Shortened simulation lengths and add reference log output

Author: athomps

examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/in.ljcov

@@ -10,7 +10,7 @@
 # adjustable parameters
 
 units           real
-variable        nsteps index 100000    # length of run
+variable        nsteps index 10000     # length of run
 variable        nthermo index  1000    # thermo output interval 
 variable        nlat equal 5           # size of box
 variable        T    equal 60.         # Temperature in K
@@ -39,7 +39,7 @@ thermo 100
 fix aL all ave/time 1 1 1 v_vol ave running
 fix NPT all npt temp $T $T 100 aniso 1. 1. 1000 fixedpoint 0. 0. 0.
 
-run 20000
+run 2000
 
 unfix NPT
 

examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/log.22Nov25.elastic.g++.1

@@ -0,0 +1,353 @@
+LAMMPS (10 Sep 2025 - Development - patch_10Sep2025-520-gd2199aa57b-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread.
+  using 1 OpenMP thread(s) per MPI task
+# Analytical calculation
+# of Born matrix
+
+# Note that because of cubic symmetry and central forces, we have:
+# C11, pure axial == positive mean value: 1,2,3
+# C44==C23, pure shear == positive mean value, exactly match in pairs: (4,12),(5,8),(6,7)
+# C14==C56, shear/axial(normal) == zero mean, exactly match in pairs: (9,21),(14,20),(18,19)
+# C15, shear/axial(in-plane) == zero mean: 10,11,13,15,16,17
+
+# adjustable parameters
+
+units           real
+variable        nsteps index 10000     # length of run
+variable        nthermo index  1000    # thermo output interval
+variable        nlat equal 5           # size of box
+variable        T    equal 60.         # Temperature in K
+variable        rho  equal 5.405       # Lattice spacing in A
+
+atom_style      atomic
+
+lattice         fcc ${rho}
+lattice         fcc 5.405
+Lattice spacing in x,y,z = 5.405 5.405 5.405
+region          box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
+region          box block 0 5 0 ${nlat} 0 ${nlat}
+region          box block 0 5 0 5 0 ${nlat}
+region          box block 0 5 0 5 0 5
+create_box      1 box
+Created orthogonal box = (0 0 0) to (27.025 27.025 27.025)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (27.025 27.025 27.025)
+  create_atoms CPU = 0.000 seconds
+
+mass            * 39.948
+
+velocity        all create ${T} 87287 loop geom
+velocity        all create 60 87287 loop geom
+velocity        all zero linear
+
+pair_style      lj/cut 12.0
+pair_coeff      1 1 0.238067 3.405
+
+neighbor        0.0 bin
+neigh_modify    every 1 delay 0 check no
+
+variable vol equal vol
+thermo 100
+fix aL all ave/time 1 1 1 v_vol ave running
+fix NPT all npt temp $T $T 100 aniso 1. 1. 1000 fixedpoint 0. 0. 0.
+fix NPT all npt temp 60 $T 100 aniso 1. 1. 1000 fixedpoint 0. 0. 0.
+fix NPT all npt temp 60 60 100 aniso 1. 1. 1000 fixedpoint 0. 0. 0.
+
+run 2000
+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 = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, 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) = 2.695 | 2.695 | 2.695 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press          Volume    
+         0   60            -974.97988      0             -885.73443     -1549.5634      19737.726    
+       100   33.504753     -943.70789      0             -893.87211      968.3116       18369.007    
+       200   26.32504      -930.72444      0             -891.56794      314.3869       18935.888    
+       300   41.132299     -931.36826      0             -870.18708     -617.04719      19632.688    
+       400   41.183387     -912.49497      0             -851.2378       485.3659       19105.509    
+       500   57.063649     -914.95616      0             -830.07831      10.213449      19451.639    
+       600   57.720228     -897.82416      0             -811.96969     -122.66415      19794.9      
+       700   55.117494     -878.27174      0             -796.28864      169.40743      19853.365    
+       800   65.753909     -877.79094      0             -779.98698     -140.35502      20145.428    
