654.8565 412.06718 20 20 + 200 9.7 -2584.8754 -2653.5532 412.06718 20 20 + 210 10 -2582.8956 -2651.5734 412.06718 20 20 + 220 10 -2580.6882 -2649.366 412.06718 20 20 + 230 10 -2578.24 -2646.9179 412.06718 20 20 + 240 11 -2575.9058 -2644.5836 412.06718 20 20 + 250 11 -2574.2875 -2642.9654 412.06718 20 20 + 260 12 -2573.8273 -2642.5052 412.06718 20 20 + 270 12 -2574.3017 -2642.9796 412.06718 20 20 + 280 12 -2574.7059 -2643.3838 412.06718 20 20 + 290 13 -2574.7745 -2643.4524 412.06718 20 20 + 300 13 -2575.3126 -2643.9904 412.06718 20 20 + 310 13 -2576.5002 -2645.178 412.06718 20 20 + 320 13 -2577.7411 -2646.419 412.06718 20 20 + 330 13 -2578.2283 -2646.9061 412.06718 20 20 + 340 13 -2577.7485 -2646.4263 412.06718 20 20 + 350 13 -2576.9631 -2645.6409 412.06718 20 20 + 360 14 -2576.0309 -2644.7088 412.06718 20 20 + 370 14 -2574.9309 -2643.6088 412.06718 20 20 + 380 14 -2573.7943 -2642.4721 412.06718 20 20 + 390 14 -2573.0353 -2641.7132 412.06718 20 20 + 400 14 -2573.4199 -2642.0977 412.06718 20 20 +Loop time of 13.9407 on 4 procs for 400 steps with 1440 atoms + +Pair time (%) = 1.92424 (13.803) +Neigh time (%) = 1.00703 (7.22368) +Comm time (%) = 7.16062 (51.3648) +Outpt time (%) = 0.231704 (1.66206) +Other time (%) = 3.61712 (25.9465) + +Nlocal: 360 ave 360 max 360 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4060 ave 4060 max 4060 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 104865 ave 104966 max 104653 min +Histogram: 1 0 0 0 0 0 0 1 0 2 +FullNghs: 209730 ave 209902 max 209521 min +Histogram: 1 0 0 0 1 0 0 1 0 1 + +Total # of neighbors = 838918 +Ave neighs/atom = 582.582 +Neighbor list builds = 40 +Dangerous builds = 0 + ATC: created nodeset lbc with 1 nodes + ATC: created nodeset rbc with 1 nodes +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 96.3294 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 400 0 -2573.4199 -2642.0977 412.06718 20 20 + 410 0.21 -2573.3989 -2643.8456 433.15262 20.515086 21.713906 + 420 0.41 -2573.4227 -2646.1086 438.04239 21.167211 21.932978 + 430 0.54 -2573.4509 -2647.2056 440.59304 21.478451 22.047254 + 440 0.62 -2573.4593 -2646.2699 439.10407 21.203492 21.980544 + 450 0.72 -2573.477 -2644.3183 435.54519 20.630023 21.821098 + 460 0.81 -2573.492 -2643.0074 433.25785 20.243891 21.71862 + 470 0.93 -2573.4972 -2642.6209 432.83341 20.12985 21.699605 + 480 1 -2573.5082 -2642.5684 433.06695 20.111322 21.710068 + 490 1.1 -2573.5206 -2642.9262 434.12535 20.211932 21.757486 + 500 1.2 -2573.5404 -2643.6737 435.95443 20.42383 21.839434 +Loop time of 1.16692 on 4 procs for 100 steps with 1440 atoms + +Pair time (%) = 0.388731 (33.3126) +Neigh time (%) = 0.187062 (16.0304) +Comm time (%) = 0.188758 (16.1757) +Outpt time (%) = 0.00402528 (0.34495) +Other time (%) = 0.398342 (34.1363) + +Nlocal: 360 ave 360 max 360 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4060 ave 4060 max 4060 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 104762 ave 105086 max 104552 min +Histogram: 2 0 0 0 1 0 0 0 0 1 +FullNghs: 209524 ave 209826 max 209318 min +Histogram: 1 0 1 1 0 0 0 0 0 1 + +Total # of neighbors = 838094 +Ave neighs/atom = 582.01 +Neighbor list builds = 10 +Dangerous builds = 0 + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 96.3294 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -2573.5404 -2643.6737 435.95443 20.42383 21.839434 + 100 1 -2573.5201 -2644.6896 441.36654 20.725607 22.081908 + 200 2.7 -2573.6986 -2641.8416 438.49489 19.844232 21.953252 + 300 9.2 -2573.8026 -2646.5126 450.6649 21.174221 22.498496 + 400 12 -2574.0076 -2641.6212 443.12147 19.690084 22.160533 + 500 13 -2573.8428 -2644.4381 451.49978 20.558381 22.5359 + 600 19 -2573.9961 -2641.9998 448.70746 19.803677 22.410798 + 700 25 -2573.8774 -2643.3051 453.67192 20.218357 22.633217 + 800 26 -2573.7077 -2642.9004 455.12598 20.149918 22.698362 + 900 36 -2573.659 -2643.8164 458.91706 20.430858 22.868211 + 1000 46 -2573.6515 -2645.0297 463.27029 20.786373 23.063246 + 1100 48 -2573.739 -2643.1888 461.37312 20.224789 22.978248 + 1200 54 -2573.8829 -2643.4916 463.51413 20.271065 23.07417 + 1300 61 -2573.6889 -2642.1642 462.75357 19.941028 23.040095 + 1400 63 -2573.6138 -2643.3131 466.83853 20.297442 23.223111 + 1500 70 -2573.6377 -2644.037 469.86295 20.501291 23.358612 + 1600 73 -2573.7132 -2642.1741 467.56259 19.936825 23.25555 + 1700 77 -2573.6318 -2644.3408 473.44986 20.591494 23.519313 + 1800 85 -2573.5331 -2645.0402 476.4419 20.823916 23.653363 + 1900 95 -2573.4381 -2643.6765 475.25076 20.454439 23.599998 + 2000 97 -2573.2109 -2643.7709 477.03683 20.548116 23.680017 + 2100 99 -2572.7952 -2641.9155 475.13352 20.128847 23.594745 + 2200 1e+02 -2572.3464 -2644.6346 482.39664 21.051379 23.920149 + 2300 1e+02 -2572.1743 -2643.3235 481.25163 20.719688 23.86885 + 2400 1e+02 -2572.003 -2641.285 478.59356 20.175918 23.749762 + 2500 1e+02 -2571.9544 -2642.3789 482.04175 20.508634 23.904249 + 2600 1e+02 -2571.5378 -2645.5591 490.12091 21.556075 24.266214 + 2700 1.1e+02 -2571.194 -2643.2392 487.04142 20.980609 24.128245 + 2800 1.1e+02 -2570.7174 -2640.0345 482.27121 20.186156 23.91453 + 2900 1.1e+02 -2570.1078 -2642.3194 488.64361 21.029079 24.200027 + 3000 1.1e+02 -2569.629 -2639.2966 484.19967 20.288221 24.000929 + 3100 1.1e+02 -2569.2046 -2639.152 485.43842 20.369711 24.056428 + 3200 1.1e+02 -2568.7882 -2639.9226 488.49663 20.715389 24.193442 + 3300 1.1e+02 -2568.3921 -2642.7345 495.61975 21.649606 24.512574 + 3400 1.1e+02 -2567.891 -2642.4061 496.56031 21.699906 24.554713 + 3500 1.1e+02 -2567.427 -2639.0374 491.37897 20.853974 24.322578 + 3600 1.1e+02 -2566.8768 -2638.0079 490.88541 20.714401 24.300465 + 3700 1.2e+02 -2566.2734 -2639.3392 495.18518 21.277842 24.493104 + 3800 1.2e+02 -2565.7852 -2641.3533 500.73283 22.006534 24.741652 + 3900 1.2e+02 -2565.7265 -2638.1821 495.43581 21.100134 24.504333 + 4000 1.2e+02 -2565.6983 -2639.4683 499.03414 21.482923 24.665547 + 4100 1.2e+02 -2565.7639 -2639.2719 499.53281 21.406617 24.687888 + 4200 1.2e+02 -2565.625 -2640.6103 503.37081 21.836828 24.859839 + 4300 1.2e+02 -2565.4337 -2638.9291 501.16899 21.40294 24.761193 + 4400 1.2e+02 -2565.2841 -2638.0978 500.53725 21.204407 24.732889 + 4500 1.2e+02 -2564.9077 -2638.3346 502.30975 21.382989 24.812301 + 4600 1.2e+02 -2564.6232 -2642.1774 511.25728 22.58494 25.213171 + 4700 1.3e+02 -2564.1627 -2641.874 512.04261 22.630698 25.248355 + 4800 1.3e+02 -2563.7451 -2638.6352 506.82273 21.809095 25.014493 + 4900 1.3e+02 -2563.1698 -2638.5762 508.19932 21.959455 25.076167 + 5000 1.3e+02 -2562.7311 -2638.9256 510.23315 22.188955 25.167288 + 5100 1.3e+02 -2562.1789 -2637.2983 508.42366 21.875875 25.086218 + 5200 1.3e+02 -2561.8603 -2638.4362 511.81985 22.300012 25.238375 + 5300 1.3e+02 -2561.4518 -2638.6128 513.46746 22.470413 25.312192 + 5400 1.3e+02 -2561.0887 -2636.5462 510.54177 21.974325 25.181115 + 5500 1.3e+02 -2560.7913 -2637.674 513.91855 22.389358 25.332402 + 5600 1.3e+02 -2560.4293 -2635.6344 511.01724 21.900824 25.202416 + 5700 1.4e+02 -2559.956 -2638.664 518.41982 22.920936 25.534069 + 5800 1.4e+02 -2559.5294 -2636.8718 516.0703 22.523257 25.428805 + 5900 1.5e+02 -2559.2184 -2637.7882 518.98207 22.880675 25.559259 + 6000 1.5e+02 -2558.7839 -2637.881 520.33211 23.034231 25.619744 + 6100 1.5e+02 -2558.2076 -2636.2274 518.42834 22.720496 25.53445 + 6200 1.5e+02 -2557.7055 -2635.5853 518.46629 22.679729 25.536151 + 6300 1.5e+02 -2557.275 -2635.3449 519.15358 22.735109 25.566943 + 6400 1.5e+02 -2556.9861 -2634.0119 517.55898 22.431055 25.495501 + 6500 1.5e+02 -2556.6947 -2636.4319 523.44577 23.220628 25.759242 + 6600 1.5e+02 -2556.3261 -2633.5874 518.88303 22.499641 25.554822 + 6700 1.5e+02 -2556.0983 -2634.3646 521.38252 22.792298 25.666804 + 6800 1.6e+02 -2555.7606 -2632.5328 518.78459 22.357197 25.550411 + 6900 1.6e+02 -2555.2965 -2634.6317 524.15767 23.103559 25.791137 + 7000 1.6e+02 -2554.8934 -2637.194 530.43216 23.967159 26.072249 + 7100 1.6e+02 -2554.5446 -2635.57 528.22644 23.595759 25.973427 + 7200 1.6e+02 -2554.0567 -2631.7969 521.8733 22.639092 25.688792 + 7300 1.6e+02 -2553.516 -2636.3304 532.21316 24.116751 26.152042 + 7400 1.6e+02 -2553.2132 -2631.2954 523.12951 22.738664 25.745074 + 7500 1.6e+02 -2552.826 -2635.2341 532.13047 23.998434 26.148337 + 7600 1.6e+02 -2552.5036 -2632.0088 526.65649 23.153076 25.90309 + 7700 1.6e+02 -2552.022 -2632.2323 528.25595 23.358404 25.97475 + 7800 1.7e+02 -2551.57 -2633.2608 531.44638 23.789544 26.117688 + 7900 1.7e+02 -2551.255 -2632.3043 530.48366 23.602743 26.074556 + 8000 1.7e+02 -2550.8499 -2632.0816 531.11588 23.655854 26.102881 + 8100 1.7e+02 -2550.5837 -2631.3645 530.61796 23.524571 26.080573 + 8200 1.7e+02 -2550.5492 -2631.2585 531.09172 23.503718 26.101798 + 8300 1.8e+02 -2550.571 -2631.4011 532.00391 23.538904 26.142667 + 8400 1.8e+02 -2550.5563 -2634.2103 538.29195 24.361265 26.424385 + 8500 1.9e+02 -2550.3181 -2631.2702 533.28023 23.574444 26.199849 + 8600 1.9e+02 -2549.8887 -2632.7932 537.36071 24.143017 26.382663 + 8700 1.9e+02 -2549.4418 -2631.583 536.05745 23.920729 26.324274 + 8800 2e+02 -2549.0389 -2633.5074 540.85459 24.598449 26.539197 + 8900 2.1e+02 -2548.632 -2630.007 534.9072 23.69757 26.27274 + 9000 2.1e+02 -2548.5009 -2631.2347 538.06423 24.093293 26.414182 + 9100 2.1e+02 -2548.1807 -2629.7776 536.11497 23.762211 26.326851 + 9200 2.2e+02 -2548.013 -2628.7314 534.75002 23.506386 26.265699 + 9300 2.3e+02 -2547.7615 -2630.5208 539.22355 24.100708 26.466123 + 9400 2.3e+02 -2547.3193 -2629.0508 537.3089 23.801401 26.380342 + 9500 2.4e+02 -2546.9048 -2632.3171 544.87205 24.873305 26.719188 + 9600 2.4e+02 -2546.4783 -2631.3151 543.83909 24.705735 26.672909 + 9700 2.4e+02 -2546.0177 -2631.6459 545.58652 24.936195 26.751198 + 9800 2.4e+02 -2545.5995 -2630.0939 543.46879 24.606005 26.656319 + 9900 2.5e+02 -2545.3065 -2628.1317 540.38322 24.119904 26.518079 + 10000 2.5e+02 -2545.0477 -2631.2427 547.46396 25.101238 26.835312 +Loop time of 249.719 on 4 procs for 10000 steps with 1440 atoms + +Pair time (%) = 42.983 (17.2126) +Neigh time (%) = 21.9303 (8.78199) +Comm time (%) = 74.6241 (29.8832) +Outpt time (%) = 0.564417 (0.226021) +Other time (%) = 109.617 (43.8962) + +Nlocal: 360 ave 360 max 360 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4060 ave 4060 max 4060 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 104819 ave 104912 max 104720 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +FullNghs: 209638 ave 210108 max 209134 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +Total # of neighbors = 838550 +Ave neighs/atom = 582.326 +Neighbor list builds = 1000 +Dangerous builds = 0 diff --git a/examples/USER/atc/thermal/bar1d_frac_step.screen b/examples/USER/atc/thermal/bar1d_frac_step.screen new file mode 100644 index 0000000000..702a06e075 --- /dev/null +++ b/examples/USER/atc/thermal/bar1d_frac_step.screen @@ -0,0 +1,176 @@ +LAMMPS (14 Aug 2013) +Reading data file ... + orthogonal box = (-27.025 -16.215 -16.215) to (27.025 16.215 16.215) + 2 by 1 by 2 MPI processor grid + 1440 atoms + 1440 velocities +Lattice spacing in x,y,z = 5.405 5.405 5.405 +1152 atoms in group internal +288 atoms in group ghost +ATC: constructing thermal coupling with parameter file Ar_thermal.mat + ATC: peratom PE compute created with ID: 3 + ATC: 3 materials defined from Ar_thermal.mat + ATC: created uniform mesh with 20 nodes, 5 unique nodes, and 4 elements + ATC: created nodeset lbc with 1 nodes + ATC: created nodeset rbc with 1 nodes +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 50.3386 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -2573.6428 -2710.8793 154.52519 39.965279 24 + 100 3.6 -2518.1866 -2595.4493 154.52519 22.500023 24 + 200 4.8 -2568.5847 -2645.8474 154.52519 22.500023 24 + 300 5.5 -2559.7999 -2637.0626 154.52519 22.500023 24 + 400 14 -2558.3822 -2635.6449 154.52519 22.500023 24 +Loop time of 13.6329 on 4 procs for 400 steps with 1440 atoms + +Pair time (%) = 1.94422 (14.2612) +Neigh time (%) = 1.12431 (8.24707) +Comm time (%) = 6.77892 (49.7248) +Outpt time (%) = 0.000810146 (0.00594259) +Other time (%) = 3.78462 (27.761) + +Nlocal: 360 ave 360 max 360 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4060 ave 4060 max 4060 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 104925 ave 105233 max 104576 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +FullNghs: 209850 ave 210159 max 209488 min +Histogram: 1 0 0 0 0 1 1 0 0 1 + +Total # of neighbors = 839402 +Ave neighs/atom = 582.918 +Neighbor list builds = 40 +Dangerous builds = 0 + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 56.989 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -2558.3822 -2635.6449 154.52519 22.500023 24 + 100 3.8 -2552.5043 -2632.8749 156.62853 23.405103 24.24501 + 200 14 -2549.8719 -2634.1326 158.91067 24.537953 24.510846 + 300 15 -2545.083 -2628.7145 161.33532 24.354702 24.793283 + 400 17 -2542.0333 -2630.2815 165.63086 25.699172 25.293653 + 500 26 -2539.6855 -2626.4322 168.67671 25.261904 25.648452 + 600 29 -2537.684 -2628.9976 171.74862 26.591857 26.006286 + 700 38 -2534.3129 -2623.8423 174.55244 26.072259 26.332891 + 800 41 -2533.4405 -2621.8368 176.45846 25.742306 26.554915 + 900 42 -2534.1228 -2623.6956 178.22609 26.084904 26.760819 + 1000 46 -2531.8714 -2622.5054 179.14012 26.393948 26.867291 + 1100 52 -2532.8133 -2624.0546 180.82964 26.57081 27.064097 + 1200 59 -2529.4099 -2622.3883 182.33958 27.076676 27.239983 + 1300 63 -2530.8526 -2622.632 183.69362 26.727531 27.39771 + 1400 65 -2524.224 -2618.001 185.22706 27.309211 27.576333 + 1500 76 -2528.5455 -2625.7848 186.81972 28.317519 27.761855 + 1600 80 -2525.517 -2623.0676 188.31399 28.408145 27.935918 + 1700 87 -2525.1661 -2618.5626 188.27434 27.198421 27.931299 + 1800 88 -2524.8789 -2622.1289 189.17398 28.320604 28.036093 + 1900 89 -2521.3182 -2616.9976 189.99006 27.863221 28.131155 + 2000 99 -2524.9482 -2622.0399 191.26094 28.274519 28.279195 + 2100 1.1e+02 -2519.3593 -2615.432 192.0516 27.977779 28.371295 + 2200 1.1e+02 -2520.8632 -2618.5921 192.79971 28.460108 28.45844 + 2300 1.1e+02 -2517.3073 -2615.3736 193.39264 28.55832 28.527508 + 2400 1.1e+02 -2520.0587 -2618.6888 194.56198 28.722533 28.66372 + 2500 1.1e+02 -2523.7628 -2620.4444 193.95494 28.155125 28.593008 + 2600 1.2e+02 -2520.3049 -2616.8463 193.8447 28.114265 28.580167 + 2700 1.2e+02 -2518.6173 -2617.33 194.44248 28.746593 28.649799 + 2800 1.2e+02 -2519.9088 -2619.7533 195.22023 29.076198 28.740396 + 2900 1.2e+02 -2518.2877 -2617.8408 195.71077 28.991324 28.797537 + 3000 1.2e+02 -2519.7894 -2619.1288 196.33228 28.929071 28.869935 + 3100 1.2e+02 -2517.6906 -2618.7609 196.62015 29.433147 28.903467 + 3200 1.2e+02 -2520.7444 -2617.9402 196.13681 28.304817 28.847164 + 3300 1.2e+02 -2519.6307 -2615.5967 196.07965 27.946722 28.840507 + 3400 1.2e+02 -2518.1719 -2616.9329 196.66214 28.76065 28.908359 + 3500 1.2e+02 -2518.6985 -2616.6925 196.59502 28.537311 28.90054 + 3600 1.2e+02 -2519.0042 -2618.7537 197.35088 29.048524 28.988587 + 3700 1.2e+02 -2518.3943 -2616.1502 196.85544 28.467961 28.930875 + 3800 1.3e+02 -2514.9161 -2613.9237 197.35119 28.832463 28.988623 + 3900 1.3e+02 -2518.3393 -2617.5157 197.36535 28.881624 28.990272 + 4000 1.3e+02 -2519.4322 -2618.5633 196.14318 28.868422 28.847906 + 4100 1.3e+02 -2519.058 -2616.3128 196.64923 28.322019 28.906854 + 4200 1.3e+02 -2518.7765 -2621.3015 197.08878 29.856777 28.958056 + 4300 1.3e+02 -2518.2567 -2618.9544 197.14618 29.324669 28.964742 + 4400 1.3e+02 -2514.8229 -2610.4412 198.37372 27.845463 29.107733 + 4500 1.3e+02 -2518.6999 -2621.3277 199.20162 29.886727 29.204172 + 4600 1.3e+02 -2517.9045 -2615.9276 198.4982 28.545758 29.122233 + 4700 1.3e+02 -2516.7228 -2615.8136 198.68483 28.856684 29.143974 + 4800 1.4e+02 -2520.2107 -2619.749 198.0603 28.986989 29.071224 + 4900 1.4e+02 -2517.4831 -2618.4664 198.0633 29.407828 29.071574 + 5000 1.4e+02 -2518.3202 -2618.3372 198.00689 29.126411 29.065003 + 5100 1.4e+02 -2517.7374 -2615.8784 198.14951 28.580106 29.081616 + 5200 1.4e+02 -2519.2208 -2617.7451 197.42033 28.691739 28.996677 + 5300 1.4e+02 -2517.6707 -2617.7618 197.94662 29.147992 29.057983 + 5400 1.4e+02 -2516.8563 -2616.1453 196.81438 28.914436 28.926093 + 5500 1.4e+02 -2518.1049 -2615.5854 196.97376 28.387729 28.944658 + 5600 1.4e+02 -2519.4547 -2617.9107 196.82232 28.67181 28.927017 + 5700 1.4e+02 -2515.4908 -2614.9193 198.10022 28.955028 29.075874 + 5800 1.4e+02 -2517.5156 -2614.7566 199.09678 28.317986 29.19196 + 5900 1.4e+02 -2514.4073 -2611.889 199.59808 28.38812 29.250354 + 6000 1.5e+02 -2515.9884 -2617.0167 199.84825 29.420913 29.279495 + 6100 1.5e+02 -2519.0803 -2616.8917 198.58963 28.484096 29.132884 + 6200 1.5e+02 -2520.7756 -2615.8458 196.59931 27.685828 28.90104 + 6300 1.5e+02 -2523.3359 -2619.8562 195.68645 28.108116 28.794704 + 6400 1.5e+02 -2520.2637 -2618.5459 195.57653 28.621217 28.7819 + 6500 1.5e+02 -2517.5582 -2617.516 196.18102 29.109158 28.852314 + 6600 1.6e+02 -2517.2535 -2616.6764 196.40618 28.953418 28.878542 + 6700 1.6e+02 -2519.3703 -2618.718 197.16334 28.931504 28.966741 + 6800 1.6e+02 -2518.4833 -2615.1878 197.01299 28.161747 28.949228 + 6900 1.7e+02 -2520.6821 -2618.6087 196.52515 28.517655 28.892402 + 7000 1.7e+02 -2520.5353 -2616.7065 195.86855 28.006459 28.815917 + 7100 1.7e+02 -2517.9476 -2620.0888 195.84161 29.745001 28.812778 + 7200 1.7e+02 -2520.3188 -2619.9923 196.29834 29.026379 28.865981 + 7300 1.7e+02 -2520.019 -2617.5856 196.51155 28.412825 28.890817 + 7400 1.7e+02 -2517.3548 -2615.9011 196.63984 28.698129 28.905761 + 7500 1.7e+02 -2519.1854 -2614.7882 197.14349 27.84093 28.964429 + 7600 1.7e+02 -2520.2412 -2618.2459 196.4216 28.540386 28.880339 + 7700 1.7e+02 -2519.5564 -2619.0182 196.41019 28.964734 28.87901 + 7800 1.7e+02 -2515.8187 -2614.3055 196.96013 28.680787 28.94307 + 7900 1.7e+02 -2517.7437 -2618.3389 197.99869 29.294776 29.064048 + 8000 1.7e+02 -2516.1958 -2615.3797 198.1845 28.883784 29.085692 + 8100 1.8e+02 -2512.7208 -2611.2195 199.13814 28.684256 29.196778 + 8200 1.8e+02 -2512.9493 -2612.2569 199.29238 28.91983 29.214744 + 8300 1.8e+02 -2513.7878 -2615.9616 199.93983 29.754506 29.290163 + 8400 1.8e+02 -2513.8883 -2612.4143 200.2124 28.692219 29.321914 + 8500 1.8e+02 -2513.5448 -2613.6577 201.25162 29.154345 29.442968 + 8600 1.8e+02 -2514.0373 -2615.8877 201.30457 29.660325 29.449136 + 8700 1.8e+02 -2516.4725 -2617.5851 202.01401 29.445459 29.531776 + 8800 1.8e+02 -2512.447 -2613.6919 202.6094 29.483999 29.601131 + 8900 1.8e+02 -2511.2282 -2614.8801 203.35526 30.18495 29.688013 + 9000 1.8e+02 -2513.6189 -2614.7829 203.42457 29.460443 29.696086 + 9100 1.8e+02 -2516.2403 -2616.7038 203.00618 29.256458 29.647349 + 9200 1.8e+02 -2513.5758 -2614.8621 202.67684 29.496061 29.608986 + 9300 1.9e+02 -2511.9519 -2611.571 202.93946 29.010549 29.639577 + 9400 1.9e+02 -2512.0828 -2613.4151 202.91769 29.509457 29.637042 + 9500 2e+02 -2513.3277 -2613.1558 203.15617 29.071383 29.664821 + 9600 2e+02 -2511.4011 -2613.9597 203.2571 29.866546 29.676579 + 9700 2e+02 -2512.7013 -2612.2983 202.78084 29.004111 29.621101 + 9800 2.1e+02 -2511.842 -2613.6997 203.42265 29.662439 29.695862 + 9900 2.1e+02 -2514.1908 -2615.9923 202.92404 29.646084 29.637782 + 10000 2.2e+02 -2515.2188 -2615.5109 202.63891 29.206539 29.604568 +Loop time of 218.096 on 4 procs for 10000 steps with 1440 atoms + +Pair time (%) = 41.8422 (19.1852) +Neigh time (%) = 20.5497 (9.4223) +Comm time (%) = 67.489 (30.9446) +Outpt time (%) = 0.374106 (0.171532) +Other time (%) = 87.8413 (40.2764) + +Nlocal: 360 ave 360 max 360 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4060 ave 4060 max 4060 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 104570 ave 104913 max 104118 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +FullNghs: 