From 335fa2e742b9d9b67dd3d30325cb036b13ec18d0 Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Sat, 19 Feb 2022 17:07:21 -0700 Subject: [PATCH] Addd born/matrix numdiff to example --- examples/numdiff/README.md | 11 +- examples/numdiff/in.numdiff | 67 +++++- .../numdiff/log.19Feb2022.log.numdiff.g++.1 | 197 ++++++++++++++++++ .../numdiff/log.19Feb2022.log.numdiff.g++.4 | 197 ++++++++++++++++++ .../numdiff/log.28Jan2022.log.numdiff.g++.1 | 175 ---------------- .../numdiff/log.28Jan2022.log.numdiff.g++.4 | 175 ---------------- 6 files changed, 461 insertions(+), 361 deletions(-) create mode 100644 examples/numdiff/log.19Feb2022.log.numdiff.g++.1 create mode 100644 examples/numdiff/log.19Feb2022.log.numdiff.g++.4 delete mode 100644 examples/numdiff/log.28Jan2022.log.numdiff.g++.1 delete mode 100644 examples/numdiff/log.28Jan2022.log.numdiff.g++.4 diff --git a/examples/numdiff/README.md b/examples/numdiff/README.md index d88f66d65c..10727fe0e3 100644 --- a/examples/numdiff/README.md +++ b/examples/numdiff/README.md @@ -1,8 +1,11 @@ -# LAMMPS FIX NUMDIFF EXAMPLE +# LAMMPS NUMDIFF EXAMPLES FOR FORCES, VIRIAL, and BORN MATRIX -## Numerical Difference Fix +## Numerical Difference Fixes and Computes -This directory contains the ingredients to run an NVE simulation using the numerical difference fix and calculate error in forces. +This directory contains the input script for an NVE simulation with +fix numdiff, fix numdiff/virial, and compute born/matrix numdiff. +In each cases, results are compared to exact analytic expressions +and the small relative differences are reported. Example: ``` @@ -10,4 +13,4 @@ NP=4 #number of processors mpirun -np $NP lmp_mpi -in.numdiff ``` -## Required LAMMPS packages: MOLECULE package +## Required LAMMPS packages: EXTRA-FIX, EXTRA-COMPUTE diff --git a/examples/numdiff/in.numdiff b/examples/numdiff/in.numdiff index cd3d44a9e7..363570da87 100644 --- a/examples/numdiff/in.numdiff +++ b/examples/numdiff/in.numdiff @@ -1,5 +1,5 @@ # Numerical difference calculation -# of error in forces and virial stress +# of error in forces, virial stress, and Born matrix # adjustable parameters @@ -8,8 +8,10 @@ variable nthermo index 10 # thermo output interval variable ndump index 500 # dump output interval variable nlat index 3 # size of box variable fdelta index 1.0e-4 # displacement size -variable vdelta index 1.0e-6 # strain size +variable vdelta index 1.0e-6 # strain size for numdiff/virial +variable bdelta index 1.0e-8 # strain size for numdiff Born matrix variable temp index 10.0 # temperature +variable nugget equal 1.0e-6 # regularization for relerr units metal atom_style atomic @@ -23,8 +25,8 @@ mass 1 39.903 velocity all create ${temp} 2357 mom yes dist gaussian -pair_style lj/cubic -pair_coeff * * 0.0102701 3.42 +pair_style lj/cut 5.0 +pair_coeff 1 1 0.0102701 3.42 neighbor 0.0 bin neigh_modify every 1 delay 0 check no @@ -42,7 +44,7 @@ variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2 compute faverrsq all reduce ave v_ferrsq variable fsq atom fx^2+fy^2+fz^2 compute favsq all reduce ave v_fsq -variable frelerr equal sqrt(c_faverrsq/c_favsq) +variable frelerr equal sqrt(c_faverrsq/(c_favsq+${nugget})) dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz # define numerical virial stress tensor calculation @@ -67,8 +69,59 @@ variable vsq equal "c_myvirial[1]^2 + & c_myvirial[4]^2 + & c_myvirial[5]^2 + & c_myvirial[6]^2" -variable vrelerr equal sqrt(v_verrsq/v_vsq) +variable vrelerr equal sqrt(v_verrsq/(v_vsq+${nugget})) -thermo_style custom step temp pe etotal press v_frelerr v_vrelerr +# define numerical Born matrix calculation + +compute bornnum all born/matrix numdiff ${bdelta} myvirial +compute born all born/matrix +variable berr vector c_bornnum-c_born +variable berrsq equal "v_berr[1]^2 + & + v_berr[2]^2 + & + v_berr[3]^2 + & + v_berr[4]^2 + & + v_berr[5]^2 + & + v_berr[6]^2 + & + v_berr[7]^2 + & + v_berr[8]^2 + & + v_berr[9]^2 + & + v_berr[10]^2 + & + v_berr[11]^2 + & + v_berr[12]^2 + & + v_berr[13]^2 + & + v_berr[14]^2 + & + v_berr[15]^2 + & + v_berr[16]^2 + & + v_berr[17]^2 + & + v_berr[18]^2 + & + v_berr[19]^2 + & + v_berr[20]^2 + & + v_berr[21]^2" + +variable bsq equal "c_born[1]^2 + & + c_born[2]^2 + & + c_born[3]^2 + & + c_born[4]^2 + & + c_born[5]^2 + & + c_born[6]^2 + & + c_born[7]^2 + & + c_born[8]^2 + & + c_born[9]^2 + & + c_born[10]^2 + & + c_born[11]^2 + & + c_born[12]^2 + & + c_born[13]^2 + & + c_born[14]^2 + & + c_born[15]^2 + & + c_born[16]^2 + & + c_born[17]^2 + & + c_born[18]^2 + & + c_born[19]^2 + & + c_born[20]^2 + & + c_born[21]^2" + +variable brelerr equal sqrt(v_berrsq/(v_bsq+${nugget})) + +thermo_style custom step temp pe etotal press v_frelerr v_vrelerr v_brelerr thermo ${nthermo} run ${nsteps} diff --git a/examples/numdiff/log.19Feb2022.log.numdiff.g++.1 b/examples/numdiff/log.19Feb2022.log.numdiff.g++.1 new file mode 100644 index 0000000000..eb2ba4fc3a --- /dev/null +++ b/examples/numdiff/log.19Feb2022.log.numdiff.g++.1 @@ -0,0 +1,197 @@ +LAMMPS (7 Jan 2022) +# Numerical difference calculation +# of error in forces, virial stress, and Born matrix + +# adjustable parameters + +variable nsteps index 500 # length of run +variable nthermo index 10 # thermo output interval +variable ndump index 500 # dump output interval +variable nlat index 3 # size of box +variable fdelta index 1.0e-4 # displacement size +variable vdelta index 1.0e-6 # strain size for numdiff/virial +variable bdelta index 1.0e-8 # strain size for numdiff Born matrix +variable temp index 10.0 # temperature +variable nugget equal 1.0e-6 # regularization for relerr + +units metal +atom_style atomic + +atom_modify map yes +lattice fcc 5.358000 +Lattice spacing in x,y,z = 5.358 5.358 5.358 +region box block 0 ${nlat} 0 ${nlat} 0 ${nlat} +region box block 0 3 0 ${nlat} 0 ${nlat} +region box block 0 3 0 3 0 ${nlat} +region box block 0 3 0 3 0 3 +create_box 1 box +Created orthogonal box = (0 0 0) to (16.074 16.074 16.074) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 108 atoms + using lattice units in orthogonal box = (0 0 0) to (16.074 16.074 16.074) + create_atoms CPU = 0.000 seconds +mass 1 39.903 + +velocity all create ${temp} 2357 mom yes dist gaussian +velocity all create 10.0 2357 mom yes dist gaussian + +pair_style lj/cut 5.0 +pair_coeff 1 1 0.0102701 3.42 + +neighbor 0.0 bin +neigh_modify every 1 delay 0 check no + +timestep 0.001 +fix nve all nve + +# define numerical force calculation + +fix numforce all numdiff ${nthermo} ${fdelta} +fix numforce all numdiff 10 ${fdelta} +fix numforce all numdiff 10 1.0e-4 +variable ferrx atom f_numforce[1]-fx +variable ferry atom f_numforce[2]-fy +variable ferrz atom f_numforce[3]-fz +variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2 +compute faverrsq all reduce ave v_ferrsq +variable fsq atom fx^2+fy^2+fz^2 +compute favsq all reduce ave v_fsq +variable frelerr equal sqrt(c_faverrsq/(c_favsq+${nugget})) +variable frelerr equal sqrt(c_faverrsq/(c_favsq+1e-06)) +dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz +dump errors all custom 500 force_error.dump v_ferrx v_ferry v_ferrz + +# define numerical virial stress tensor calculation + +compute myvirial all pressure NULL virial +fix numvirial all numdiff/virial ${nthermo} ${vdelta} +fix numvirial all numdiff/virial 10 ${vdelta} +fix numvirial all numdiff/virial 10 1.0e-6 +variable errxx equal f_numvirial[1]-c_myvirial[1] +variable erryy equal f_numvirial[2]-c_myvirial[2] +variable errzz equal f_numvirial[3]-c_myvirial[3] +variable erryz equal f_numvirial[4]-c_myvirial[6] +variable errxz equal f_numvirial[5]-c_myvirial[5] +variable errxy equal f_numvirial[6]-c_myvirial[4] +variable verrsq equal "v_errxx^2 + v_erryy^2 + v_errzz^2 + v_erryz^2 + v_errxz^2 + v_errxy^2" +variable vsq equal "c_myvirial[1]^2 + c_myvirial[3]^2 + c_myvirial[3]^2 + c_myvirial[4]^2 + c_myvirial[5]^2 + c_myvirial[6]^2" +variable vrelerr equal sqrt(v_verrsq/(v_vsq+${nugget})) +variable vrelerr equal sqrt(v_verrsq/(v_vsq+1e-06)) + +# define numerical Born matrix calculation + +compute bornnum all born/matrix numdiff ${bdelta} myvirial +compute bornnum all born/matrix numdiff 1.0e-8 myvirial +compute born all born/matrix +variable berr vector c_bornnum-c_born +variable berrsq equal "v_berr[1]^2 + v_berr[2]^2 + v_berr[3]^2 + v_berr[4]^2 + v_berr[5]^2 + v_berr[6]^2 + v_berr[7]^2 + v_berr[8]^2 + v_berr[9]^2 + v_berr[10]^2 + v_berr[11]^2 + v_berr[12]^2 + v_berr[13]^2 + v_berr[14]^2 + v_berr[15]^2 + v_berr[16]^2 + v_berr[17]^2 + v_berr[18]^2 + v_berr[19]^2 + v_berr[20]^2 + v_berr[21]^2" + +variable bsq equal "c_born[1]^2 + c_born[2]^2 + c_born[3]^2 + c_born[4]^2 + c_born[5]^2 + c_born[6]^2 + c_born[7]^2 + c_born[8]^2 + c_born[9]^2 + c_born[10]^2 + c_born[11]^2 + c_born[12]^2 + c_born[13]^2 + c_born[14]^2 + c_born[15]^2 + c_born[16]^2 + c_born[17]^2 + c_born[18]^2 + c_born[19]^2 + c_born[20]^2 + c_born[21]^2" + +variable brelerr equal sqrt(v_berrsq/(v_bsq+${nugget})) +variable brelerr equal sqrt(v_berrsq/(v_bsq+1e-06)) + +thermo_style custom step temp pe etotal press v_frelerr v_vrelerr v_brelerr +thermo ${nthermo} +thermo 10 +run ${nsteps} +run 500 + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5 + ghost atom cutoff = 5 + binsize = 2.5, bins = 7 7 7 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard + (2) compute born/matrix, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 6.823 | 6.823 | 6.823 Mbytes +Step Temp PotEng TotEng Press v_frelerr v_vrelerr v_brelerr + 0 10 -6.6101864 -6.471878 947.70558 5.7012262e-09 1.4849734e-08 9.072204e-09 + 10 9.9357441 -6.6092976 -6.471878 949.3486 1.3828998e-08 1.9248385e-09 3.0140952e-09 + 20 9.7444561 -6.6066519 -6.4718779 954.23637 1.385204e-08 1.7476399e-09 2.8104946e-09 + 30 9.4311148 -6.6023181 -6.4718779 962.23331 1.4147226e-08 1.7647816e-09 3.038408e-09 + 40 9.0043293 -6.5964152 -6.4718778 973.10762 1.4128155e-08 1.6390138e-09 3.1677083e-09 + 50 8.4762135 -6.5891108 -6.4718777 986.53572 1.4168048e-08 2.3910821e-09 3.2880496e-09 + 60 7.8621735 -6.5806179 -6.4718775 1002.1092 1.411958e-08 2.0683414e-09 2.650625e-09 + 70 7.1805874 -6.5711908 -6.4718773 1019.3448 1.4139911e-08 1.6084571e-09 2.7690475e-09 + 80 6.4523557 -6.5611186 -6.4718771 1037.6974 