+       900   61.5708       -870.58334      0             -779.00144     -6.2782272      20132.09     
+      1000   59.71058      -873.44425      0             -784.62929      18.589753      20063.414    
+      1100   59.887921     -878.67927      0             -789.60053     -53.049476      20034.152    
+      1200   59.121142     -881.97593      0             -794.03771      31.110495      19909.638    
+      1300   60.931065     -887.19784      0             -796.5675       6.5972135      19859.309    
+      1400   60.086091     -890.68151      0             -801.308       -26.605388      19827.013    
+      1500   58.240958     -892.81245      0             -806.18344      32.781814      19743.494    
+      1600   59.997061     -896.10853      0             -806.86745      1.8694388      19731.408    
+      1700   62.500416     -900.56177      0             -807.59714     -58.405946      19717.51     
+      1800   60.950957     -905.28688      0             -814.62695      13.287333      19580.499    
+      1900   57.643425     -908.35702      0             -822.61679      80.300088      19476.931    
+      2000   54.860033     -904.52282      0             -822.92268      28.955012      19564.956    
+Loop time of 3.77963 on 1 procs for 2000 steps with 500 atoms
+
+Performance: 45.719 ns/day, 0.525 hours/ns, 529.153 timesteps/s, 264.576 katom-step/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.4902     | 1.4902     | 1.4902     |   0.0 | 39.43
+Neigh   | 2.1869     | 2.1869     | 2.1869     |   0.0 | 57.86
+Comm    | 0.062232   | 0.062232   | 0.062232   |   0.0 |  1.65
+Output  | 0.00039628 | 0.00039628 | 0.00039628 |   0.0 |  0.01
+Modify  | 0.030281   | 0.030281   | 0.030281   |   0.0 |  0.80
+Other   |            | 0.009542   |            |       |  0.25
+
+Nlocal:            500 ave         500 max         500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           2930 ave        2930 max        2930 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          46401 ave       46401 max       46401 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 46401
+Ave neighs/atom = 92.802
+Neighbor list builds = 2000
+Dangerous builds not checked
+
+unfix NPT
+
+variable newL equal "f_aL^(1./3.)"
+change_box all x final 0 ${newL} y final 0. ${newL} z final 0. ${newL} remap units box
+change_box all x final 0 26.9850129540338 y final 0. ${newL} z final 0. ${newL} remap units box
+change_box all x final 0 26.9850129540338 y final 0. 26.9850129540338 z final 0. ${newL} remap units box
+change_box all x final 0 26.9850129540338 y final 0. 26.9850129540338 z final 0. 26.9850129540338 remap units box
+Changing box ...
+  orthogonal box = (0 0 0) to (26.985013 26.94049 27.008247)
+  orthogonal box = (0 0 0) to (26.985013 26.985013 27.008247)
+  orthogonal box = (0 0 0) to (26.985013 26.985013 26.985013)
+
+unfix aL
+
+reset_timestep 0
+
+# Conversion variables
+variable kb        equal 1.38065e-23    # J/K
+variable Myvol     equal "vol*10^-30" # Volume in m^3
+variable kbt       equal "v_kb*v_T"
+variable Nat       equal atoms
+variable Rhokbt    equal "v_kbt*v_Nat/v_Myvol"
+variable at2Pa     equal 101325
+variable kcalmol2J equal "4183.9954/(6.022e23)"
+variable C1        equal "v_kcalmol2J/v_Myvol" # Convert Cb from energy to pressure units
+variable C2        equal "v_Myvol/v_kbt"       # Factor for Cfl terms
+variable Pa2GPa    equal 1e-9
+
+# Born compute giving <C^b> terms
+compute     born all born/matrix
+# The six virial stress component to compute <C^fl>
+compute     VIR all pressure NULL virial
+variable s1 equal "-c_VIR[1]*v_at2Pa"
+variable s2 equal "-c_VIR[2]*v_at2Pa"
+variable s3 equal "-c_VIR[3]*v_at2Pa"
+variable s6 equal "-c_VIR[4]*v_at2Pa"
+variable s5 equal "-c_VIR[5]*v_at2Pa"
+variable s4 equal "-c_VIR[6]*v_at2Pa"
+variable press equal press
+
+
+# Average of Born term and vector to store stress
+# for post processing
+fix CB all ave/time 1 ${nthermo} ${nthermo} c_born[*] ave running file born.out overwrite
+fix CB all ave/time 1 1000 ${nthermo} c_born[*] ave running file born.out overwrite
