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ATC (Atom To Continuum methods)
Reese Jones, Jeremy Templeton, Jonathan Zimmerman
rjones@sandia.gov
September 2009
--------------
This directory contains examples run using the AtC library in LAMMPS
in its various coupling and post-processing modes. Descriptions of
the files in each are provided below. In addition to the included
output these examples will "dump" mesh-based data either in binary
(Ensight) format or simple column-based text format (for gnuplot, for
example).
bar1d_thermal:
input files:
in.bar1d - Atoms comprise a subset of a 1D finite element bar,
heated at the left end and cooled at the right end.
A Gaussian isokinetic thermostat is used to keep the atomic
kinetic temperature equal to the finite element temperature
at the boundaries.
in.bar1d_flux - Same setup and geometry as in.bar1d.
A Gaussian isokinetic thermostat is used to transfer
the FE heat flux to the atoms at the boundaries.
Ar_thermal.mat - Material parameter file specifying
the thermal properties of argon.
temp.init - Initial set of atomic positions and velocities.
output files:
bar1d.log - LAMMPS log file generated by running in.bar1d.
bar1d_flux.log - LAMMPS log file generated by running in.bar1d_flux.
bar1d_two_temperature:
input files:
in.bar1d_ttm - Atoms comprise a subset of a 1D finite element bar,
with a high fixed electron temperature on the left end
and low fixed phonon and electron temperatures on the right end.
A Gaussian isokinetic thermostat is used to transfer energy
from the electron temperature field to the atoms.
in.gaussianIC_ttm - Atoms fully overlap an FE mesh with an initially
elevated electron temperature having a Gaussian distribution.
in.no_atoms - Heating followed by relaxation is simulated on a FE mesh.
in.uniform_exchange - Electron and kinetic temperatures are initially
spatially uniform but out of equilibrium, followed by relaxation.
in.uniform_heating - Initially equal electron and kinetic temperatures
are subjected to heating of the kinetic temperature only. The kinetic
temperature is fixed at both ends while the electrons are insulated.
Ar_ttm.mat - Material parameter file specifying
the kinetic and electric thermal properties of argon.
Cu_ttm.mat - Material parameter file specifying
the kinetic and electric thermal properties of copper.
temp.init - Initial set of atomic positions and velocities for most cases.
uniform_exchange_init.data - Initial set of atomic positions and velocities
for in.uniform_exchange
uniform_heating_init.data - Initial set of atomic positions and velocities
for in.uniform_heating
output files:
bar1d_ttm.log - LAMMPS log file generated by running in.bar1d_ttm.
gaussianIC_ttm.log - log file generated by running in.gaussianIC_ttm.
no_atoms.log - LAMMPS log file generated by running in.no_atoms.
uniform_exchange.log - log file generated by running in.uniform_exchange.
uniform_heating.log - LAMMPS log file generated by running in.uniform_heating.
hardy:
input files:
in.consistency - Small block of EAM Copper is used to confirm the
consistency between the atc calculations of 1st Piola-Kirchhoff (P-K)
stress, displacment gradient, and strain energy density for various
amounts of uniaxial strain.
in.eam_kernel_convergence - Block of EAM Gold is used to examine the
variation of the atc estimate of 1st P-K stress with size of localization
(averaging) volume. Volume is spherical, and kernel function
is quartic depending on radial distance from sphere center.
in.eam_unistrain_xxxx - Long block of EAM Copper is subjected to uniaxial
stretching and estimates of 1st P-K stress, energy density, displacement
and displacement gradient are calculated. The end-suffix denotes the
localization volume shape and kernel function type:
cell - 3D rectangular elements with step-functions at cell boundary
mesh - 3D rectangular elements with linear "tent" functions
qcylinder - cylindrical volume with quartic function dependent on
distance from cylinder axis
qsphere - spherical volume with quartic function dependent on
distance from sphere center
step - spherical volume with step-function at sphere boundary
in.eam_volume_stretch - Small block of EAM Copper is equitriaxially
stretched and estimates of 1st P-K stress, energy density, and mass
density are calculated.
in.nvt - Block of Lennard-Jones Argon is simulated at 30K for 1000 timesteps.
output files:
consistency.log - LAMMPS log file generated by running in.consistency
consistency.screen - Screen/console output generated by running
in.consistency
eam_kernel_convergence.log - LAMMPS log file generated by running
in.eam_kernel_convergence
eam_kernel_convergence.screen - Screen/console output generated by running
in.eam_kernel_convergence
eam_unistrain_xxxx.log - LAMMPS log file generated by running
in.eam_unistrain_xxxx
eam_unistrain_xxxx.screen - Screen/console output generated by running
in.eam_unistrain_xxxx ( xxxx = cell, mesh, qcylinder, qsphere, step )
eam_volume_stretch.log - LAMMPS log file generated by running
in.eam_volume_stretch
eam_volume_stretchscreen - Screen/console output generated by running
in.eam_volume_stretch
nvt.log - LAMMPS log file generated by running in.nvt
nvt.screen - Screen/console output generated by running in.nvt

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material Ar
heat_flux linear
conductivity .00000000168
end
end
material Ar2
heat_flux linear
conductivity .00000000316
end
end