1.4105096e-08 1.9929271e-09 3.7464396e-09 + 90 5.7003071 -6.5507169 -6.4718769 1056.5767 1.4084183e-08 1.750579e-09 4.1502319e-09 + 100 4.9484503 -6.5403179 -6.4718767 1075.3674 1.4063796e-08 1.0250271e-09 3.0940885e-09 + 110 4.221081 -6.5302576 -6.4718765 1093.4526 1.400901e-08 1.389277e-09 3.3111451e-09 + 120 3.5417733 -6.520862 -6.4718763 1110.2388 1.4038158e-08 8.6231891e-10 2.6872042e-09 + 130 2.9323072 -6.5124324 -6.4718762 1125.183 1.4048645e-08 7.0840985e-10 2.5616823e-09 + 140 2.411607 -6.5052306 -6.471876 1137.8182 1.3968429e-08 1.8508015e-09 3.984183e-09 + 150 1.9947801 -6.4994654 -6.4718759 1147.7764 1.395965e-08 1.9484728e-09 3.8459442e-09 + 160 1.6923481 -6.4952825 -6.4718759 1154.8063 1.3948606e-08 1.5275137e-09 3.4566825e-09 + 170 1.5097515 -6.492757 -6.4718759 1158.7853 1.3845523e-08 1.5455e-09 2.4291888e-09 + 180 1.4471795 -6.4918916 -6.4718759 1159.7221 1.3788451e-08 1.578099e-09 2.2452653e-09 + 190 1.4997431 -6.4926187 -6.471876 1157.7529 1.374841e-08 2.142073e-09 2.3614867e-09 + 200 1.6579637 -6.4948072 -6.4718761 1153.1286 1.3674788e-08 2.111894e-09 3.4774073e-09 + 210 1.908522 -6.4982727 -6.4718763 1146.1965 1.3639408e-08 1.2386489e-09 2.1550029e-09 + 220 2.23518 -6.5027908 -6.4718764 1137.3775 1.3524209e-08 1.7016573e-09 3.3806952e-09 + 230 2.6197892 -6.5081105 -6.4718766 1127.1415 1.3344007e-08 1.5843477e-09 2.9517742e-09 + 240 3.043298 -6.5139681 -6.4718768 1115.9815 1.3245227e-08 1.5502368e-09 3.7751316e-09 + 250 3.4866901 -6.5201007 -6.4718769 1104.3906 1.3080142e-08 1.369987e-09 3.1015926e-09 + 260 3.9318061 -6.5262572 -6.4718771 1092.84 1.2885339e-08 1.0743728e-09 3.2781775e-09 + 270 4.3620216 -6.5322076 -6.4718772 1081.7617 1.2705966e-08 1.3618619e-09 3.2074528e-09 + 280 4.7627723 -6.5377504 -6.4718773 1071.5341 1.2480463e-08 1.4346869e-09 2.6014531e-09 + 290 5.1219322 -6.542718 -6.4718774 1062.4716 1.2434727e-08 2.1935942e-09 2.8738025e-09 + 300 5.4300557 -6.5469796 -6.4718774 1054.8177 1.2321314e-08 8.2365886e-10 3.0321861e-09 + 310 5.6804997 -6.5504435 -6.4718774 1048.7409 1.2300884e-08 1.4855741e-09 3.0631008e-09 + 320 5.8694423 -6.5530567 -6.4718774 1044.3341 1.2483087e-08 1.8711589e-09 3.9505726e-09 + 330 5.9958115 -6.5548045 -6.4718774 1041.6165 1.2627617e-08 1.9256986e-09 2.0214697e-09 + 340 6.0611353 -6.555708 -6.4718774 1040.5369 1.2935701e-08 1.6609255e-09 3.0860271e-09 + 350 6.0693222 -6.5558211 -6.4718773 1040.9803 1.3218179e-08 1.985355e-09 2.8012116e-09 + 360 6.0263776 -6.5552271 -6.4718773 1042.7755 1.3471701e-08 1.5125203e-09 2.8686484e-09 + 370 5.9400629 -6.5540332 -6.4718772 1045.7049 1.3676495e-08 1.7364093e-09 2.578312e-09 + 380 5.8195019 -6.5523657 -6.4718771 1049.515 1.3859995e-08 1.6834835e-09 2.9599336e-09 + 390 5.6747442 -6.5503635 -6.471877 1053.9288 1.3987553e-08 1.7893896e-09 2.5163687e-09 + 400 5.5162948 -6.5481719 -6.4718769 1058.6583 1.4091878e-08 1.4468098e-09 2.1565248e-09 + 410 5.3546269 -6.5459358 -6.4718768 1063.4182 1.4188438e-08 1.7231047e-09 2.8650537e-09 + 420 5.1996958 -6.5437929 -6.4718768 1067.9384 1.4205207e-08 1.3551982e-09 4.5778887e-09 + 430 5.0604771 -6.5418673 -6.4718767 1071.9767 1.4267199e-08 1.361845e-09 3.0381078e-09 + 440 4.9445529 -6.5402639 -6.4718766 1075.3292 1.4253464e-08 1.3945282e-09 2.820632e-09 + 450 4.8577717 -6.5390637 -6.4718766 1077.8394 1.4240998e-08 1.8767323e-09 3.4379833e-09 + 460 4.8040023 -6.53832 -6.4718766 1079.4048 1.4242259e-08 1.4785379e-09 4.399133e-09 + 470 4.7849977 -6.5380571 -6.4718766 1079.9795 1.4227939e-08 1.8623848e-09 3.0102588e-09 + 480 4.8003794 -6.5382699 -6.4718766 1079.5756 1.4215836e-08 1.2821795e-09 3.0643976e-09 + 490 4.8477405 -6.538925 -6.4718767 1078.2596 1.4186541e-08 2.47604e-09 3.3809071e-09 + 500 4.9228588 -6.539964 -6.4718767 1076.1469 1.4099819e-08 1.6653302e-09 3.4324143e-09 +Loop time of 0.476785 on 1 procs for 500 steps with 108 atoms + +Performance: 90.607 ns/day, 0.265 hours/ns, 1048.692 timesteps/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0043699 | 0.0043699 | 0.0043699 | 0.0 | 0.92 +Neigh | 0.026529 | 0.026529 | 0.026529 | 0.0 | 5.56 +Comm | 0.0026272 | 0.0026272 | 0.0026272 | 0.0 | 0.55 +Output | 0.014971 | 0.014971 | 0.014971 | 0.0 | 3.14 +Modify | 0.42777 | 0.42777 | 0.42777 | 0.0 | 89.72 +Other | | 0.0005208 | | | 0.11 + +Nlocal: 108 ave 108 max 108 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 256 ave 256 max 256 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 648 ave 648 max 648 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 648 +Ave neighs/atom = 6 +Neighbor list builds = 500 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/numdiff/log.19Feb2022.log.numdiff.g++.4 b/examples/numdiff/log.19Feb2022.log.numdiff.g++.4 new file mode 100644 index 0000000000..e20efd7f68 --- /dev/null +++ b/examples/numdiff/log.19Feb2022.log.numdiff.g++.4 @@ -0,0 +1,197 @@ +LAMMPS (7 Jan 2022) +# Numerical difference calculation +# of error in forces, virial stress, and Born matrix + +# adjustable parameters + +variable nsteps index 500 # length of run +variable nthermo index 10 # thermo output interval +variable ndump index 500 # dump output interval +variable nlat index 3 # size of box +variable fdelta index 1.0e-4 # displacement size +variable vdelta index 1.0e-6 # strain size for numdiff/virial +variable bdelta index 1.0e-8 # strain size for numdiff Born matrix +variable temp index 10.0 # temperature +variable nugget equal 1.0e-6 # regularization for relerr + +units metal +atom_style atomic + +atom_modify map yes +lattice fcc 5.358000 +Lattice spacing in x,y,z = 5.358 5.358 5.358 +region box block 0 ${nlat} 0 ${nlat} 0 ${nlat} +region box block 0 3 0 ${nlat} 0 ${nlat} +region box block 0 3 0 3 0 ${nlat} +region box block 0 3 0 3 0 3 +create_box 1 box +Created orthogonal box = (0 0 0) to (16.074 16.074 16.074) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 108 atoms + using lattice units in orthogonal box = (0 0 0) to (16.074 16.074 16.074) + create_atoms CPU = 0.000 seconds +mass 1 39.903 + +velocity all create ${temp} 2357 mom yes dist gaussian +velocity all create 10.0 2357 mom yes dist gaussian + +pair_style lj/cut 5.0 +pair_coeff 1 1 0.0102701 3.42 + +neighbor 0.0 bin +neigh_modify every 1 delay 0 check no + +timestep 0.001 +fix nve all nve + +# define numerical force calculation + +fix numforce all numdiff ${nthermo} ${fdelta} +fix numforce all numdiff 10 ${fdelta} +fix numforce all numdiff 10 1.0e-4 +variable ferrx atom f_numforce[1]-fx +variable ferry atom f_numforce[2]-fy +variable ferrz atom f_numforce[3]-fz +variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2 +compute faverrsq all reduce ave v_ferrsq +variable fsq atom fx^2+fy^2+fz^2 +compute favsq all reduce ave v_fsq +variable frelerr equal sqrt(c_faverrsq/(c_favsq+${nugget})) +variable frelerr equal sqrt(c_faverrsq/(c_favsq+1e-06)) +dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz +dump errors all custom 500 force_error.dump v_ferrx v_ferry v_ferrz + +# define numerical virial stress tensor calculation + +compute myvirial all pressure NULL virial +fix numvirial all numdiff/virial ${nthermo} ${vdelta} +fix numvirial all numdiff/virial 10 ${vdelta} +fix numvirial all numdiff/virial 10 1.0e-6 +variable errxx equal f_numvirial[1]-c_myvirial[1] +variable erryy equal f_numvirial[2]-c_myvirial[2] +variable errzz equal f_numvirial[3]-c_myvirial[3] +variable erryz equal f_numvirial[4]-c_myvirial[6] +variable errxz equal f_numvirial[5]-c_myvirial[5] +variable errxy equal f_numvirial[6]-c_myvirial[4] +variable verrsq equal "v_errxx^2 + v_erryy^2 + v_errzz^2 + v_erryz^2 + v_errxz^2 + v_errxy^2" +variable vsq equal "c_myvirial[1]^2 + c_myvirial[3]^2 + c_myvirial[3]^2 + c_myvirial[4]^2 + c_myvirial[5]^2 + c_myvirial[6]^2" +variable vrelerr equal sqrt(v_verrsq/(v_vsq+${nugget})) +variable vrelerr equal sqrt(v_verrsq/(v_vsq+1e-06)) + +# define numerical Born matrix calculation + +compute bornnum all born/matrix numdiff ${bdelta} myvirial +compute bornnum all born/matrix numdiff 1.0e-8 myvirial +compute born all born/matrix +variable berr vector c_bornnum-c_born +variable berrsq equal "v_berr[1]^2 + v_berr[2]^2 + v_berr[3]^2 + v_berr[4]^2 + v_berr[5]^2 + v_berr[6]^2 + v_berr[7]^2 + v_berr[8]^2 + v_berr[9]^2 + v_berr[10]^2 + v_berr[11]^2 + v_berr[12]^2 + v_berr[13]^2 + v_berr[14]^2 + v_berr[15]^2 + v_berr[16]^2 + v_berr[17]^2 + v_berr[18]^2 + v_berr[19]^2 + v_berr[20]^2 + v_berr[21]^2" + +variable bsq equal "c_born[1]^2 + c_born[2]^2 + c_born[3]^2 + c_born[4]^2 + c_born[5]^2 + c_born[6]^2 + c_born[7]^2 + c_born[8]^2 + c_born[9]^2 + c_born[10]^2 + c_born[11]^2 + c_born[12]^2 + c_born[13]^2 + c_born[14]^2 + c_born[15]^2 + c_born[16]^2 + c_born[17]^2 + c_born[18]^2 + c_born[19]^2 + c_born[20]^2 + c_born[21]^2" + +variable brelerr equal sqrt(v_berrsq/(v_bsq+${nugget})) +variable brelerr equal sqrt(v_berrsq/(v_bsq+1e-06)) + +thermo_style custom step temp pe etotal press v_frelerr v_vrelerr v_brelerr +thermo ${nthermo} +thermo 10 +run ${nsteps} +run 500 + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5 + ghost atom cutoff = 5 + binsize = 2.5, bins = 7 7 7 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard + (2) compute born/matrix, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 6.816 | 6.816 | 6.816 Mbytes +Step Temp PotEng TotEng Press v_frelerr v_vrelerr v_brelerr + 0 10 -6.6101864 -6.471878 947.70558 1.9110624e-09 9.4407596e-10 3.6112548e-09 + 10 9.9369961 -6.6093149 -6.471878 949.31222 1.3055176e-08 4.996456e-10 1.8135199e-09 + 20 9.7500224 -6.6067289 -6.4718779 954.07898 1.3721178e-08 5.6039795e-10 1.6247414e-09 + 30 9.4448115 -6.6025075 -6.4718779 961.85502 1.3813156e-08 6.8451692e-10 1.3087974e-09 + 40 9.0305392 -6.5967776 -6.4718777 972.39819 1.3961749e-08 3.1134064e-10 2.0036072e-09 + 50 8.5196068 -6.5897109 -6.4718776 985.38158 1.3996941e-08 7.0149406e-10 1.6670043e-09 + 60 7.9273388 -6.5815192 -6.4718775 1000.4024 1.4000005e-08 3.5766629e-10 2.53484e-09 + 70 7.2715879 -6.5724494 -6.4718773 1016.9932 1.3996503e-08 6.2731503e-10 1.9890841e-09 + 80 6.5722375 -6.5627766 -6.4718771 1034.6361 1.3973603e-08 3.1142917e-10 1.3798878e-09 + 90 5.8505991 -6.5527956 -6.4718769 1052.7794 1.3983301e-08 3.9931135e-10 2.7529755e-09 + 100 5.128708 -6.542811 -6.4718767 1070.8561 