209141 ave 210354 max 207940 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 836564 +Ave neighs/atom = 580.947 +Neighbor list builds = 1000 +Dangerous builds = 0 diff --git a/examples/USER/atc/thermal/bar1d_hoover.screen b/examples/USER/atc/thermal/bar1d_hoover.screen new file mode 100644 index 0000000000..dbae569b95 --- /dev/null +++ b/examples/USER/atc/thermal/bar1d_hoover.screen @@ -0,0 +1,129 @@ +LAMMPS (14 Aug 2013) +Reading data file ... + orthogonal box = (-37.835 -16.215 -16.215) to (37.835 16.215 16.215) + 4 by 1 by 1 MPI processor grid + 2016 atoms + 2016 velocities +Lattice spacing in x,y,z = 5.405 5.405 5.405 +1728 atoms in group internal +288 atoms in group ghost +ATC: constructing thermal coupling with parameter file Ar_thermal.mat + ATC: peratom PE compute created with ID: 3 + ATC: 3 materials defined from Ar_thermal.mat + ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements + ATC: created faceset obndy with 2 faces + ATC: created faceset lbndy with 1 faces + ATC: created faceset rbndy with 1 faces + ATC: created nodeset lbc with 1 nodes + ATC: created nodeset rbc with 1 nodes +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 94.9757 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -3635.4921 -3841.4065 412.06718 39.976852 20 + 100 1.4 -3633.2821 -3735.9436 412.06718 19.931021 20 + 200 2.5 -3633.7032 -3745.5364 412.06718 21.711641 20 + 300 3.8 -3633.3886 -3737.9656 412.06718 20.30289 20 + 400 4.8 -3633.276 -3743.2469 412.06718 21.350106 20 +Loop time of 4.81586 on 4 procs for 400 steps with 2016 atoms + +Pair time (%) = 2.08209 (43.2341) +Neigh time (%) = 0.873464 (18.1372) +Comm time (%) = 0.629725 (13.0761) +Outpt time (%) = 0.00164068 (0.0340682) +Other time (%) = 1.22894 (25.5186) + +Nlocal: 504 ave 504 max 504 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5411 ave 6594 max 4228 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 153096 ave 168828 max 137834 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 306192 ave 336609 max 275767 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1224770 +Ave neighs/atom = 607.525 +Neighbor list builds = 40 +Dangerous builds = 0 + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 101.722 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -3633.276 -3743.2469 412.06718 21.350106 20 + 100 1.2 -3633.0184 -3737.5606 433.0597 20.296137 21.709743 + 200 2.3 -3630.978 -3736.759 437.07782 20.536657 21.889764 + 300 4.5 -3630.2807 -3738.4664 441.08703 21.003524 22.069386 + 400 5.8 -3628.7648 -3738.253 445.01494 21.256382 22.245365 + 500 7.2 -3628.6774 -3736.2098 448.44051 20.876689 22.398838 + 600 8.3 -3629.0146 -3738.7086 451.21751 21.296345 22.523254 + 700 9.5 -3629.4762 -3735.9701 453.6179 20.675069 22.630797 + 800 11 -3628.5517 -3737.9603 455.96852 21.240918 22.73611 + 900 12 -3627.9946 -3734.9525 458.36001 20.765138 22.843254 + 1000 13 -3627.1175 -3734.63 460.8795 20.872814 22.956133 + 1100 14 -3625.5617 -3736.2377 463.50068 21.486986 23.073567 + 1200 15 -3625.1174 -3735.9751 466.03 21.522261 23.186887 + 1300 25 -3623.7322 -3738.0095 468.52626 22.186143 23.298725 + 1400 35 -3622.477 -3733.4261 471.32308 21.540006 23.424029 + 1500 38 -3620.9818 -3734.3366 474.23412 22.007035 23.55445 + 1600 44 -3619.2598 -3731.8302 477.03372 21.854767 23.679878 + 1700 49 -3617.6892 -3731.965 479.84714 22.185839 23.805926 + 1800 59 -3616.4338 -3730.6552 482.89708 22.175296 23.94257 + 1900 60 -3614.9486 -3731.4426 485.8722 22.616502 24.075862 + 2000 62 -3612.9578 -3730.0656 488.82273 22.735673 24.208052 + 2100 72 -3611.6636 -3730.1037 491.71943 22.994329 24.337831 + 2200 74 -3609.638 -3726.0041 494.55968 22.591684 24.465081 + 2300 83 -3607.7636 -3726.2043 497.44291 22.994443 24.594256 + 2400 85 -3606.1931 -3729.5114 500.355 23.9414 24.724724 + 2500 86 -3605.654 -3728.5288 502.92122 23.85529 24.839697 + 2600 96 -3604.6683 -3726.5822 505.03954 23.668739 24.934602 + 2700 97 -3603.4727 -3727.5047 507.08456 24.079967 25.026224 + 2800 1.1e+02 -3601.3844 -3722.0574 509.55631 23.42783 25.136963 + 2900 1.1e+02 -3599.1203 -3724.1692 512.37703 24.277383 25.263338 + 3000 1.2e+02 -3597.4403 -3722.913 515.29334 24.359653 25.393995 + 3100 1.2e+02 -3596.4637 -3721.0822 517.95476 24.193817 25.513233 + 3200 1.3e+02 -3595.7063 -3720.5662 520.17135 24.240706 25.612541 + 3300 1.3e+02 -3594.7208 -3723.5103 522.05786 25.003593 25.697061 + 3400 1.4e+02 -3595.1342 -3723.1049 523.68038 24.844616 25.769754 + 3500 1.5e+02 -3594.1992 -3722.8206 524.96184 24.970947 25.827166 + 3600 1.5e+02 -3592.921 -3718.6757 526.62229 24.414414 25.901558 + 3700 1.5e+02 -3592.0787 -3722.0021 528.37927 25.223739 25.980275 + 3800 1.6e+02 -3591.4326 -3720.3866 529.9943 25.035536 26.052632 + 3900 1.7e+02 -3591.1339 -3719.2518 531.21478 24.873215 26.107312 + 4000 1.7e+02 -3588.7466 -3717.6921 532.70635 25.033882 26.174138 + 4100 1.8e+02 -3586.8667 -3716.2661 534.88978 25.121998 26.27196 + 4200 1.8e+02 -3585.4841 -3715.0705 537.1895 25.158292 26.374993 + 4300 1.9e+02 -3583.4751 -3715.4056 539.48252 25.613395 26.477725 + 4400 2e+02 -3582.8059 -3716.1375 541.63579 25.885404 26.574196 + 4500 2e+02 -3582.2104 -3717.0156 543.25614 26.171504 26.646792 + 4600 2e+02 -3580.8062 -3712.9347 545.04092 25.65184 26.726754 + 4700 2.1e+02 -3579.0105 -3714.252 547.03816 26.256204 26.816235 + 4800 2.1e+02 -3577.652 -3714.1416 549.10337 26.49851 26.908761 + 4900 2.2e+02 -3576.446 -3714.0514 551.00751 26.715137 26.994071 + 5000 2.2e+02 -3574.4655 -3713.6631 553.07998 27.024264 27.086922 +Loop time of 224.114 on 4 procs for 5000 steps with 2016 atoms + +Pair time (%) = 32.9838 (14.7175) +Neigh time (%) = 16.9606 (7.56785) +Comm time (%) = 45.4395 (20.2752) +Outpt time (%) = 0.171835 (0.0766732) +Other time (%) = 128.558 (57.3628) + +Nlocal: 504 ave 504 max 504 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5411 ave 6594 max 4228 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 152764 ave 169189 max 136700 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 305528 ave 336475 max 273769 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1222110 +Ave neighs/atom = 606.205 +Neighbor list builds = 500 +Dangerous builds = 0 diff --git a/examples/USER/atc/thermal/bar1d_interpolate.screen b/examples/USER/atc/thermal/bar1d_interpolate.screen new file mode 100644 index 0000000000..aecb0116bb --- /dev/null +++ b/examples/USER/atc/thermal/bar1d_interpolate.screen @@ -0,0 +1,206 @@ +LAMMPS (14 Aug 2013) +Reading data file ... + orthogonal box = (-27.025 -16.215 -16.215) to (27.025 16.215 16.215) + 2 by 1 by 2 MPI processor grid + 1440 atoms + 1440 velocities +Lattice spacing in x,y,z = 5.405 5.405 5.405 +1152 atoms in group internal +288 atoms in group ghost +ATC: constructing thermal coupling with parameter file Ar_thermal.mat + ATC: peratom PE compute created with ID: 3 + ATC: 3 materials defined from Ar_thermal.mat + ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements + ATC: created faceset ibndy with 2 faces + ATC: created faceset obndy with 2 faces +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 91.5825 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -2573.6428 -2710.8793 412.06718 39.965279 20 + 100 0.74 -2537.6764 -2606.3542 412.06718 20 20 + 200 1.5 -2584.8754 -2653.5532 412.06718 20 20 + 300 2.3 -2575.3126 -2643.9904 412.06718 20 20 + 400 3.2 -2573.4199 -2642.0977 412.06718 20 20 +Loop time of 3.18614 on 4 procs for 400 steps with 1440 atoms + +Pair time (%) = 1.44382 (45.3157) +Neigh time (%) = 0.593548 (18.6291) +Comm time (%) = 0.384184 (12.058) +Outpt time (%) = 0.00157028 (0.0492849) +Other time (%) = 0.763013 (23.9479) + +Nlocal: 360 ave 360 max 360 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4060 ave 4060 max 4060 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 104865 ave 104966 max 104653 min +Histogram: 1 0 0 0 0 0 0 1 0 2 +FullNghs: 209730 ave 209902 max 209521 min +Histogram: 1 0 0 0 1 0 0 1 0 1 + +Total # of neighbors = 838918 +Ave neighs/atom = 582.582 +Neighbor list builds = 40 +Dangerous builds = 0 + ATC: created nodeset lbc with 1 nodes + ATC: created nodeset rbc with 1 nodes +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 96.3294 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 400 0 -2573.4199 -2642.0977 412.06718 20 20 + 500 1.1 -2573.5342 -2643.6832 433.11971 20.428433 21.712432 +Loop time of 1.09966 on 4 procs for 100 steps with 1440 atoms + +Pair time (%) = 0.359811 (32.7203) +Neigh time (%) = 0.172976 (15.73) +Comm time (%) = 0.139441 (12.6804) +Outpt time (%) = 0.000396669 (0.0360721) +Other time (%) = 0.427031 (38.8331) + +Nlocal: 360 ave 360 max 360 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4060 ave 4060 max 4060 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 104761 ave 105083 max 104555 min +Histogram: 2 0 0 0 1 0 0 0 0 1 +FullNghs: 209522 ave 209825 max 209317 min +Histogram: 1 0 1 1 0 0 0 0 0 1 + +Total # of neighbors = 838088 +Ave neighs/atom = 582.006 +Neighbor list builds = 10 +Dangerous builds = 0 + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 96.3294 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -2573.5342 -2643.6832 433.11971 20.428433 21.712432 + 100 0.88 -2573.5097 -2644.702 436.57572 20.732249 21.867268 + 200 1.7 -2573.5112 -2641.7502 439.66841 19.872211 22.005828 + 300 2.6 -2573.3491 -2646.3078 442.69161 21.246649 22.141274 + 400 3.5 -2573.2822 -2641.2514 445.36751 19.793633 22.261161 + 500 4.4 -2572.8845 -2643.9862 447.90976 20.705853 22.375059 + 600 6 -2572.6755 -2641.3224 450.33699 19.990965 22.483804 + 700 6.8 -2572.2821 -2642.5297 452.633 20.457107 22.586671 + 800 7.7 -2571.8547 -2641.9891 454.79418 20.424169 22.683497 + 900 8.9 -2571.4933 -2642.7882 456.85387 20.762116 22.775775 + 1000 14 -2571.0496 -2643.7527 458.82574 21.172182 22.86412 + 1100 21 -2570.5809 -2641.69 460.75038 20.708018 22.950348 + 1200 22 -2570.1887 -2641.7751 462.58586 20.847009 23.032581 + 1300 22 -2569.6728 -2640.1746 464.33069 20.531153 23.110754 + 1400 23 -2569.1102 -2641.2988 465.97998 21.022351 23.184646 + 1500 24 -2568.6933 -2641.6758 467.72853 21.25356 23.262985 + 1600 25 -2568.3126 -2639.4799 469.33389 20.724972 23.334908 + 1700 26 -2567.8917 -2641.4173 470.85034 21.411743 23.402849 + 1800 27 -2567.416 -2642.3747 472.3574 21.829085 23.470369 + 1900 28 -2567.0152 -2640.9335 473.92673 21.526078 23.540678 + 2000 28 -2566.5969 -2640.5435 475.40816 21.534312 23.607049 + 2100 31 -2566.1052 -2638.4679 476.80477 21.073068 23.66962 + 2200 31 -2565.5495 -2641.5032 478.14213 22.118844 23.729537 + 2300 32 -2565.1398 -2639.5956 479.53019 21.682594 23.791726 + 2400 33 -2564.732 -2637.9249 480.87877 21.314827 23.852145 + 2500 34 -2564.3944 -2638.6441 482.2304 21.622593 23.912701 + 2600 35 -2563.8222 -2641.7424 483.47432 22.691525 23.968431 + 2700 36 -2563.3329 -2639.2173 484.77559 22.098628 24.026731 + 2800 37 -2562.8806 -2636.6059 486.01573 21.469866 24.082292 + 2900 38 -2562.3465 -2638.8817 487.25366 22.288159 24.137755 + 3000 39 -2561.8757 -2635.0869 488.43148 21.320176 24.190523 + 3100 39 -2561.4471 -2635.1227 489.60154 21.455403 24.242945 + 3200 40 -2561.0263 -2636.215 490.82935 21.896066 24.297953 + 3300 41 -2560.5777 -2639.0266 491.97068 22.845446 24.349088 + 3400 46 -2560.0712 -2638.4176 493.06997 22.815602 24.398338 + 3500 48 -2559.6348 -2634.4135 494.16582 21.776629 24.447435 + 3600 51 -2559.1842 -2635.4811 495.30605 22.218778 24.49852 + 3700 52 -2558.7086 -2636.2754 496.34541 22.588602 24.545086 + 3800 59 -2558.2562 -2636.6903 497.40496 22.841163 24.592556 + 3900 62 -2557.9356 -2635.0878 498.49911 22.467843 24.641576 + 4000 65 -2557.6063 -2635.2544 499.51434 22.612267 24.687061 + 4100 75 -2557.2943 -2635.0249 500.49246 22.636293 24.730882 + 4200 79 -2556.9353 -2635.4961 501.50868 22.878043 24.776412 + 4300 86 -2556.6277 -2635.8313 502.53051 23.065232 24.822192 + 4400 87 -2556.3739 -2632.5904 503.57744 22.195375 24.869096 + 4500 88 -2556.0212 -2633.6191 504.49147 22.59766 24.910047 + 4600 94 -2555.6736 -2637.0356 505.44829 23.693808 24.952915 + 4700 1e+02 -2555.3469 -2635.8282 506.40204 23.437311 24.995645 + 4800 1.1e+02 -2555.0683 -2637.0806 507.39281 23.883194 25.040034 + 4900 1.1e+02 -2554.6933 -2634.0013 508.23979 23.095678 25.07798 + 5000 1.1e+02 -2554.4138 -2634.5914 509.20047 23.34888 25.121021 + 5100 1.2e+02 -2554.0316 -2631.8029 510.10292 22.648143 25.161453 + 5200 1.2e+02 -2553.7548 -2635.4247 511.03731 23.783481 25.203316 + 5300 1.2e+02 -2553.3812 -2634.282 511.87478 23.559504 25.240836 + 5400 1.2e+02 -2553.0678 -2632.9241 512.77374 23.255322 25.281111 + 5500 1.3e+02 -2552.7082 -2634.3549 513.6816 23.776717 25.321786 + 5600 1.4e+02 -2552.3171 -2634.1375 514.44071 23.827315 25.355796 + 5700 1.4e+02 -2551.9607 -2631.5049 515.35773 23.164428 25.39688 + 5800 1.5e+02 -2551.496 -2633.1155 516.19921 23.768789 25.43458 + 5900 1.5e+02 -2551.2035 -2632.1116 517.07471 23.561628 25.473805 + 6000 1.5e+02 -2550.7722 -2637.2148 517.87274 25.173338 25.509558 + 6100 1.6e+02 -2550.3729 -2635.223 518.677 24.709601 25.545591 + 6200 1.6e+02 -2550.0239 -2633.7077 519.50465 24.369948 25.582672 + 6300 1.6e+02 -2549.7022 -2634.9153 520.32051 24.815296 25.619224 + 6400 1.6e+02 -2549.2302 -2630.2767 521.18099 23.601923 25.657775 + 6500 1.7e+02 -2548.7701 -2632.1853 521.991 24.291732 25.694065 + 6600 1.8e+02 -2548.3382 -2629.8213 522.69988 23.729068 25.725825 + 6700 1.8e+02 -2547.9544 -2634.3457 523.47285 25.158407 25.760456 + 6800 1.8e+02 -2547.6099 -2632.3242 524.24129 24.670057 25.794884 + 6900 1.8e+02 -2547.3857 -2630.1042 524.9806 24.088828 25.828006 + 7000 1.9e+02 -2547.1211 -2631.9693 525.7776 24.70903 25.863714 + 7100 1.9e+02 -2546.7539 -2631.6181 526.45984 24.713697 25.89428 + 7200 2e+02 -2546.4777 -2629.7492 527.21059 24.249884 25.927915 + 7300 2e+02 -2546.2406 -2629.7818 528.01912 24.32843 25.964139 + 7400 2e+02 -2545.9694 -2632.4927 528.64586 25.196846 25.992218 + 7500 2.1e+02 -2545.8619 -2630.0613 529.38653 24.520088 26.025402 + 7600 2.2e+02 -2545.7138 -2632.8388 530.16874 25.372085 26.060447 + 7700 2.3e+02 -2545.4529 -2628.921 530.86231 24.307131 26.09152 + 7800 2.3e+02 -2545.166 -2629.3814 531.58154 24.524736 26.123743 + 7900 2.4e+02 -2544.8001 -2625.4882 532.26268 23.497557 26.15426 + 8000 2.4e+02 -2544.4118 -2628.3746 532.9236 24.451192 26.183871 + 8100 2.4e+02 -2544.1166 -2629.2914 533.60356 24.804137 26.214334 + 8200 2.5e+02 -2543.7942 -2627.1091 534.28788 24.262513 26.244994 + 8300 2.5e+02 -2543.4804 -2630.0029 534.94382 25.196642 26.274381 + 8400 2.5e+02 -2543.104 -2632.0263 535.55146 25.895456 26.301605 + 8500 2.6e+02 -2542.7117 -2627.3589 536.21003 24.650511 26.33111 + 8600 2.6e+02 -2542.3628 -2627.7464 536.92095 24.86496 26.362961 + 8700 2.7e+02 -2542.0845 -2628.3592 537.58922 25.124445 26.392901 + 8800 2.7e+02 -2541.7327 -2628.2907 538.11331 25.206956 26.416381 + 8900 2.8e+02 -2541.5205 -2628.8127 538.78583 25.420763 26.446512 + 9000 2.8e+02 -2541.4308 -2628.532 539.48656 25.36513 26.477906 + 9100 2.8e+02 -2541.3427 -2624.8856 540.08761 24.328917 26.504834 + 9200 2.8e+02 -2541.2405 -2626.8739 540.65481 24.937701 26.530246 + 9300 2.8e+02 -2541.1638 -2628.2134 541.35281 25.350118 26.561518 + 9400 2.8e+02 -2541.0394 -2629.2501 541.97029 25.688239 26.589183 + 9500 2.8e+02 -2540.8064 -2629.0064 542.46763 25.685128 26.611465 + 9600 2.8e+02 -2540.6384 -2628.7742 543.13578 25.666436 26.641399 + 9700 2.9e+02 -2540.3957 -2628.1981 543.7668 25.56933 26.669671 + 9800 2.9e+02 -2540.1324 -2627.8582 544.32985 25.547048 26.694896 + 9900 2.9e+02 -2539.8497 -2629.5669 544.90695 26.12696 26.720752 + 10000 2.9e+02 -2539.5955 -2628.0303 545.50615 25.753491 26.747597 +Loop time of 288.276 on 4 procs for 10000 steps with 1440 atoms + +Pair time (%) = 43.2003 (14.9858) +Neigh time (%) = 21.8684 (7.58594) +Comm time (%) = 65.1973 (22.6163) +Outpt time (%) = 0.233757 (0.0810881) +Other time (%) = 157.776 (54.7309) + +Nlocal: 360 ave 360 max 360 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4060 ave 4060 max 4060 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 104778 ave 104928 max 104669 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +FullNghs: 209556 ave 210121 max 208975 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +Total # of neighbors = 838224 +Ave neighs/atom = 582.1 +Neighbor list builds = 1000 +Dangerous builds = 0 diff --git a/examples/USER/atc/thermal/bar1d_lumped.screen b/examples/USER/atc/thermal/bar1d_lumped.screen new file mode 100644 index 0000000000..b5e588cd7d --- /dev/null +++ b/examples/USER/atc/thermal/bar1d_lumped.screen @@ -0,0 +1,294 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init +Reading data file ... + orthogonal box = (-27.025 -16.215 -16.215) to (27.025 16.215 16.215) + 2 by 1 by 2 MPI processor grid + 1440 atoms + 1440 velocities +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region simRegion block -12 12 -3 3 -3 3 +# create atoms, NOTE commented out for restart +#region mdRegion block -5 5 -3 3 -3 3 +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 +# specify interal/ghost atoms +region mdInternal block -4 4 -3 3 -3 3 +group internal region mdInternal +1152 atoms in group internal +group ghost subtract all internal +288 atoms in group ghost +# velocities have Vcm = 0, NOTE next three lines commented out for restart +#velocity internal create 40. 87287 mom yes loop geom +#pair_style lj/cut 13.5 +#pair_coeff 1 1 .238 3.405 13.5 +neighbor 5. bin +neigh_modify every 10 delay 0 check no +# ID group atc PhysicsType ParameterFile +fix AtC internal atc thermal Ar_thermal.mat +ATC: constructing thermal coupling with parameter file Ar_thermal.mat + ATC: peratom PE compute created with ID: 3 + ATC: 3 materials defined from Ar_thermal.mat +fix_modify AtC boundary ghost +# numerical parameters +fix_modify AtC time_integration fractional_step +fix_modify AtC internal_quadrature off +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p + ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements +fix_modify AtC mesh create_faceset ibndy box -4.0 4.0 -INF INF -INF INF in + ATC: created faceset ibndy with 2 faces +fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -INF INF -INF INF outward + ATC: created faceset obndy with 2 faces +# fix a temperature +fix_modify AtC fix temperature all 20. +#fix_modify AtC fix temperature all linear 0 0 0 -0.154 0 0 30. +#fix_modify AtC fix temperature all quadratic 0 0 0 -0.154 0 0 30. 