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LAMMPS (7 Jul 2009)
#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
orthogonal box = (-27.025 -16.215 -16.215) to (27.025 16.215 16.215)
1 by 1 by 1 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
# ID part keywords nx ny nz region
#fix_modify AtC fem create mesh 12 2 2 simRegion f p p
fix_modify AtC fem create mesh 12 1 1 simRegion f p p
# specify atom types
#fix_modify AtC transfer internal type internal
fix_modify AtC transfer boundary type ghost
# fix a temperature
fix_modify AtC transfer fix temperature all 20.
# turn on thermostat
fix_modify AtC transfer thermal control rescale 10
# equilibrate MD field
#dump D1 all atom 100 dump.bar1d
#fix_modify AtC transfer 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
Memory usage per processor = 8.7506 Mbytes
Step CPU TotEng PotEng AtC[1] Temp AtC[2]
0 0 -2573.6428 -2710.8793 412.06718 39.965279 20
100 2.7 -2537.6764 -2606.3542 412.06718 20 20
200 5.5 -2584.8754 -2653.5532 412.06718 20 20
300 8.2 -2575.3126 -2643.9904 412.06718 20 20
400 11 -2573.4199 -2642.0977 412.06718 20 20
Loop time of 10.9925 on 1 procs for 400 steps with 1440 atoms
Pair time (%) = 4.30201 (39.1358)
Neigh time (%) = 1.867 (16.9842)
Comm time (%) = 0.0373757 (0.34001)
Outpt time (%) = 0.00606346 (0.0551598)
Other time (%) = 4.78008 (43.4848)
Nlocal: 1440 ave 1440 max 1440 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5320 ave 5320 max 5320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 419459 ave 419459 max 419459 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 838918 ave 838918 max 838918 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 838918
Ave neighs/atom = 582.582
Neighbor list builds = 40
Dangerous builds = 0
# change thermostat to hoover
fix_modify AtC transfer unfix temperature all
fix_modify AtC transfer thermal control hoover
fix_modify AtC transfer filter type exponential
fix_modify AtC transfer filter scale 10000.0
fix_modify AtC transfer filter on
fix_modify AtC transfer internal_quadrature off
# add nodesets
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -12 12 -12 12
fix_modify AtC transfer fix temperature lbc 40.
fix_modify AtC transfer fix temperature rbc 20.
# initialize filter
#thermo 1
run 100
Memory usage per processor = 8.97948 Mbytes
Step CPU TotEng PotEng AtC[1] Temp AtC[2]
400 0 -2573.4199 -2642.0977 274.71145 20 20
500 2.7 -2573.7738 -2643.7447 295.61002 20.376549 21.713472
Loop time of 2.67287 on 1 procs for 100 steps with 1440 atoms
Pair time (%) = 1.07427 (40.1917)
Neigh time (%) = 0.466434 (17.4507)
Comm time (%) = 0.00930166 (0.348003)
Outpt time (%) = 0.00103688 (0.0387928)
Other time (%) = 1.12183 (41.9709)
Nlocal: 1440 ave 1440 max 1440 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5320 ave 5320 max 5320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 419059 ave 419059 max 419059 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 838118 ave 838118 max 838118 min
Histogram: 1 0 0 0 0 0 0 0 0 0
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 transfer output bar1dFE 100 text
# ouput command
#dump D1 all atom 1000 dump.bar1d
fix_modify AtC transfer atomic_output bar1dMD 100
# run with FE
reset_timestep 0
thermo 100
run 10000
Memory usage per processor = 8.97948 Mbytes
Step CPU TotEng PotEng AtC[1] Temp AtC[2]
0 0 -2573.7738 -2643.7447 295.61002 20.376549 21.713472
100 2.7 -2573.654 -2645.0562 298.997 20.793359 21.86901
200 5.4 -2574.0035 -2642.057 302.05784 19.818184 22.007349
300 8 -2573.5186 -2646.5507 304.88852 21.268004 22.143129
400 11 -2573.2662 -2641.032 307.48549 19.734394 22.262531
500 13 -2573.5673 -2644.7553 309.92162 20.730998 22.376015
600 16 -2572.9368 -2641.5818 312.18796 19.990452 22.483808
700 19 -2573.2457 -2642.9406 314.3431 20.296183 22.586025
800 21 -2573.215 -2642.7311 316.37915 20.244129 22.681635
900 24 -2572.7227 -2643.5215 318.29866 20.617655 22.772405
1000 27 -2572.411 -2644.5969 320.08215 21.021606 22.85772
1100 29 -2571.4099 -2642.08 321.74721 20.580181 22.940424
1200 32 -2570.5495 -2641.7296 323.29152 20.728698 23.01806
1300 35 -2570.2491 -2640.8115 324.79381 20.548784 23.09183
1400 37 -2570.159 -2641.2853 326.14846 20.713008 23.158731
1500 40 -2569.5061 -2642.2055 327.46482 21.171117 23.230527
1600 43 -2568.7522 -2639.5246 328.68994 20.609988 23.295442
1700 45 -2569.1809 -2642.0975 329.85636 21.234392 23.355365
1800 48 -2568.7484 -2643.2103 330.95066 21.684387 23.414458
1900 51 -2568.258 -2641.5017 332.02069 21.329638 23.476702
2000 54 -2568.192 -2641.4646 333.04827 21.338079 23.534077
2100 56 -2568.0746 -2639.9335 334.04476 20.926349 23.588633
2200 59 -2567.2717 -2642.2868 334.99014 21.84549 23.639739
2300 62 -2566.7209 -2639.9022 335.89195 21.311463 23.692327
2400 64 -2566.6054 -2638.8118 336.73569 21.02756 23.743177
2500 67 -2565.7629 -2639.6423 337.51835 21.514764 23.792702
2600 70 -2565.9251 -2642.5797 338.26277 22.322947 23.837067
2700 72 -2564.9995 -2640.0503 339.00006 21.855897 23.885327
2800 75 -2565.2468 -2638.033 339.72187 21.196396 23.929976
2900 78 -2565.0496 -2639.4905 340.4486 21.678289 23.975728
3000 80 -2565.1382 -2637.5132 341.15766 21.076651 24.018275
3100 83 -2564.4793 -2636.786 341.85076 21.056788 24.060818
3200 86 -2564.1799 -2637.5024 342.51347 21.352563 24.105465
3300 88 -2564.4531 -2641.3463 343.13584 22.392438 24.145599
3400 91 -2564.2323 -2641.0072 343.75483 22.357976 24.184764
3500 94 -2563.378 -2635.3819 344.36945 20.968577 24.22365
3600 96 -2563.5014 -2637.8324 345.00242 21.646292 24.265399
3700 99 -2563.4092 -2638.0479 345.63031 21.73589 24.302306
3800 1e+02 -2563.0307 -2637.5397 346.23705 21.698125 24.340069
3900 1e+02 -2562.1415 -2637.2704 346.79157 21.878655 24.379583
4000 1.1e+02 -2561.9968 -2637.3928 347.2934 21.956417 24.413166
4100 1.1e+02 -2560.7688 -2636.0902 347.76126 21.934696 24.449405
4200 1.1e+02 -2561.3033 -2638.2325 348.21187 22.402893 24.48165
4300 1.2e+02 -2560.9897 -2637.0909 348.67188 22.161792 24.517482
4400 1.2e+02 -2561.1676 -2638.5003 349.1221 22.52042 24.551399
4500 1.2e+02 -2560.4797 -2637.3716 349.57016 22.392068 24.58389
4600 1.2e+02 -2560.5787 -2637.0577 350.03085 22.2718 24.616821
4700 1.3e+02 -2560.9645 -2639.5114 350.46283 22.874034 24.648359
4800 1.3e+02 -2560.445 -2637.6681 350.93668 22.488484 24.682119
4900 1.3e+02 -2559.5243 -2635.9383 351.38797 22.252882 24.713605
5000 1.3e+02 -2559.4948 -2637.7238 351.82736 22.781448 24.746433
5100 1.4e+02 -2559.6822 -2636.169 352.25581 22.274077 24.77752
5200 1.4e+02 -2559.6398 -2637.3169 352.67163 22.620718 24.810244
5300 1.4e+02 -2558.6285 -2634.5293 353.06226 22.103426 24.836256
5400 1.4e+02 -2558.6394 -2637.9486 353.46662 23.096021 24.869663
5500 1.5e+02 -2558.1403 -2636.176 353.85792 22.725147 24.897758
5600 1.5e+02 -2558.0703 -2635.1367 354.27521 22.442874 24.929906
5700 1.5e+02 -2558.0656 -2636.7197 354.66462 22.905238 24.956168
5800 1.6e+02 -2557.3776 -2634.8266 355.06619 22.554271 24.987034
5900 1.6e+02 -2557.2526 -2635.9743 355.44501 22.924934 25.016353
6000 1.6e+02 -2557.3833 -2637.2292 355.80121 23.252296 25.043949
6100 1.6e+02 -2556.0263 -2633.5408 356.13412 22.573353 25.072447
6200 1.7e+02 -2555.7442 -2634.4378 356.46167 22.916748 25.100704
6300 1.7e+02 -2555.855 -2635.6231 356.75569 23.22965 25.127725
6400 1.7e+02 -2555.933 -2634.2031 357.04516 22.793407 25.152406
6500 1.7e+02 -2555.6529 -2635.6086 357.33016 23.28426 25.178081
6600 1.8e+02 -2554.8702 -2633.8043 357.60713 22.986754 25.203066
6700 1.8e+02 -2555.4594 -2637.4198 357.91044 23.868096 25.228913
6800 1.8e+02 -2555.1344 -2633.0306 358.23055 22.684511 25.254519
6900 1.8e+02 -2555.203 -2635.8935 358.56704 23.498239 25.281995
7000 1.9e+02 -2554.4151 -2634.9963 358.89735 23.466408 25.305952
7100 1.9e+02 -2555.5652 -2636.9959 359.27174 23.713819 25.334106
7200 1.9e+02 -2554.6218 -2632.7376 359.62885 22.748439 25.361455
7300 2e+02 -2553.7347 -2633.5173 359.96531 23.233845 25.386903
7400 2e+02 -2553.6833 -2632.7482 360.28731 23.024868 25.412373
7500 2e+02 -2554.1584 -2634.2224 360.62311 23.31579 25.437173
7600 2e+02 -2553.7146 -2636.4165 360.95078 24.084027 25.461273
7700 2.1e+02 -2553.0976 -2633.1652 361.2731 23.316874 25.488376
7800 2.1e+02 -2553.7234 -2633.641 361.58496 23.273177 25.51462
7900 2.1e+02 -2553.1572 -2635.2359 361.88331 23.902505 25.537243
8000 2.1e+02 -2553.0069 -2632.9284 362.20064 23.274304 25.562883
8100 2.2e+02 -2552.2172 -2632.9342 362.5047 23.505977 25.58597
8200 2.2e+02 -2552.6328 -2633.7047 362.84446 23.609337 25.610996
8300 2.2e+02 -2553.0514 -2636.536 363.15344 24.311943 25.634632
8400 2.3e+02 -2551.9163 -2634.5593 363.4457 24.066867 25.656569
8500 2.3e+02 -2551.1621 -2632.5819 363.73408 23.710645 25.680723
8600 2.3e+02 -2551.3228 -2631.8791 364.03489 23.459181 25.706041
8700 2.3e+02 -2551.3997 -2634.1928 364.32604 24.110586 25.728322
8800 2.4e+02 -2551.5524 -2635.9592 364.60259 24.58049 25.751881
8900 2.4e+02 -2550.9861 -2634.5125 364.87711 24.324098 25.772874
9000 2.4e+02 -2550.3983 -2630.9444 365.15409 23.456228 25.797098
9100 2.4e+02 -2550.2259 -2632.4851 365.42126 23.955067 25.819654
9200 2.5e+02 -2549.7275 -2633.251 365.67315 24.323271 25.84363
9300 2.5e+02 -2549.2312 -2632.0116 365.91463 24.106861 25.865763
9400 2.5e+02 -2549.1796 -2631.7916 366.12014 24.057833 25.884164
9500 2.5e+02 -2549.3237 -2632.8582 366.34704 24.326456 25.907195
9600 2.6e+02 -2548.7761 -2630.2005 366.56572 23.711991 25.926896
9700 2.6e+02 -2548.5538 -2631.9243 366.75569 24.278711 25.946464
9800 2.6e+02 -2548.3631 -2632.4881 366.94867 24.498431 25.965165
9900 2.7e+02 -2548.2213 -2631.2185 367.15325 24.169994 25.986899
10000 2.7e+02 -2547.7789 -2631.2241 367.37155 24.30047 26.007162
Loop time of 267.8 on 1 procs for 10000 steps with 1440 atoms
Pair time (%) = 107.528 (40.1525)
Neigh time (%) = 46.6868 (17.4335)
Comm time (%) = 0.952441 (0.355655)
Outpt time (%) = 0.106937 (0.0399319)
Other time (%) = 112.525 (42.0184)
Nlocal: 1440 ave 1440 max 1440 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5320 ave 5320 max 5320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 419294 ave 419294 max 419294 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 838588 ave 838588 max 838588 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 838588
Ave neighs/atom = 582.353
Neighbor list builds = 1000
Dangerous builds = 0