+fix CB all ave/time 1 1000 1000 c_born[*] ave running file born.out overwrite
+fix CPR all ave/time 1 1 1 c_VIR[*] file vir.out
+fix APR all ave/time 1 1 1 v_press ave running
+fix VEC all vector 1 v_s1 v_s2 v_s3 v_s4 v_s5 v_s6
+
+thermo      ${nthermo}
+thermo      1000
+thermo_style    custom step temp press f_APR c_born[1] f_CB[1] c_born[12] f_CB[12] c_born[4] f_CB[4]
+thermo_modify line multi
+
+fix     1 all nvt temp $T $T 100
+fix     1 all nvt temp 60 $T 100
+fix     1 all nvt temp 60 60 100
+
+run         ${nsteps}
+run         10000
+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 = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  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
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.326 | 3.326 | 3.326 Mbytes
+------------ Step              0 ----- CPU =            0 (sec) -------------
+Step     =              0 Temp     =        54.8600 Press    =       -74.9874 
+f_APR    =       -74.9874 c_born[1] =      9269.2848 f_CB[1]  =         0.0000 
+c_born[12] =      5315.9657 f_CB[12] =         0.0000 c_born[4] =      5315.9657 
+f_CB[4]  =         0.0000
+------------ Step           1000 ----- CPU =     9.120759 (sec) -------------
+Step     =           1000 Temp     =        56.1005 Press    =        93.2723 
+f_APR    =       104.8993 c_born[1] =      9899.7837 f_CB[1]  =      9738.6101 
+c_born[12] =      5515.1091 f_CB[12] =      5497.0605 c_born[4] =      5515.1091 
+f_CB[4]  =      5497.0605
+------------ Step           2000 ----- CPU =     18.76019 (sec) -------------
+Step     =           2000 Temp     =        59.2245 Press    =       164.2019 
+f_APR    =        90.3569 c_born[1] =     10127.7921 f_CB[1]  =      9762.5811 
+c_born[12] =      5582.5570 f_CB[12] =      5512.1775 c_born[4] =      5582.5570 
+f_CB[4]  =      5512.1775
+------------ Step           3000 ----- CPU =     27.88892 (sec) -------------
+Step     =           3000 Temp     =        62.3421 Press    =       138.9920 
+f_APR    =       103.8105 c_born[1] =      9784.0632 f_CB[1]  =      9805.4617 
+c_born[12] =      5558.8869 f_CB[12] =      5514.3234 c_born[4] =      5558.8869 
+f_CB[4]  =      5514.3234
+------------ Step           4000 ----- CPU =     36.92665 (sec) -------------
+Step     =           4000 Temp     =        58.1487 Press    =       136.4624 
+f_APR    =       107.3823 c_born[1] =      9996.9126 f_CB[1]  =      9821.2552 
+c_born[12] =      5439.8328 f_CB[12] =      5518.8966 c_born[4] =      5439.8328 
+f_CB[4]  =      5518.8966
+------------ Step           5000 ----- CPU =     45.77529 (sec) -------------
+Step     =           5000 Temp     =        60.3351 Press    =       -21.9127 
+f_APR    =       101.0136 c_born[1] =      9631.2101 f_CB[1]  =      9798.9441 
+c_born[12] =      5352.0607 f_CB[12] =      5519.0345 c_born[4] =      5352.0607 
+f_CB[4]  =      5519.0345
+------------ Step           6000 ----- CPU =     54.63388 (sec) -------------
+Step     =           6000 Temp     =        57.7282 Press    =       157.6900 
+f_APR    =       100.3234 c_born[1] =     10030.8342 f_CB[1]  =      9800.1967 
+c_born[12] =      5740.8579 f_CB[12] =      5521.0716 c_born[4] =      5740.8579 
+f_CB[4]  =      5521.0716
+------------ Step           7000 ----- CPU =     63.63728 (sec) -------------
+Step     =           7000 Temp     =        59.5948 Press    =       135.9651 
+f_APR    =       101.9810 c_born[1] =     10058.4542 f_CB[1]  =      9817.6242 
+c_born[12] =      5511.2599 f_CB[12] =      5521.8274 c_born[4] =      5511.2599 
+f_CB[4]  =      5521.8274
+------------ Step           8000 ----- CPU =     73.14265 (sec) -------------
+Step     =           8000 Temp     =        61.7547 Press    =        41.1860 
+f_APR    =       105.3152 c_born[1] =      9554.9451 f_CB[1]  =      9830.6704 
+c_born[12] =      5292.0749 f_CB[12] =      5520.3055 c_born[4] =      5292.0749 
+f_CB[4]  =      5520.3055
+------------ Step           9000 ----- CPU =      82.2176 (sec) -------------