0.01 0.0 0.0 0 0 0 +# turn on thermostat +fix_modify AtC control thermal rescale 10 +# output +thermo 100 +variable xdof equal 3*count(ghost) +compute_modify thermo_temp extra ${xdof} +compute_modify thermo_temp extra 864 +thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] +thermo_modify format 1 %6i format 2 %7.2g +# equilibrate MD field +#fix_modify AtC output bar1d_lumped_initFE 1 text +timestep 5 +run 400 +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 91.5825 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -2573.6428 -2710.8793 412.06718 39.965279 20 + 100 5.4 -2537.6764 -2606.3542 412.06718 20 20 + 200 13 -2584.8754 -2653.5532 412.06718 20 20 + 300 17 -2575.3126 -2643.9904 412.06718 20 20 + 400 18 -2573.4199 -2642.0977 412.06718 20 20 +Loop time of 18.3995 on 4 procs for 400 steps with 1440 atoms + +Pair time (%) = 2.1463 (11.665) +Neigh time (%) = 1.32344 (7.19278) +Comm time (%) = 9.14841 (49.721) +Outpt time (%) = 0.00160271 (0.00871062) +Other time (%) = 5.77975 (31.4125) + +Nlocal: 360 ave 360 max 360 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4060 ave 4060 max 4060 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 104865 ave 104966 max 104653 min +Histogram: 1 0 0 0 0 0 0 1 0 2 +FullNghs: 209730 ave 209902 max 209521 min +Histogram: 1 0 0 0 1 0 0 1 0 1 + +Total # of neighbors = 838918 +Ave neighs/atom = 582.582 +Neighbor list builds = 40 +Dangerous builds = 0 +#run 100 +# change thermostat to hoover +fix_modify AtC unfix temperature all +#fix_modify AtC thermal control flux interpolate +fix_modify AtC control thermal flux faceset obndy +fix_modify AtC control localized_lambda on +fix_modify AtC filter type exponential +fix_modify AtC filter scale 10000.0 +fix_modify AtC filter on +# add nodesets +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF + ATC: created nodeset lbc with 1 nodes +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF + ATC: created nodeset rbc with 1 nodes +fix_modify AtC fix temperature lbc 80. +fix_modify AtC fix temperature rbc 80. +# initialize +thermo 10 +run 100 +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 96.3294 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 400 0 -2573.4199 -2642.0977 412.06718 20 20 + 410 0.089 -2573.3989 -2643.8455 517.30661 20.515089 29.330348 + 420 0.17 -2573.4223 -2646.1083 519.64166 21.16724 29.434964 + 430 0.25 -2573.4498 -2647.2051 521.96898 21.478626 29.539233 + 440 0.34 -2573.4569 -2646.2686 524.27182 21.203839 29.642406 + 450 0.5 -2573.4737 -2644.3159 526.53414 20.63027 29.743762 + 460 2.9 -2573.4879 -2643.0036 528.75499 20.243982 29.843261 + 470 3.1 -2573.4922 -2642.6172 530.94429 20.130226 29.941347 + 480 3.3 -2573.5022 -2642.5663 533.10876 20.112489 30.03832 + 490 3.4 -2573.5141 -2642.9253 535.25201 20.213567 30.134343 + 500 3.6 -2573.5321 -2643.6709 537.37935 20.425453 30.229652 +Loop time of 3.6034 on 4 procs for 100 steps with 1440 atoms + +Pair time (%) = 0.532621 (14.7811) +Neigh time (%) = 0.227121 (6.30295) +Comm time (%) = 1.37573 (38.1786) +Outpt time (%) = 0.00399309 (0.110814) +Other time (%) = 1.46394 (40.6266) + +Nlocal: 360 ave 360 max 360 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4060 ave 4060 max 4060 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 104761 ave 105083 max 104555 min +Histogram: 2 0 0 0 1 0 0 0 0 1 +FullNghs: 209522 ave 209825 max 209318 min +Histogram: 1 0 1 1 0 0 0 0 0 1 + +Total # of neighbors = 838090 +Ave neighs/atom = 582.007 +Neighbor list builds = 10 +Dangerous builds = 0 +# relax +fix_modify AtC unfix temperature all +# output +fix_modify AtC output bar1d_lumpedFE 100 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +# run with FE +reset_timestep 0 +thermo 100 +run 10000 +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 96.3294 Mbytes +Step CPU TotEng PotEng AtC[1] Temp AtC[2] + 0 0 -2573.5321 -2643.6709 537.37935 20.425453 30.229652 + 100 8.4 -2573.4714 -2644.6628 537.59712 20.731964 29.437439 + 200 18 -2573.5166 -2641.7664 537.63735 19.875333 28.850231 + 300 19 -2573.3454 -2646.2939 537.8469 21.243688 28.422511 + 400 30 -2573.0942 -2641.1809 537.90867 19.827861 28.095231 + 500 31 -2572.3083 -2643.707 538.005 20.792348 27.845793 + 600 38 -2571.6518 -2640.8182 538.12895 20.142273 27.652618 + 700 42 -2570.5731 -2641.7027 538.24696 20.713971 27.499382 + 800 43 -2569.3231 -2640.7761 538.33555 20.808172 27.374616 + 900 44 -2568.1073 -2641.2144 538.42259 21.289869 27.27217 + 1000 48 -2566.8774 -2641.7627 538.50252 21.807716 27.186491 + 1100 52 -2565.6817 -2639.3847 538.60769 21.463413 27.11518 + 1200 54 -2564.5291 -2639.0021 538.6921 21.687625 27.053351 + 1300 57 -2563.046 -2636.8175 538.75291 21.483334 26.998775 + 1400 66 -2561.7374 -2637.9846 538.75622 22.204304 26.948354 + 1500 67 -2560.5922 -2638.0152 538.92825 22.546707 26.911016 + 1600 68 -2559.5712 -2634.9079 538.98874 21.939138 26.873272 + 1700 69 -2558.4498 -2637.4043 539.01552 22.992706 26.83788 + 1800 71 -2557.3572 -2637.6783 539.06504 23.390689 26.806789 + 1900 71 -2556.3318 -2635.4587 539.21528 23.042919 26.783029 + 2000 72 -2555.2491 -2634.8649 539.3077 23.185278 26.759119 + 2100 74 -2554.0813 -2632.5651 539.34324 22.855611 26.734792 + 2200 75 -2552.9667 -2635.7107 539.36679 24.096274 26.711802 + 2300 76 -2552.2327 -2633.1401 539.45717 23.561421 26.693468 + 2400 76 -2551.6044 -2632.5536 539.53752 23.573606 26.676165 + 2500 77 -2551.1734 -2631.6954 539.62757 23.449169 26.660623 + 2600 78 -2550.381 -2634.669 539.66971 24.545902 26.644129 + 2700 79 -2549.624 -2633.4682 539.75068 24.41666 26.630457 + 2800 80 -2548.8206 -2630.6519 539.80156 23.830481 26.616417 + 2900 81 -2547.8861 -2632.5638 539.88361 24.659393 26.604667 + 3000 83 -2547.084 -2627.427 539.9225 23.397054 26.5918 + 3100 84 -2546.394 -2629.4378 539.94648 24.183576 26.579016 + 3200 86 -2545.7683 -2629.3918 540.06149 24.352372 26.571 + 3300 87 -2545.2615 -2631.3813 540.12465 25.079335 26.5613 + 3400 88 -2544.6024 -2630.0895 540.12814 24.895105 26.549518 + 3500 88 -2543.9337 -2628.4156 540.13502 24.602369 26.53844 + 3600 89 -2543.3099 -2628.0721 540.25751 24.684014 26.533053 + 3700 90 -2542.6958 -2628.8619 540.25488 25.092829 26.522541 + 3800 91 -2542.218 -2630.3008 540.2971 25.651004 26.514488 + 3900 92 -2542.2329 -2626.6554 540.40242 24.585058 26.509685 + 4000 93 -2542.345 -2628.0992 540.4246 24.972878 26.501556 + 4100 93 -2542.444 -2628.9863 540.4438 25.202383 26.493668 + 4200 94 -2542.4625 -2630.9619 540.43077 25.772324 26.484689 + 4300 95 -2542.4932 -2628.6896 540.46659 25.101648 26.47823 + 4400 96 -2542.4649 -2626.3615 540.52486 24.431935 26.473089 + 4500 97 -2542.3848 -2629.9464 540.56942 25.49921 26.467627 + 4600 98 -2542.2156 -2630.1917 540.57345 25.619915 26.460625 + 4700 99 -2542.0968 -2628.4423 540.65789 25.145095 26.457485 + 4800 1e+02 -2541.8766 -2630.6991 540.69403 25.866389 26.452428 + 4900 1e+02 -2541.7652 -2628.337 540.65021 25.210979 26.444021 + 5000 1e+02 -2541.667 -2627.5891 540.75066 25.021773 26.442299 + 5100 1e+02 -2541.4455 -2626.9354 540.74526 24.895894 26.436045 + 5200 1.1e+02 -2541.3524 -2626.9293 540.80011 24.92126 26.432691 + 5300 1.1e+02 -2541.4921 -2627.9353 540.85481 25.173531 26.429523 + 5400 1.2e+02 -2541.4091 -2627.4363 540.77756 25.052378 26.420627 + 5500 1.2e+02 -2541.2364 -2627.0322 540.8409 24.985021 26.418205 + 5600 1.2e+02 -2541.0146 -2626.1809 540.84749 24.801661 26.41341 + 5700 1.2e+02 -2540.7658 -2626.3892 540.83392 24.934789 26.407875 + 5800 1.2e+02 -2540.5557 -2625.5238 540.86784 24.74395 26.404623 + 5900 1.2e+02 -2540.2613 -2628.8094 540.88157 25.7865 26.400618 + 6000 1.2e+02 -2540.023 -2628.3564 540.89421 25.723987 26.39671 + 6100 1.2e+02 -2539.7369 -2626.2678 540.8886 25.199056 26.392126 + 6200 1.2e+02 -2539.4247 -2626.9787 540.88107 25.496996 26.387593 + 6300 1.2e+02 -2539.2795 -2628.1038 540.94239 25.866954 26.386278 + 6400 1.3e+02 -2539.2702 -2625.3721 540.99133 25.07412 26.384539 + 6500 1.3e+02 -2539.0339 -2627.6649 541.01851 25.810661 26.381951 + 6600 1.3e+02 -2538.7604 -2630.2595 540.93819 26.645879 26.37467 + 6700 1.3e+02 -2538.5609 -2627.2764 541.00702 25.835243 26.374189 + 6800 1.3e+02 -2538.4781 -2628.4908 541.04647 26.213023 26.372508 + 6900 1.3e+02 -2538.3363 -2626.3948 541.0421 25.643922 26.368975 + 7000 1.3e+02 -2538.1096 -2624.3062 541.07424 25.101732 26.367185 + 7100 1.3e+02 -2538.1297 -2625.2825 541.13737 25.380157 26.366889 + 7200 1.3e+02 -2537.9558 -2625.6952 541.11622 25.550998 26.362917 + 7300 1.3e+02 -2537.7777 -2623.8467 541.12479 25.064554 26.360375 + 7400 1.4e+02 -2537.691 -2626.362 541.12857 25.822305 26.357713 + 7500 1.4e+02 -2537.6017 -2627.6258 541.11665 26.216328 26.354439 + 7600 1.4e+02 -2537.5881 -2626.5336 541.09525 25.902252 26.350828 + 7700 1.4e+02 -2537.4503 -2626.5011 541.10444 25.932897 26.348674 + 7800 1.4e+02 -2537.4247 -2625.6606 541.16841 25.695575 26.349056 + 7900 1.5e+02 -2537.221 -2626.6494 541.16553 26.042851 26.346524 + 8000 1.5e+02 -2536.9786 -2624.3886 541.16948 25.455068 26.344375 + 8100 1.5e+02 -2537.0091 -2626.1267 541.19675 25.952348 26.343346 + 8200 1.6e+02 -2536.8966 -2626.9415 541.24047 26.222385 26.343126 + 8300 1.6e+02 -2536.7301 -2627.422 541.17563 26.4108 26.338112 + 8400 1.7e+02 -2536.5639 -2626.9772 541.22236 26.329686 26.338165 + 8500 1.7e+02 -2536.2761 -2623.6142 541.20754 25.434125 26.335526 + 8600 1.8e+02 -2536.1413 -2624.8573 541.2923 25.835401 26.337411 + 8700 1.8e+02 -2535.8015 -2627.0616 541.217 26.576282 26.332188 + 8800 1.8e+02 -2535.645 -2625.4677 541.22666 26.157671 26.33083 + 8900 1.9e+02 -2535.5467 -2622.6362 541.21146 25.361737 26.328417 + 9000 1.9e+02 -2535.5706 -2622.2805 541.23307 25.251184 26.32771 + 9100 1.9e+02 -2535.6698 -2627.18 541.28442 26.649119 26.328389 + 9200 2e+02 -2535.6724 -2623.9823 541.29366 25.717136 26.327233 + 9300 2e+02 -2535.4543 -2624.9706 541.21196 26.06848 26.322051 + 9400 2.1e+02 -2535.4415 -2625.439 541.31268 26.20861 26.325088 + 9500 2.1e+02 -2535.4949 -2622.6035 541.29414 25.367306 26.322824 + 9600 2.1e+02 -2535.6083 -2623.7154 541.32785 25.658066 26.322941 + 9700 2.2e+02 -2535.569 -2624.6231 541.28832 25.933859 26.319815 + 9800 2.2e+02 -2535.4348 -2624.787 541.27797 26.020648 26.318031 + 9900 2.2e+02 -2535.3781 -2626.4373 541.30541 26.517775 26.317973 + 10000 2.3e+02 -2535.4286 -2624.7326 541.30648 26.006646 26.316764 +Loop time of 232.78 on 4 procs for 10000 steps with 1440 atoms + +Pair time (%) = 43.634 (18.7448) +Neigh time (%) = 20.911 (8.98318) +Comm time (%) = 68.5468 (29.447) +Outpt time (%) = 0.2765 (0.118782) +Other time (%) = 99.4116 (42.7063) + +Nlocal: 360 ave 360 max 360 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4060 ave 4060 max 4060 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 104746 ave 104843 max 104627 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +FullNghs: 209492 ave 209713 max 209341 min +Histogram: 1 1 0 0 1 0 0 0 0 1 + +Total # of neighbors = 837970 +Ave neighs/atom = 581.924 +Neighbor list builds = 1000 +Dangerous builds = 0 diff --git a/examples/USER/atc/thermal/in.bar1d b/examples/USER/atc/thermal/in.bar1d new file mode 100644 index 0000000000..7c091a7c87 --- /dev/null +++ b/examples/USER/atc/thermal/in.bar1d @@ -0,0 +1,79 @@ +#AtC Thermal Coupling +# This benchmark tests heat conducting into and out of the MD region. The +# temperature is intially 20 everywhere and the left boundary BC is fixed at 40. +# The result should show heat diffusing through the FEM to the MD and back out +# to the FEM on the right. Insufficient time is captured to reach the linear +# steady state, but heat crossing both boundaries should be observed. + +units real +atom_style atomic +echo both +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init +lattice fcc 5.405 origin 0.25 0.25 0.25 +region simRegion block -12 12 -3 3 -3 3 +# create atoms, NOTE commented out for restart +#region mdRegion block -5 5 -3 3 -3 3 +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 +# specify interal/ghost atoms +region mdInternal block -4 4 -3 3 -3 3 +group internal region mdInternal +group ghost subtract all internal +# velocities have Vcm = 0, NOTE next four lines commented out for restart +#velocity internal create 40. 87287 mom yes loop geom +#pair_style lj/cut 13.5 +##pair_coeff 1 1 0.010323166 3.405 13.5 +#pair_coeff 1 1 .238 3.405 13.5 +neighbor 5. bin +neigh_modify every 10 delay 0 check no +# ID group atc PhysicsType ParameterFile +fix AtC internal atc thermal Ar_thermal.mat +fix_modify AtC boundary ghost +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p +fix_modify AtC internal_quadrature off +# fix a temperature +fix_modify AtC fix temperature all 20. +# turn on thermostat +fix_modify AtC control thermal rescale 10 +# equilibrate MD field +#dump D1 all atom 100 dump.bar1d +#fix_modify AtC output bar1dfe 100 +timestep 5 +variable xdof equal 3*count(ghost) +compute_modify thermo_temp extra ${xdof} +thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] +thermo_modify format 1 %6i format 2 %7.2g +thermo 100 +run 400 +# change thermostat to hoover +fix_modify AtC unfix temperature all +fix_modify AtC control thermal hoover +#fix_modify AtC localized_lambda on +fix_modify AtC filter type exponential +fix_modify AtC filter scale 10000.0 +fix_modify AtC filter on +# add nodesets +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF +fix_modify AtC fix temperature lbc 40. +fix_modify AtC fix temperature rbc 20. +# initialize filter +#thermo 1 +run 100 +# set up output, should be before a "run" +fix_modify AtC output bar1dFE 100 text binary +# ouput command +#dump D1 all atom 1000 dump.bar1d +# run with FE +reset_timestep 0 +thermo 100 +run 10000 diff --git a/examples/USER/atc/thermal/in.bar1d_all_atoms b/examples/USER/atc/thermal/in.bar1d_all_atoms new file mode 100644 index 0000000000..6b855f37b1 --- /dev/null +++ b/examples/USER/atc/thermal/in.bar1d_all_atoms @@ -0,0 +1,101 @@ +#AtC Thermal Coupling +# This benchmark tests thermostats applied in all atom simulations. The +# temperature is intially 20 everywhere and the left boundary BC is fixed at +# 40.# The result should show heat diffusing through the FEM to the MD and back +# out # to the FEM on the right. Insufficient time is captured to reach the +# linear # steady state, but heat crossing both boundaries should be observed. +units real +atom_style atomic +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13.5 +read_data all_atoms.init +lattice fcc 5.405 origin 0.25 0.25 0.25 +region simRegion block -7 7 -3 3 -3 3 +# create atoms, NOTE commented out for restart +#boundary f p p +#create_box 1 simRegion +#create_atoms 1 region simRegion +#mass 1 39.95 +# specify interal/ghost atoms +region mdInternal block -6 6 -3 3 -3 3 +group internal region mdInternal +group ghost subtract all internal +# velocities have Vcm = 0, NOTE next four lines commented out for restart +#velocity internal create 40. 87287 mom yes loop geom +#pair_style lj/cut 13.5 +##pair_coeff 1 1 0.010323166 3.405 13.5 +#pair_coeff 1 1 .238 3.405 13.5 +#write_restart all_atoms.init +neighbor 5. bin +neigh_modify every 10 delay 0 check no +# ID group atc PhysicsType ParameterFile +fix AtC internal atc thermal Ar_thermal.mat +# ID part keywords nx ny nz region +fix_modify AtC mesh create 6 1 1 mdInternal f p p +fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward +fix_modify AtC mesh create_faceset lbndy box -6.0 16.0 -INF INF -INF INF outward +fix_modify AtC mesh create_faceset rbndy box -16.0 6.0 -INF INF -INF INF outward +# fix a temperature +fix_modify AtC fix temperature all 20. +# turn on thermostat +fix_modify AtC control thermal rescale 10 +fix_modify AtC internal_quadrature off +# equilibrate MD field +#dump D1 all atom 100 dump.bar1d +#fix_modify AtC output bar1dfe 100 +#fix_modify AtC time_integration frac_step +timestep 5 +variable xdof equal 3*count(ghost) +compute_modify thermo_temp extra ${xdof} +thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] +thermo_modify format 1 %6i format 2 %7.2g +thermo 100 +run 400 +# change thermostat to hoover +fix_modify AtC control thermal hoover +#fix_modify AtC thermal control flux interpolate +#fix_modify AtC thermal control flux faceset obndy +fix_modify AtC filter scale 1000.0 +#fix_modify AtC filter equilibrate +#fix_modify AtC filter on +#fix_modify AtC localized_lambda on +fix_modify AtC boundary_faceset is obndy +# initialize filter +#fix_modify AtC output bar1d_all_atoms_preqFE 1 +reset_timestep 0 +thermo 1 +#run 5000 +# add nodesets and ramp temperature +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +#fix_modify AtC mesh create_nodeset lbc -6.1 -5.9 -INF INF -INF INF +#fix_modify AtC mesh create_nodeset rbc 5.9 6.1 -INF INF -INF INF +#fix_modify AtC fix temperature lbc temporal_ramp 20. 40. 25000. +#fix_modify AtC fix temperature rbc 20. +# initialize filter +#fix_modify AtC output bar1d_all_atoms_eqFE 200 +reset_timestep 0 +fix_modify AtC reset_time +#run 5000 +# release and let run +#fix_modify AtC filter on +fix_modify AtC unfix temperature all +#fix_modify AtC localized_lambda on +fix_modify AtC control lumped_lambda_solve on +# dirichlet boundaries +#fix_modify AtC fix temperature lbc 40. +#fix_modify AtC fix temperature rbc 20. +# neumann boundaries +fix_modify AtC control thermal flux no_boundary +fix_modify AtC fix_flux temperature lbndy 0.0000000001 +fix_modify AtC fix_flux temperature rbndy -0.0000000001 +# set up output, should be before a "run" +fix_modify AtC output bar1d_all_atomsFE 200 text binary +# ouput command +#dump D1 all atom 1000 dump.bar1d +# run with FE +reset_timestep 0 +thermo 200 +run 5000 diff --git a/examples/USER/atc/thermal/in.bar1d_combined b/examples/USER/atc/thermal/in.bar1d_combined new file mode 100644 index 0000000000..1f960dbab7 --- /dev/null +++ b/examples/USER/atc/thermal/in.bar1d_combined @@ -0,0 +1,87 @@ +#AtC Thermal Coupling +# This benchmark tests heat conducting into an MD region at a fixed temperature at one end. The +# temperature is intially 20 everywhere and the left boundary BC is fixed at +# 40.# The result should show heat diffusing through the FEM to the MD and back +# out # to the FEM on the right. Insufficient time is captured to reach the +# linear # steady state, but heat crossing the boundaries should be observed, +# as should the interaction of the two themostat types. +#echo both +units real +atom_style atomic +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init +lattice fcc 5.405 origin 0.25 0.25 0.25 +region simRegion block -16 4 -3 3 -3 3 +# create atoms, NOTE commented out for restart +#region mdRegion block -5 5 -3 3 -3 3 +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 +# specify interal/ghost atoms +region mdInternal block -4 4 -3 3 -3 3 +group internal region mdInternal +region mdGhost block -5 -4 -3 3 -3 3 +group ghost region mdGhost +# velocities have Vcm = 0, NOTE next four lines commented out for restart +#velocity internal create 40. 87287 mom yes loop geom +#pair_style lj/cut 13.5 +##pair_coeff 1 1 0.010323166 3.405 13.5 +#pair_coeff 1 1 .238 3.405 13.5 +neighbor 5. bin +neigh_modify every 10 delay 0 check no +#write_restart tinit.dat +# ID group atc PhysicsType ParameterFile +fix AtC internal atc thermal Ar_thermal.mat +fix_modify AtC boundary ghost +fix_modify AtC time_integration fractional_step +fix_modify AtC internal_quadrature off +# ID part keywords nx ny nz region +fix_modify AtC mesh create 10 1 1 simRegion f p p +fix_modify AtC mesh create_faceset ibndy box -4.0 40.0 -INF INF -INF INF in +fix_modify AtC mesh create_faceset obndy box -4.0 40.0 -INF INF -INF INF outward +# fix a temperature +fix_modify AtC fix temperature all 20. +# turn on thermostat +fix_modify AtC control thermal rescale 10 +variable xdof equal 3*count(ghost) +compute_modify thermo_temp extra ${xdof} +thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] +thermo_modify format 1 %6i format 2 %7.2g +# equilibrate MD field +#fix_modify AtC output bar1dfe_combined_init 100 +timestep 5 +thermo 10 +run 400 +# change thermostat to flux +fix_modify AtC unfix temperature all +fix_modify AtC control thermal flux faceset obndy +#fix_modify AtC control thermal hoover +fix_modify AtC control localized_lambda on +#fix_modify AtC control tolerance 1.e-16 # this tolerance seems necessary to prevent noticeable drift +# add nodesets +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -16.1 -15.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 3.9 4.1 -INF INF -INF INF +fix_modify AtC fix temperature lbc 40. +fix_modify AtC fix temperature rbc 20. + +# equilibrate filter +fix_modify AtC filter type exponential +fix_modify AtC filter scale 1000.0 +#fix_modify AtC filter on +thermo 100 +#run 100 + +# set up output, should be before a "run" +fix_modify AtC output bar1d_combinedFE 100 text +# ouput command +#dump D1 all atom 100 dump.bar1d_combined +# run with FE +reset_timestep 0 +thermo 100 +run 5000 diff --git a/examples/USER/atc/thermal/in.bar1d_flux b/examples/USER/atc/thermal/in.bar1d_flux new file mode 100644 index 0000000000..0103f00b5b --- /dev/null +++ b/examples/USER/atc/thermal/in.bar1d_flux @@ -0,0 +1,79 @@ +#AtC Thermal Coupling +# This benchmark tests heat conducting into and out of the MD region. The +# temperature is intially 20 everywhere and the left boundary BC is fixed at +# 40.