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LAMMPS (7 Jul 2009)
#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
orthogonal box = (-27.025 -16.215 -16.215) to (27.025 16.215 16.215)
1 by 1 by 1 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
#write_restart tinit.dat
# ID group atc PhysicsType ParameterFile
fix AtC internal atc thermal Ar_thermal.mat
# ID part keywords nx ny nz region
#fix_modify AtC fem create mesh 12 2 2 simRegion f p p
fix_modify AtC fem create mesh 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset ibndy box -4.0 4.0 -12 12 -12 12 in
fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 outward
# specify atom types
#fix_modify AtC transfer internal type internal
fix_modify AtC transfer boundary type ghost
# fix a temperature
fix_modify AtC transfer fix temperature all 20.
#fix_modify AtC transfer fix temperature all linear 0 0 0 -0.154 0 0 30.
# turn on thermostat
fix_modify AtC transfer thermal control rescale 10
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 transfer output bar1dfe_flux_init 100
timestep 5
thermo 10
run 400
Memory usage per processor = 8.7506 Mbytes
Step CPU TotEng PotEng AtC[1] Temp AtC[2]
0 0 -2573.6428 -2710.8793 412.06718 39.965279 20
10 0.28 -2626.7498 -2695.4276 412.06718 20 20
20 0.56 -2600.7022 -2669.38 412.06718 20 20
30 0.84 -2570.0142 -2638.6921 412.06718 20 20
40 1.1 -2548.1494 -2616.8273 412.06718 20 20
50 1.4 -2541.6409 -2610.3188 412.06718 20 20
60 1.7 -2539.3355 -2608.0134 412.06718 20 20
70 2 -2534.3684 -2603.0463 412.06718 20 20
80 2.2 -2530.2415 -2598.9194 412.06718 20 20
90 2.5 -2531.3411 -2600.019 412.06718 20 20
100 2.8 -2537.6764 -2606.3542 412.06718 20 20
110 3.1 -2546.506 -2615.1838 412.06718 20 20
120 3.4 -2555.0937 -2623.7716 412.06718 20 20
130 3.6 -2562.4178 -2631.0957 412.06718 20 20
140 3.9 -2568.7827 -2637.4606 412.06718 20 20
150 4.2 -2574.6292 -2643.307 412.06718 20 20
160 4.5 -2579.7542 -2648.432 412.06718 20 20
170 4.8 -2583.6629 -2652.3408 412.06718 20 20
180 5 -2585.9113 -2654.5892 412.06718 20 20
190 5.3 -2586.1786 -2654.8565 412.06718 20 20
200 5.6 -2584.8754 -2653.5532 412.06718 20 20
210 5.9 -2582.8956 -2651.5734 412.06718 20 20
220 6.2 -2580.6882 -2649.366 412.06718 20 20
230 6.5 -2578.24 -2646.9179 412.06718 20 20
240 6.7 -2575.9058 -2644.5836 412.06718 20 20
250 7 -2574.2875 -2642.9654 412.06718 20 20
260 7.3 -2573.8273 -2642.5052 412.06718 20 20
270 7.6 -2574.3017 -2642.9796 412.06718 20 20
280 7.8 -2574.7059 -2643.3838 412.06718 20 20
290 8.1 -2574.7745 -2643.4524 412.06718 20 20
300 8.4 -2575.3126 -2643.9904 412.06718 20 20
310 8.7 -2576.5002 -2645.178 412.06718 20 20
320 9 -2577.7411 -2646.419 412.06718 20 20
330 9.3 -2578.2283 -2646.9061 412.06718 20 20
340 9.5 -2577.7485 -2646.4263 412.06718 20 20
350 9.8 -2576.9631 -2645.6409 412.06718 20 20
360 10 -2576.0309 -2644.7088 412.06718 20 20
370 10 -2574.9309 -2643.6088 412.06718 20 20
380 11 -2573.7943 -2642.4721 412.06718 20 20
390 11 -2573.0353 -2641.7132 412.06718 20 20
400 11 -2573.4199 -2642.0977 412.06718 20 20
Loop time of 11.2102 on 1 procs for 400 steps with 1440 atoms
Pair time (%) = 4.45575 (39.7474)
Neigh time (%) = 1.86555 (16.6416)
Comm time (%) = 0.0379353 (0.338401)
Outpt time (%) = 0.0610819 (0.54488)
Other time (%) = 4.78984 (42.7277)
Nlocal: 1440 ave 1440 max 1440 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5320 ave 5320 max 5320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 419459 ave 419459 max 419459 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 838918 ave 838918 max 838918 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 838918
Ave neighs/atom = 582.582
Neighbor list builds = 40
Dangerous builds = 0
# change thermostat to hoover
fix_modify AtC transfer unfix temperature all
fix_modify AtC transfer thermal control flux faceset obndy
fix_modify AtC transfer filter type exponential
fix_modify AtC transfer filter scale 10000.0
fix_modify AtC transfer 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 -12 12 -12 12
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -12 12 -12 12
fix_modify AtC transfer fix temperature lbc 40.
fix_modify AtC transfer fix temperature rbc 20.
# initialize filter
run 100
Memory usage per processor = 8.97948 Mbytes
Step CPU TotEng PotEng AtC[1] Temp AtC[2]
400 0 -2573.4199 -2642.0977 412.06718 20 20
410 0.3 -2573.399 -2643.8456 429.61396 20.515068 21.555366
420 0.6 -2573.4225 -2646.1086 430.028 21.16726 21.573916
430 0.91 -2573.4498 -2647.2056 430.455 21.478791 21.593046
440 1.2 -2573.4565 -2646.2695 430.87731 21.204227 21.611967
450 1.5 -2573.4725 -2644.3172 431.27891 20.631017 21.62996
460 1.8 -2573.4862 -2643.0051 431.65927 20.244924 21.647001
470 2.1 -2573.4906 -2642.6175 432.02801 20.130768 21.663521
480 2.4 -2573.5014 -2642.5644 432.3911 20.112138 21.679788
490 2.7 -2573.5132 -2642.9216 432.75177 20.212768 21.695947
500 3 -2573.5326 -2643.6695 433.11495 20.424906 21.712218
Loop time of 3.0217 on 1 procs for 100 steps with 1440 atoms
Pair time (%) = 1.11102 (36.7679)
Neigh time (%) = 0.465189 (15.3949)
Comm time (%) = 0.0091815 (0.303852)
Outpt time (%) = 0.0152943 (0.506148)
Other time (%) = 1.42102 (47.0272)
Nlocal: 1440 ave 1440 max 1440 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5320 ave 5320 max 5320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 419046 ave 419046 max 419046 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 838092 ave 838092 max 838092 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 838092
Ave neighs/atom = 582.008
Neighbor list builds = 10
Dangerous builds = 0
# set up output, should be before a "run"
fix_modify AtC transfer output bar1d_fluxFE 100 text
# ouput command
#dump D1 all atom 1000 dump.bar1d
fix_modify AtC transfer atomic_output bar1d_fluxMD 100
# run with FE
reset_timestep 0
thermo 100
run 10000
Memory usage per processor = 8.97948 Mbytes
Step CPU TotEng PotEng AtC[1] Temp AtC[2]
0 0 -2573.5326 -2643.6695 433.11495 20.424906 21.712218
100 3 -2573.4996 -2644.68 436.56595 20.728783 21.866831
200 6 -2573.6452 -2641.8181 439.65242 19.852963 22.005112
300 8.9 -2573.7003 -2646.4622 442.67272 21.189339 22.140428
400 12 -2573.8123 -2641.5274 445.34109 19.719609 22.259977
500 15 -2573.523 -2644.2791 447.87899 20.605203 22.373681
600 18 -2573.5066 -2641.7526 450.30082 19.874234 22.482184
700 21 -2573.1755 -2642.9899 452.59197 20.330998 22.584833
800 24 -2572.7532 -2642.4538 454.74808 20.297842 22.681431
900 27 -2572.4242 -2643.2186 456.80456 20.616377 22.773566
1000 30 -2572.1111 -2644.2513 458.77119 21.008267 22.861675
1100 33 -2571.8664 -2642.2676 460.69037 20.501859 22.947659
1200 36 -2571.6698 -2642.4072 462.52036 20.599778 23.029647
1300 39 -2571.1188 -2640.8357 464.26327 20.302568 23.107733
1400 42 -2570.6841 -2642.0319 465.90618 20.777507 23.181339
1500 45 -2570.3755 -2642.5393 467.64779 21.015167 23.259367
1600 48 -2570.1086 -2640.3963 469.24937 20.468802 23.331122
1700 51 -2569.7084 -2642.3964 470.76324 21.167807 23.398946
1800 53 -2569.2903 -2643.213 472.26485 21.527379 23.466222
1900 56 -2568.8699 -2641.4957 473.83022 21.149691 23.536354
2000 59 -2568.3377 -2641.3608 475.30209 21.265411 23.602297
2100 62 -2567.6236 -2639.3792 476.69625 20.896274 23.664759
2200 65 -2566.8936 -2642.0946 478.02908 21.899656 23.724472
2300 68 -2566.4627 -2640.2742 479.41262 21.494985 23.786458
2400 71 -2566.0253 -2638.6268 480.76007 21.142611 23.846827
2500 74 -2565.8021 -2639.6421 482.09822 21.503291 23.906779
2600 77 -2565.2093 -2642.2012 483.3378 22.421166 23.962315
2700 80 -2564.6901 -2639.8567 484.63598 21.889625 24.020477
2800 83 -2564.0658 -2636.9481 485.8689 21.22441 24.075714
2900 86 -2563.3168 -2639.3155 487.10404 22.131928 24.131051
3000 89 -2562.6825 -2635.5318 488.27527 21.214781 24.183525
3100 92 -2562.1212 -2635.4426 489.43761 21.352279 24.2356
3200 95 -2561.6126 -2636.3019 490.64892 21.750607 24.28987
3300 98 -2561.1335 -2639.0741 491.78462 22.697438 24.340752
3400 1e+02 -2560.4828 -2638.3251 492.87662 22.66881 24.389676
3500 1e+02 -2559.8843 -2635.4238 493.96107 21.998211 24.438262
3600 1.1e+02 -2559.2443 -2634.7161 495.09564 21.97848 24.489093
3700 1.1e+02 -2558.5654 -2636.1565 496.14063 22.595663 24.535911
3800 1.1e+02 -2558.0214 -2636.7671 497.17918 22.931888 24.58244
3900 1.2e+02 -2557.9398 -2634.982 498.30063 22.435836 24.632684
4000 1.2e+02 -2557.8749 -2635.5655 499.26966 22.624655 24.676098
4100 1.2e+02 -2557.8331 -2635.3677 500.27412 22.579214 24.721101
4200 1.2e+02 -2557.6329 -2635.9432 501.25564 22.805115 24.765075
4300 1.3e+02 -2557.4707 -2636.512 502.24607 23.017987 24.809448
4400 1.3e+02 -2557.3019 -2632.8823 503.29942 22.010137 24.856641
4500 1.3e+02 -2556.8882 -2633.5726 504.19269 22.331634 24.896661
4600 1.4e+02 -2556.5255 -2637.0121 505.14884 23.438878 24.939499
4700 1.4e+02 -2556.1965 -2636.3657 506.12562 23.346446 24.983261
4800 1.4e+02 -2555.728 -2636.154 507.0392 23.421248 25.024191
4900 1.5e+02 -2555.3573 -2634.8572 507.93584 23.151538 25.064363
5000 1.5e+02 -2554.8839 -2635.3615 508.86307 23.436248 25.105905
5100 1.5e+02 -2554.5001 -2632.2863 509.79029 22.652461 25.147447
5200 1.5e+02 -2554.2786 -2635.3015 510.67821 23.595069 25.187227
5300 1.6e+02 -2554.1208 -2633.4672 511.56223 23.106822 25.226833
5400 1.6e+02 -2553.8571 -2632.9509 512.411 23.033282 25.26486
5500 1.6e+02 -2553.4771 -2633.4831 513.27749 23.29891 25.303681
5600 1.7e+02 -2552.995 -2634.0399 514.08357 23.601475 25.339795
5700 1.7e+02 -2552.6786 -2632.23 514.99251 23.166531 25.380517
5800 1.7e+02 -2552.1989 -2634.2926 515.83523 23.906877 25.418273
5900 1.8e+02 -2551.9275 -2633.7331 516.69181 23.822967 25.45665
6000 1.8e+02 -2551.5879 -2633.4709 517.50304 23.845533 25.492995
6100 1.8e+02 -2551.1096 -2633.3576 518.27013 23.951824 25.527362
6200 1.8e+02 -2550.6066 -2634.4431 519.07898 24.414427 25.5636
6300 1.9e+02 -2550.1427 -2633.9705 519.85788 24.411888 25.598497
6400 1.9e+02 -2549.6148 -2630.7643 520.70201 23.631931 25.636316
6500 1.9e+02 -2549.2143 -2629.4555 521.48165 23.3674 25.671246
6600 2e+02 -2548.823 -2629.4952 522.21153 23.492935 25.703946
6700 2e+02 -2548.6124 -2631.6154 523.03499 24.171693 25.740839
6800 2e+02 -2548.314 -2627.4378 523.72811 23.041997 25.771892
6900 2e+02 -2548.0996 -2632.112 524.53399 24.465645 25.807997
7000 2.1e+02 -2547.8468 -2630.457 525.24887 24.057291 25.840026
7100 2.1e+02 -2547.5093 -2630.8501 526.01815 24.27005 25.874491
7200 2.1e+02 -2547.1919 -2630.0362 526.75581 24.125462 25.90754
7300 2.2e+02 -2546.8056 -2631.0682 527.4846 24.538524 25.940191
7400 2.2e+02 -2546.541 -2632.4362 528.24198 25.01394 25.974124
7500 2.2e+02 -2546.1286 -2629.6863 528.94188 24.33324 26.005481
7600 2.3e+02 -2545.959 -2629.3922 529.57701 24.296979 26.033936
7700 2.3e+02 -2546.0743 -2629.693 530.30436 24.351001 26.066523
7800 2.3e+02 -2546.1431 -2631.6521 530.98889 24.901471 26.097191
7900 2.3e+02 -2546.1056 -2629.3749 531.66127 24.249239 26.127315
8000 2.4e+02 -2546.0454 -2630.0836 532.37925 24.473159 26.159482
8100 2.4e+02 -2545.9725 -2630.5976 533.05102 24.644071 26.18958
8200 2.4e+02 -2545.5772 -2629.4844 533.65121 24.435002 26.216469
8300 2.5e+02 -2545.5178 -2631.6842 534.43183 25.092927 26.251443
8400 2.5e+02 -2545.3432 -2629.5904 535.02156 24.534025 26.277864
8500 2.5e+02 -2545.2097 -2631.2853 535.66213 25.06648 26.306563
8600 2.6e+02 -2544.9173 -2629.2314 536.3311 24.553498 26.336535
8700 2.6e+02 -2544.5414 -2628.3855 536.99695 24.416625 26.366366
8800 2.6e+02 -2543.8563 -2629.5985 537.57029 24.969392 26.392053
8900 2.6e+02 -2543.2906 -2628.292 538.33031 24.753655 26.426103
9000 2.7e+02 -2542.5357 -2627.1708 538.87931 24.64698 26.4507
9100 2.7e+02 -2542.1926 -2627.894 539.53269 24.957511 26.479973
9200 2.7e+02 -2542.0567 -2627.6595 540.14474 24.928803 26.507394
9300 2.8e+02 -2542.1288 -2626.8786 540.80469 24.680402 26.536961
9400 2.8e+02 -2541.8301 -2627.2829 541.36001 24.885088 26.561841
9500 2.8e+02 -2541.6773 -2628.1451 541.99633 25.180691 26.590349
9600 2.9e+02 -2541.3762 -2629.589 542.51985 25.688852 26.613804
9700 2.9e+02 -2541.0314 -2625.3135 543.15786 24.544177 26.642389
9800 2.9e+02 -2540.6298 -2625.8733 543.76425 24.824163 26.669556
9900 2.9e+02 -2540.2376 -2628.1266 544.31076 25.594543 26.694041
10000 3e+02 -2540.0111 -2625.9159 544.89126 25.016719 26.720049
Loop time of 297.023 on 1 procs for 10000 steps with 1440 atoms
Pair time (%) = 107.376 (36.1506)
Neigh time (%) = 46.5622 (15.6763)
Comm time (%) = 0.924362 (0.311209)
Outpt time (%) = 0.154094 (0.0518793)
Other time (%) = 142.007 (47.81)
Nlocal: 1440 ave 1440 max 1440 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5320 ave 5320 max 5320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 419203 ave 419203 max 419203 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 838406 ave 838406 max 838406 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 838406
Ave neighs/atom = 582.226
Neighbor list builds = 1000
Dangerous builds = 0