+Step     =           9000 Temp     =        59.2478 Press    =       146.6808 
+f_APR    =       104.7030 c_born[1] =      9860.2050 f_CB[1]  =      9823.1198 
+c_born[12] =      5543.4620 f_CB[12] =      5518.4889 c_born[4] =      5543.4620 
+f_CB[4]  =      5518.4889
+------------ Step          10000 ----- CPU =     91.68689 (sec) -------------
+Step     =          10000 Temp     =        59.4645 Press    =        96.1963 
+f_APR    =       107.2322 c_born[1] =      9779.2285 f_CB[1]  =      9836.0535 
+c_born[12] =      5617.0229 f_CB[12] =      5525.6584 c_born[4] =      5617.0229 
+f_CB[4]  =      5525.6584
+Loop time of 91.6869 on 1 procs for 10000 steps with 500 atoms
+
+Performance: 9.423 ns/day, 2.547 hours/ns, 109.067 timesteps/s, 54.533 katom-step/s
+99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.8446     | 7.8446     | 7.8446     |   0.0 |  8.56
+Neigh   | 11.559     | 11.559     | 11.559     |   0.0 | 12.61
+Comm    | 0.37942    | 0.37942    | 0.37942    |   0.0 |  0.41
+Output  | 0.047699   | 0.047699   | 0.047699   |   0.0 |  0.05
+Modify  | 71.807     | 71.807     | 71.807     |   0.0 | 78.32
+Other   |            | 0.04957    |            |       |  0.05
+
+Nlocal:            500 ave         500 max         500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           2930 ave        2930 max        2930 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          46195 ave       46195 max       46195 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:        92390 ave       92390 max       92390 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 92390
+Ave neighs/atom = 184.78
+Neighbor list builds = 10000
+Dangerous builds not checked
+
+# Compute vector averages
+# Note the indice switch.
+# LAMMPS convention is NOT the Voigt notation.
+variable aves1 equal "ave(f_VEC[1])"
+variable aves2 equal "ave(f_VEC[2])"
+variable aves3 equal "ave(f_VEC[3])"
+variable aves4 equal "ave(f_VEC[6])"
+variable aves5 equal "ave(f_VEC[5])"
+variable aves6 equal "ave(f_VEC[4])"
+
+# Computing the covariance through the <s_{i}s_{j}>-<s_i><s_j>
+# is numerically instable. Here we go through the <(s-<s>)^2>
+# definition.
+
+# Computing difference relative to average values
+variable ds1 vector "f_VEC[1]-v_aves1"
+variable ds2 vector "f_VEC[2]-v_aves2"
+variable ds3 vector "f_VEC[3]-v_aves3"
+variable ds4 vector "f_VEC[4]-v_aves4"
+variable ds5 vector "f_VEC[5]-v_aves5"
+variable ds6 vector "f_VEC[6]-v_aves6"
+
+# Squaring and averaging
+variable dds1 vector "v_ds1*v_ds1"
+variable dds2 vector "v_ds2*v_ds2"
+variable dds3 vector "v_ds3*v_ds3"
+variable vars1 equal "ave(v_dds1)"
+variable vars2 equal "ave(v_dds2)"
+variable vars3 equal "ave(v_dds3)"
+variable C11 equal "v_Pa2GPa*(v_C1*f_CB[1] - v_C2*v_vars1 + 2*v_Rhokbt)"
+variable C22 equal "v_Pa2GPa*(v_C1*f_CB[2] - v_C2*v_vars2 + 2*v_Rhokbt)"
+variable C33 equal "v_Pa2GPa*(v_C1*f_CB[3] - v_C2*v_vars3 + 2*v_Rhokbt)"
+
+variable dds12 vector "v_ds1*v_ds2"
+variable dds13 vector "v_ds1*v_ds3"
+variable dds23 vector "v_ds2*v_ds3"
+variable vars12 equal "ave(v_dds12)"
+variable vars13 equal "ave(v_dds13)"
+variable vars23 equal "ave(v_dds23)"
+variable C12 equal "v_Pa2GPa*(v_C1*f_CB[7] - v_C2*v_vars12)"
+variable C13 equal "v_Pa2GPa*(v_C1*f_CB[8] - v_C2*v_vars13)"
+variable C23 equal "v_Pa2GPa*(v_C1*f_CB[12] - v_C2*v_vars23)"
+
+variable dds4 vector "v_ds4*v_ds4"
+variable dds5 vector "v_ds5*v_ds5"
+variable dds6 vector "v_ds6*v_ds6"
+variable vars4 equal "ave(v_dds4)"
+variable vars5 equal "ave(v_dds5)"
+variable vars6 equal "ave(v_dds6)"
+variable C44 equal "v_Pa2GPa*(v_C1*f_CB[4] - v_C2*v_vars4 + v_Rhokbt)"
+variable C55 equal "v_Pa2GPa*(v_C1*f_CB[5] - v_C2*v_vars5 + v_Rhokbt)"
+variable C66 equal "v_Pa2GPa*(v_C1*f_CB[6] - v_C2*v_vars6 + v_Rhokbt)"
+
+variable aC11 equal "(v_C11 + v_C22 + v_C33)/3."
+variable aC12 equal "(v_C12 + v_C13 + v_C23)/3."
+variable aC44 equal "(v_C44 + v_C55 + v_C66)/3."
+
+print """
+C11 = ${aC11}
+C12 = ${aC12}
+C44 = ${aC44}
+"""
+
+C11 = 2.43259565469463
+C12 = 1.31707509521887
+C44 = 1.46049163278008
+
+Total wall time: 0:01:35