# The result should show heat diffusing through the FEM to the MD and back +# out # to the FEM on the right. Insufficient time is captured to reach the +# linear # steady state, but heat crossing both boundaries should be observed. +#echo both +units real +atom_style atomic +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init +lattice fcc 5.405 origin 0.25 0.25 0.25 +region simRegion block -12 12 -3 3 -3 3 +# create atoms, NOTE commented out for restart +#region mdRegion block -5 5 -3 3 -3 3 +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 +# specify interal/ghost atoms +region mdInternal block -4 4 -3 3 -3 3 +group internal region mdInternal +group ghost subtract all internal +# velocities have Vcm = 0, NOTE next four lines commented out for restart +#velocity internal create 40. 87287 mom yes loop geom +#pair_style lj/cut 13.5 +##pair_coeff 1 1 0.010323166 3.405 13.5 +#pair_coeff 1 1 .238 3.405 13.5 +neighbor 5. bin +neigh_modify every 10 delay 0 check no +#write_restart tinit.dat +# ID group atc PhysicsType ParameterFile +fix AtC internal atc thermal Ar_thermal.mat +fix_modify AtC boundary ghost +fix_modify AtC time_integration fractional_step +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p +fix_modify AtC mesh create_faceset ibndy box -4.0 4.0 -INF INF -INF INF in +fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -INF INF -INF INF outward +# fix a temperature +fix_modify AtC fix temperature all 20. +#fix_modify AtC fix temperature all linear 0 0 0 -0.154 0 0 30. +# turn on thermostat +fix_modify AtC control thermal rescale 10 +variable xdof equal 3*count(ghost) +compute_modify thermo_temp extra ${xdof} +thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] +thermo_modify format 1 %6i format 2 %7.2g +# equilibrate MD field +#fix_modify AtC output bar1dfe_flux_init 100 +timestep 5 +thermo 10 +run 400 +# change thermostat to hoover +fix_modify AtC unfix temperature all +fix_modify AtC control thermal flux faceset obndy +fix_modify AtC filter type exponential +fix_modify AtC filter scale 10000.0 +#fix_modify AtC filter on +# add nodesets +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF +fix_modify AtC fix temperature lbc 40. +fix_modify AtC fix temperature rbc 20. +# initialize filter +run 100 +# set up output, should be before a "run" +fix_modify AtC output bar1d_fluxFE 100 text binary +# ouput command +#dump D1 all atom 1000 dump.bar1d +# run with FE +reset_timestep 0 +thermo 100 +run 10000 diff --git a/examples/USER/atc/thermal/in.bar1d_frac_step b/examples/USER/atc/thermal/in.bar1d_frac_step new file mode 100644 index 0000000000..1e5a23a5d6 --- /dev/null +++ b/examples/USER/atc/thermal/in.bar1d_frac_step @@ -0,0 +1,78 @@ +#AtC Thermal Coupling +# This benchmark tests heat conducting into and out of the MD region. The +# temperature is intially 20 everywhere and the left boundary BC is fixed at +# 40.# The result should show heat diffusing through the FEM to the MD and back +# out # to the FEM on the right. Insufficient time is captured to reach the +# linear # steady state, but heat crossing both boundaries should be observed. +units real +atom_style atomic +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init +lattice fcc 5.405 origin 0.25 0.25 0.25 +region simRegion block -12 12 -3 3 -3 3 +# create atoms, NOTE commented out for restart +#region mdRegion block -5 5 -3 3 -3 3 +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 +# specify interal/ghost atoms +region mdInternal block -4 4 -3 3 -3 3 +group internal region mdInternal +group ghost subtract all internal +# velocities have Vcm = 0, NOTE next four lines commented out for restart +#velocity internal create 40. 87287 mom yes loop geom +#pair_style lj/cut 13.5 +##pair_coeff 1 1 0.010323166 3.405 13.5 +#pair_coeff 1 1 .238 3.405 13.5 +neighbor 5. bin +neigh_modify every 10 delay 0 check no +# ID group atc PhysicsType ParameterFile +fix AtC internal atc thermal Ar_thermal.mat +# ID part keywords nx ny nz region +fix_modify AtC mesh create 4 1 1 mdInternal f p p +fix_modify AtC time_integration fractional_step +fix_modify AtC internal_quadrature off +# fix a temperature +fix_modify AtC fix temperature all 20. +# add nodesets +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -4.1 -3.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 3.9 4.1 -INF INF -INF INF +fix_modify AtC fix temperature lbc 40. +fix_modify AtC fix temperature rbc 20. +# turn on thermostat +fix_modify AtC control thermal rescale 10 +# equilibrate MD field +#dump D1 all atom 100 dump.bar1d +#fix_modify AtC output bar1dfe 100 text +timestep 5 +variable xdof equal 3*count(ghost) +compute_modify thermo_temp extra ${xdof} +thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] +thermo_modify format 1 %6i format 2 %7.2g +thermo 100 +run 400 +# change thermostat to hoover +fix_modify AtC unfix temperature all +fix_modify AtC fix temperature lbc 40. +fix_modify AtC fix temperature rbc 20. +fix_modify AtC control thermal flux no_boundary +fix_modify AtC control tolerance 1.e-9 # this is to remove looser benchmark tolerance because the lambda solution was reacting to numerical noise, but it results in a slight drift in the constraints +#fix_modify AtC thermal control none +fix_modify AtC control localized_lambda on +fix_modify AtC filter type exponential +fix_modify AtC filter scale 1000.0 +fix_modify AtC filter on +# set up output, should be before a "run" +fix_modify AtC output bar1d_frac_stepFE 200 text +# ouput command +#dump D1 all atom 1000 dump.bar1d +# run with FE +reset_timestep 0 +thermo 100 +run 10000 diff --git a/examples/USER/atc/thermal/in.bar1d_hoover b/examples/USER/atc/thermal/in.bar1d_hoover new file mode 100644 index 0000000000..50e8f02166 --- /dev/null +++ b/examples/USER/atc/thermal/in.bar1d_hoover @@ -0,0 +1,138 @@ +# AtC Thermal Coupling +# This benchmark tests thermostats applied in all atom simulations. The +# temperature is intially 20 everywhere and the left boundary BC is fixed at +# 40.# The result should show heat diffusing through the FEM to the MD and back +# out # to the FEM on the right. Insufficient time is captured to reach the +# linear # steady state, but heat crossing both boundaries should be observed. +units real +atom_style atomic +log bar1d_hoover.log +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13.5 +read_data all_atoms.init +lattice fcc 5.405 origin 0.25 0.25 0.25 +region simRegion block -7 7 -3 3 -3 3 +# create atoms, NOTE commented out for restart +#boundary f p p +#create_box 1 simRegion +#create_atoms 1 region simRegion +#mass 1 39.95 +#atom_modify sort 0 0 +# specify interal/ghost atoms +region mdInternal block -6 6 -3 3 -3 3 +group internal region mdInternal +group ghost subtract all internal +# velocities have Vcm = 0, NOTE next four lines commented out for restart +#velocity internal create 40. 87287 mom yes loop geom +#pair_style lj/cut 13.5 +##pair_coeff 1 1 0.010323166 3.405 13.5 +#pair_coeff 1 1 .238 3.405 13.5 +#write_restart all_atoms.init +neighbor 5. bin +neigh_modify every 10 delay 0 check no +# ID group atc PhysicsType ParameterFile +fix AtC internal atc thermal Ar_thermal.mat +# ID part keywords nx ny nz region + +# switch depending on application of BCs or coupling +#variable nEls equal 6 # for boundary conditions +variable nEls equal 12 # for coupling +fix_modify AtC boundary ghost # for coupling + +region atcRegion block -${nEls} ${nEls} -3 3 -3 3 +fix_modify AtC mesh create ${nEls} 1 1 atcRegion f p p +fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward +fix_modify AtC mesh create_faceset lbndy box -6.0 16.0 -INF INF -INF INF outward +fix_modify AtC mesh create_faceset rbndy box -16.0 6.0 -INF INF -INF INF outward +variable tol equal 0.1 +variable uBnd equal ${nEls}+${tol} +variable lBnd equal ${nEls}-${tol} +fix_modify AtC mesh create_nodeset lbc -${uBnd} -${lBnd} -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc ${lBnd} ${uBnd} -INF INF -INF INF +# fix a temperature +fix_modify AtC fix temperature all 20. +#fix_modify AtC initial temperature all 20. +#fix_modify AtC consistent_fe_initialization on +# turn on thermostat +fix_modify AtC control thermal rescale 10 +fix_modify AtC internal_quadrature off +# equilibrate MD field +#dump D1 all atom 100 dump.bar1d_hoover_init +#fix_modify AtC output bar1d_hoover_init 100 text binary +fix_modify AtC time_integration fractional_step +fix_modify AtC temperature_definition total +timestep 5 +variable xdof equal 3*count(ghost) +compute_modify thermo_temp extra ${xdof} +thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] +thermo_modify format 1 %6i format 2 %7.2g +thermo 100 +run 400 + +fix_modify AtC unfix temperature all + +fix_modify AtC filter type exponential +fix_modify AtC filter scale 1000.0 +fix_modify AtC filter on + + +# boundary conditions------------------------ +# dirichlet with ramp (unstable when filtered due to instantaneous change in rate) +#fix_modify AtC fix temperature lbc temporal_ramp 20. 40. 25000. +#fix_modify AtC fix temperature rbc 20. +#fix_modify AtC localized_lambda on +#fix_modify AtC control thermal flux no_boundary +#fix_modify AtC output test_rampFE 200 text binary +#dump D1 all atom 200 dump.test_ramp +#reset_timestep 0 +#fix_modify AtC reset_time +#thermo 100 +#run 5000 +#fix_modify AtC fix temperature lbc 40. + +# dirichlet with rescaling +#fix_modify AtC filter off +#fix_modify AtC fix temperature all 20. +#fix_modify AtC fix temperature lbc 40. +#fix_modify AtC output test_rampFE 200 text binary +#dump D1 all atom 200 dump.test_ramp +#reset_timestep 0 +#fix_modify AtC reset_time +#thermo 100 +#run 1000 +#fix_modify AtC unfix temperature all +#fix_modify AtC fix temperature lbc 40. +#fix_modify AtC fix temperature rbc 20. +#fix_modify AtC control thermal flux no_boundary +#fix_modify AtC localized_lambda on +#fix_modify AtC filter on + +# neumann +#fix_modify AtC fix_flux temperature lbndy 0.0000000005 +#fix_modify AtC fix_flux temperature rbndy -0.0000000005 +#fix_modify AtC control thermal flux no_boundary +#fix_modify AtC lumped_lambda_solve on + +# coupling------------------------------------ +fix_modify AtC fix temperature lbc 40. +fix_modify AtC fix temperature rbc 20. + +# flux +#fix_modify AtC control thermal flux interpolate +#fix_modify AtC control thermal flux faceset obndy +#fix_modify AtC lumped_lambda_solve on + +# hoover +fix_modify AtC control thermal hoover +fix_modify AtC control localized_lambda on + +fix_modify AtC control tolerance 1.e-14 +fix_modify AtC output bar1d_hooverFE 200 text binary +#dump D1 all atom 200 dump.bar1d_hoover +reset_timestep 0 +fix_modify AtC reset_time +thermo 100 +run 5000 diff --git a/examples/USER/atc/thermal/in.bar1d_interpolate b/examples/USER/atc/thermal/in.bar1d_interpolate new file mode 100644 index 0000000000..e7db0d3856 --- /dev/null +++ b/examples/USER/atc/thermal/in.bar1d_interpolate @@ -0,0 +1,80 @@ +#AtC Thermal Coupling +# This benchmark tests heat conducting into and out of the MD region. The +# temperature is intially 20 everywhere and the left boundary BC is fixed at +# 40.# The result should show heat diffusing through the FEM to the MD and back +# out # to the FEM on the right. Insufficient time is captured to reach the +# linear # steady state, but heat crossing both boundaries should be observed. +units real +atom_style atomic +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init +lattice fcc 5.405 origin 0.25 0.25 0.25 +region simRegion block -12 12 -3 3 -3 3 +# create atoms, NOTE commented out for restart +#region mdRegion block -5 5 -3 3 -3 3 +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 +# specify interal/ghost atoms +region mdInternal block -4 4 -3 3 -3 3 +group internal region mdInternal +group ghost subtract all internal +# velocities have Vcm = 0, NOTE next three lines commented out for restart +#velocity internal create 40. 87287 mom yes loop geom +#pair_style lj/cut 13.5 +#pair_coeff 1 1 .238 3.405 13.5 +neighbor 5. bin +neigh_modify every 10 delay 0 check no +# ID group atc PhysicsType ParameterFile +fix AtC internal atc thermal Ar_thermal.mat +fix_modify AtC boundary ghost +# numerical parameters +fix_modify AtC time_integration fractional_step +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p +fix_modify AtC mesh create_faceset ibndy box -4.0 4.0 -INF INF -INF INF in +fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -INF INF -INF INF outward +# fix a temperature +fix_modify AtC fix temperature all 20. +#fix_modify AtC fix temperature all linear 0 0 0 -0.154 0 0 30. +#fix_modify AtC fix temperature all quadratic 0 0 0 -0.154 0 0 30. 0.01 0.0 0.0 0 0 0 +# turn on thermostat +fix_modify AtC control thermal rescale 10 +# equilibrate MD field +#fix_modify AtC output bar1dfe_flux_init 100 +timestep 5 +variable xdof equal 3*count(ghost) +compute_modify thermo_temp extra ${xdof} +thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] +thermo_modify format 1 %6i format 2 %7.2g +thermo 100 +run 400 +# change thermostat to hoover +fix_modify AtC unfix temperature all +fix_modify AtC control thermal none +fix_modify AtC control thermal flux interpolate +fix_modify AtC control localized_lambda on +#fix_modify AtC thermal control flux faceset obndy +fix_modify AtC filter type exponential +fix_modify AtC filter scale 10000.0 +fix_modify AtC filter on +# add nodesets +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF +fix_modify AtC fix temperature lbc 40. +fix_modify AtC fix temperature rbc 20. +# initialize filter +run 100 +# set up output, should be before a "run" +fix_modify AtC output bar1d_interpolateFE 100 text +# run with FE +reset_timestep 0 +thermo 100 +#run 10 +run 10000 diff --git a/examples/USER/atc/thermal/in.bar1d_lumped b/examples/USER/atc/thermal/in.bar1d_lumped new file mode 100644 index 0000000000..eb305a6252 --- /dev/null +++ b/examples/USER/atc/thermal/in.bar1d_lumped @@ -0,0 +1,85 @@ +#AtC Thermal Coupling +# This benchmark tests heat conducting into and out of the MD region. The +# temperature is intially 20 everywhere and the left boundary BC is fixed at +# 40.# The result should show heat diffusing through the FEM to the MD and back +# out # to the FEM on the right. Insufficient time is captured to reach the +# linear # steady state, but heat crossing both boundaries should be observed. +echo both +units real +atom_style atomic +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +# NOTE following 3 lines added for restart +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init +lattice fcc 5.405 origin 0.25 0.25 0.25 +region simRegion block -12 12 -3 3 -3 3 +# create atoms, NOTE commented out for restart +#region mdRegion block -5 5 -3 3 -3 3 +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 +# specify interal/ghost atoms +region mdInternal block -4 4 -3 3 -3 3 +group internal region mdInternal +group ghost subtract all internal +# velocities have Vcm = 0, NOTE next three lines commented out for restart +#velocity internal create 40. 87287 mom yes loop geom +#pair_style lj/cut 13.5 +#pair_coeff 1 1 .238 3.405 13.5 +neighbor 5. bin +neigh_modify every 10 delay 0 check no +# ID group atc PhysicsType ParameterFile +fix AtC internal atc thermal Ar_thermal.mat +fix_modify AtC boundary ghost +# numerical parameters +fix_modify AtC time_integration fractional_step +fix_modify AtC internal_quadrature off +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 simRegion f p p +fix_modify AtC mesh create_faceset ibndy box -4.0 4.0 -INF INF -INF INF in +fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -INF INF -INF INF outward +# fix a temperature +fix_modify AtC fix temperature all 20. +#fix_modify AtC fix temperature all linear 0 0 0 -0.154 0 0 30. +#fix_modify AtC fix temperature all quadratic 0 0 0 -0.154 0 0 30. 0.01 0.0 0.0 0 0 0 +# turn on thermostat +fix_modify AtC control thermal rescale 10 +# output +thermo 100 +variable xdof equal 3*count(ghost) +compute_modify thermo_temp extra ${xdof} +thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] +thermo_modify format 1 %6i format 2 %7.2g +# equilibrate MD field +#fix_modify AtC output bar1d_lumped_initFE 1 text +timestep 5 +run 400 +#run 100 +# change thermostat to hoover +fix_modify AtC unfix temperature all +#fix_modify AtC thermal control flux interpolate +fix_modify AtC control thermal flux faceset obndy +fix_modify AtC control localized_lambda on +fix_modify AtC filter type exponential +fix_modify AtC filter scale 10000.0 +fix_modify AtC filter on +# add nodesets +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF +fix_modify AtC fix temperature lbc 80. +fix_modify AtC fix temperature rbc 80. +# initialize +thermo 10 +run 100 +# relax +fix_modify AtC unfix temperature all +# output +fix_modify AtC output bar1d_lumpedFE 100 text +# run with FE +reset_timestep 0 +thermo 100 +run 10000 diff --git a/examples/USER/atc/thermal/in.no_atoms b/examples/USER/atc/thermal/in.no_atoms new file mode 100644 index 0000000000..cf8def8c6c --- /dev/null +++ b/examples/USER/atc/thermal/in.no_atoms @@ -0,0 +1,56 @@ +# needs description +#AtC thermal Coupling +# +echo both + +units real +atom_style atomic +lattice fcc 5.405 origin 0.25 0.25 0.25 +region feRegion block -10 10 -1 1 -1 1 +boundary f p p +create_box 1 feRegion +mass 1 39.95 # need to keep this +atom_modify sort 0 1 +region dummyRegion block -100 -99 -1 1 -1 1 +group dummy region dummyRegion + +# ID group atc PhysicsType ParameterFile +fix AtC dummy atc thermal Ar_thermal.mat +timestep 5.0 + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 10 1 1 feRegion f p p + +# fix end temperatures and an internal source +fix_modify AtC initial temperature all 20.0 +fix_modify AtC source temperature all 0.0000000000632 +fix_modify AtC mesh create_nodeset lbc -10.1 -9.