100
examples/USER/atc/bar1d_thermal/in.bar1d Normal file
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@ -0,0 +1,100 @@
#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 fem create mesh 12 2 2 simRegion f p p
fix_modify AtC fem create mesh 12 1 1 simRegion f p p
# specify atom types
#fix_modify AtC transfer internal type internal
fix_modify AtC transfer boundary type ghost
# fix a temperature
fix_modify AtC transfer fix temperature all 20.
# turn on thermostat
fix_modify AtC transfer thermal control rescale 10
# equilibrate MD field
#dump D1 all atom 100 dump.bar1d
#fix_modify AtC transfer 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 transfer unfix temperature all
fix_modify AtC transfer thermal control hoover
fix_modify AtC transfer filter type exponential
fix_modify AtC transfer filter scale 10000.0
fix_modify AtC transfer filter on
fix_modify AtC transfer internal_quadrature off
# add nodesets
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -12 12 -12 12
fix_modify AtC transfer fix temperature lbc 40.
fix_modify AtC transfer fix temperature rbc 20.
# initialize filter
#thermo 1
run 100
# set up output, should be before a "run"
fix_modify AtC transfer output bar1dFE 100 text
# ouput command
#dump D1 all atom 1000 dump.bar1d
fix_modify AtC transfer atomic_output bar1dMD 100
# run with FE
reset_timestep 0
thermo 100
run 10000

103
examples/USER/atc/bar1d_thermal/in.bar1d_flux Normal file
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@ -0,0 +1,103 @@
#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
# ID part keywords nx ny nz region
#fix_modify AtC fem create mesh 12 2 2 simRegion f p p
fix_modify AtC fem create mesh 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset ibndy box -4.0 4.0 -12 12 -12 12 in
fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 outward
# specify atom types
#fix_modify AtC transfer internal type internal
fix_modify AtC transfer boundary type ghost
# fix a temperature
fix_modify AtC transfer fix temperature all 20.
#fix_modify AtC transfer fix temperature all linear 0 0 0 -0.154 0 0 30.
# turn on thermostat
fix_modify AtC transfer thermal control 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 transfer output bar1dfe_flux_init 100
timestep 5
thermo 10
run 400
# change thermostat to hoover
fix_modify AtC transfer unfix temperature all
fix_modify AtC transfer thermal control flux faceset obndy
fix_modify AtC transfer filter type exponential
fix_modify AtC transfer filter scale 10000.0
fix_modify AtC transfer 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 -12 12 -12 12
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -12 12 -12 12
fix_modify AtC transfer fix temperature lbc 40.
fix_modify AtC transfer fix temperature rbc 20.
# initialize filter
run 100
# set up output, should be before a "run"
fix_modify AtC transfer output bar1d_fluxFE 100 text
# ouput command
#dump D1 all atom 1000 dump.bar1d
fix_modify AtC transfer atomic_output bar1d_fluxMD 100
# run with FE
reset_timestep 0
thermo 100
run 10000

112
examples/USER/atc/bar1d_thermal/in.bar1d_frac_step Normal file
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#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 fem create mesh 12 2 2 simRegion f p p
fix_modify AtC fem create mesh 4 1 1 mdInternal f p p
#fix_modify AtC mesh create_faceset ibndy box -4.0 4.0 -12 12 -12 12 in
#fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 outward
# specify atom types
#fix_modify AtC transfer internal type internal
#fix_modify AtC transfer boundary type ghost
# fix a temperature
fix_modify AtC transfer fix temperature all 20.
# turn on thermostat
fix_modify AtC transfer thermal control rescale 10
# equilibrate MD field
#dump D1 all atom 100 dump.bar1d
#fix_modify AtC transfer 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
# add nodesets
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -4.1 -3.9 -12 12 -12 12
fix_modify AtC mesh create_nodeset rbc 3.9 4.1 -12 12 -12 12
fix_modify AtC transfer fix temperature lbc 40.
fix_modify AtC transfer fix temperature rbc 20.
# initialize filter
#timestep 0.5
#fix_modify AtC transfer output bar1d_frac_stepFE 1
#thermo 1
run 400
# change thermostat to hoover
fix_modify AtC transfer pmfc
fix_modify AtC transfer unfix temperature all
fix_modify AtC transfer fix temperature lbc 40.
fix_modify AtC transfer fix temperature rbc 20.
# fix_modify AtC transfer thermal control none
#fix_modify AtC transfer thermal control hoover
fix_modify AtC transfer thermal control flux no_boundary
# #fix_modify AtC transfer thermal control flux interpolate
# #fix_modify AtC transfer thermal control flux faceset obndy
fix_modify AtC transfer filter type exponential
fix_modify AtC transfer filter scale 10000.0
#fix_modify AtC transfer filter on
fix_modify AtC transfer internal_quadrature off
# #fix_modify AtC transfer localized_lambda on
# set up output, should be before a "run"
fix_modify AtC transfer output bar1d_frac_stepFE 100 text
# ouput command
#dump D1 all atom 1000 dump.bar1d
fix_modify AtC transfer atomic_output bar1d_frac_stepMD 100
# run with FE
reset_timestep 0
thermo 100
run 10000

2903
examples/USER/atc/bar1d_thermal/temp.init Normal file
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File diff suppressed because it is too large Load Diff

35
examples/USER/atc/bar1d_two_temperature/Ar_ttm.mat Normal file
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material Ar
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
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

17
examples/USER/atc/bar1d_two_temperature/Cu_ttm.mat Normal file
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material Cu
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