1.395586e-08 2.3152413e-10 2.0674207e-09 + 110 4.4285344 -6.5331269 -6.4718766 1088.305 1.3938374e-08 4.2173005e-10 1.5662067e-09 + 120 3.7711361 -6.5240343 -6.4718764 1104.5919 1.3915264e-08 2.5458038e-10 1.5849397e-09 + 130 3.1757964 -6.5158002 -6.4718762 1119.2319 1.3858843e-08 5.7490448e-10 3.0296967e-09 + 140 2.6591997 -6.5086551 -6.4718761 1131.8095 1.3814891e-08 3.5434633e-10 1.6789888e-09 + 150 2.2347034 -6.5027839 -6.471876 1141.9961 1.3781115e-08 5.0639594e-10 2.9776968e-09 + 160 1.9117661 -6.4983173 -6.471876 1149.564 1.3734288e-08 3.1954962e-10 1.3139064e-09 + 170 1.6955808 -6.4953273 -6.471876 1154.3946 1.3682252e-08 3.5426781e-10 2.5537158e-09 + 180 1.586949 -6.4938249 -6.471876 1156.4812 1.363e-08 4.0804881e-10 1.5958563e-09 + 190 1.5824056 -6.4937621 -6.4718761 1155.925 1.3532637e-08 4.0767685e-10 2.3016751e-09 + 200 1.6745831 -6.4950371 -6.4718762 1152.926 1.3455927e-08 2.953369e-10 2.1101198e-09 + 210 1.8527803 -6.4975018 -6.4718763 1147.7684 1.335224e-08 3.5042319e-10 1.7878344e-09 + 220 2.1036825 -6.5009721 -6.4718764 1140.8026 1.3239176e-08 3.5988448e-10 1.9695755e-09 + 230 2.4121721 -6.5052389 -6.4718766 1132.4243 1.3090019e-08 3.5004036e-10 1.5993755e-09 + 240 2.7621668 -6.5100798 -6.4718767 1123.0538 1.2946525e-08 4.1216361e-10 2.1544908e-09 + 250 3.1374274 -6.5152701 -6.4718768 1113.1152 1.277789e-08 5.9848318e-10 2.5891141e-09 + 260 3.5222906 -6.5205932 -6.471877 1103.0171 1.2591089e-08 2.0080182e-10 1.9280289e-09 + 270 3.9022942 -6.5258491 -6.4718771 1093.1369 1.2432232e-08 4.2494727e-10 2.2260348e-09 + 280 4.2646753 -6.5308612 -6.4718772 1083.8072 1.2268238e-08 6.1239266e-10 1.7606971e-09 + 290 4.598736 -6.5354816 -6.4718772 1075.306 1.2181179e-08 4.9338341e-10 1.5542041e-09 + 300 4.896078 -6.5395941 -6.4718773 1067.85 1.2098274e-08 3.4564838e-10 1.9030041e-09 + 310 5.150715 -6.543116 -6.4718773 1061.5918 1.2184958e-08 4.2383299e-10 1.6691938e-09 + 320 5.3590742 -6.5459978 -6.4718773 1056.6189 1.2312948e-08 3.5194185e-10 1.340539e-09 + 330 5.5199009 -6.5482222 -6.4718773 1052.9565 1.2573918e-08 4.2401322e-10 1.6425443e-09 + 340 5.6340787 -6.5498013 -6.4718773 1050.5719 1.2821551e-08 5.8802825e-10 1.9791699e-09 + 350 5.7043792 -6.5507736 -6.4718772 1049.3813 1.3067314e-08 4.0014945e-10 1.0305017e-09 + 360 5.7351548 -6.5511992 -6.4718772 1049.2581 1.331283e-08 4.1684815e-10 1.3051661e-09 + 370 5.7319891 -6.5511553 -6.4718771 1050.042 1.354018e-08 3.8495426e-10 1.5606716e-09 + 380 5.7013193 -6.5507311 -6.4718771 1051.5496 1.3734888e-08 3.5333605e-10 1.6933716e-09 + 390 5.6500487 -6.5500219 -6.471877 1053.5847 1.3892287e-08 3.8154957e-10 1.5483204e-09 + 400 5.5851679 -6.5491245 -6.471877 1055.9489 1.3988171e-08 5.8769536e-10 1.860034e-09 + 410 5.5134009 -6.5481319 -6.4718769 1058.4508 1.4088779e-08 3.6754739e-10 3.0708184e-09 + 420 5.4408957 -6.547129 -6.4718769 1060.9152 1.4139924e-08 4.9030281e-10 2.8908455e-09 + 430 5.3729707 -6.5461895 -6.4718768 1063.1898 1.4173041e-08 5.2345074e-10 1.9816809e-09 + 440 5.3139284 -6.5453729 -6.4718768 1065.1506 1.4191516e-08 5.9481094e-10 1.6654998e-09 + 450 5.2669383 -6.5447229 -6.4718768 1066.7054 1.4168424e-08 3.0799668e-10 2.0838273e-09 + 460 5.2339881 -6.5442672 -6.4718768 1067.7958 1.4163444e-08 6.3927736e-10 2.7292416e-09 + 470 5.2158979 -6.544017 -6.4718768 1068.3968 1.413819e-08 5.5108262e-10 1.3969622e-09 + 480 5.2123873 -6.5439685 -6.4718768 1068.5155 1.4083227e-08 3.9249548e-10 1.6717922e-09 + 490 5.2221849 -6.544104 -6.4718768 1068.188 1.4035287e-08 2.1988631e-10 1.75155e-09 + 500 5.2431716 -6.5443943 -6.4718768 1067.4759 1.3968666e-08 3.9100701e-10 1.9215444e-09 +Loop time of 0.169723 on 4 procs for 500 steps with 108 atoms + +Performance: 254.532 ns/day, 0.094 hours/ns, 2945.973 timesteps/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0012438 | 0.0014032 | 0.0015571 | 0.4 | 0.83 +Neigh | 0.0048166 | 0.0051267 | 0.0054319 | 0.4 | 3.02 +Comm | 0.0075482 | 0.0081723 | 0.0087409 | 0.6 | 4.82 +Output | 0.0081869 | 0.0082763 | 0.0085015 | 0.1 | 4.88 +Modify | 0.14635 | 0.14641 | 0.14646 | 0.0 | 86.26 +Other | | 0.0003391 | | | 0.20 + +Nlocal: 27 ave 31 max 24 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Nghost: 135 ave 138 max 131 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Neighs: 162 ave 191 max 148 min +Histogram: 1 2 0 0 0 0 0 0 0 1 + +Total # of neighbors = 648 +Ave neighs/atom = 6 +Neighbor list builds = 500 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/numdiff/log.28Jan2022.log.numdiff.g++.1 b/examples/numdiff/log.28Jan2022.log.numdiff.g++.1 deleted file mode 100644 index f32e72834f..0000000000 --- a/examples/numdiff/log.28Jan2022.log.numdiff.g++.1 +++ /dev/null @@ -1,175 +0,0 @@ -LAMMPS (7 Jan 2022) -# Numerical difference calculation -# of error in forces and virial stress - -# adjustable parameters - -variable nsteps index 500 # length of run -variable nthermo index 10 # thermo output interval -variable ndump index 500 # dump output interval -variable nlat index 3 # size of box -variable fdelta index 1.0e-4 # displacement size -variable vdelta index 1.0e-6 # strain size -variable temp index 10.0 # temperature - -units metal -atom_style atomic - -atom_modify map yes -lattice fcc 5.358000 -Lattice spacing in x,y,z = 5.358 5.358 5.358 -region box block 0 ${nlat} 0 ${nlat} 0 ${nlat} -region box block 0 3 0 ${nlat} 0 ${nlat} -region box block 0 3 0 3 0 ${nlat} -region box block 0 3 0 3 0 3 -create_box 1 box -Created orthogonal box = (0 0 0) to (16.074 16.074 16.074) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 108 atoms - using lattice units in orthogonal box = (0 0 0) to (16.074 16.074 16.074) - create_atoms CPU = 0.000 seconds -mass 1 39.903 - -velocity all create ${temp} 2357 mom yes dist gaussian -velocity all create 10.0 2357 mom yes dist gaussian - -pair_style lj/cubic -pair_coeff * * 0.0102701 3.42 - -neighbor 0.0 bin -neigh_modify every 1 delay 0 check no - -timestep 0.001 -fix nve all nve - -# define numerical force calculation - -fix numforce all numdiff ${nthermo} ${fdelta} -fix numforce all numdiff 10 ${fdelta} -fix numforce all numdiff 10 1.0e-4 -variable ferrx atom f_numforce[1]-fx -variable ferry atom f_numforce[2]-fy -variable ferrz atom f_numforce[3]-fz -variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2 -compute faverrsq all reduce ave v_ferrsq -variable fsq atom fx^2+fy^2+fz^2 -compute favsq all reduce ave v_fsq -variable frelerr equal sqrt(c_faverrsq/c_favsq) -dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz -dump errors all custom 500 force_error.dump v_ferrx v_ferry v_ferrz - -# define numerical virial stress tensor calculation - -compute myvirial all pressure NULL virial -fix numvirial all numdiff/virial ${nthermo} ${vdelta} -fix numvirial all numdiff/virial 10 ${vdelta} -fix numvirial all numdiff/virial 10 1.0e-6 -variable errxx equal f_numvirial[1]-c_myvirial[1] -variable erryy equal f_numvirial[2]-c_myvirial[2] -variable errzz equal f_numvirial[3]-c_myvirial[3] -variable erryz equal f_numvirial[4]-c_myvirial[6] -variable errxz equal f_numvirial[5]-c_myvirial[5] -variable errxy equal f_numvirial[6]-c_myvirial[4] -variable verrsq equal "v_errxx^2 + v_erryy^2 + v_errzz^2 + v_erryz^2 + v_errxz^2 + v_errxy^2" -variable vsq equal "c_myvirial[1]^2 + c_myvirial[3]^2 + c_myvirial[3]^2 + c_myvirial[4]^2 + c_myvirial[5]^2 + c_myvirial[6]^2" -variable vrelerr equal sqrt(v_verrsq/v_vsq) - -thermo_style custom step temp pe etotal press v_frelerr v_vrelerr -thermo ${nthermo} -thermo 10 -run ${nsteps} -run 500 - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 5.9407173 - ghost atom cutoff = 5.9407173 - binsize = 2.9703587, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cubic, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.083 | 6.083 | 6.083 Mbytes -Step Temp PotEng TotEng Press v_frelerr v_vrelerr - 0 10 -7.0259569 -6.8876486 28.564278 19203.344 1.5660292e-06 - 10 9.9376583 -7.0250947 -6.8876486 30.254762 1.5040965e-08 2.1991382e-07 - 20 9.7520139 -7.022527 -6.8876485 35.28505 1.4756358e-08 2.6265315e-06 - 30 9.4477557 -7.0183188 -6.8876485 43.519863 1.4688198e-08 2.6356166e-07 - 40 9.0330215 -7.0125826 -6.8876484 54.727797 1.4637921e-08 5.2292327e-08 - 50 8.5192918 -7.0054772 -6.8876483 68.585553 1.4587854e-08 7.1324716e-08 - 60 7.9212026 -6.997205 -6.8876481 84.684636 1.4525561e-08 3.1108149e-08 - 70 7.2562592 -6.9880081 -6.8876479 102.54088 1.450885e-08 3.2311094e-08 - 80 6.5444294 -6.9781627 -6.8876478 121.60715 1.4444738e-08 2.1776998e-08 - 90 5.8075961 -6.9679715 -6.8876476 141.2895 1.4493562e-08 2.0400898e-08 - 100 5.0688629 -6.957754 -6.8876474 160.9668 1.445455e-08 1.2636688e-08 - 110 4.3517145 -6.947835 -6.8876472 180.0135 1.4460371e-08 1.2528038e-08 - 120 3.6790589 -6.9385314 -6.887647 197.82486 1.4371757e-08 1.4489522e-08 - 130 3.0721984 -6.9301379 -6.8876468 213.84331 1.4364708e-08 1.2461922e-08 - 140 2.5497991 -6.9229125 -6.8876467 227.58429 1.4330926e-08 9.3913926e-09 - 150 2.1269443 -6.917064 -6.8876466 238.6596 1.4287002e-08 4.1510266e-09 - 160 1.8143642 -6.9127407 -6.8876465 246.79599 1.4282669e-08 7.7048281e-09 - 170 1.6179191 -6.9100237 -6.8876465 251.84748 1.42726e-08 1.2719973e-08 - 180 1.5383946 -6.9089239 -6.8876466 253.79991 1.4236534e-08 8.1200831e-09 - 190 1.5716287 -6.9093836 -6.8876467 252.76745 1.41706e-08 6.5670612e-09 - 200 1.7089493 -6.911283 -6.8876468 248.98142 1.4096463e-08 1.1685863e-08 - 210 1.9378716 -6.9144493 -6.8876469 242.77289 1.4008978e-08 1.1226902e-08 - 220 2.2429731 -6.9186692 -6.887647 234.55055 1.3886901e-08 9.9914102e-09 - 230 2.606862 -6.9237023 -6.8876472 224.77626 1.3864576e-08 1.1540228e-08 - 240 3.0111524 -6.9292941 -6.8876474 213.93996 1.3696314e-08 1.1697747e-08 - 250 3.4373794 -6.9351893 -6.8876475 202.53583 1.3626701e-08 1.0398197e-08 - 260 3.8678047 -6.9411426 -6.8876476 191.04084 1.3489489e-08 6.6603364e-09 - 270 4.2860853 -6.9469279 -6.8876478 179.89646 1.3312014e-08 1.1687917e-08 - 280 4.6777954 -6.9523457 -6.8876479 169.49404 1.3081144e-08 1.1336675e-08 - 290 5.030805 -6.9572282 -6.887648 160.16371 1.2947385e-08 1.7342825e-08 - 300 5.3355278 -6.9614428 -6.887648 152.16682 1.2893673e-08 1.7510534e-08 - 310 5.5850532 -6.964894 -6.887648 145.69148 1.2842022e-08 1.2782546e-08 - 320 5.7751794 -6.9675236 -6.8876481 140.85102 1.2903488e-08 1.5319437e-08 - 330 5.9043601 -6.9693103 -6.887648 137.68497 1.3076809e-08 1.1208999e-08 - 340 5.9735784 -6.9702676 -6.887648 136.16232 1.3296904e-08 1.891087e-08 - 350 5.9861549 -6.9704415 -6.887648 136.18679 1.3504051e-08 2.5783601e-08 - 360 5.947496 -6.9699067 -6.8876479 137.60397 1.3731112e-08 2.0556839e-08 - 370 5.8647874 -6.9687627 -6.8876478 140.2101 1.4009878e-08 2.1771736e-08 - 380 5.7466376 -6.9671285 -6.8876477 143.76234 1.4092054e-08 1.1085162e-08 - 390 5.6026773 -6.9651374 -6.8876477 147.99019 1.4282872e-08 2.0221602e-08 - 400 5.4431231 -6.9629305 -6.8876476 152.60787 1.4317739e-08 1.7076065e-08 - 410 5.2783192 -6.960651 -6.8876475 157.32722 1.4415075e-08 2.5031776e-08 - 420 5.1182723 -6.9584374 -6.8876474 161.87063 1.4441435e-08 2.2519289e-08 - 430 4.9722 -6.956417 -6.8876473 165.98344 1.4550624e-08 2.4512613e-08 - 440 4.8481153 -6.9547008 -6.8876473 169.44527 1.4544672e-08 1.4758301e-08 - 450 4.7524707 -6.9533779 -6.8876472 172.07964 1.4546492e-08 1.324687e-08 - 460 4.6898817 -6.9525122 -6.8876472 173.76132 1.4537475e-08 1.351367e-08 - 470 4.6629495 -6.9521397 -6.8876472 174.42109 1.4530458e-08 1.521106e-08 - 480 4.6721922 -6.9522675 -6.8876472 174.04742 1.4543785e-08 1.0905422e-08 - 490 4.7160887 -6.9528747 -6.8876473 172.68525 1.4545591e-08 2.0128525e-08 - 500 4.7912313 -6.953914 -6.8876473 170.43183 1.4438981e-08 1.6062775e-08 -Loop time of 0.837333 on 1 procs for 500 steps with 108 atoms - -Performance: 51.592 ns/day, 0.465 hours/ns, 597.134 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0097726 | 0.0097726 | 0.0097726 | 0.0 | 1.17 -Neigh | 0.03095 | 0.03095 | 0.03095 | 0.0 | 3.70 -Comm | 0.005564 | 0.005564 | 0.005564 | 0.0 | 0.66 -Output | 0.0042451 | 0.0042451 | 0.0042451 | 0.0 | 0.51 -Modify | 0.78618 | 0.78618 | 0.78618 | 0.0 | 93.89 -Other | | 0.0006258 | | | 0.07 - -Nlocal: 108 ave 108 max 108 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 558 ave 558 max 558 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 972 ave 972 max 972 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 972 -Ave neighs/atom = 9 -Neighbor list builds = 500 -Dangerous builds not checked -Total wall time: 0:00:00 diff --git a/examples/numdiff/log.28Jan2022.log.numdiff.g++.4 b/examples/numdiff/log.28Jan2022.log.numdiff.g++.4 deleted file mode 100644 index fc56c4aee8..0000000000 --- a/examples/numdiff/log.28Jan2022.log.numdiff.g++.4 +++ /dev/null @@ -1,175 +0,0 @@ -LAMMPS (7 Jan 2022) -# Numerical difference calculation -# of error in forces and virial stress - -# adjustable parameters - -variable nsteps index 500 # length of run -variable nthermo index 10 # thermo output interval -variable ndump index 500 # dump output interval -variable nlat index 3 # size of box -variable fdelta index 1.0e-4 # displacement size -variable vdelta index 1.0e-6 # strain size -variable temp index 10.0 # temperature - -units metal -atom_style atomic - -atom_modify map yes -lattice fcc 5.358000 -Lattice spacing in x,y,z = 5.358 5.358 5.358 -region box block 0 ${nlat} 0 ${nlat} 0 ${nlat} -region box block 0 3 0 ${nlat} 0 ${nlat} -region box block 0 3 0 3 0 ${nlat} -region box block 0 3 0 3 0 3 -create_box 1 box -Created orthogonal box = (0 0 0) to (16.074 16.074 16.074) - 1 by 2 by 2 MPI processor grid -create_atoms 1 box -Created 108 atoms - using lattice units in orthogonal box = (0 0 0) to (16.074 16.074 16.074) - create_atoms CPU = 0.000 seconds -mass 1 39.903 - -velocity all create ${temp} 2357 mom yes dist gaussian -velocity all create 10.0 2357 mom yes dist gaussian - -pair_style lj/cubic -pair_coeff * * 0.0102701 3.42 - -neighbor 0.0 bin -neigh_modify every 1 delay 0 check no - -timestep 0.001 -fix nve all nve - -# define numerical force calculation - -fix numforce all numdiff ${nthermo} ${fdelta} -fix numforce all numdiff 10 ${fdelta} -fix numforce all numdiff 10 1.0e-4 -variable ferrx atom f_numforce[1]-fx -variable ferry atom f_numforce[2]-fy -variable ferrz atom f_numforce[3]-fz -variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2 -compute faverrsq all reduce ave v_ferrsq -variable fsq atom fx^2+fy^2+fz^2 -compute favsq all reduce ave v_fsq -variable frelerr equal sqrt(c_faverrsq/c_favsq) -dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz -dump errors all custom 500 force_error.dump v_ferrx v_ferry v_ferrz - -# define numerical virial stress tensor calculation - -compute myvirial all pressure NULL virial -fix numvirial all numdiff/virial ${nthermo} ${vdelta} -fix numvirial all numdiff/virial 10 ${vdelta} -fix numvirial all numdiff/virial 10 1.0e-6 -variable errxx equal f_numvirial[1]-c_myvirial[1] -variable erryy equal f_numvirial[2]-c_myvirial[2] -variable errzz equal f_numvirial[3]-c_myvirial[3] -variable erryz equal f_numvirial[4]-c_myvirial[6] -variable errxz equal f_numvirial[5]-c_myvirial[5] -variable errxy equal f_numvirial[6]-c_myvirial[4] -variable verrsq equal "v_errxx^2 + v_erryy^2 + v_errzz^2 + v_erryz^2 + v_errxz^2 + v_errxy^2" -variable vsq equal "c_myvirial[1]^2 + c_myvirial[3]^2 + c_myvirial[3]^2 + c_myvirial[4]^2 + c_myvirial[5]^2 + c_myvirial[6]^2" -variable vrelerr equal sqrt(v_verrsq/v_vsq) - -thermo_style custom step temp pe etotal press v_frelerr v_vrelerr -thermo ${nthermo} -thermo 10 -run ${nsteps} -run 500 - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 5.9407173 - ghost atom cutoff = 5.9407173 - binsize = 2.9703587, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cubic, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.067 | 6.067 | 6.067 Mbytes -Step Temp PotEng TotEng Press v_frelerr v_vrelerr - 0 10 -7.0259569 -6.8876486 28.564278 10664.391 9.1481187e-08 - 10 9.9388179 -7.0251107 -6.8876486 30.21736 1.4771865e-08 1.3452512e-07 - 20 9.7572185 -7.022599 -6.8876485 35.123527 1.437525e-08 8.0966999e-07 - 30 9.4606673 -7.0184974 -6.8876484 43.132052 1.4375468e-08 1.990012e-08 - 40 9.0579092 -7.0129268 -6.8876483 54.000927 1.4350331e-08 1.7239028e-08 - 50 8.5607685 -7.0060508 -6.8876482 67.403151 1.4353284e-08 7.813181e-09 - 60 7.9838726 -6.9980717 -6.8876481 82.935358 1.4398078e-08 2.022316e-08 - 70 7.3442875 -6.9892255 -6.8876479 100.12892 1.434409e-08 7.5938179e-09 - 80 6.6610579 -6.9797757 -6.8876477 118.46358 1.4324787e-08 7.1972571e-09 - 90 5.9546462 -6.9700053 -6.8876476 137.38365 1.4322718e-08 4.3978378e-09 - 100 5.2462727 -6.9602077 -6.8876474 156.31651 1.4273172e-08 4.6728038e-09 - 110 4.5571706 -6.9506767 -6.8876472 174.69294 1.4266163e-08 3.522225e-09 - 120 3.9077807 -6.9416949 -6.887647 191.96859 1.42241e-08 3.5357511e-09 - 130 3.3169241 -6.9335227 -6.8876469 207.64566 1.4203813e-08 2.5182488e-09 - 140 2.8010028 -6.926387 -6.8876468 221.29333 1.4164215e-08 2.3112509e-09 - 150 2.3732854 -6.9204712 -6.8876467 232.5658 1.4134122e-08 1.9368963e-09 - 160 2.0433329 -6.9159076 -6.8876466 241.21647 1.4095473e-08 3.6806452e-09 - 170 1.8166184 -6.912772 -6.8876466 247.10715 1.4049531e-08 2.5319322e-09 - 180 1.6943727 -6.9110813 -6.8876467 250.21143 1.3997912e-08 1.952404e-09 - 190 1.6736731 -6.910795 -6.8876467 250.61203 1.3915487e-08 1.4271767e-09 - 200 1.7477659 -6.9118199 -6.8876468 248.49223 1.3850618e-08 2.4515718e-09 - 210 1.9065921 -6.9140167 -6.8876469 244.12226 1.3747916e-08 1.7957531e-09 - 220 2.1374676 -6.91721 -6.887647 237.84173 1.3674779e-08 2.6613511e-09 - 230 2.4258607 -6.9211989 -6.8876472 230.0395 1.3565712e-08 3.0777067e-09 - 240 2.7562034 -6.9257679 -6.8876473 221.13265 1.3440442e-08 1.7111501e-09 - 250 3.1126827 -6.9306984 -6.8876474 211.54566 1.3270914e-08 1.6690112e-09 - 260 3.4799641 -6.9357784 -6.8876476 201.69126 1.3105092e-08 2.1637558e-09 - 270 3.8438148 -6.9408108 -6.8876477 191.95361 1.2962846e-08 4.4613506e-09 - 280 4.191607 -6.9456212 -6.8876478 182.6745 1.2846383e-08 3.3730203e-09 - 290 4.5126922 -6.9500621 -6.8876478 174.14285 1.2710692e-08 2.2809889e-09 - 300 4.7986487 -6.9540172 -6.8876479 166.58747 1.2657778e-08 6.9880891e-09 - 310 5.0434083 -6.9574025 -6.8876479 160.17316 1.266381e-08 4.2486217e-09 - 320 5.243275 -6.9601668 -6.8876479 154.99974 1.279856e-08 5.1505673e-09 - 330 5.3968455 -6.9622908 -6.8876479 151.1038 1.2981831e-08 3.3339333e-09 - 340 5.5048468 -6.9637845 -6.8876479 148.46296 1.3159021e-08 1.7881393e-09 - 350 5.569902 -6.9646843 -6.8876479 147.00205 1.3439465e-08 5.6876219e-09 - 360 5.5962378 -6.9650485 -6.8876478 146.60113 1.3645943e-08 7.233847e-09 - 370 5.5893468 -6.9649531 -6.8876478 147.10471 1.3829581e-08 4.5514318e-09 - 380 5.5556199 -6.9644866 -6.8876477 148.33195 1.4005893e-08 4.2971846e-09 - 390 5.5019639 -6.9637444 -6.8876476 150.08725 1.4157454e-08 3.3564262e-09 - 400 5.4354239 -6.962824 -6.8876476 152.17073 1.4226422e-08 4.2393923e-09 - 410 5.3628267 -6.9618199 -6.8876475 154.38825 1.4302679e-08 3.8937698e-09 - 420 5.2904639 -6.960819 -6.8876475 156.56034 1.4381099e-08 4.315875e-09 - 430 5.2238282 -6.9598973 -6.8876474 158.52969 1.4426567e-08 4.2658185e-09 - 440 5.1674149 -6.9591171 -6.8876474 160.16704 1.4453381e-08 5.7055268e-09 - 450 5.1245913 -6.9585248 -6.8876474 161.37513 1.4449488e-08 4.4308801e-09 - 460 5.0975361 -6.9581506 -6.8876474 162.09077 1.4445596e-08 5.8269923e-09 - 470 5.0872416 -6.9580082 -6.8876474 162.28517 1.4444348e-08 4.8263194e-09 - 480 5.0935712 -6.9580957 -6.8876474 161.96268 1.4411666e-08 6.222228e-09 - 490 5.115362 -6.9583971 -6.8876474 161.15816 1.4369716e-08 3.3926077e-09 - 500 5.1505605 -6.958884 -6.8876474 159.9333 1.4288515e-08 3.8845251e-09 -Loop time of 0.252598 on 4 procs for 500 steps with 108 atoms - -Performance: 171.023 ns/day, 0.140 hours/ns, 1979.430 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0021545 | 0.0022845 | 0.0023794 | 0.2 | 0.90 -Neigh | 0.0063887 | 0.0067604 | 0.0069752 | 0.3 | 2.68 -Comm | 0.01048 | 0.010916 | 0.011408 | 0.3 | 4.32 -Output | 0.0026603 | 0.0027399 | 0.0029738 | 0.3 | 1.08 -Modify | 0.2295 | 0.22952 | 0.22954 | 0.0 | 90.86 -Other | | 0.0003814 | | | 0.15 - -Nlocal: 27 ave 29 max 25 min -Histogram: 1 0 1 0 0 0 0 1 0 1 -Nghost: 325 ave 327 max 323 min -Histogram: 1 0 1 0 0 0 0 1 0 1 -Neighs: 243 ave 273 max 228 min -Histogram: 1 1 1 0 0 0 0 0 0 1 - -Total # of neighbors = 972 -Ave neighs/atom = 9 -Neighbor list builds = 500 -Dangerous builds not checked -Total wall time: 0:00:00