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 9.9 10.1 -INF INF -INF INF +fix_modify AtC fix temperature lbc 20. +fix_modify AtC fix temperature rbc 20. + +fix_modify AtC mesh create_elementset middle -4.1 4.1 -INF INF -INF INF +fix_modify AtC material middle Ar2 + +thermo_style custom step cpu f_AtC[1] f_AtC[2] +fix_modify AtC output no_atomsFE 1000 text binary +thermo 100 +run 10000 + + +fix_modify AtC remove_source temperature all +fix_modify AtC unfix temperature rbc + +fix_modify AtC fix temperature all 20. +run 1 +fix_modify AtC unfix temperature all +reset_timestep 0 + +# fix one end temperature and the a source at the other +fix_modify AtC fix temperature lbc 20. +fix_modify AtC mesh create_faceset rbcFace plane x 10.0 +fix_modify AtC fix_flux temperature rbcFace 0.000000001 + +fix_modify AtC output no_atoms_flux_FE 1000 text binary # NOTE not used +thermo 100 +run 10000 diff --git a/examples/USER/atc/thermal/no_atoms.screen b/examples/USER/atc/thermal/no_atoms.screen new file mode 100644 index 0000000000..f336072041 --- /dev/null +++ b/examples/USER/atc/thermal/no_atoms.screen @@ -0,0 +1,350 @@ +LAMMPS (14 Aug 2013) + +units real +atom_style atomic +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region feRegion block -10 10 -1 1 -1 1 +boundary f p p +create_box 1 feRegion +Created orthogonal box = (-54.05 -5.405 -5.405) to (54.05 5.405 5.405) + 4 by 1 by 1 MPI processor grid +mass 1 39.95 # need to keep this +atom_modify sort 0 1 +region dummyRegion block -100 -99 -1 1 -1 1 +group dummy region dummyRegion +0 atoms in group dummy + +# ID group atc PhysicsType ParameterFile +fix AtC dummy atc thermal Ar_thermal.mat +ATC: constructing thermal coupling with parameter file Ar_thermal.mat + ATC: peratom PE compute created with ID: 3 + ATC: 3 materials defined from Ar_thermal.mat +timestep 5.0 + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 10 1 1 feRegion f p p + ATC: created uniform mesh with 44 nodes, 11 unique nodes, and 10 elements + +# fix end temperatures and an internal source +fix_modify AtC initial temperature all 20.0 +fix_modify AtC source temperature all 0.0000000000632 +fix_modify AtC mesh create_nodeset lbc -10.1 -9.9 -INF INF -INF INF + ATC: created nodeset lbc with 1 nodes +fix_modify AtC mesh create_nodeset rbc 9.9 10.1 -INF INF -INF INF + ATC: created nodeset rbc with 1 nodes +fix_modify AtC fix temperature lbc 20. +fix_modify AtC fix temperature rbc 20. + +fix_modify AtC mesh create_elementset middle -4.1 4.1 -INF INF -INF INF + ATC: created elementset middle with 4 elements +fix_modify AtC material middle Ar2 + +thermo_style custom step cpu f_AtC[1] f_AtC[2] +fix_modify AtC output no_atomsFE 1000 text binary + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +thermo 100 +run 10000 +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 0.432198 Mbytes +Step CPU AtC[1] AtC[2] + 0 0 38.154369 20 + 100 0.198596 38.998362 20.402191 + 200 0.33823085 39.827109 20.797116 + 300 0.47814584 40.638112 21.183586 + 400 0.674582 41.432837 21.562299 + 500 0.87166095 42.212497 21.933833 + 600 1.0095859 42.978107 22.298671 + 700 1.1372099 43.730523 22.657222 + 800 1.2767439 44.470481 23.009836 + 900 1.3687179 45.198615 23.356816 + 1000 1.4402959 45.915477 23.698425 + 1100 1.5109999 46.621553 24.034893 + 1200 1.5813069 47.317274 24.366427 + 1300 1.651567 48.003024 24.69321 + 1400 1.7221079 48.679146 25.015404 + 1500 1.7923758 49.345952 25.333159 + 1600 1.8629169 50.003724 25.64661 + 1700 1.933373 50.652719 25.955877 + 1800 2.0037959 51.293174 26.261075 + 1900 2.0746109 51.925305 26.562306 + 2000 2.145087 52.549313 26.859667 + 2100 2.215744 53.165384 27.153245 + 2200 2.2863379 53.773691 27.443124 + 2300 2.3566098 54.374397 27.72938 + 2400 2.4366989 54.967653 28.012086 + 2500 2.5044408 55.553601 28.29131 + 2600 2.5741239 56.132378 28.567116 + 2700 2.6417909 56.70411 28.839565 + 2800 2.7091548 57.268918 29.108715 + 2900 2.7765369 57.826919 29.37462 + 3000 2.8588939 58.37822 29.637334 + 3100 2.9269259 58.922929 29.896906 + 3200 2.9947858 59.461146 30.153384 + 3300 3.0632079 59.992968 30.406815 + 3400 3.131222 60.518488 30.657243 + 3500 3.199235 61.037798 30.90471 + 3600 3.2675898 61.550983 31.14926 + 3700 3.3352199 62.058128 31.390932 + 3800 3.4026849 62.559317 31.629765 + 3900 3.470047 63.054627 31.865797 + 4000 3.5383139 63.544138 32.099064 + 4100 3.606086 64.027924 32.329605 + 4200 3.6737199 64.50606 32.557452 + 4300 3.741308 64.978617 32.782641 + 4400 3.8089309 65.445666 33.005206 + 4500 3.8761919 65.907277 33.225178 + 4600 3.9435189 66.363516 33.442591 + 4700 4.011107 66.814451 33.657477 + 4800 4.0784218 67.260145 33.869865 + 4900 4.1459188 67.700665 34.079787 + 5000 4.2139089 68.136071 34.287272 + 5100 4.2817738 68.566425 34.492351 + 5200 4.3494208 68.99179 34.695051 + 5300 4.4170818 69.412224 34.895401 + 5400 4.4845729 69.827786 35.09343 + 5500 4.612407 70.238534 35.289165 + 5600 4.7415109 70.644525 35.482634 + 5700 4.8686008 71.045816 35.673862 + 5800 5.005605 71.442462 35.862877 + 5900 5.137594 71.834517 36.049704 + 6000 5.275028 72.222037 36.23437 + 6100 5.4125428 72.605073 36.4169 + 6200 5.5497239 72.983679 36.597318 + 6300 5.6767418 73.357906 36.77565 + 6400 5.803622 73.727806 36.951919 + 6500 5.8905358 74.093429 37.12615 + 6600 6.0176079 74.454825 37.298367 + 6700 6.1476219 74.812042 37.468594 + 6800 6.2646389 75.165131 37.636852 + 6900 6.3316889 75.514139 37.803166 + 7000 6.3994029 75.859112 37.967557 + 7100 6.4671588 76.200099 38.130048 + 7200 6.5343359 76.537145 38.290662 + 7300 6.6116469 76.870297 38.44942 + 7400 6.6786668 77.199598 38.606343 + 7500 6.7457249 77.525095 38.761453 + 7600 6.8126168 77.84683 38.91477 + 7700 6.8796759 78.164848 39.066317 + 7800 6.9466639 78.479192 39.216112 + 7900 7.0136268 78.789904 39.364176 + 8000 7.0817449 79.097027 39.51053 + 8100 7.1496539 79.400601 39.655193 + 8200 7.227 79.700668 39.798185 + 8300 7.294349 79.997268 39.939525 + 8400 7.3613229 80.290442 40.079232 + 8500 7.4285059 80.580229 40.217325 + 8600 7.5257459 80.866668 40.353823 + 8700 7.59304 81.149798 40.488744 + 8800 7.6604259 81.429658 40.622106 + 8900 7.727886 81.706285 40.753928 + 9000 7.7962129 81.979716 40.884227 + 9100 7.863817 82.249989 41.013021 + 9200 7.9611189 82.517139 41.140327 + 9300 8.04863 82.781204 41.266162 + 9400 8.116328 83.042218 41.390544 + 9500 8.2232919 83.300217 41.51349 + 9600 8.3302848 83.555236 41.635014 + 9700 8.4073069 83.807309 41.755136 + 9800 8.5042849 84.056471 41.873869 + 9900 8.6116118 84.302754 41.991231 + 10000 8.6993539 84.546192 42.107238 +Loop time of 8.69972 on 4 procs for 10000 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 0.00606805 (0.0697499) +Outpt time (%) = 0.0389953 (0.448236) +Other time (%) = 8.65466 (99.482) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + +fix_modify AtC remove_source temperature all +fix_modify AtC unfix temperature rbc + +fix_modify AtC fix temperature all 20. +run 1 +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 0.432198 Mbytes +Step CPU AtC[1] AtC[2] + 10000 0 84.546192 42.107238 + 10001 0.00071191788 38.154369 20 +Loop time of 0.00105554 on 4 procs for 1 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 7.15256e-07 (0.0677622) +Outpt time (%) = 0.000342309 (32.4298) +Other time (%) = 0.000712514 (67.5024) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +fix_modify AtC unfix temperature all +reset_timestep 0 + +# fix one end temperature and the a source at the other +fix_modify AtC fix temperature lbc 20. +fix_modify AtC mesh create_faceset rbcFace plane x 10.0 + ATC: created faceset rbcFace with 1 faces +fix_modify AtC fix_flux temperature rbcFace 0.000000001 + +fix_modify AtC output no_atoms_flux_FE 1000 text binary # NOTE not used + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +thermo 100 +run 10000 +Setting up run ... + ATC: WARNING: material: [vacuum] cannot find heat_flux + ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null +Memory usage per processor = 0.432198 Mbytes +Step CPU AtC[1] AtC[2] + 0 0 38.154369 20 + 100 0.083673954 38.293317 20.125706 + 200 0.19899392 38.432963 20.241114 + 300 0.29243803 38.57261 20.348568 + 400 0.36600494 38.712256 20.45016 + 500 0.48900485 38.851902 20.547358 + 600 0.56217504 38.991549 20.641205 + 700 0.65521789 39.131195 20.732446 + 800 0.75310206 39.270841 20.821625 + 900 0.89797902 39.410488 20.90914 + 1000 1.0122259 39.550134 20.99529 + 1100 1.1407759 39.68978 21.080301 + 1200 1.214483 39.829426 21.164346 + 1300 1.308712 39.969071 21.247561 + 1400 1.4200881 40.108714 21.330051 + 1500 1.548327 40.248357 21.411904 + 1600 1.67171 40.387997 21.493188 + 1700 1.778965 40.527634 21.57396 + 1800 1.902406 40.667266 21.654269 + 1900 1.9758 40.806892 21.734154 + 2000 2.0998969 40.946511 21.813649 + 2100 2.2233069 41.08612 21.892782 + 2200 2.2966919 41.225716 21.971578 + 2300 2.390126 41.365298 22.050059 + 2400 2.4832549 41.504861 22.128243 + 2500 2.576612 41.644403 22.206146 + 2600 2.6688199 41.78392 22.283782 + 2700 2.7717919 41.923408 22.361164 + 2800 2.8780448 42.062861 22.438302 + 2900 2.9616508 42.202276 22.515205 + 3000 3.0891819 42.341647 22.591883 + 3100 3.1626549 42.480969 22.668342 + 3200 3.289422 42.620236 22.744588 + 3300 4.5723 42.759443 22.820628 + 3400 4.6451941 42.898584 22.896465 + 3500 4.7988889 43.037652 22.972105 + 3600 4.9616499 43.176641 23.047551 + 3700 5.0750909 43.315544 23.122806 + 3800 5.158251 43.454355 23.197872 + 3900 5.2814069 43.593068 23.272753 + 4000 5.365943 43.731674 23.347449 + 4100 5.5499399 43.870169 23.421963 + 4200 5.7134259 44.008544 23.496296 + 4300 5.8402519 44.146792 23.570449 + 4400 5.914254 44.284907 23.644422 + 4500 6.059108 44.422882 23.718217 + 4600 6.173615 44.56071 23.791833 + 4700 6.2584949 44.698385 23.865272 + 4800 6.390687 44.835898 23.938532 + 4900 6.5018079 44.973245 24.011614 + 5000 6.6458249 45.110417 24.084519 + 5100 6.7996399 45.247409 24.157245 + 5200 6.947237 45.384214 24.229793 + 5300 7.065861 45.520826 24.302161 + 5400 7.1804399 45.657238 24.37435 + 5500 7.329967 45.793445 24.44636 + 5600 7.403404 45.92944 24.518189 + 5700 7.532212 46.065217 24.589837 + 5800 7.636107 46.200772 24.661303 + 5900 7.7702749 46.336097 24.732587 + 6000 7.8824019 46.471189 24.803688 + 6100 8.0066459 46.60604 24.874606 + 6200 13.214045 46.740647 24.94534 + 6300 13.892477 46.875004 25.015889 + 6400 14.292473 47.009107 25.086252 + 6500 14.535074 47.14295 25.156429 + 6600 14.988646 47.276528 25.22642 + 6700 15.313997 47.409838 25.296223 + 6800 15.648461 47.542875 25.365838 + 6900 15.970553 47.675634 25.435265 + 7000 16.191319 47.808113 25.504502 + 7100 16.827143 47.940306 25.57355 + 7200 17.610442 48.072209 25.642407 + 7300 18.375779 48.20382 25.711073 + 7400 18.552067 48.335135 25.779548 + 7500 18.625211 48.46615 25.847831 + 7600 18.777196 48.596861 25.915922 + 7700 18.860914 48.727267 25.98382 + 7800 19.056963 48.857363 26.051525 + 7900 19.143181 48.987147 26.119036 + 8000 19.217513 49.116615 26.186353 + 8100 19.291583 49.245766 26.253475 + 8200 19.365672 49.374597 26.320403 + 8300 19.439444 49.503104 26.387136 + 8400 19.513173 49.631286 26.453674 + 8500 19.586943 49.759141 26.520016 + 8600 19.660707 49.886666 26.586162 + 8700 19.734394 50.013859 26.652112 + 8800 19.808109 50.140719 26.717866 + 8900 19.881979 50.267243 26.783423 + 9000 19.9564 50.393429 26.848784 + 9100 20.030697 50.519276 26.913949 + 9200 20.104676 50.644783 26.978916 + 9300 20.178579 50.769947 27.043687 + 9400 20.252333 50.894768 27.10826 + 9500 20.326012 51.019243 27.172637 + 9600 20.399727 51.143372 27.236816 + 9700 20.473378 51.267153 27.300799 + 9800 20.547044 51.390586 27.364584 + 9900 20.620753 51.513669 27.428173 + 10000 20.695237 51.636401 27.491564 +Loop time of 20.6956 on 4 procs for 10000 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 0.0139726 (0.0675151) +Outpt time (%) = 0.0488307 (0.235948) +Other time (%) = 20.6328 (99.6965) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/two_temperature/Ar_ttm.mat b/examples/USER/atc/two_temperature/Ar_ttm.mat new file mode 100644 index 0000000000..9f80303cda --- /dev/null +++ b/examples/USER/atc/two_temperature/Ar_ttm.mat @@ -0,0 +1,35 @@ +material Ar real +heat_capacity constant +capacity 0.000000063363 +end +electron_heat_capacity constant +capacity 0.000000063363 +end +heat_flux linear +conductivity 0.0000000030111 +end +electron_heat_flux linear +conductivity 0.0000000030111 +end +electron_phonon_exchange linear +coefficient 0.00000000001 +end +end + +material Null real +heat_capacity constant +capacity 1.0 +end +electron_heat_capacity constant +capacity 1.0 +end +heat_flux linear +conductivity 0.0 +end +electron_heat_flux linear +conductivity 0.0 +end +electron_phonon_exchange linear +coefficient 0.0 +end +end diff --git a/examples/USER/atc/two_temperature/Cu_ttm.mat b/examples/USER/atc/two_temperature/Cu_ttm.mat new file mode 100644 index 0000000000..fac8957bda --- /dev/null +++ b/examples/USER/atc/two_temperature/Cu_ttm.mat @@ -0,0 +1,17 @@ +material Cu metal +heat_capacity constant +capacity 0.211977459280654 +end +heat_flux linear +conductivity 67.4479848 +end +electron_heat_flux linear +conductivity 441.362750535 +end +electron_heat_capacity constant +capacity 0.005817388689 +end +electron_phonon_exchange linear +coefficient 0.0156575679 +end +end diff --git a/examples/USER/atc/two_temperature/bar1d_ttm.screen b/examples/USER/atc/two_temperature/bar1d_ttm.screen new file mode 100644 index 0000000000..ce15293d24 --- /dev/null +++ b/examples/USER/atc/two_temperature/bar1d_ttm.screen @@ -0,0 +1,446 @@ +LAMMPS (14 Aug 2013) +Reading data file ... + orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215) + 4 by 1 by 1 MPI processor grid + 3456 atoms + 3456 velocities +Lattice spacing in x,y,z = 5.405 5.405 5.405 +2880 atoms in group internal +576 atoms in group ghost +ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat + ATC: peratom PE compute created with ID: 3 + ATC: 2 materials defined from Ar_ttm.mat + ATC: creating two_temperature extrinsic model + ATC: 2 materials defined from Ar_ttm.mat + ATC: created uniform mesh with 60 nodes, 15 unique nodes, and 14 elements + ATC: created faceset bndy with 2 faces + ATC: created nodeset lbc with 1 nodes + ATC: created nodeset rbc with 1 nodes + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +Setting up run ... +Memory usage per processor = 100.664 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 16.671491 -6505.7593 0 -6334.0647 -1236.2423 + 10 16.651702 -6505.5537 0 -6334.0628 -1236.063 + 20 16.530147 -6504.2726 0 -6334.0336 -1232.9375 + 30 16.484722 -6503.7603 0 -6333.9891 -1231.0693 + 40 16.543921 -6504.3216 0 -6333.9407 -1231.4896 + 50 16.594956 -6504.742 0 -6333.8355 -1231.8563 + 60 16.569017 -6504.3692 0 -6333.7298 -1230.774 + 70 16.505606 -6503.6167 0 -6333.6304 -1229.192 + 80 16.499938 -6503.445 0 -6333.5172 -1229.1013 + 90 16.523216 -6503.6045 0 -6333.4369 -1229.6947 + 100 16.50815 -6503.3717 0 -6333.3592 -1229.2848 + 110 16.515727 -6503.3742 0 -6333.2837 -1229.1999 + 120 16.568227 -6503.8633 0 -6333.2321 -1230.0838 + 130 16.554875 -6503.6751 0 -6333.1814 -1229.6147 + 140 16.473418 -6502.736 0 -6333.0812 -1227.7488 + 150 16.469779 -6502.5515 0 -6332.9342 -1227.6072 + 160 16.579808 -6503.5343 0 -6332.7839 -1229.6569 + 170 16.624355 -6503.8397 0 -6332.6305 -1229.6117 + 180 16.501717 -6502.3771 0 -6332.4309 -1225.3561 + 190 16.38836 -6500.9674 0 -6332.1886 -1221.4976 + 200 16.484583 -6501.7505 0 -6331.9808 -1223.1581 + 210 16.699218 -6503.7793 0 -6331.7991 -1228.2054 + 220 16.791883 -6504.5481 0 -6331.6135 -1230.5561 + 230 16.748089 -6503.9202 0 -6331.4366 -1229.2129 + 240 16.665848 -6502.849 0 -6331.2124 -1226.4068 + 250 16.621244 -6502.1715 0 -6330.9943 -1224.5035 + 260 16.658103 -6502.3533 0 -6330.7965 -1224.8892 + 270 16.73917 -6502.9656 0 -6330.5739 -1226.6044 + 280 16.804864 -6503.449 0 -6330.3807 -1227.9288 + 290 16.798754 -6503.1257 0 -6330.1204 -1227.0908 + 300 16.696317 -6501.801 0 -6329.8507 -1223.5728 + 310 16.591132 -6500.3983 0 -6329.5312 -1219.6957 + 320 16.562111 -6499.7683 0 -6329.2001 -1217.6592 + 330 16.629363 -6500.1642 0 -6328.9034 -1218.1364 + 340 16.735603 -6500.9663 0 -6328.6114 -1219.8661 + 350 16.849016 -6501.8915 0 -6328.3686 -1222.1919 + 360 16.987179 -6503.0918 0 -6328.146 -1225.3559 + 370 17.069822 -6503.7253 0 -6327.9283 -1227.2178 + 380 16.971748 -6502.4322 0 -6327.6452 -1224.4888 + 390 16.743421 -6499.7171 0 -6327.2816 -1218.0665 + 400 16.574707 -6497.5174 0 -6326.8195 -1212.3609 + 410 16.567165 -6496.9841 0 -6326.3639 -1210.1955 + 420 16.671594 -6497.63 0 -6325.9343 -1210.904 + 430 16.808398 -6498.6163 0 -6325.5117 -1212.8577 + 440 16.918714 -6499.3848 0 -6325.1441 -1214.747 + 450 16.998405 -6499.8251 0 -6324.7637 -1216.1874 + 460 17.10197 -6500.4966 0 -6324.3686 -1217.9781 + 470 17.199373 -6501.0956 0 -6323.9645 -1219.067 + 480 17.13357 -6500.0354 0 -6323.5819 -1216.039 + 490 16.93992 -6497.6895 0 -6323.2304 -1210.2729 + 500 16.919171 -6497.0726 0 -6322.8272 -1209.112 + 510 17.178559 -6499.324 0 -6322.4072 -1215.185 + 520 17.480271 -6502.0281 0 -6322.004 -1222.3709 + 530 17.559599 -6502.4375 0 -6321.5964 -1223.4721 + 540 17.389395 -6500.2917 0 -6321.2036 -1217.4915 + 550 17.142307 -6497.3088 0 -6320.7653 -1209.0976 + 560 17.016535 -6495.5085 0 -6320.2603 -1204.0875 + 570 17.15099 -6496.3909 0 -6319.7581 -1206.2345 + 580 17.393207 -6498.4177 0 -6319.2903 -1211.648 + 590 17.504872 -6499.1261 0 -6318.8487 -1213.8125 + 600 17.50042 -6498.6414 0 -6318.4099 -1212.1098 + 610 17.4061 -6497.2202 0 -6317.9601 -1207.3648 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+ 3720 26.536195 -6408.9585 0 -6135.6702 -928.38906 + 3730 26.508798 -6408.1755 0 -6135.1694 -925.86117 + 3740 26.462861 -6407.1721 0 -6134.639 -922.36984 + 3750 26.397047 -6405.9529 0 -6134.0977 -918.40406 + 3760 26.441038 -6405.7917 0 -6133.4834 -917.5207 + 3770 26.745497 -6408.2489 0 -6132.805 -923.15559 + 3780 27.041387 -6410.638 0 -6132.1469 -928.93182 + 3790 27.003103 -6409.6198 0 -6131.523 -927.08557 + 3800 26.811297 -6407.0724 0 -6130.9509 -921.49064 + 3810 26.74993 -6405.8938 0 -6130.4043 -918.72164 + 3820 26.795927 -6405.8497 0 -6129.8865 -918.36389 + 3830 26.820327 -6405.6002 0 -6129.3857 -917.30195 + 3840 26.781033 -6404.61 0 -6128.8002 -914.61209 + 3850 26.812615 -6404.3012 0 -6128.1661 -913.53658 + 3860 26.89712 -6404.5103 0 -6127.505 -913.76078 + 3870 26.922323 -6404.1069 0 -6126.842 -912.84013 + 3880 27.101213 -6405.3838 0 -6126.2766 -915.25469 + 3890 27.279626 -6406.7429 0 -6125.7983 -917.5866 + 3900 27.221817 -6405.6018 0 -6125.2525 -914.50773 + 3910 27.107351 -6403.8119 0 -6124.6414 -910.05769 + 3920 27.116841 -6403.2638 0 -6123.9956 -908.36736 + 3930 27.081747 -6402.2285 0 -6123.3218 -905.83791 + 3940 26.935403 -6400.0723 0 -6122.6727 -901.12718 + 3950 26.934802 -6399.4344 0 -6122.041 -899.91808 + 3960 27.238985 -6401.9825 0 -6121.4564 -905.50671 + 3970 27.502303 -6404.1848 0 -6120.9469 -910.11508 + 3980 27.430392 -6402.8753 0 -6120.378 -907.1389 + 3990 27.280815 -6400.7088 0 -6119.7519 -902.24647 + 4000 27.271626 -6399.937 0 -6119.0747 -900.07961 +Loop time of 297.534 on 4 procs for 4000 steps with 3456 atoms + +Pair time (%) = 47.024 (15.8045) +Neigh time (%) = 23.741 (7.97924) +Comm time (%) = 52.1483 (17.5268) +Outpt time (%) = 3.25944 (1.09548) +Other time (%) = 171.362 (57.5939) + +Nlocal: 864 ave 864 max 864 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 6741 ave 7924 max 5558 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 272272 ave 288060 max 256050 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 544544 ave 574446 max 513814 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 2178178 +Ave neighs/atom = 630.26 +Neighbor list builds = 400 +Dangerous builds = 0 diff --git a/examples/USER/atc/two_temperature/cutout.screen b/examples/USER/atc/two_temperature/cutout.screen new file mode 100644 index 0000000000..ac474d8408 --- /dev/null +++ b/examples/USER/atc/two_temperature/cutout.screen @@ -0,0 +1,278 @@ +LAMMPS (14 Aug 2013) +units metal +variable INF equal 1000 + +variable T equal 20 + +atom_style atomic + +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region FE block -8 8 -6 6 0 3 +region MD block -7 7 -6 0 0 3 +region FREE block -4 4 -6 0 0 3 + +boundary f f p + +# create atoms +#create_box 1 FE +#create_atoms 1 region MD +#group internal region FREE +#mass 1 39.95 +#read_data cutout.data +#pair_coeff * * .238 3.405 13.5 +#velocity internal create 40 87287 mom yes loop geom +#fix NVE internal nve +#thermo 100 +#dump CONFIG all atom 100 cutout.dump +##run 1000 +#unfix NVE +#write_restart cutout.rst + +pair_style lj/cut 13.5 +read_data cutout.data +Reading data file ... + orthogonal box = (-43.24 -32.43 0) to (43.24 32.43 16.215) + 2 by 2 by 1 MPI processor grid + 1008 atoms + 1008 velocities +group internal region FREE +576 atoms in group internal +group ghost subtract all internal +432 atoms in group ghost + +timestep 0.002 +thermo 20 + +# allow initial state to relax +fix NVT internal nvt temp $T $T 10 drag 0.2 +fix NVT internal nvt temp 20 $T 10 drag 0.2 +fix NVT internal nvt temp 20 20 10 drag 0.2 +fix RESCALE internal temp/rescale 25 $T $T 0.05 1.0 +fix RESCALE internal temp/rescale 25 20 $T 0.05 1.0 +fix RESCALE internal