537
examples/USER/atc/bar1d_two_temperature/bar1d_ttm.log Normal file
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LAMMPS (7 Jul 2009)
# 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
orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215)
1 by 1 by 1 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 -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
2880 atoms in group internal
group ghost subtract all internal
576 atoms in group ghost
# 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
# ID part keywords nx ny nz region
fix_modify AtC fem create mesh 14 1 1 feRegion f p p
# specify atom types for the atc fix
#fix_modify AtC transfer internal type internal
fix_modify AtC transfer boundary type ghost
# fix initial temperatures
#if !{restart}
#velocity internal create 40 87287 mom yes loop geom
#endif
fix_modify AtC transfer initial temperature all 20
fix_modify AtC transfer fix temperature all 20
fix_modify AtC transfer initial electron_temperature all 20
fix_modify AtC transfer fix electron_temperature all 20
# equilibrate MD field with rescale
fix_modify AtC extrinsic exchange off
fix_modify AtC transfer thermal control rescale 10
#if !{restart}
#run 1000
#endif
# change thermostat
fix_modify AtC extrinsic exchange on
fix_modify AtC transfer unfix temperature all
fix_modify AtC transfer 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 transfer thermal control flux faceset bndy
# .. this controls the time filtering ....
#fix_modify AtC transfer 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 -6 6 -6 6
fix_modify AtC mesh create_nodeset rbc 13.9 14.1 -6 6 -6 6
fix_modify AtC transfer fix electron_temperature lbc 40.
fix_modify AtC transfer fix electron_temperature rbc 20.
fix_modify AtC transfer fix temperature rbc 20.
#fix_modify AtC transfer source electron_temperature all 0.0015
fix_modify AtC transfer source electron_temperature all 9.50445e-11
# output filename frequency [text output]
fix_modify AtC transfer output bar1d_ttmFE 100 text
# run transient to steady state
thermo 10
reset_timestep 0
run 4000
Memory usage per processor = 20.4457 Mbytes
Step Temp E_pair E_mol TotEng Press
0 16.671491 -6505.7593 0 -6334.0647 -1236.2423
10 16.651705 -6505.5537 0 -6334.0628 -1236.063
20 16.530158 -6504.2726 0 -6334.0335 -1232.9374
30 16.484745 -6503.7602 0 -6333.9888 -1231.0691
40 16.543953 -6504.3215 0 -6333.9403 -1231.4891
50 16.594988 -6504.7418 0 -6333.835 -1231.8556
60 16.569044 -6504.3689 0 -6333.7293 -1230.7731
70 16.505629 -6503.6163 0 -6333.6298 -1229.1909
80 16.499955 -6503.4447 0 -6333.5166 -1229.1002
90 16.523227 -6503.6042 0 -6333.4365 -1229.6937
100 16.508157 -6503.3717 0 -6333.3591 -1229.2842
110 16.515733 -6503.374 0 -6333.2834 -1229.1993
120 16.568236 -6503.8632 0 -6333.2319 -1230.0834
130 16.554884 -6503.675 0 -6333.1812 -1229.6144
140 16.473429 -6502.736 0 -6333.0811 -1227.7486
150 16.469794 -6502.5514 0 -6332.934 -1227.607
160 16.579831 -6503.5343 0 -6332.7836 -1229.6567
170 16.624378 -6503.8396 0 -6332.6301 -1229.6114
180 16.501732 -6502.377 0 -6332.4306 -1225.3556
190 16.388366 -6500.9672 0 -6332.1884 -1221.4971
200 16.484582 -6501.7504 0 -6331.9806 -1223.1577
210 16.699214 -6503.7792 0 -6331.799 -1228.2052
220 16.791874 -6504.548 0 -6331.6136 -1230.5561
230 16.748075 -6503.9202 0 -6331.4368 -1229.213
240 16.665833 -6502.8491 0 -6331.2127 -1226.4072
250 16.621232 -6502.1717 0 -6330.9946 -1224.5041
260 16.658091 -6502.3535 0 -6330.7969 -1224.89
270 16.739152 -6502.9658 0 -6330.5744 -1226.6051
280 16.804835 -6503.4492 0 -6330.3813 -1227.9296
290 16.798717 -6503.126 0 -6330.121 -1227.0917
300 16.696278 -6501.8014 0 -6329.8514 -1223.5739
310 16.591095 -6500.3987 0 -6329.532 -1219.6969
320 16.562079 -6499.7687 0 -6329.2009 -1217.6605
330 16.629333 -6500.1646 0 -6328.9041 -1218.1376
340 16.735568 -6500.9667 0 -6328.6121 -1219.8673
350 16.848974 -6501.8919 0 -6328.3694 -1222.1931
360 16.98713 -6503.0922 0 -6328.1469 -1225.3572
370 17.06977 -6503.7257 0 -6327.9293 -1227.2193
380 16.971691 -6502.4327 0 -6327.6463 -1224.4904
390 16.743361 -6499.7176 0 -6327.2828 -1218.0682
400 16.574649 -6497.518 0 -6326.8207 -1212.3628
410 16.56711 -6496.9847 0 -6326.3651 -1210.1976
420 16.671542 -6497.6307 0 -6325.9355 -1210.9062
430 16.808348 -6498.617 0 -6325.5129 -1212.8599
440 16.918663 -6499.3855 0 -6325.1453 -1214.7492
450 16.998348 -6499.8258 0 -6324.7649 -1216.1894
460 17.101907 -6500.4972 0 -6324.3698 -1217.98
470 17.199306 -6501.0962 0 -6323.9657 -1219.0689
480 17.133501 -6500.0357 0 -6323.5829 -1216.0406
490 16.939851 -6497.6902 0 -6323.2317 -1210.2749
500 16.919105 -6497.0735 0 -6322.8287 -1209.1143
510 17.178498 -6499.3244 0 -6322.4083 -1215.1868
520 17.48021 -6502.0287 0 -6322.0053 -1222.3728
530 17.559531 -6502.438 0 -6321.5977 -1223.4739
540 17.38932 -6500.2923 0 -6321.2049 -1217.4934
550 17.142234 -6497.3094 0 -6320.7667 -1209.0997
560 17.01647 -6495.5092 0 -6320.2617 -1204.0898
570 17.150938 -6496.3914 0 -6319.7591 -1206.2366
580 17.393162 -6498.4183 0 -6319.2914 -1211.65
590 17.504817 -6499.1265 0 -6318.8497 -1213.8141
600 17.500349 -6498.6418 0 -6318.411 -1212.1111
610 17.406024 -6497.2206 0 -6317.9612 -1207.3661
620 17.220843 -6494.8037 0 -6317.4514 -1200.5909
630 17.102363 -6493.032 0 -6316.8999 -1196.203
640 17.148333 -6492.9097 0 -6316.3042 -1196.5894
650 17.311596 -6493.9994 0 -6315.7125 -1200.1099
660 17.48294 -6495.2118 0 -6315.1602 -1203.3122
670 17.519633 -6495.0681 0 -6314.6387 -1202.4983
680 17.457125 -6493.9797 0 -6314.194 -1198.8656
690 17.470863 -6493.6507 0 -6313.7235 -1197.0165
700 17.576148 -6494.2454 0 -6313.2339 -1197.8281
710 17.697902 -6495.025 0 -6312.7596 -1199.4344
720 17.743065 -6494.9543 0 -6312.2238 -1199.2455
730 17.699788 -6493.9456 0 -6311.6608 -1196.7949
740 17.627877 -6492.6298 0 -6311.0856 -1193.4101
750 17.550154 -6491.244 0 -6310.5002 -1189.7954
760 17.539095 -6490.5769 0 -6309.947 -1187.8995
770 17.673363 -6491.4351 0 -6309.4225 -1189.7523
780 17.882147 -6493.062 0 -6308.8991 -1193.7188
790 18.00966 -6493.8707 0 -6308.3947 -1195.8005
800 17.980583 -6493.0714 0 -6307.8948 -1193.6851
810 17.825824 -6490.9588 0 -6307.376 -1188.1017
820 17.692317 -6489.0401 0 -6306.8322 -1183.0295
830 17.710419 -6488.6573 0 -6306.2631 -1181.9387
840 17.808262 -6489.0855 0 -6305.6836 -1183.0468
850 17.829578 -6488.7143 0 -6305.0928 -1182.1899
860 17.771342 -6487.5008 0 -6304.4791 -1179.1217
870 17.820295 -6487.3695 0 -6303.8436 -1178.575
880 18.063537 -6489.2637 0 -6303.2327 -1183.0663
890 18.369284 -6491.8496 0 -6302.6699 -1189.4275
900 18.525872 -6492.9961 0 -6302.2037 -1192.342
910 18.472235 -6492.0343 0 -6301.7943 -1190.0811
920 18.372321 -6490.5617 0 -6301.3507 -1186.1654
930 18.288123 -6489.2163 0 -6300.8724 -1181.9829
940 18.096622 -6486.6631 0 -6300.2914 -1174.8569
950 17.882153 -6483.7861 0 -6299.6232 -1167.0973
960 17.867323 -6482.9268 0 -6298.9166 -1164.4853
970 18.09915 -6484.6345 0 -6298.2368 -1168.6545
980 18.443545 -6487.5728 0 -6297.6283 -1176.2602
990 18.703733 -6489.7042 0 -6297.0801 -1181.8804
1000 18.753218 -6489.6818 0 -6296.548 -1181.8673
1010 18.610779 -6487.6703 0 -6296.0035 -1176.534
1020 18.39336 -6484.8445 0 -6295.4168 -1168.9352
1030 18.247821 -6482.6945 0 -6294.7657 -1162.956
1040 18.27653 -6482.3647 0 -6294.1402 -1161.3767
1050 18.418106 -6483.2621 0 -6293.5796 -1163.05
1060 18.573973 -6484.3115 0 -6293.0237 -1165.571
1070 18.664801 -6484.6987 0 -6292.4755 -1166.7949
1080 18.621552 -6483.6737 0 -6291.896 -1164.8778
1090 18.53927 -6482.1938 0 -6291.2635 -1161.868
1100 18.568833 -6481.8649 0 -6290.6301 -1161.2524
1110 18.683765 -6482.4291 0 -6290.0106 -1162.4768
1120 18.808147 -6483.0831 0 -6289.3837 -1163.5972
1130 18.884946 -6483.3252 0 -6288.8348 -1163.2843
1140 18.846682 -6482.3961 0 -6288.2998 -1160.2541
1150 18.748976 -6480.8337 0 -6287.7436 -1156.1965
1160 18.759994 -6480.3843 0 -6287.1808 -1155.1103
1170 18.901967 -6481.2895 0 -6286.6238 -1157.2721
1180 19.011261 -6481.9017 0 -6286.1104 -1158.6901
1190 19.040255 -6481.7192 0 -6285.6293 -1158.1377
1200 19.106103 -6481.8954 0 -6285.1274 -1158.289
1210 19.229265 -6482.6335 0 -6284.5971 -1159.6899
1220 19.239111 -6482.1951 0 -6284.0573 -1158.6039
1230 19.157688 -6480.7877 0 -6283.4884 -1155.4514
1240 19.174743 -6480.4215 0 -6282.9466 -1154.4926
1250 19.286153 -6481.0811 0 -6282.4589 -1155.5921
1260 19.320062 -6480.9602 0 -6281.9887 -1154.5954
1270 19.190466 -6479.1585 0 -6281.5217 -1149.413
1280 18.995019 -6476.6109 0 -6280.9869 -1142.6018
1290 18.914422 -6475.1574 0 -6280.3635 -1138.9829
1300 19.050226 -6475.8748 0 -6279.6823 -1141.1071
1310 19.272645 -6477.5322 0 -6279.049 -1145.5684
1320 19.357581 -6477.7617 0 -6278.4038 -1146.3936
1330 19.266387 -6476.2235 0 -6277.8047 -1142.4125
1340 19.168211 -6474.5602 0 -6277.1526 -1137.831
1350 19.257232 -6474.8149 0 -6276.4904 -1137.9089
1360 19.550412 -6477.2011 0 -6275.8573 -1143.4638
1370 19.796833 -6479.1494 0 -6275.2678 -1148.551
1380 19.7815 -6478.4409 0 -6274.7172 -1147.5698
1390 19.631575 -6476.3413 0 -6274.1616 -1142.7018
1400 19.521048 -6474.5989 0 -6273.5575 -1138.0212
1410 19.519644 -6473.9613 0 -6272.9343 -1135.7628
1420 19.608168 -6474.2556 0 -6272.317 -1136.0104
1430 19.764525 -6475.2719 0 -6271.723 -1138.215
1440 19.912587 -6476.2047 0 -6271.131 -1140.1734
1450 19.913759 -6475.6003 0 -6270.5145 -1138.3693
1460 19.79157 -6473.6952 0 -6269.8678 -1133.2856
1470 19.714636 -6472.2575 0 -6269.2224 -1129.0564
1480 19.737365 -6471.846 0 -6268.5768 -1127.3107
1490 19.766194 -6471.5403 0 -6267.9742 -1126.1998
1500 19.7696 -6470.9664 0 -6267.3653 -1124.9092
1510 19.827695 -6470.9018 0 -6266.7023 -1124.9431
1520 19.944447 -6471.4439 0 -6266.042 -1126.1254
1530 19.973951 -6471.1382 0 -6265.4325 -1125.053
1540 19.886531 -6469.6311 0 -6264.8257 -1121.0356
1550 19.818466 -6468.3255 0 -6264.221 -1117.3869
1560 19.839194 -6467.8989 0 -6263.5811 -1115.9427
1570 19.921311 -6468.101 0 -6262.9374 -1116.1766
1580 20.015732 -6468.4487 0 -6262.3127 -1116.9107
1590 20.110315 -6468.7904 0 -6261.6803 -1117.8602
1600 20.264876 -6469.7349 0 -6261.0331 -1120.2718
1610 20.380324 -6470.3096 0 -6260.4188 -1121.7548
1620 20.322098 -6469.1089 0 -6259.8178 -1119.0178
1630 20.232717 -6467.5453 0 -6259.1747 -1115.1644
1640 20.313706 -6467.7411 0 -6258.5363 -1115.2943
1650 20.575967 -6469.8346 0 -6257.9289 -1120.0993
1660 20.793996 -6471.5219 0 -6257.3708 -1124.1915
1670 20.736006 -6470.3925 0 -6256.8386 -1121.5447
1680 20.444958 -6466.8331 0 -6256.2767 -1112.7298
1690 20.22674 -6463.9901 0 -6255.681 -1105.0268
1700 20.274891 -6463.902 0 -6255.097 -1103.5997
1710 20.45142 -6465.094 0 -6254.471 -1105.8914
1720 20.56919 -6465.7092 0 -6253.8733 -1107.7881
1730 20.641711 -6465.8219 0 -6253.2392 -1108.9745
1740 20.728211 -6466.1028 0 -6252.6292 -1110.0176
1750 20.722246 -6465.3722 0 -6251.96 -1107.879
1760 20.538713 -6462.7849 0 -6251.2629 -1100.8039
1770 20.35658 -6460.178 0 -6250.5317 -1093.4872
1780 20.411269 -6460.0611 0 -6249.8516 -1092.0689
1790 20.661313 -6461.9598 0 -6249.1752 -1096.0711
1800 20.95287 -6464.3187 0 -6248.5314 -1101.9506
1810 21.25238 -6466.7902 0 -6247.9183 -1108.1806
1820 21.413306 -6467.889 0 -6247.3598 -1110.7541
1830 21.265567 -6465.8163 0 -6246.8086 -1105.462
1840 20.904899 -6461.4789 0 -6246.1856 -1094.6349
1850 20.604956 -6457.7007 0 -6245.4965 -1085.2083
1860 20.577858 -6456.6395 0 -6244.7144 -1082.4955
1870 20.79238 -6458.0326 0 -6243.8981 -1085.8989
1880 21.103689 -6460.5343 0 -6243.1938 -1091.8916
1890 21.349681 -6462.4189 0 -6242.545 -1096.2855
1900 21.424808 -6462.6294 0 -6241.9818 -1096.4936
1910 21.349347 -6461.3082 0 -6241.4377 -1092.941
1920 21.18517 -6459.1076 0 -6240.928 -1087.3369
1930 21.036065 -6457.0235 0 -6240.3794 -1082.2115
1940 21.024255 -6456.3164 0 -6239.794 -1080.5427
1950 21.289969 -6458.4084 0 -6239.1495 -1085.3514
1960 21.667609 -6461.6896 0 -6238.5414 -1092.5154
1970 21.745842 -6461.9113 0 -6237.9574 -1092.2463
1980 21.479887 -6458.5535 0 -6237.3386 -1083.5811
1990 21.293202 -6456.0149 0 -6236.7226 -1076.7027
2000 21.279875 -6455.261 0 -6236.106 -1074.3201
2010 21.209986 -6453.9211 0 -6235.4858 -1071.2596
2020 21.123158 -6452.3385 0 -6234.7975 -1068.0754
2030 21.231892 -6452.7558 0 -6234.0949 -1069.5067
2040 21.508927 -6454.8747 0 -6233.3608 -1074.7487
2050 21.689676 -6456.0738 0 -6232.6984 -1077.5956
2060 21.647006 -6455.0083 0 -6232.0723 -1075.0067
2070 21.595825 -6453.8924 0 -6231.4835 -1072.0624
2080 21.722464 -6454.6421 0 -6230.929 -1073.3487
2090 21.936202 -6456.321 0 -6230.4066 -1076.6812
2100 21.94343 -6455.8658 0 -6229.877 -1075.0841
2110 21.710389 -6452.8983 0 -6229.3096 -1067.7357
2120 21.539354 -6450.4365 0 -6228.6092 -1061.8052
2130 21.625914 -6450.5981 0 -6227.8793 -1062.4766
2140 21.960668 -6453.3298 0 -6227.1635 -1069.5494
2150 22.310957 -6456.2864 0 -6226.5125 -1077.1038
2160 22.442785 -6457.0871 0 -6225.9556 -1078.9487
2170 22.307481 -6455.1658 0 -6225.4278 -1073.5529
2180 22.01895 -6451.6169 0 -6224.8504 -1063.9995
2190 21.809231 -6448.8289 0 -6224.2222 -1056.4997
2200 21.834738 -6448.4131 0 -6223.5437 -1055.247
2210 22.053404 -6449.9713 0 -6222.8499 -1059.0126
2220 22.211871 -6450.9665 0 -6222.2131 -1061.1631
2230 22.136256 -6449.519 0 -6221.5444 -1057.005
2240 21.95616 -6446.9579 0 -6220.838 -1049.819
2250 21.923576 -6445.8406 0 -6220.0563 -1046.3662
2260 22.155568 -6447.4761 0 -6219.3026 -1050.0877
2270 22.472144 -6450.0957 0 -6218.6619 -1056.7086
2280 22.625353 -6451.0829 0 -6218.0712 -1059.4587
2290 22.542977 -6449.6972 0 -6217.5338 -1055.8674
2300 22.353808 -6447.0998 0 -6216.8847 -1048.8464
2310 22.199672 -6444.8501 0 -6216.2224 -1042.6858
2320 22.168149 -6443.8627 0 -6215.5596 -1040.2713
2330 22.326947 -6444.8459 0 -6214.9074 -1043.2191
2340 22.619445 -6447.2547 0 -6214.3038 -1049.6256
2350 22.841953 -6448.9708 0 -6213.7284 -1054.0085
2360 22.832357 -6448.29 0 -6213.1464 -1052.3278
2370 22.676181 -6446.0942 0 -6212.559 -1046.8884
2380 22.573679 -6444.4435 0 -6211.964 -1042.7352
2390 22.582663 -6443.8955 0 -6211.3234 -1041.3299
2400 22.653145 -6443.9587 0 -6210.6608 -1041.3709
2410 22.763485 -6444.4279 0 -6209.9936 -1042.0924
2420 22.873423 -6444.9515 0 -6209.385 -1042.6384
2430 22.906275 -6444.7449 0 -6208.8401 -1041.5096
2440 22.910306 -6444.2555 0 -6208.3092 -1039.9263
2450 23.026189 -6444.906 0 -6207.7662 -1040.9903
2460 23.150543 -6445.6549 0 -6207.2345 -1042.0974
2470 23.03306 -6443.8888 0 -6206.6783 -1037.2926
2480 22.842772 -6441.2953 0 -6206.0445 -1030.4331
2490 22.911334 -6441.3197 0 -6205.3627 -1029.7119
2500 23.153003 -6443.2121 0 -6204.7663 -1033.9009
2510 23.302474 -6444.2371 0 -6204.252 -1036.5887
2520 23.252259 -6443.2208 0 -6203.7528 -1034.4441
2530 23.053919 -6440.6493 0 -6203.2239 -1028.2518
2540 22.849407 -6437.9368 0 -6202.6177 -1021.2949
2550 22.71295 -6435.8556 0 -6201.9418 -1015.6613
2560 22.715354 -6435.146 0 -6201.2074 -1013.3958
2570 22.864096 -6435.9504 0 -6200.48 -1015.1761
2580 23.14749 -6438.1503 0 -6199.7612 -1020.6574
2590 23.497133 -6441.031 0 -6199.0411 -1027.6059
2600 23.697975 -6442.4482 0 -6198.3899 -1030.8199
2610 23.740349 -6442.2782 0 -6197.7835 -1030.0732
2620 23.75572 -6441.8591 0 -6197.206 -1028.6315
2630 23.699131 -6440.7117 0 -6196.6415 -1025.8508
2640 23.5571 -6438.6417 0 -6196.0342 -1021.2352
2650 23.389543 -6436.2703 0 -6195.3884 -1015.7993
2660 23.267974 -6434.3342 0 -6194.7043 -1011.0616
2670 23.287404 -6433.8493 0 -6194.0194 -1009.2211
2680 23.400854 -6434.3704 0 -6193.372 -1009.3078
2690 23.416634 -6433.8866 0 -6192.7257 -1007.2707
2700 23.427232 -6433.3541 0 -6192.0841 -1005.4693
2710 23.635545 -6434.8406 0 -6191.4252 -1008.7624
2720 24.010565 -6438.1027 0 -6190.8251 -1016.3862
2730 24.23397 -6439.8767 0 -6190.2984 -1020.4547
2740 24.078692 -6437.7148 0 -6189.7356 -1015.0876
2750 23.670633 -6432.8931 0 -6189.1164 -1003.3684
2760 23.373655 -6429.1855 0 -6188.4673 -994.51945
2770 23.482791 -6429.5982 0 -6187.756 -995.83147
2780 23.872126 -6432.9614 0 -6187.1096 -1004.3236
2790 24.162 -6435.438 0 -6186.6008 -1010.2907
2800 24.108594 -6434.4173 0 -6186.1301 -1007.1844
2810 23.814401 -6430.8633 0 -6185.606 -997.59405
2820 23.671042 -6428.7616 0 -6184.9807 -991.50142
2830 23.904253 -6430.4417 0 -6184.259 -994.88526
2840 24.222253 -6433.0419 0 -6183.5843 -1001.3792
2850 24.366623 -6433.9188 0 -6182.9743 -1004.2837
2860 24.357528 -6433.2663 0 -6182.4155 -1003.1189
2870 24.267904 -6431.8546 0 -6181.9268 -999.3335
2880 24.1373 -6429.9704 0 -6181.3876 -994.19805
2890 24.088236 -6428.8913 0 -6180.8138 -991.20406
2900 24.237479 -6429.859 0 -6180.2445 -993.58209
2910 24.537221 -6432.4491 0 -6179.7477 -1000.1557
2920 24.725978 -6433.9593 0 -6179.3139 -1004.2865
2930 24.666397 -6432.9221 0 -6178.8903 -1002.0287
2940 24.431333 -6430.0101 0 -6178.3992 -994.8963
2950 24.205387 -6427.1163 0 -6177.8323 -987.58777
2960 24.165998 -6426.0758 0 -6177.1974 -984.54957
2970 24.304869 -6426.8576 0 -6176.5491 -985.75023
2980 24.507852 -6428.3077 0 -6175.9087 -988.49496
2990 24.71811 -6429.8823 0 -6175.3179 -991.35348
3000 24.795515 -6430.196 0 -6174.8344 -991.38382
3010 24.684857 -6428.5861 0 -6174.3641 -987.38566
3020 24.566106 -6426.8412 0 -6173.8422 -983.14118
3030 24.5132 -6425.7553 0 -6173.3012 -980.29245
3040 24.445354 -6424.4783 0 -6172.7229 -977.31599
3050 24.449132 -6423.8964 0 -6172.1021 -976.31361
3060 24.574974 -6424.5399 0 -6171.4496 -978.26691
3070 24.694342 -6425.1325 0 -6170.8129 -979.70901
3080 24.649447 -6424.071 0 -6170.2138 -976.60226
3090 24.476494 -6421.6191 0 -6169.5431 -970.00913
3100 24.513281 -6421.3556 0 -6168.9007 -968.37295
3110 24.821876 -6423.9501 0 -6168.3171 -973.82404
3120 25.101656 -6426.3352 0 -6167.8208 -979.74497
3130 25.270758 -6427.6016 0 -6167.3457 -983.50283
3140 25.403423 -6428.5364 0 -6166.9142 -985.98587
3150 25.397638 -6428.0315 0 -6166.4689 -984.51906
3160 25.128712 -6424.8064 0 -6166.0133 -976.55331
3170 24.797216 -6420.8279 0 -6165.4489 -967.18014
3180 24.861755 -6420.8636 0 -6164.8199 -966.99651
3190 25.218012 -6423.92 0 -6164.2073 -973.58189
3200 25.337601 -6424.6054 0 -6163.6611 -974.78523
3210 25.107309 -6421.6886 0 -6163.1159 -967.83802
3220 24.898576 -6418.9494 0 -6162.5265 -961.26736
3230 24.956173 -6418.9898 0 -6161.9737 -960.87585
3240 25.076431 -6419.7207 0 -6161.4661 -962.14002
3250 25.08389 -6419.2993 0 -6160.9679 -960.88619
3260 25.079853 -6418.7103 0 -6160.4205 -959.28426
3270 25.215389 -6419.4987 0 -6159.813 -961.04963
3280 25.54459 -6422.342 0 -6159.2659 -967.73074
3290 25.87554 -6425.2881 0 -6158.8037 -974.74344
3300 25.903164 -6425.1578 0 -6158.3889 -974.55815
3310 25.680487 -6422.4196 0 -6157.944 -967.79715
3320 25.436459 -6419.4634 0 -6157.501 -959.93171
3330 25.271552 -6417.219 0 -6156.955 -953.99906
3340 25.346444 -6417.3919 0 -6156.3565 -954.0175
3350 25.587077 -6419.3 0 -6155.7864 -958.22206
3360 25.695996 -6419.8737 0 -6155.2383 -959.6718
3370 25.720883 -6419.6273 0 -6154.7357 -959.2484
3380 25.879074 -6420.7997 0 -6154.2789 -961.83955
3390 26.036918 -6421.9789 0 -6153.8325 -964.45572
3400 25.948629 -6420.6132 0 -6153.3761 -961.19626
3410 25.603577 -6416.4955 0 -6152.812 -951.49936
3420 25.277837 -6412.527 0 -6152.1982 -941.89472
3430 25.230926 -6411.4805 0 -6151.6348 -938.85197
3440 25.407463 -6412.7782 0 -6151.1144 -941.42569
3450 25.617358 -6414.4021 0 -6150.5766 -944.96905
3460 25.786076 -6415.5599 0 -6149.9968 -947.32234
3470 25.922851 -6416.4053 0 -6149.4336 -949.06813
3480 26.119347 -6417.8636 0 -6148.8683 -952.68886
3490 26.218974 -6418.4654 0 -6148.4441 -954.69743
3500 26.049233 -6416.2679 0 -6147.9947 -950.18839
3510 25.693394 -6412.0535 0 -6147.445 -940.43261
3520 25.499588 -6409.4156 0 -6146.803 -933.41544
3530 25.586974 -6409.6226 0 -6146.11 -932.74156
3540 25.860392 -6411.7931 0 -6145.4647 -937.15348
3550 26.188484 -6414.6069 0 -6144.8996 -943.87737
3560 26.461464 -6416.9396 0 -6144.421 -949.90349
3570 26.589315 -6417.8021 0 -6143.9668 -952.4457
3580 26.56993 -6417.1574 0 -6143.5217 -950.92142
3590 26.455909 -6415.5203 0 -6143.0589 -946.16358
3600 26.152282 -6411.8875 0 -6142.5531 -936.37401
3610 25.775567 -6407.352 0 -6141.8973 -924.87198
3620 25.668894 -6405.556 0 -6141.1997 -920.34854
3630 25.978149 -6408.0811 0 -6140.5399 -926.56734
3640 26.564553 -6413.4864 0 -6139.9061 -939.48639
3650 26.909124 -6416.5404 0 -6139.4115 -946.37805
3660 26.724717 -6414.1574 0 -6138.9276 -940.42555
3670 26.422189 -6410.5082 0 -6138.394 -931.50617
3680 26.398635 -6409.7042 0 -6137.8326 -929.4103
3690 26.570748 -6410.9307 0 -6137.2866 -932.34441
3700 26.651417 -6411.2063 0 -6136.7314 -933.36511
3710 26.589807 -6410.0585 0 -6136.2181 -931.02997
3720 26.533858 -6408.9543 0 -6135.6901 -928.38574
3730 26.50668 -6408.1736 0 -6135.1892 -925.86436
3740 26.46159 -6407.1775 0 -6134.6575 -922.39462
3750 26.396595 -6405.9681 0 -6134.1175 -918.45094
3760 26.440196 -6405.8064 0 -6133.5068 -917.56053
3770 26.743112 -6408.2451 0 -6132.8259 -923.15375
3780 27.038748 -6410.6332 0 -6132.1693 -928.92314
3790 27.002397 -6409.6317 0 -6131.5421 -927.11925
3800 26.812667 -6407.1061 0 -6130.9705 -921.57646
3810 26.751391 -6405.9331 0 -6130.4286 -918.81768
3820 26.79566 -6405.8688 0 -6129.9083 -918.41904
3830 26.818814 -6405.6095 0 -6129.4106 -917.33046
3840 26.779516 -6404.6176 0 -6128.8234 -914.63692
3850 26.811121 -6404.3106 0 -6128.1909 -913.56294
3860 26.8958 -6404.519 0 -6127.5273 -913.78855
3870 26.921326 -6404.1181 0 -6126.8635 -912.87443
3880 27.099964 -6405.3939 0 -6126.2995 -915.28328
3890 27.27787 -6406.7453 0 -6125.8188 -917.59696
3900 27.219648 -6405.6017 0 -6125.2748 -914.50763
3910 27.105833 -6403.8204 0 -6124.6656 -910.07587
3920 27.116709 -6403.2885 0 -6124.0216 -908.42333
3930 27.081527 -6402.2517 0 -6123.3472 -905.89446
3940 26.932756 -6400.0687 0 -6122.6964 -901.1286
3950 26.930705 -6399.4167 0 -6122.0655 -899.88995
3960 27.236836 -6401.9835 0 -6121.4795 -905.52465
3970 27.502217 -6404.206 0 -6120.969 -910.18191
3980 27.430879 -6402.9045 0 -6120.4021 -907.21813
3990 27.280358 -6400.7263 0 -6119.7741 -902.29762
4000 27.27069 -6399.9508 0 -6119.0981 -900.12014
Loop time of 344.483 on 1 procs for 4000 steps with 3456 atoms
Pair time (%) = 115.899 (33.6442)
Neigh time (%) = 49.9152 (14.4899)
Comm time (%) = 1.06949 (0.310462)
Outpt time (%) = 0.0676758 (0.0196456)
Other time (%) = 177.532 (51.5358)
Nlocal: 3456 ave 3456 max 3456 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 12768 ave 12768 max 12768 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.0891e+06 ave 1.0891e+06 max 1.0891e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 2.1782e+06 ave 2.1782e+06 max 2.1782e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2178196
Ave neighs/atom = 630.265
Neighbor list builds = 400
Dangerous builds = 0

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LAMMPS (7 Jul 2009)
#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
orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215)
1 by 1 by 1 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
# ID part keywords nx ny nz region
fix_modify AtC fem create mesh 10 1 1 feRegion f p p
# specify atom types
#fix_modify AtC transfer internal type internal
# fix a temperature
fix_modify AtC transfer fix temperature all 20.0
fix_modify AtC transfer initial temperature all 20.0
fix_modify AtC transfer initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC transfer 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 transfer thermal control 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 transfer output gaussianIC_ttmFE 10 text
# change thermostat
fix_modify AtC transfer unfix temperature all
fix_modify AtC transfer unfix electron_temperature all
fix_modify AtC transfer thermal control 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
Memory usage per processor = 20.4457 Mbytes
Step Temp PotEng AtC[2] AtC[4]
0 16.671491 -6505.7593 20 21.852118
10 16.677475 -6505.5427 20.002541 21.837728
20 16.576352 -6504.1927 19.867309 21.822847
30 16.543006 -6503.5347 19.829679 21.807329
40 16.606315 -6503.9098 19.948237 21.79227
50 16.657241 -6504.1495 20.063768 21.77819
60 16.632334 -6503.6282 20.043346 21.764516
70 16.575817 -6502.7756 19.922594 21.750359
80 16.582959 -6502.556 19.854482 21.735666
90 16.619481 -6502.6709 19.843443 21.720989
100 16.61416 -6502.3553 19.823604 21.706411
110 16.63 -6502.2515 19.868881 21.692096
120 16.693117 -6502.6546 19.982758 21.67865
130 16.690721 -6502.395 19.998489 21.665851
140 16.614049 -6501.3546 19.912824 21.652674
150 16.61038 -6501.0505 19.922441 21.639146
160 16.722799 -6501.9758 20.079964 21.626427
170 16.770602 -6502.2509 20.17121 21.614856
180 16.650892 -6500.7765 20.054544 21.603105
190 16.541447 -6499.381 19.906876 21.590204
200 16.645228 -6500.2039 19.964842 21.577132
210 16.869527 -6502.3001 20.162483 21.565509
220 16.964383 -6503.0601 20.257183 21.55523
230 16.911611 -6502.3326 20.238311 21.545157
240 16.817036 -6501.1565 20.182711 21.534754
250 16.768709 -6500.4545 20.137714 21.524032
260 16.815288 -6500.7352 20.15617 21.51338
270 16.910049 -6501.5019 20.224357 21.50326
280 16.977499 -6502.0383 20.29341 21.493767
290 16.956659 -6501.6276 20.291231 21.484565
300 16.835262 -6500.213 20.164202 21.474772
310 16.71985 -6498.8264 20.004642 21.463806
320 16.69098 -6498.3213 19.932827 21.452076
330 16.761703 -6498.8528 20.012407 21.440668
340 16.868998 -6499.7478 20.16924 21.430476
350 16.984511 -6500.7709 20.340112 21.421697
360 17.123542 -6502.0546 20.527447 21.414404
370 17.196695 -6502.6994 20.623027 21.408269
380 17.078535 -6501.3567 20.479029 21.401788
390 16.82808 -6498.6218 20.180491 21.393274
400 16.644633 -6496.5257 19.969187 21.382648
Loop time of 38.0403 on 1 procs for 400 steps with 3456 atoms
Pair time (%) = 11.5723 (30.4211)
Neigh time (%) = 4.98386 (13.1015)
Comm time (%) = 0.111562 (0.293273)
Outpt time (%) = 0.00291038 (0.00765077)
Other time (%) = 21.3697 (56.1764)
Nlocal: 3456 ave 3456 max 3456 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 12768 ave 12768 max 12768 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.09177e+06 ave 1.09177e+06 max 1.09177e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 2.18354e+06 ave 2.18354e+06 max 2.18354e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2183544
Ave neighs/atom = 631.812
Neighbor list builds = 40
Dangerous builds = 0