temp/rescale 25 20 20 0.05 1.0 +run 200 +Setting up run ... +Memory usage per processor = 2.20651 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 22.840119 -1789.5949 0 -1786.6219 -15765.333 + 20 13.566839 -1788.3853 0 -1786.6194 -15277.27 + 40 33.553913 -1791.7417 0 -1787.3741 -14707.846 + 60 19.256223 -1794.1032 0 -1791.5967 -14029.132 + 80 13.368297 -1796.2574 0 -1794.5173 -13523.457 + 100 11.42006 -1798.2698 0 -1796.7833 -13103.079 + 120 21.491111 -1799.819 0 -1797.0216 -12688.96 + 140 16.977999 -1801.1896 0 -1798.9797 -12265.345 + 160 13.938224 -1802.0525 0 -1800.2382 -11790.033 + 180 12.23396 -1802.7 0 -1801.1076 -11276.872 + 200 11.42006 -1803.1286 0 -1801.6421 -10730.804 +Loop time of 8.50337 on 4 procs for 200 steps with 1008 atoms + +Pair time (%) = 0.668509 (7.86169) +Neigh time (%) = 0 (0) +Comm time (%) = 4.23724 (49.8301) +Outpt time (%) = 0.237265 (2.79024) +Other time (%) = 3.36036 (39.518) + +Nlocal: 252 ave 504 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 1368 ave 1656 max 1080 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 36492 ave 74116 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 145968 +Ave neighs/atom = 144.81 +Neighbor list builds = 0 +Dangerous builds = 0 +unfix RESCALE +run 800 +Setting up run ... +Memory usage per processor = 2.20651 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 11.42006 -1803.1286 0 -1801.6421 -10730.804 + 220 12.634668 -1803.4525 0 -1801.8079 -10188.88 + 240 12.389545 -1803.5125 0 -1801.8998 -9656.8881 + 260 11.317877 -1803.4182 0 -1801.945 -9236.1616 + 280 9.7270274 -1803.2416 0 -1801.9754 -8947.2355 + 300 7.9370805 -1803.0419 0 -1802.0087 -8750.7074 + 320 6.4067491 -1802.861 0 -1802.027 -8623.9069 + 340 5.3573492 -1802.7311 0 -1802.0338 -8577.8953 + 360 4.9188235 -1802.6872 0 -1802.0469 -8637.0036 + 380 4.8156229 -1802.6667 0 -1802.0399 -8806.2763 + 400 5.0090105 -1802.6545 0 -1802.0025 -9077.449 + 420 5.6421616 -1802.6821 0 -1801.9477 -9435.9659 + 440 6.5180667 -1802.7415 0 -1801.8931 -9843.0718 + 460 7.8021978 -1802.8463 0 -1801.8307 -10243.525 + 480 9.1986451 -1802.9578 0 -1801.7604 -10581.685 + 500 10.560896 -1803.0497 0 -1801.675 -10833.653 + 520 11.604474 -1803.1302 0 -1801.6197 -11011.347 + 540 11.844791 -1803.1128 0 -1801.571 -11122.58 + 560 11.304866 -1803.0402 0 -1801.5687 -11161.742 + 580 9.8313387 -1802.8722 0 -1801.5925 -11124.258 + 600 7.7333706 -1802.6641 0 -1801.6575 -11030.299 + 620 5.3793592 -1802.408 0 -1801.7078 -10901.73 + 640 3.3272825 -1802.1725 0 -1801.7394 -10761.774 + 660 2.0314815 -1802.0222 0 -1801.7578 -10622.656 + 680 2.0077988 -1802.0353 0 -1801.7739 -10487.867 + 700 3.3843921 -1802.2247 0 -1801.7842 -10372.664 + 720 5.9780298 -1802.565 0 -1801.7869 -10302.637 + 740 9.0173322 -1802.9596 0 -1801.7858 -10280.842 + 760 11.766779 -1803.3181 0 -1801.7865 -10288.676 + 780 13.733393 -1803.5291 0 -1801.7415 -10302.17 + 800 14.164962 -1803.566 0 -1801.7222 -10302.618 + 820 12.863097 -1803.4368 0 -1801.7625 -10272.719 + 840 10.393884 -1803.1903 0 -1801.8374 -10192.543 + 860 7.4184997 -1802.8426 0 -1801.877 -10058.512 + 880 4.3613644 -1802.4882 0 -1801.9205 -9897.1119 + 900 2.2361845 -1802.2402 0 -1801.9491 -9736.3308 + 920 1.7719305 -1802.1979 0 -1801.9672 -9590.9833 + 940 2.9237629 -1802.3563 0 -1801.9757 -9472.0013 + 960 5.061993 -1802.6395 0 -1801.9806 -9381.0823 + 980 7.6242849 -1802.9731 0 -1801.9807 -9319.9173 + 1000 10.04544 -1803.2677 0 -1801.9601 -9298.5324 +Loop time of 3.52358 on 4 procs for 800 steps with 1008 atoms + +Pair time (%) = 1.13774 (32.2892) +Neigh time (%) = 0 (0) +Comm time (%) = 1.88566 (53.5154) +Outpt time (%) = 0.00261962 (0.0743455) +Other time (%) = 0.497567 (14.1211) + +Nlocal: 252 ave 504 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 1368 ave 1656 max 1080 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 37230.2 ave 75593 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 148921 +Ave neighs/atom = 147.739 +Neighbor list builds = 0 +Dangerous builds = 0 +unfix NVT + +# ID group atc PhysicsType ParameterFile +fix AtC internal atc two_temperature Ar_ttm.mat +ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat + ATC: peratom PE compute created with ID: 3 + ATC: WARNING: material units real do not match lammps + ATC: WARNING: material units real do not match lammps + ATC: 2 materials defined from Ar_ttm.mat + ATC: creating two_temperature extrinsic model + ATC: WARNING: material units real do not match lammps + ATC: WARNING: material units real do not match lammps + ATC: 2 materials defined from Ar_ttm.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 8 6 1 FE f f p + ATC: created uniform mesh with 126 nodes, 63 unique nodes, and 48 elements + +fix_modify AtC mesh create_elementset wire -4 4 -INF 0 -INF INF + ATC: created elementset wire with 12 elements +fix_modify AtC mesh create_nodeset gap -4 4 -0 INF -INF INF + ATC: created nodeset gap with 20 nodes +fix_modify AtC mesh create_elementset gap -4 4 -0 INF -INF INF + ATC: created elementset gap with 12 elements +fix_modify AtC mesh delete_elements gap + +fix_modify AtC mesh create_faceset bndy box -4 4 -INF 0 -INF INF + ATC: created faceset bndy with 10 faces +fix_modify AtC control thermal flux faceset bndy + +# fix a temperature +fix_modify AtC initial temperature all 20.0 +fix_modify AtC initial electron_temperature all 30.0 +fix_modify AtC initial temperature gap 0.0 + +# relaxation +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] +fix_modify AtC output cutoutFE 10 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +fix_modify AtC extrinsic electron_integration implicit + +# heating +fix_modify AtC mesh create_nodeset lbc -8 -8 -INF INF -INF INF + ATC: created nodeset lbc with 7 nodes +fix_modify AtC mesh create_nodeset rbc 8 8 -INF INF -INF INF + ATC: created nodeset rbc with 7 nodes +fix_modify AtC fix electron_temperature lbc 20. +fix_modify AtC fix electron_temperature rbc 20. +fix_modify AtC source electron_temperature wire 0.001 +run 200 +Setting up run ... +Memory usage per processor = 52.1308 Mbytes +Step CPU AtC[1] AtC[2] AtC[3] AtC[4] + 1000 0 7.5905384e-06 13.650794 1.7918648e-05 30 + 1020 0.42264199 8.0867497e-06 14.386397 0.00011143616 168.06236 + 1040 0.89445806 8.2236256e-06 14.569133 0.00020569969 308.34605 + 1060 1.512279 7.9547417e-06 14.139358 0.00029996263 448.62886 + 1080 2.0000911 7.47106e-06 13.387177 0.00039422497 588.91078 + 1100 2.334769 6.9291851e-06 12.597525 0.00048848671 729.19182 + 1120 2.6742702 6.4666101e-06 11.970788 0.00058274785 869.47196 + 1140 3.0125241 6.1269287e-06 11.536337 0.0006770084 1009.7512 + 1160 3.3478191 5.9463401e-06 11.304155 0.00077126834 1150.0296 + 1180 4.02788 5.7757317e-06 11.035914 0.0008655277 1290.307 + 1200 4.612457 5.6534832e-06 10.819941 0.00095978645 1430.5836 +Loop time of 4.61523 on 4 procs for 200 steps with 1008 atoms + +Pair time (%) = 0.437437 (9.47811) +Neigh time (%) = 0 (0) +Comm time (%) = 0.583825 (12.65) +Outpt time (%) = 0.0544528 (1.17985) +Other time (%) = 3.53952 (76.6921) + +Nlocal: 252 ave 504 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 1368 ave 1656 max 1080 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 37569 ave 75414 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 75138 ave 150278 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 300552 +Ave neighs/atom = 298.167 +Neighbor list builds = 0 +Dangerous builds = 0 + +# relaxation +fix_modify AtC remove_source electron_temperature wire +run 200 +Setting up run ... +Memory usage per processor = 52.1308 Mbytes +Step CPU AtC[1] AtC[2] AtC[3] AtC[4] + 1200 0 5.6534832e-06 10.819941 0.00095978645 1430.5836 + 1220 0.39391184 5.6247016e-06 10.745001 0.0009597804 1430.5746 + 1240 0.98758292 5.6705058e-06 10.77004 0.00095977436 1430.5656 + 1260 1.461138 5.9348763e-06 11.132668 0.00095976831 1430.5566 + 1280 1.794466 6.3878919e-06 11.792006 0.00095976227 1430.5477 + 1300 2.124989 6.8588119e-06 12.489994 0.00095975623 1430.5387 + 1320 2.46228 7.3682728e-06 13.289603 0.00095975019 1430.5297 + 1340 2.8012109 7.8680354e-06 14.125224 0.00095974416 1430.5207 + 1360 3.1344459 8.1759187e-06 14.694182 0.00095973813 1430.5117 + 1380 3.47153 8.187909e-06 14.802618 0.0009597321 1430.5028 + 1400 3.8077469 7.7666161e-06 14.187723 0.00095972607 1430.4938 +Loop time of 3.81041 on 4 procs for 200 steps with 1008 atoms + +Pair time (%) = 0.410787 (10.7806) +Neigh time (%) = 0 (0) +Comm time (%) = 0.46719 (12.2609) +Outpt time (%) = 0.0359789 (0.944226) +Other time (%) = 2.89646 (76.0143) + +Nlocal: 252 ave 504 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 1368 ave 1656 max 1080 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 37178.8 ave 74546 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 74357.5 ave 148715 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 297430 +Ave neighs/atom = 295.069 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/two_temperature/gaussianIC_ttm.screen b/examples/USER/atc/two_temperature/gaussianIC_ttm.screen new file mode 100644 index 0000000000..1aecc56102 --- /dev/null +++ b/examples/USER/atc/two_temperature/gaussianIC_ttm.screen @@ -0,0 +1,168 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, +# where N = 4 for fcc, +# s = 3.405 A (Wagner) +# a = 5.25 A (Ashcroft & Mermin, p. 70) +# to create restart : +# write_restart temp.bin +# then : restart2data temp.bin temp.init +#if {restart} +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init +Reading data file ... + orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215) + 4 by 1 by 1 MPI processor grid + 3456 atoms + 3456 velocities +#endif + +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region feRegion block -10 10 -3 3 -3 3 +region mdRegion block -12 12 -3 3 -3 3 +region mdInternal block -10 10 -3 3 -3 3 + + +# create atoms, NOTE commented out for restart +#if !{restart} +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 +#pair_style lj/cut 13.5 +#pair_coeff 1 1 .238 3.405 13.5 +#velocity internal create 40 87287 mom yes loop geom +#endif + +# specify interal/ghost atoms +group internal region mdInternal +2880 atoms in group internal +# do not define ghosts if outside fe region +#group ghost subtract all internal + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# ID group atc PhysicsType ParameterFile +fix AtC internal atc two_temperature Ar_ttm.mat +ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat + ATC: peratom PE compute created with ID: 3 + ATC: 2 materials defined from Ar_ttm.mat + ATC: creating two_temperature extrinsic model + ATC: 2 materials defined from Ar_ttm.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 10 1 1 feRegion f p p + ATC: created uniform mesh with 44 nodes, 11 unique nodes, and 10 elements + +# fix a temperature +fix_modify AtC fix temperature all 20.0 +fix_modify AtC initial temperature all 20.0 +fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 +fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 + + +# turn on thermostat +fix_modify AtC extrinsic exchange off +fix_modify AtC control thermal rescale 10 + +# equilibrate MD field +timestep 5.0 +#timestep 0.1 +thermo 10 +#if !{restart} +#run 1000 +#endif + +# write restart file (for atoms) +#if !{restart} +#write_restart gaussianT0.dat +#endif + +#output +fix_modify AtC output gaussianIC_ttmFE 10 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + + +# change thermostat +fix_modify AtC unfix temperature all +fix_modify AtC unfix electron_temperature all +fix_modify AtC control thermal flux +fix_modify AtC extrinsic exchange on +fix_modify AtC extrinsic electron_integration explicit 10 + +# run with FE +thermo_style custom step temp pe f_AtC[2] f_AtC[4] +reset_timestep 0 +run 400 +Setting up run ... +Memory usage per processor = 57.2223 Mbytes +Step Temp PotEng AtC[2] AtC[4] + 0 16.671491 -6505.7593 20 21.852118 + 10 16.677473 -6505.5427 20.002889 21.837729 + 20 16.576343 -6504.1927 19.867968 21.822852 + 30 16.542988 -6503.5347 19.830499 21.807341 + 40 16.606289 -6503.9099 19.949187 21.792289 + 50 16.657212 -6504.1497 20.064794 21.778216 + 60 16.632306 -6503.6285 20.04415 21.764548 + 70 16.575792 -6502.7759 19.922657 21.750393 + 80 16.582942 -6502.5564 19.85354 21.735697 + 90 16.619478 -6502.6712 19.841821 21.721009 + 100 16.61417 -6502.3556 19.821932 21.706419 + 110 16.630014 -6502.2516 19.867656 21.692093 + 120 16.693128 -6502.6546 19.982069 21.678641 + 130 16.690728 -6502.3949 19.998086 21.665838 + 140 16.614054 -6501.3545 19.912572 21.652659 + 150 16.610384 -6501.0503 19.92245 21.63913 + 160 16.722801 -6501.9756 20.080186 21.626412 + 170 16.770605 -6502.2507 20.171452 21.614843 + 180 16.650901 -6500.7763 20.054669 21.603093 + 190 16.541463 -6499.3809 19.906639 21.590191 + 200 16.645253 -6500.2037 19.963942 21.577114 + 210 16.869564 -6502.3 20.16097 21.565481 + 220 16.964432 -6503.0598 20.255544 21.55519 + 230 16.911666 -6502.3323 20.237187 21.545107 + 240 16.817088 -6501.156 20.182306 21.534699 + 250 16.768753 -6500.4538 20.137553 21.523975 + 260 16.815333 -6500.7346 20.155564 21.51332 + 270 16.910106 -6501.5013 20.223111 21.503193 + 280 16.977575 -6502.0376 20.291942 21.49369 + 290 16.956748 -6501.627 20.290033 21.484478 + 300 16.835354 -6500.2122 20.163353 21.474677 + 310 16.719943 -6498.8256 20.003858 21.463706 + 320 16.691075 -6498.3204 19.931873 21.451971 + 330 16.761802 -6498.8518 20.011315 21.440557 + 340 16.869104 -6499.7468 20.168181 21.430357 + 350 16.984625 -6500.7698 20.339225 21.421572 + 360 17.123663 -6502.0535 20.526715 21.414273 + 370 17.19682 -6502.6982 20.622354 21.408133 + 380 17.078663 -6501.3555 20.478377 21.401648 + 390 16.828211 -6498.6205 20.179895 21.393129 + 400 16.644766 -6496.5243 19.968603 21.3825 +Loop time of 18.4436 on 4 procs for 400 steps with 3456 atoms + +Pair time (%) = 3.74164 (20.2869) +Neigh time (%) = 1.71663 (9.30746) +Comm time (%) = 2.39567 (12.9891) +Outpt time (%) = 0.0720797 (0.390811) +Other time (%) = 10.5176 (57.0257) + +Nlocal: 864 ave 864 max 864 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 6741 ave 7924 max 5558 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 272943 ave 288483 max 257454 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 545886 ave 575873 max 515774 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 2183544 +Ave neighs/atom = 631.812 +Neighbor list builds = 40 +Dangerous builds = 0 diff --git a/examples/USER/atc/two_temperature/in.bar1d_ttm b/examples/USER/atc/two_temperature/in.bar1d_ttm new file mode 100644 index 0000000000..78bb81d263 --- /dev/null +++ b/examples/USER/atc/two_temperature/in.bar1d_ttm @@ -0,0 +1,86 @@ +# in this example the electron temperature on the left is ramped up in time +# and held fixed on the right. the phonon temperature is free on the left +# and fixed and consistent with the electron temperature on the right. +# this mimics some simplified pumped system +# also a volume source is added to mimic Joule heating +#echo both +# units +units real +atom_style atomic +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, +# where N = 4 for fcc, +# s = 3.405 A (Wagner) +# a = 5.25 A (Ashcroft & Mermin, p. 70) +#if {restart} +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init +#endif +lattice fcc 5.405 origin 0.25 0.25 0.25 +region feRegion block -14 14 -3 3 -3 3 +region mdRegion block -12 12 -3 3 -3 3 +region mdInternal block -10 10 -3 3 -3 3 +# NOTE: don't define ghosts if they are outside the feRegion +group internal region mdInternal +group ghost subtract all internal +# create atoms +#if !{restart} +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 +#pair_style lj/cut 13.5 +#pair_coeff 1 1 .238 3.405 13.5 +#velocity internal create 40 87287 mom yes loop geom +#endif +# timestep & neighboring +timestep 5.0 +thermo 10 +neighbor 5. bin +neigh_modify every 10 delay 0 check no +# ID group atc PhysicsType ParameterFile +fix AtC internal atc two_temperature Ar_ttm.mat +fix_modify AtC boundary ghost +# ID part keywords nx ny nz region +fix_modify AtC mesh create 14 1 1 feRegion f p p +# fix initial temperatures +#if !{restart} +#velocity internal create 40 87287 mom yes loop geom +#endif +fix_modify AtC initial temperature all 20 +fix_modify AtC fix temperature all 20 +fix_modify AtC initial electron_temperature all 20 +fix_modify AtC fix electron_temperature all 20 +# equilibrate MD field with rescale +fix_modify AtC extrinsic exchange off +fix_modify AtC control thermal rescale 10 +#if !{restart} +#run 1000 +#endif +# change thermostat +fix_modify AtC extrinsic exchange on +fix_modify AtC unfix temperature all +fix_modify AtC unfix electron_temperature all +# note does not handle "inf"s +#fix_modify AtC mesh create_faceset bndy -8 8 inf inf inf inf +fix_modify AtC mesh create_faceset bndy box -10 10 -10 10 -10 10 +fix_modify AtC control thermal flux faceset bndy +# .. this controls the time filtering .... +#fix_modify AtC filter scale 500.0 +# add nodesets & boundary temperature controls +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +# NOTE create_nodeset doesn't handle "inf" +fix_modify AtC mesh create_nodeset lbc -14.1 -13.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 13.9 14.1 -INF INF -INF INF +fix_modify AtC fix electron_temperature lbc 40. +fix_modify AtC fix electron_temperature rbc 20. +fix_modify AtC fix temperature rbc 20. +#fix_modify AtC source electron_temperature all 0.0015 +fix_modify AtC source electron_temperature all 9.50445e-11 +# output filename frequency [text output] +fix_modify AtC output bar1d_ttmFE 100 text +# run transient to steady state +thermo 10 +reset_timestep 0 +run 4000 diff --git a/examples/USER/atc/two_temperature/in.cutout b/examples/USER/atc/two_temperature/in.cutout new file mode 100644 index 0000000000..4afba57e52 --- /dev/null +++ b/examples/USER/atc/two_temperature/in.cutout @@ -0,0 +1,87 @@ +# needs description +#AtC Two temperature Coupling +# DESCRIPTION: +# delete elements from the mesh +# heating and then relaxation + +echo both +units metal +variable INF equal 1000 + +variable T equal 20 + +atom_style atomic + +lattice fcc 5.405 origin 0.25 0.25 0.25 +region FE block -8 8 -6 6 0 3 +region MD block -7 7 -6 0 0 3 +region FREE block -4 4 -6 0 0 3 + +boundary f f p + +# create atoms +#create_box 1 FE +#create_atoms 1 region MD +#group internal region FREE +#mass 1 39.95 +#read_data cutout.data +#pair_coeff * * .238 3.405 13.5 +#velocity internal create 40 87287 mom yes loop geom +#fix NVE internal nve +#thermo 100 +#dump CONFIG all atom 100 cutout.dump +##run 1000 +#unfix NVE +#write_restart cutout.rst + +pair_style lj/cut 13.5 +read_data cutout.data +group internal region FREE +group ghost subtract all internal + +timestep 0.002 +thermo 20 + +# allow initial state to relax +fix NVT internal nvt temp $T $T 10 drag 0.2 +fix RESCALE internal temp/rescale 25 $T $T 0.05 1.0 +run 200 +unfix RESCALE +run 800 +unfix NVT + +# ID group atc PhysicsType ParameterFile +fix AtC internal atc two_temperature Ar_ttm.