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# 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
# ID part keywords nx ny nz region
fix_modify AtC fem create mesh 14 1 1 feRegion f p p
# specify atom types for the atc fix
#fix_modify AtC transfer internal type internal
fix_modify AtC transfer boundary type ghost
# fix initial temperatures
#if !{restart}
#velocity internal create 40 87287 mom yes loop geom
#endif
fix_modify AtC transfer initial temperature all 20
fix_modify AtC transfer fix temperature all 20
fix_modify AtC transfer initial electron_temperature all 20
fix_modify AtC transfer fix electron_temperature all 20
# equilibrate MD field with rescale
fix_modify AtC extrinsic exchange off
fix_modify AtC transfer thermal control rescale 10
#if !{restart}
#run 1000
#endif
# change thermostat
fix_modify AtC extrinsic exchange on
fix_modify AtC transfer unfix temperature all
fix_modify AtC transfer 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 transfer thermal control flux faceset bndy
# .. this controls the time filtering ....
#fix_modify AtC transfer 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 -6 6 -6 6
fix_modify AtC mesh create_nodeset rbc 13.9 14.1 -6 6 -6 6
fix_modify AtC transfer fix electron_temperature lbc 40.
fix_modify AtC transfer fix electron_temperature rbc 20.
fix_modify AtC transfer fix temperature rbc 20.
#fix_modify AtC transfer source electron_temperature all 0.0015
fix_modify AtC transfer source electron_temperature all 9.50445e-11
# output filename frequency [text output]
fix_modify AtC transfer output bar1d_ttmFE 100 text
# run transient to steady state
thermo 10
reset_timestep 0
run 4000