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 8 6 1 FE f f p + +fix_modify AtC mesh create_elementset wire -4 4 -INF 0 -INF INF +fix_modify AtC mesh create_nodeset gap -4 4 -0 INF -INF INF +fix_modify AtC mesh create_elementset gap -4 4 -0 INF -INF INF +fix_modify AtC mesh delete_elements gap + +fix_modify AtC mesh create_faceset bndy box -4 4 -INF 0 -INF INF +fix_modify AtC control thermal flux faceset bndy + +# fix a temperature +fix_modify AtC initial temperature all 20.0 +fix_modify AtC initial electron_temperature all 30.0 +fix_modify AtC initial temperature gap 0.0 + +# relaxation +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] +fix_modify AtC output cutoutFE 10 text +fix_modify AtC extrinsic electron_integration implicit + +# heating +fix_modify AtC mesh create_nodeset lbc -8 -8 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 8 8 -INF INF -INF INF +fix_modify AtC fix electron_temperature lbc 20. +fix_modify AtC fix electron_temperature rbc 20. +fix_modify AtC source electron_temperature wire 0.001 +run 200 + +# relaxation +fix_modify AtC remove_source electron_temperature wire +run 200 diff --git a/examples/USER/atc/two_temperature/in.gaussianIC_ttm b/examples/USER/atc/two_temperature/in.gaussianIC_ttm new file mode 100644 index 0000000000..600e3e95dd --- /dev/null +++ b/examples/USER/atc/two_temperature/in.gaussianIC_ttm @@ -0,0 +1,94 @@ +#AtC Two temperature Coupling +# DESCRIPTION: +# full overlap of MD and FE regions w/ free ends & lateral periodic bcs +# initial gaussian electron temperature profile and uniform phonon temperature +# results in fast exchange followed by slower diffusion and finally relaxation +# to equilibrium +# +echo both +units real +atom_style atomic + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, +# where N = 4 for fcc, +# s = 3.405 A (Wagner) +# a = 5.25 A (Ashcroft & Mermin, p. 70) +# to create restart : +# write_restart temp.bin +# then : restart2data temp.bin temp.init +#if {restart} +boundary f p p +pair_style lj/cut 13.5 +read_data temp.init +#endif + +lattice fcc 5.405 origin 0.25 0.25 0.25 +region feRegion block -10 10 -3 3 -3 3 +region mdRegion block -12 12 -3 3 -3 3 +region mdInternal block -10 10 -3 3 -3 3 + + +# create atoms, NOTE commented out for restart +#if !{restart} +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 +#pair_style lj/cut 13.5 +#pair_coeff 1 1 .238 3.405 13.5 +#velocity internal create 40 87287 mom yes loop geom +#endif + +# specify interal/ghost atoms +group internal region mdInternal +# do not define ghosts if outside fe region +#group ghost subtract all internal + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# ID group atc PhysicsType ParameterFile +fix AtC internal atc two_temperature Ar_ttm.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 10 1 1 feRegion f p p + +# fix a temperature +fix_modify AtC fix temperature all 20.0 +fix_modify AtC initial temperature all 20.0 +fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 +fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 + + +# turn on thermostat +fix_modify AtC extrinsic exchange off +fix_modify AtC control thermal rescale 10 + +# equilibrate MD field +timestep 5.0 +#timestep 0.1 +thermo 10 +#if !{restart} +#run 1000 +#endif + +# write restart file (for atoms) +#if !{restart} +#write_restart gaussianT0.dat +#endif + +#output +fix_modify AtC output gaussianIC_ttmFE 10 text + +# change thermostat +fix_modify AtC unfix temperature all +fix_modify AtC unfix electron_temperature all +fix_modify AtC control thermal flux +fix_modify AtC extrinsic exchange on +fix_modify AtC extrinsic electron_integration explicit 10 + +# run with FE +thermo_style custom step temp pe f_AtC[2] f_AtC[4] +reset_timestep 0 +run 400 diff --git a/examples/USER/atc/two_temperature/in.no_atoms b/examples/USER/atc/two_temperature/in.no_atoms new file mode 100644 index 0000000000..7bbeec183d --- /dev/null +++ b/examples/USER/atc/two_temperature/in.no_atoms @@ -0,0 +1,61 @@ +# needs description +#AtC Two temperature Coupling +# DESCRIPTION: +# no atoms and FE regions with periodic boundary conditions. +# heating and then relaxation + +echo both +#units real +units metal + +atom_style atomic + +lattice fcc 5.405 origin 0.25 0.25 0.25 +region simRegion block -14 14 -3 3 -3 3 +region feRegion block -12 12 -3 3 -3 3 + +# need to create atoms or lammps throws an error +region mdRegion block -12 12 -3 3 -3 3 +boundary f p p +create_box 1 mdRegion +mass 1 39.95 # need to keep this +atom_modify sort 0 1 +region dummyRegion block -100 -99 -1 1 -1 1 +group dummy region dummyRegion + +# ID group atc PhysicsType ParameterFile +fix AtC dummy atc two_temperature Cu_ttm.mat +timestep 0.002 +thermo 20 + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 feRegion f p p + +# fix a temperature +fix_modify AtC initial temperature all 20.0 +#fix_modify AtC initial electron_temperature all 30.0 +fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 + +# relaxation +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] +fix_modify AtC output no_atomsFE 10 text +#fix_modify AtC extrinsic electron_integration subcycle 100 +fix_modify AtC extrinsic electron_integration implicit +run 400 + +# heating +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF +fix_modify AtC fix electron_temperature lbc 20. +fix_modify AtC fix electron_temperature rbc 20. +#fix_modify AtC extrinsic exchange off +#fix_modify AtC fix temperature lbc 20. +#fix_modify AtC fix temperature rbc 20. +#fix_modify AtC extrinsic electron_integration lockstep +#fix_modify AtC source electron_temperature all 1000.0 +fix_modify AtC source electron_temperature all 0.521981 +run 400 + +# relaxation +fix_modify AtC remove_source electron_temperature all +run 400 diff --git a/examples/USER/atc/two_temperature/in.restart b/examples/USER/atc/two_temperature/in.restart new file mode 100644 index 0000000000..ebf924dafb --- /dev/null +++ b/examples/USER/atc/two_temperature/in.restart @@ -0,0 +1,117 @@ +# in this example the electron temperature on the left is ramped up in time +# and held fixed on the right. the phonon temperature is free on the left +# and fixed and consistent with the electron temperature on the right. +# ATC restarting is used to eliminate the need to redo the equilibration phase. +# This benchmark tests restarting and the fractional step method with the TTM. +#echo both +# units +units real +atom_style atomic +variable restart equal 0 # NOTE add support for ifs when we update to new lammps +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, +# where N = 4 for fcc, +# s = 3.405 A (Wagner) +# a = 5.25 A (Ashcroft & Mermin, p. 70) +boundary f p p +pair_style lj/cut 13.5 +#if "${restart}" +#read_data atom_restart.data # NOTE reading in text atom data results in minor differences due to truncation +#else +read_data temp.init +#endif +lattice fcc 5.405 origin 0.25 0.25 0.25 +region feRegion block -14 14 -3 3 -3 3 +region mdRegion block -12 12 -3 3 -3 3 +region mdInternal block -10 10 -3 3 -3 3 +# NOTE: don't define ghosts if they are outside the feRegion +group internal region mdInternal +group ghost subtract all internal +# create atoms +#boundary f p p +#create_box 1 mdRegion +#create_atoms 1 region mdRegion +#mass 1 39.95 +#pair_style lj/cut 13.5 +#pair_coeff 1 1 .238 3.405 13.5 +#velocity internal create 40 87287 mom yes loop geom +# timestep & neighboring +timestep 5.0 +thermo 10 +neighbor 5. bin +neigh_modify every 10 delay 0 check no +# ID group atc PhysicsType ParameterFile +fix AtC internal atc two_temperature Ar_ttm.mat +fix_modify AtC boundary ghost +# ID part keywords nx ny nz region +fix_modify AtC mesh create 14 1 1 feRegion f p p +fix_modify AtC time_integration fractional_step +fix_modify AtC internal_quadrature off +# fix initial temperatures +fix_modify AtC initial temperature all 20 +fix_modify AtC fix temperature all 20 +fix_modify AtC initial electron_temperature all 20 +fix_modify AtC fix electron_temperature all 20 +# equilibrate MD field with rescale +fix_modify AtC extrinsic exchange off +fix_modify AtC control thermal rescale 10 +thermo 100 +run 1000 + +# change thermostat +fix_modify AtC extrinsic exchange on +fix_modify AtC unfix temperature all +fix_modify AtC unfix electron_temperature all +fix_modify AtC mesh create_faceset bndy box -10 10 -10 10 -10 10 +fix_modify AtC control thermal flux faceset bndy +# add nodesets & boundary temperature controls +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +# NOTE create_nodeset doesn't handle "inf" +fix_modify AtC mesh create_nodeset lbc -14.1 -13.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 13.9 14.1 -INF INF -INF INF +fix_modify AtC fix electron_temperature lbc 40. +fix_modify AtC fix electron_temperature rbc 20. +fix_modify AtC fix temperature rbc 20. +fix_modify AtC source electron_temperature all 9.50445e-11 +# run transient +thermo 100 +reset_timestep 0 +run 2000 +write_restart atom_restart.bin +fix_modify AtC write_restart atc_restart.bin + +unfix AtC +fix AtC internal atc two_temperature Ar_ttm.mat +fix_modify AtC boundary ghost +# ID part keywords nx ny nz region +fix_modify AtC mesh create 14 1 1 feRegion f p p +fix_modify AtC time_integration fractional_step +fix_modify AtC internal_quadrature off +# fix initial temperatures +fix_modify AtC initial temperature all 20 +fix_modify AtC initial electron_temperature all 20 +# change thermostat +fix_modify AtC mesh create_faceset bndy box -10 10 -10 10 -10 10 +fix_modify AtC control thermal flux faceset bndy +# add nodesets & boundary temperature controls +# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax +# NOTE create_nodeset doesn't handle "inf" +fix_modify AtC mesh create_nodeset lbc -14.1 -13.9 -INF INF -INF INF +fix_modify AtC mesh create_nodeset rbc 13.9 14.1 -INF INF -INF INF +fix_modify AtC fix electron_temperature lbc 40. +fix_modify AtC fix electron_temperature rbc 20. +fix_modify AtC fix temperature rbc 20. +fix_modify AtC source electron_temperature all 9.50445e-11 +# read in reference positions +fix_modify AtC reset_atomic_reference_positions temp.init +fix_modify AtC consistent_fe_initialization on +# output filename frequency [text output] +fix_modify AtC output restartFE 100 text +# ATC restart command +fix_modify AtC read_restart atc_restart.bin + +# run to steady state +thermo 100 +reset_timestep 0 +fix_modify AtC reset_time +run 2000 diff --git a/examples/USER/atc/two_temperature/in.uniform_exchange b/examples/USER/atc/two_temperature/in.uniform_exchange new file mode 100644 index 0000000000..a12ac1dc47 --- /dev/null +++ b/examples/USER/atc/two_temperature/in.uniform_exchange @@ -0,0 +1,66 @@ +#AtC Two temperature Coupling +# DESCRIPTION: +# full overlap of MD and FE regions with full periodic boundary conditions. +# initial electron and phonon temperatures are different and then allowed to +# relax. +# + +units real +atom_style atomic +boundary p p p + +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, +# where N = 4 for fcc, +# s = 3.405 A (Wagner) +# a = 5.25 A (Ashcroft & Mermin, p. 70) +lattice fcc 5.405 origin 0.25 0.25 0.25 + +pair_style lj/cut 13.5 + +read_data uniform_exchange_init.data + +region simRegion block -12 12 -3 3 -3 3 +region feRegion block -12 12 -3 3 -3 3 + +# create atoms +region mdRegion block -12 12 -3 3 -3 3 + +# specify interal/ghost atoms +region mdInternal block -12 12 -3 3 -3 3 +group internal region mdInternal + +neighbor 5. bin +neigh_modify every 10 delay 0 check no + +# ID group atc PhysicsType ParameterFile +fix AtC internal atc two_temperature Ar_ttm.mat + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 4 1 1 feRegion p p p + +# fix a temperature +fix_modify AtC fix temperature all 20.0 +fix_modify AtC fix electron_temperature all 30.0 + +timestep 5.0 + +# output +thermo_style custom step pe temp f_AtC[2] f_AtC[4] +thermo 10 + +# equilibrate MD field +fix_modify AtC control thermal rescale 13 +run 500 + +# relax +fix_modify AtC output uniform_exchangeFE 100 text +fix_modify AtC filter type exponential +fix_modify AtC filter scale 5.0e2 +fix_modify AtC filter on +fix_modify AtC unfix temperature all +fix_modify AtC unfix electron_temperature all +fix_modify AtC control thermal flux + +# run with FE +run 5000 diff --git a/examples/USER/atc/two_temperature/in.uniform_heating b/examples/USER/atc/two_temperature/in.uniform_heating new file mode 100644 index 0000000000..fb4c2f93f2 --- /dev/null +++ b/examples/USER/atc/two_temperature/in.uniform_heating @@ -0,0 +1,53 @@ +# needs description +#AtC Thermal Coupling +echo both +units real +atom_style atomic +boundary f p p +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +pair_style lj/cut 13.5 +read_data uniform_heating_init.data +lattice fcc 5.405 origin 0.25 0.25 0.25 +region mdRegion block -8 8 -3 3 -3 3 +region mdInternal block -6 6 -3 3 -3 3 +group internal region mdInternal +neighbor 5. bin +neigh_modify every 10 delay 0 check no +# ID group atc PhysicsType ParameterFile +fix AtC internal atc two_temperature Ar_ttm.mat +# ID part keywords nx ny nz region +fix_modify AtC mesh create 6 1 1 mdInternal f p p +fix_modify AtC internal_quadrature on +# fix a temperature +fix_modify AtC initial temperature all 20. +fix_modify AtC fix temperature all 20. +fix_modify AtC initial electron_temperature all 20. +fix_modify AtC fix electron_temperature all 20. +# turn on thermostat +fix_modify AtC control thermal rescale 10 +# output +thermo_style custom step cpu pe etotal temp f_AtC[1] f_AtC[2] +thermo 100 +log uniform_heating.log +# make thermo output the correct temperature by removing ghost dof +# variable xdof equal 3*count(ghost) +# compute_modify thermo_temp extra ${xdof} +# equilibrate MD field +timestep 5 +run 400 +# change thermostat +fix_modify AtC output uniform_heatingFE 100 text +fix_modify AtC unfix temperature all +fix_modify AtC control thermal flux +# fix boundary +fix_modify AtC mesh create_nodeset lbc -6.1 -5.9 -INF INF -INF INF +fix_modify AtC fix temperature lbc 20. +fix_modify AtC mesh create_nodeset rbc 5.9 6.1 -INF INF -INF INF +fix_modify AtC fix temperature rbc 20. +# add source +#fix_modify AtC source temperature all 0.01 +fix_modify AtC source temperature all 6.3363e-10 +# run with FE +reset_timestep 0 +run 1000 diff --git a/examples/USER/atc/two_temperature/no_atoms.screen b/examples/USER/atc/two_temperature/no_atoms.screen new file mode 100644 index 0000000000..6140e4b8c6 --- /dev/null +++ b/examples/USER/atc/two_temperature/no_atoms.screen @@ -0,0 +1,202 @@ +LAMMPS (14 Aug 2013) +#units real +units metal + +atom_style atomic + +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region simRegion block -14 14 -3 3 -3 3 +region feRegion block -12 12 -3 3 -3 3 + +# need to create atoms or lammps throws an error +region mdRegion block -12 12 -3 3 -3 3 +boundary f p p +create_box 1 mdRegion +Created orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215) + 4 by 1 by 1 MPI processor grid +mass 1 39.95 # need to keep this +atom_modify sort 0 1 +region dummyRegion block -100 -99 -1 1 -1 1 +group dummy region dummyRegion +0 atoms in group dummy + +# ID group atc PhysicsType ParameterFile +fix AtC dummy atc two_temperature Cu_ttm.mat +ATC: constructing two_temperature coupling with parameter file Cu_ttm.mat + ATC: peratom PE compute created with ID: 3 + ATC: 1 materials defined from Cu_ttm.mat + ATC: creating two_temperature extrinsic model + ATC: 1 materials defined from Cu_ttm.mat +timestep 0.002 +thermo 20 + +# ID part keywords nx ny nz region +fix_modify AtC mesh create 12 1 1 feRegion f p p + ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements + +# fix a temperature +fix_modify AtC initial temperature all 20.0 +#fix_modify AtC initial electron_temperature all 30.0 +fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20 + +# relaxation +thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] +fix_modify AtC output no_atomsFE 10 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +#fix_modify AtC extrinsic electron_integration subcycle 100 +fix_modify AtC extrinsic electron_integration implicit +run 400 +Setting up run ... +Memory usage per processor = 0.432198 Mbytes +Step CPU AtC[1] AtC[2] AtC[3] AtC[4] + 0 0 59.94586 20 1.7847722 21.567177 + 20 0.51286197 59.95972 20.00454 1.770575 21.52456 + 40 3.5349412 59.97247 20.008795 1.7578608 21.370605 + 60 5.626349 59.983888 20.012606 1.7464745 21.232182 + 80 5.8213 59.994113 20.016019 1.7362775 21.108216 + 100 6.004406 60.00327 20.019076 1.7271457 20.997198 + 120 6.1875122 60.01147 20.021814 1.7189676 20.897776 + 140 6.3812881 60.018815 20.024266 1.7116438 20.808739 + 160 7.63975 60.025391 20.026462 1.7050849 20.729002 + 180 8.937978 60.031281 20.028429 1.6992111 20.657594 + 200 9.1152291 60.036556 20.030191 1.6939509 20.593644 + 220 9.2659261 60.04128 20.031768 1.6892401 20.536374 + 240 9.351284 60.045511 20.033181 1.6850213 20.485086 + 260 9.5723131 60.049299 20.034447 1.6812432 20.439154 + 280 9.656342 60.052692 20.035581 1.6778597 20.398021 + 300 9.7407582 60.05573 20.036596 1.6748297 20.361184 + 320 9.8237951 60.058451 20.037506 1.6721161 20.328194 + 340 9.9057951 60.060888 20.03832 1.6696859 20.298651 + 360 9.9871891 60.063071 20.03905 1.6675096 20.272193 + 380 10.070899 60.065025 20.039703 1.6655606 20.248499 + 400 10.151502 60.066775 20.040289 1.6638152 20.227279 +Loop time of 10.1472 on 4 procs for 400 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000468552 (0.00461755) +Outpt time (%) = 0.038277 (0.377217) +Other time (%) = 10.1085 (99.6182) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +# heating +fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF + ATC: created nodeset lbc with 1 nodes +fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF + ATC: created nodeset rbc with 1 nodes +fix_modify AtC fix electron_temperature lbc 20. +fix_modify AtC fix electron_temperature rbc 20. +#fix_modify AtC extrinsic exchange off +#fix_modify AtC fix temperature lbc 20. +#fix_modify AtC fix temperature rbc 20. +#fix_modify AtC extrinsic electron_integration lockstep +#fix_modify AtC source electron_temperature all 1000.0 +fix_modify AtC source electron_temperature all 0.521981 +run 400 +Setting up run ... +Memory usage per processor = 0.432198 Mbytes +Step CPU AtC[1] AtC[2] AtC[3] AtC[4] + 400 0 60.066775 20.040289 1.6638152 20.227279 + 420 0.09581995 60.074057 20.042563 1.7526734 21.206964 + 440 0.19161606 60.08642 20.046435 1.7697616 21.398727 + 460 0.28751802 60.099602 20.050578 1.7726213 21.43082 + 480 0.38343 60.112889 20.054768 1.7731138 21.436346 + 500 0.4793241 60.126162 20.058968 1.7732124 21.437452 + 520 0.57561994 60.139402 20.063168 1.7732452 21.437821 + 540 0.67192292 60.152606 20.067367 1.773267 21.438066 + 560 0.76804209 60.165773 20.071564 1.7732869 21.438289 + 580 0.86413407 60.178904 20.075757 1.7733063 21.438507 + 600 0.96042204 60.191997 20.079946 1.7733256 21.438723 + 620 1.0565081 60.205055 20.084131 1.7733447 21.438937 + 640 1.152534 60.218075 20.08831 1.7733637 21.43915 + 660 1.248451 60.23106 20.092484 1.7733825 21.439362 + 680 1.34378 60.244008 20.096653 1.7734013 21.439572 + 700 1.439183 60.256919 20.100815 1.7734199 21.439781 + 720 1.533103 60.269795 20.10497 1.7734384 21.439989 + 740 1.6269159 60.282635 20.109119 1.7734568 21.440195 + 760 1.720458 60.295439 20.11326 1.7734751 21.4404 + 780 1.8143139 60.308207 20.117395 1.7734932 21.440604 + 800 1.9079239 60.320939 20.121522 1.7735113 21.440807 +Loop time of 1.90864 on 4 procs for 400 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000290334 (0.0152116) +Outpt time (%) = 0.0181738 (0.952187) +Other time (%) = 1.89018 (99.0326) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +# relaxation +fix_modify AtC remove_source electron_temperature all +run 400 +Setting up run ... +Memory usage per processor = 0.432198 Mbytes +Step CPU AtC[1] AtC[2] AtC[3] AtC[4] + 800 0 60.320939 20.121522 1.7735113 21.440807 + 820 0.094663858 60.326208 20.123317 1.6666305 20.24139 + 840 0.19028497 60.326191 20.123452 1.6491438 20.045155 + 860 0.28605103 60.325301 20.123302 1.6462322 20.012481 + 880 0.38183498 60.324267 20.123096 1.6457454 20.007018 + 900 0.47761798 60.323212 20.122873 1.6456621 20.006083 + 920 0.57323003 60.322156 20.122641 1.6456459 20.005902 + 940 0.66837287 60.321102 20.122402 1.645641 20.005846 + 960 0.76329494 60.320051 20.122158 1.645638 20.005813 + 980 0.85846591 60.319003 20.121908 1.6456354 20.005783 + 1000 0.95354199 60.317957 20.121654 1.6456328 20.005754 + 1020 1.0488029 60.316914 20.121396 1.6456303 20.005726 + 1040 1.144012 60.315874 20.121135 1.6456279 20.005699 + 1060 1.2391 60.314837 20.120871 1.6456255 20.005672 + 1080 1.3342969 60.313803 20.120603 1.6456231 20.005645 + 1100 1.429821 60.312771 20.120334 1.6456208 20.005619 + 1120 1.525784 60.311742 20.120061 1.6456185 20.005593 + 1140 1.6198239 60.310716 20.119787 1.6456162 20.005568 + 1160 1.713886 60.309693 20.119511 1.645614 20.005543 + 1180 1.8080029 60.308673 20.119234 1.6456118 20.005519 + 1200 1.9020278 60.307655 20.118954 1.6456097 20.005495 +Loop time of 1.90272 on 4 procs for 400 steps with 0 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000293195 (0.0154092) +Outpt time (%) = 0.0181384 (0.953286) +Other time (%) = 1.88429 (99.0313) + +Nlocal: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/USER/atc/two_temperature/restart.screen b/examples/USER/atc/two_temperature/restart.screen new file mode 100644 index 0000000000..89c8a041d4 --- /dev/null +++ b/examples/USER/atc/two_temperature/restart.screen @@ -0,0 +1,158 @@ +LAMMPS (14 Aug 2013) +Reading data file ... + orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215) + 4 by 1 by 1 MPI processor grid + 3456 atoms + 3456 velocities +Lattice spacing in x,y,z = 5.405 5.405 5.405 +2880 atoms in group internal +576 atoms in group ghost +ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat + ATC: peratom PE compute created with ID: 3 + ATC: 2 materials defined from Ar_ttm.mat + ATC: creating two_temperature extrinsic model + ATC: 2 materials defined from Ar_ttm.mat + ATC: created uniform mesh with 60 nodes, 15 unique nodes, and 14 elements +Setting up run ... +Memory usage per processor = 97.9907 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 16.671491 -6505.7593 0 -6334.0647 -1236.2423 + 100 16.671491 -6501.3833 0 -6329.6886 -1223.1536 + 200 16.671491 -6500.6894 0 -6328.9948 -1219.3362 + 300 16.671491 -6503.1069 0 -6331.4122 -1227.3602 + 400 16.671491 -6500.6574 0 -6328.9628 -1220.86 + 500 16.671491 -6502.4882 0 -6330.7935 -1225.3148 + 600 16.671491 -6505.0003 0 -6333.3057 -1232.9704 + 700 16.671491 -6501.3022 0 -6329.6075 -1221.089 + 800 16.671491 -6503.8814 0 -6332.1868 -1228.9533 + 900 16.671491 -6505.846 0 -6334.1514 -1235.4657 + 1000 16.671491 -6504.4261 0 -6332.7314 -1231.2716 +Loop time of 37.7773 on 4 procs for 1000 steps with 3456 atoms + +Pair time (%) = 10.8992 (28.8511) +Neigh time (%) = 4.99517 (13.2227) +Comm time (%) = 6.46988 (17.1264) +Outpt time (%) = 0.0506067 (0.13396) +Other time (%) = 15.3625 (40.6659) + +Nlocal: 864 ave 864 max 864 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 6741 ave 7924 max 5558 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 273177 ave 289116 max 257307 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 546354 ave 576160 max 516664 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 2185418 +Ave neighs/atom = 632.355 +Neighbor list builds = 100 +Dangerous builds = 0 + ATC: created faceset bndy with 2 faces + ATC: created nodeset lbc with 1 nodes + ATC: created nodeset rbc with 1 nodes +Setting up run ... +Memory usage per processor = 102.974 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 16.671491 -6504.4261 0 -6332.7314 -1231.2716 + 100 16.530548 -6502.2979 0 -6332.0547 -1225.9982 + 200 16.768382 -6503.3792 0 -6330.6867 -1227.3237 + 300 16.645261 -6500.2867 0 -6328.8622 -1218.8568 + 400 16.895022 -6499.7419 0 -6325.7451 -1218.3147 + 500 17.025324 -6497.5028 0 -6322.1641 -1209.3964 + 600 17.357415 -6496.5551 0 -6317.7963 -1206.7087 + 700 17.318832 -6491.6971 0 -6313.3357 -1193.3844 + 800 17.899936 -6492.264 0 -6307.9179 -1191.1732 + 900 18.450923 -6492.0033 0 -6301.9828 -1190.2234 + 1000 18.293629 -6484.9144 0 -6296.5138 -1169.3319 + 1100 18.566253 -6481.8954 0 -6290.6872 -1161.7547 + 1200 18.884588 -6479.22 0 -6284.7334 -1152.6827 + 1300 19.428205 -6477.9973 0 -6277.9121 -1147.8183 + 1400 19.653142 -6473.9811 0 -6271.5793 -1136.5497 + 1500 19.9352 -6470.4382 0 -6265.1316 -1122.9541 + 1600 20.587115 -6470.6124 0 -6258.5919 -1122.3456 + 1700 20.433936 -6462.792 0 -6252.349 -1100.3298 + 1800 21.314998 -6465.4549 0 -6245.9382 -1104.9574 + 1900 21.353208 -6458.9075 0 -6238.9973 -1085.5335 + 2000 21.394021 -6453.327 0 -6232.9964 -1069.954 +Loop time of 235.783 on 4 procs for 2000 steps with 3456 atoms + +Pair time (%) = 26.6899 (11.3197) +Neigh time (%) = 13.9674 (5.92386) +Comm time (%) = 42.2094 (17.9018) +Outpt time (%) = 0.572407 (0.242769) +Other time (%) = 152.344 (64.6118) + +Nlocal: 864 ave 864 max 864 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 6741 ave 7924 max 5558 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 272686 ave 287488 max 257348 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 545372 ave 575305 max 514897 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 2181486 +Ave neighs/atom = 631.217 +Neighbor list builds = 200 +Dangerous builds = 0 +System init for write_restart ... +ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat + ATC: peratom PE compute created with ID: 3 + ATC: 2 materials defined from Ar_ttm.mat + ATC: creating two_temperature extrinsic model + ATC: 2 materials defined from Ar_ttm.mat + ATC: created uniform mesh with 60 nodes, 15 unique nodes, and 14 elements + ATC: created faceset bndy with 2 faces + ATC: created nodeset lbc with 1 nodes + ATC: created nodeset rbc with 1 nodes + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +Setting up run ... + ATC: P0, found 3456 atoms in reference file + ATC: P0, read 3456 reference positions +Memory usage per processor = 102.974 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 21.394021 -6453.327 0 -6232.9964 -1069.954 + 100 21.611528 -6449.5788 0 -6227.0081 -1058.3224 + 200 21.976031 -6447.3787 0 -6221.0542 -1050.4447 + 300 22.453535 -6446.5516 0 -6215.3094 -1047.2794 + 400 23.061538 -6447.4669 0 -6209.9631 -1048.3359 + 500 23.0435 -6441.8867 0 -6204.5687 -1031.0775 + 600 23.434674 -6439.8253 0 -6198.4787 -1023.8681 + 700 23.661242 -6436.051 0 -6192.371 -1012.9536 + 800 23.855535 -6432.3914 0 -6186.7104 -1002.6094 + 900 24.57972 -6434.1846 0 -6181.0454 -1005.6096 + 1000 24.591901 -6427.6437 0 -6174.3791 -986.79755 + 1100 24.564542 -6420.9496 0 -6167.9668 -967.60512 + 1200 25.124526 -6420.7193 0 -6161.9694 -965.13516 + 1300 25.451194 -6418.1572 0 -6156.043 -957.51898 + 1400 25.392119 -6411.6404 0 -6150.1346 -940.17651 + 1500 25.941448 -6411.8573 0 -6144.6941 -937.00901 + 1600 26.068719 -6407.9609 0 -6139.4871 -925.02968 + 1700 26.556302 -6407.3907 0 -6133.8954 -921.78016 + 1800 27.343301 -6410.2665 0 -6128.6661 -928.15556 + 1900 27.586019 -6407.6536 0 -6123.5535 -917.44798 + 2000 27.450662 -6401.9839 0 -6119.2778 -903.28749 +Loop time of 65.9952 on 4 procs for 2000 steps with 3456 atoms + +Pair time (%) = 19.756 (29.9355) +Neigh time (%) = 8.36309 (12.6723) +Comm time (%) = 7.43406 (11.2645) +Outpt time (%) = 0.0658885 (0.0998383) +Other time (%) = 30.3762 (46.0278) + +Nlocal: 864 ave 864 max 864 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 6741 ave 7924 max 5558 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 272377 ave 288250 max 256633 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 544754 ave 574451 max 514186 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 2179016 +Ave neighs/atom = 630.502 +Neighbor list builds = 200 +Dangerous builds = 0 diff --git a/examples/USER/atc/two_temperature/uniform_exchange.screen b/examples/USER/atc/two_temperature/uniform_exchange.screen new file mode 100644 index 0000000000..7ea8ac7870 --- /dev/null +++ b/examples/USER/atc/two_temperature/uniform_exchange.screen @@ -0,0 +1,617 @@ +LAMMPS (14 Aug 2013) +Lattice spacing in x,y,z = 5.405 5.405 5.405 +Reading data file ... + orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215) + 4 by 1 by 1 MPI processor grid + 3456 atoms + 3456 velocities +3456 atoms in group internal +ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat + ATC: peratom PE compute created with ID: 3 + ATC: 2 materials defined from Ar_ttm.mat + ATC: creating two_temperature extrinsic model + ATC: 2 materials defined from Ar_ttm.mat + ATC: created uniform mesh with 20 nodes, 4 unique nodes, and 4 elements +Setting up run ... +Memory usage per processor = 55.3317 Mbytes +Step PotEng Temp AtC[2] AtC[4] + 0 -6783.1469 40 20 30 + 10 -6735.22 35.347373 20 30 + 20 -6638.0676 13.590854 20 30 + 30 -6546.9613 16.073857 20 30 + 40 -6490.431 19.681958 20 30 + 50 -6479.6344 18.576331 20 30 + 60 -6478.1607 19.820313 20 30 + 70 -6466.4024 19.347063 20 30 + 80 -6460.4965 20.043544 20 30 + 90 -6475.7847 21.525054 20 30 + 100 -6506.4571 22.734929 20 30 + 110 -6537.5028 21.72233 20 30 + 120 -6560.5557 20.545507 20 30 + 130 -6574.1125 20.005789 20 30 + 140 -6580.4816 20.638888 20 30 + 150 -6583.1325 20.170952 20 30 + 160 -6585.5219 20.117764 20 30 + 170 -6590.0974 20.060397 20 30 + 180 -6596.3875 20.679965 20 30 + 190 -6600.9942 20.347234 20 30 + 200 -6601.4311 19.975895 20 30 + 210 -6598.8067 19.945866 20 30 + 220 -6595.9852 19.679031 20 30 + 230 -6595.1077 19.944269 20 30 + 240 -6595.9943 20.070388 20 30 + 250 -6596.6556 20.011201 20 30 + 260 -6595.7678 20.005789 20 30 + 270 -6593.2664 19.759981 20 30 + 280 -6589.8904 19.770089 20 30 + 290 -6586.5561 19.876762 20 30 + 300 -6583.355 19.976674 20 30 + 310 -6580.8402 19.728887 20 30 + 320 -6579.781 19.931828 20 30 + 330 -6579.6954 20.004298 20 30 + 340 -6579.3344 19.991891 20 30 + 350 -6577.9943 19.863213 20 30 + 360 -6576.2366 19.850666 20 30 + 370 -6575.6064 19.992817 20 30 + 380 -6577.2176 20.076185 20 30 + 390 -6580.379 20.005789 20 30 + 400 -6584.1107 20.372789 20 30 + 410 -6587.9805 20.271504 20 30 + 420 -6590.8266 20.093685 20 30 + 430 -6591.9592 20.011482 20 30 + 440 -6592.611 20.077122 20 30 + 450 -6593.5045 20.07691 20 30 + 460 -6593.8748 20.010686 20 30 + 470 -6593.217 19.98456 20 30 + 480 -6591.7933 19.843386 20 30 + 490 -6589.9573 19.837677 20 30 + 500 -6587.2689 19.832888 20 30 +Loop time of 15.8836 on 4 procs for 500 steps with 3456 atoms + +Pair time (%) = 6.08595 (38.316) +Neigh time (%) = 2.65869 (16.7386) +Comm time (%) = 1.88057 (11.8397) +Outpt time (%) = 0.146439 (0.921951) +Other time (%) = 5.11194 (32.1838) + +Nlocal: 864 ave 864 max 864 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 7924 ave 7924 max 7924 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 287824 ave 289277 max 286558 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +FullNghs: 575647 ave 575980 max 575238 min +Histogram: 1 0 0 1 0 0 0 0 1 1 + +Total # of neighbors = 2302588 +Ave neighs/atom = 666.258 +Neighbor list builds = 50 +Dangerous builds = 0 + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +Setting up run ... +Memory usage per processor = 57.6419 Mbytes +Step PotEng Temp AtC[2] AtC[4] + 500 -6587.2689 19.832888 20 30 + 510 -6583.6679 19.63388 19.99067 29.921403 + 520 -6580.4044 19.465899 19.964127 29.843272 + 530 -6578.0632 19.385556 19.929008 29.765503 + 540 -6576.7688 19.408521 19.894578 29.688066 + 550 -6577.5441 19.634385 19.875757 29.611022 + 560 -6580.0311 20.033796 19.890374 29.53457 + 570 -6582.692 20.453288 19.943612 29.459004 + 580 -6584.4988 20.792548 20.027892 29.384591 + 590 -6584.8106 20.986315 20.129173 29.311509 + 600 -6583.0642 20.973002 20.22873 29.239803 + 610 -6579.3187 20.764597 20.306625 29.16936 + 620 -6575.2098 20.510314 20.35374 29.099949 + 630 -6571.8246 20.325665 20.375584 29.031339 + 640 -6569.5494 20.242631 20.383183 28.96337 + 650 -6568.5339 20.279067 20.388292 28.895976 + 660 -6569.1807 20.481136 20.404722 28.82919 + 670 -6571.8804 20.888192 20.449466 28.763169 + 680 -6575.8853 21.427509 20.536803 28.698198 + 690 -6578.9633 21.878187 20.664173 28.634605 + 700 -6578.9118 22.022487 20.807267 28.572603 + 710 -6575.3783 21.818746 20.931312 28.51215 + 720 -6570.6353 21.492478 21.01549 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25.307292 25.294483 25.298049 + 5150 -6537.5767 25.271715 25.31233 25.298102 + 5160 -6536.3151 25.151468 25.319554 25.298254 + 5170 -6535.9253 25.114159 25.317924 25.298416 + 5180 -6536.4798 25.167001 25.318871 25.29857 + 5190 -6536.1179 25.13136 25.321013 25.298741 + 5200 -6534.9204 25.015115 25.314484 25.298895 + 5210 -6534.1763 24.937377 25.298689 25.298953 + 5220 -6534.5267 24.971824 25.282929 25.298879 + 5230 -6535.3186 25.047097 25.274949 25.298714 + 5240 -6535.931 25.108109 25.273956 25.298519 + 5250 -6536.915 25.207033 25.280379 25.298348 + 5260 -6538.452 25.359021 25.298594 25.298277 + 5270 -6539.799 25.494657 25.329406 25.298406 + 5280 -6539.8899 25.507179 25.364409 25.298803 + 5290 -6538.0806 25.333634 25.38759 25.299432 + 5300 -6535.0967 25.042437 25.384622 25.300131 + 5310 -6533.6581 24.896657 25.359623 25.300693 + 5320 -6535.3135 25.05354 25.339645 25.301057 + 5330 -6537.5649 25.272889 25.342371 25.301359 + 5340 -6537.8096 25.296808 25.356372 25.301742 + 5350 -6535.8768 25.106661 25.35918 25.302196 + 5360 -6533.9006 24.911221 25.341369 25.302578 + 5370 -6533.6914 24.885198 25.31523 25.302769 + 5380 -6535.164 25.024726 25.298244 25.302783 + 5390 -6536.8589 25.192828 25.299421 25.302741 + 5400 -6536.3929 25.145908 25.306382 25.30275 + 5410 -6534.017 24.912722 25.29671 25.302751 + 5420 -6532.4608 24.759447 25.268065 25.302588 + 5430 -6533.6554 24.873379 25.240968 25.302189 + 5440 -6537.273 25.22677 25.241143 25.301685 + 5450 -6540.5201 25.548408 25.275716 25.301341 + 5460 -6540.799 25.581769 25.32313 25.301347 + 5470 -6538.9726 25.411274 25.35642 25.301676 + 5480 -6538.0259 25.322264 25.372916 25.302183 + 5490 -6538.1544 25.3361 25.386454 25.302798 + 5500 -6536.8742 25.212636 25.393996 25.303497 +Loop time of 325.113 on 4 procs for 5000 steps with 3456 atoms + +Pair time (%) = 60.4693 (18.5995) +Neigh time (%) = 30.21 (9.29214) +Comm time (%) = 53.3399 (16.4066) +Outpt time (%) = 1.67016 (0.513718) +Other time (%) = 179.424 (55.1881) + +Nlocal: 864 ave 864 max 864 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 7924 ave 7924 max 7924 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 287658 ave 288864 max 286341 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +FullNghs: 575316 ave 576116 max 574315 min +Histogram: 1 0 0 0 0 1 1 0 0 1 + +Total # of neighbors = 2301264 +Ave neighs/atom = 665.875 +Neighbor list builds = 500 +Dangerous builds = 0 diff --git a/examples/USER/atc/two_temperature/uniform_heating.screen b/examples/USER/atc/two_temperature/uniform_heating.screen new file mode 100644 index 0000000000..292cf95875 --- /dev/null +++ b/examples/USER/atc/two_temperature/uniform_heating.screen @@ -0,0 +1,133 @@ +LAMMPS (14 Aug 2013) +units real +atom_style atomic +boundary f p p +# create domain +#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) +pair_style lj/cut 13.5 +read_data uniform_heating_init.data +Reading data file ... + orthogonal box = (-43.24 -16.215 -16.215) to (43.24 16.215 16.215) + 4 by 1 by 1 MPI processor grid + 2304 atoms + 2304 velocities +lattice fcc 5.405 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 5.405 5.405 5.405 +region mdRegion block -8 8 -3 3 -3 3 +region mdInternal block -6 6 -3 3 -3 3 +group internal region mdInternal +1728 atoms in group internal +neighbor 5. bin +neigh_modify every 10 delay 0 check no +# ID group atc PhysicsType ParameterFile +fix AtC internal atc two_temperature Ar_ttm.mat +ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat + ATC: peratom PE compute created with ID: 3 + ATC: 2 materials defined from Ar_ttm.mat + ATC: creating two_temperature extrinsic model + ATC: 2 materials defined from Ar_ttm.mat +# ID part keywords nx ny nz region +fix_modify AtC mesh create 6 1 1 mdInternal f p p + ATC: created uniform mesh with 28 nodes, 7 unique nodes, and 6 elements +fix_modify AtC internal_quadrature on +# fix a temperature +fix_modify AtC initial temperature all 20. +fix_modify AtC fix temperature all 20. +fix_modify AtC initial electron_temperature all 20. +fix_modify AtC fix electron_temperature all 20. +# turn on thermostat +fix_modify AtC control thermal rescale 10 +# output +thermo_style custom step cpu pe etotal temp f_AtC[1] f_AtC[2] +thermo 100 +log uniform_heating.log +# make thermo output the correct temperature by removing ghost dof +# variable xdof equal 3*count(ghost) +# compute_modify thermo_temp extra ${xdof} +# equilibrate MD field +timestep 5 +run 400 +Setting up run ... +Memory usage per processor = 52.5067 Mbytes +Step CPU PotEng TotEng Temp AtC[1] AtC[2] + 0 0 -4406.6687 -4200.7544 29.995658 206.60693 20 + 100 7.4800179 -4258.7421 -4155.7253 15.006513 206.60693 20 + 200 10.47899 -4317.7651 -4214.7483 15.006513 206.60693 20 + 300 12.109694 -4308.7092 -4205.6924 15.006513 206.60693 20 + 400 13.610023 -4305.0489 -4202.0322 15.006513 206.60693 20 +Loop time of 13.6154 on 4 procs for 400 steps with 2304 atoms + +Pair time (%) = 2.90979 (21.3713) +Neigh time (%) = 1.344 (9.87119) +Comm time (%) = 2.62009 (19.2435) +Outpt time (%) = 0.0412001 (0.302599) +Other time (%) = 6.70033 (49.2114) + +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5677 ave 6860 max 4494 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 177099 ave 193893 max 161681 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +FullNghs: 354198 ave 384150 max 324339 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1416792 +Ave neighs/atom = 614.927 +Neighbor list builds = 40 +Dangerous builds = 0 +# change thermostat +fix_modify AtC output uniform_heatingFE 100 text + ATC: Warning : text output can create _LARGE_ files + ATC: output custom names: + +fix_modify AtC unfix temperature all +fix_modify AtC control thermal flux +# fix boundary +fix_modify AtC mesh create_nodeset lbc -6.1 -5.9 -INF INF -INF INF + ATC: created nodeset lbc with 1 nodes +fix_modify AtC fix temperature lbc 20. +fix_modify AtC mesh create_nodeset rbc 5.9 6.1 -INF INF -INF INF + ATC: created nodeset rbc with 1 nodes +fix_modify AtC fix temperature rbc 20. +# add source +#fix_modify AtC source temperature all 0.01 +fix_modify AtC source temperature all 6.3363e-10 +# run with FE +reset_timestep 0 +run 1000 +Setting up run ... +Memory usage per processor = 54.7588 Mbytes +Step CPU PotEng TotEng Temp AtC[1] AtC[2] + 0 0 -4305.0489 -4202.0322 15.006513 206.60693 20 + 100 1.581583 -4284.0298 -4161.843 17.799025 245.0222 23.187441 + 200 3.199868 -4271.7421 -4126.3033 21.186144 291.62707 27.054401 + 300 4.951031 -4252.1549 -4092.7431 23.221609 319.6337 29.378203 + 400 6.5261829 -4243.1541 -4066.5034 25.732803 354.18694 32.245198 + 500 8.1686139 -4220.6621 -4038.0194 26.605675 366.20291 33.242203 + 600 9.6777399 -4216.5541 -4017.5256 28.992598 399.04557 35.967267 + 700 12.2501 -4214.2511 -3996.8158 31.673922 435.9421 39.028693 + 800 14.206697 -4198.8979 -3978.4057 32.119215 442.05328 39.535758 + 900 15.72 -4186.3755 -3963.2872 32.4974 447.23922 39.966052 + 1000 24.377633 -4182.9374 -3949.4046 34.018855 468.17471 41.703139 +Loop time of 24.3779 on 4 procs for 1000 steps with 2304 atoms + +Pair time (%) = 6.42443 (26.3535) +Neigh time (%) = 2.68509 (11.0145) +Comm time (%) = 2.88995 (11.8548) +Outpt time (%) = 0.00563473 (0.0231141) +Other time (%) = 12.3728 (50.7541) + +Nlocal: 576 ave 576 max 576 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5677 ave 6860 max 4494 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 175875 ave 189472 max 162330 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 351750 ave 379061 max 324517 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1407002 +Ave neighs/atom = 610.678 +Neighbor list builds = 100 +Dangerous builds = 0