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#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 fem create mesh 10 1 1 feRegion f p p
# specify atom types
#fix_modify AtC transfer internal type internal
# fix a temperature
fix_modify AtC transfer fix temperature all 20.0
fix_modify AtC transfer initial temperature all 20.0
fix_modify AtC transfer initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC transfer 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 transfer thermal control 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 transfer output gaussianIC_ttmFE 10 text
# change thermostat
fix_modify AtC transfer unfix temperature all
fix_modify AtC transfer unfix electron_temperature all
fix_modify AtC transfer thermal control 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

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#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
# create atoms
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
# ID group atc PhysicsType ParameterFile
fix AtC all atc two_temperature Cu_ttm.mat
timestep 0.002
thermo 20
# ID part keywords nx ny nz region
fix_modify AtC fem create mesh 12 1 1 feRegion f p p
# fix a temperature
fix_modify AtC transfer initial temperature all 20.0
#fix_modify AtC transfer initial electron_temperature all 30.0
fix_modify AtC transfer 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 transfer 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 -12 12 -12 12
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -12 12 -12 12
fix_modify AtC transfer fix electron_temperature lbc 20.
fix_modify AtC transfer fix electron_temperature rbc 20.
#fix_modify AtC extrinsic exchange off
#fix_modify AtC transfer fix temperature lbc 20.
#fix_modify AtC transfer fix temperature rbc 20.
#fix_modify AtC extrinsic electron_integration lockstep
#fix_modify AtC transfer source electron_temperature all 1000.0
fix_modify AtC transfer source electron_temperature all 0.521981
run 400
# relaxation
fix_modify AtC transfer remove_source electron_temperature all
run 400

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#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 fem create mesh 4 1 1 feRegion p p p
# fix a temperature
fix_modify AtC transfer fix temperature all 20.0
fix_modify AtC transfer 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 transfer thermal control rescale 13
run 500
# relax
fix_modify AtC transfer output uniform_exchangeFE 100 text
fix_modify AtC transfer atomic_output uniform_exchangeMD 10000
fix_modify AtC transfer filter type exponential
fix_modify AtC transfer filter scale 5.0e2
fix_modify AtC transfer filter on
fix_modify AtC transfer unfix temperature all
fix_modify AtC transfer unfix electron_temperature all
fix_modify AtC transfer thermal control flux
# run with FE
run 5000

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#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 fem create mesh 6 1 1 mdInternal f p p
# specify atom types
#fix_modify AtC transfer internal type internal
# fix a temperature
fix_modify AtC transfer initial temperature all 20.
fix_modify AtC transfer fix temperature all 20.
fix_modify AtC transfer initial electron_temperature all 20.
fix_modify AtC transfer fix electron_temperature all 20.
# turn on thermostat
fix_modify AtC transfer thermal control 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 transfer output uniform_heatingFE 100 text
fix_modify AtC transfer unfix temperature all
fix_modify AtC transfer thermal control flux
# fix boundary
fix_modify AtC mesh create_nodeset lbc -6.1 -5.9 -12 12 -12 12
fix_modify AtC transfer fix temperature lbc 20.
fix_modify AtC mesh create_nodeset rbc 5.9 6.1 -12 12 -12 12
fix_modify AtC transfer fix temperature rbc 20.
# add source
fix_modify AtC transfer internal_quadrature on
#fix_modify AtC transfer source temperature all 0.01
fix_modify AtC transfer source temperature all 6.3363e-10
# run with FE
reset_timestep 0
run 1000

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LAMMPS (7 Jul 2009)
#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
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
# create atoms
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)
1 by 1 by 1 processor grid
mass 1 39.95 # need to keep this
# ID group atc PhysicsType ParameterFile
fix AtC all atc two_temperature Cu_ttm.mat
timestep 0.002
thermo 20
# ID part keywords nx ny nz region
fix_modify AtC fem create mesh 12 1 1 feRegion f p p
# fix a temperature
fix_modify AtC transfer initial temperature all 20.0
#fix_modify AtC transfer initial electron_temperature all 30.0
fix_modify AtC transfer 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 transfer output no_atomsFE 10 text
#fix_modify AtC extrinsic electron_integration subcycle 100
fix_modify AtC extrinsic electron_integration implicit
run 400
Memory usage per processor = 0.412468 Mbytes
Step CPU AtC[1] AtC[2] AtC[3] AtC[4]
0 0 59.94586 20 1.7847722 21.567177
20 0.46597385 59.95972 20.00454 1.770575 21.52456
40 0.93160486 59.97247 20.008795 1.7578608 21.370605
60 1.368351 59.983888 20.012606 1.7464745 21.232182
80 1.8008358 59.994113 20.016019 1.7362775 21.108216
100 2.2340729 60.00327 20.019076 1.7271457 20.997198
120 2.667372 60.01147 20.021814 1.7189676 20.897776
140 3.101615 60.018815 20.024266 1.7116438 20.808739
160 3.5347569 60.025391 20.026462 1.7050849 20.729002
180 3.9713268 60.031281 20.028429 1.6992111 20.657594
200 4.4060199 60.036556 20.030191 1.6939509 20.593644
220 4.8383729 60.04128 20.031768 1.6892401 20.536374
240 5.2700989 60.045511 20.033181 1.6850213 20.485086
260 5.702713 60.049299 20.034447 1.6812432 20.439154
280 6.1313 60.052692 20.035581 1.6778597 20.398021
300 6.552902 60.05573 20.036596 1.6748297 20.361184
320 6.978493 60.058451 20.037506 1.6721161 20.328194
340 7.3976619 60.060888 20.03832 1.6696859 20.298651
360 7.817637 60.063071 20.03905 1.6675096 20.272193
380 8.227901 60.065025 20.039703 1.6655606 20.248499
400 8.6359458 60.066775 20.040289 1.6638152 20.227279
Loop time of 8.63894 on 1 procs for 400 steps with 0 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000214577 (0.00248383)
Outpt time (%) = 0.0595214 (0.68899)
Other time (%) = 8.5792 (99.3085)
Nlocal: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min
Histogram: 1 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 -12 12 -12 12
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -12 12 -12 12
fix_modify AtC transfer fix electron_temperature lbc 20.
fix_modify AtC transfer fix electron_temperature rbc 20.
#fix_modify AtC extrinsic exchange off
#fix_modify AtC transfer fix temperature lbc 20.
#fix_modify AtC transfer fix temperature rbc 20.
#fix_modify AtC extrinsic electron_integration lockstep
#fix_modify AtC transfer source electron_temperature all 1000.0
fix_modify AtC transfer source electron_temperature all 0.521981
run 400
Memory usage per processor = 0.412468 Mbytes
Step CPU AtC[1] AtC[2] AtC[3] AtC[4]
400 0 60.066775 20.040289 1.6638152 20.227279
420 0.46465707 60.074057 20.042563 1.7526734 21.206964
440 0.93380594 60.08642 20.046435 1.7697616 21.398727
460 1.4028659 60.099602 20.050578 1.7726213 21.43082
480 1.872489 60.112889 20.054768 1.7731138 21.436346
500 2.341527 60.126162 20.058968 1.7732124 21.437452
520 2.8146279 60.139402 20.063168 1.7732452 21.437821
540 3.2863479 60.152606 20.067367 1.773267 21.438066
560 3.7559209 60.165773 20.071564 1.7732869 21.438289
580 4.2253721 60.178904 20.075757 1.7733063 21.438507
600 4.696142 60.191997 20.079946 1.7733256 21.438723
620 5.164628 60.205055 20.084131 1.7733447 21.438937
640 5.633961 60.218075 20.08831 1.7733637 21.43915
660 6.1026099 60.23106 20.092484 1.7733825 21.439362
680 6.5716951 60.244008 20.096653 1.7734013 21.439572
700 7.0413561 60.256919 20.100815 1.7734199 21.439781
720 7.5101869 60.269795 20.10497 1.7734384 21.439989
740 7.9797149 60.282635 20.109119 1.7734568 21.440195
760 8.4487319 60.295439 20.11326 1.7734751 21.4404
780 8.9184639 60.308207 20.117395 1.7734932 21.440604
800 9.3883049 60.320939 20.121522 1.7735113 21.440807
Loop time of 9.39129 on 1 procs for 400 steps with 0 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000202179 (0.00215284)
Outpt time (%) = 0.0597332 (0.636049)
Other time (%) = 9.33135 (99.3618)
Nlocal: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Neighbor list builds = 0
Dangerous builds = 0
# relaxation
fix_modify AtC transfer remove_source electron_temperature all
run 400
Memory usage per processor = 0.412468 Mbytes
Step CPU AtC[1] AtC[2] AtC[3] AtC[4]
800 0 60.320939 20.121522 1.7735113 21.440807
820 0.46552801 60.326208 20.123317 1.6666305 20.24139
840 0.93443298 60.326191 20.123452 1.6491438 20.045155
860 1.4037609 60.325301 20.123302 1.6462322 20.012481
880 1.87309 60.324267 20.123096 1.6457454 20.007018
900 2.341542 60.323212 20.122873 1.6456621 20.006083
920 2.810395 60.322156 20.122641 1.6456459 20.005902
940 3.279598 60.321102 20.122402 1.645641 20.005846
960 3.7478158 60.320051 20.122158 1.645638 20.005813
980 4.21626 60.319003 20.121908 1.6456354 20.005783
1000 4.6847739 60.317957 20.121654 1.6456328 20.005754
1020 5.1538019 60.316914 20.121396 1.6456303 20.005726
1040 5.622643 60.315874 20.121135 1.6456279 20.005699
1060 6.0918579 60.314837 20.120871 1.6456255 20.005672
1080 6.561069 60.313803 20.120603 1.6456231 20.005645
1100 7.0291269 60.312771 20.120334 1.6456208 20.005619
1120 7.497472 60.311742 20.120061 1.6456185 20.005593
1140 7.9661739 60.310716 20.119787 1.6456162 20.005568
1160 8.4346058 60.309693 20.119511 1.645614 20.005543
1180 8.9034901 60.308673 20.119234 1.6456118 20.005519
1200 9.373548 60.307655 20.118954 1.6456097 20.005495
Loop time of 9.37655 on 1 procs for 400 steps with 0 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000205755 (0.00219436)
Outpt time (%) = 0.0598149 (0.637921)
Other time (%) = 9.31653 (99.3599)
Nlocal: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (7 Jul 2009)
#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
Lattice spacing in x,y,z = 5.405 5.405 5.405
pair_style lj/cut 13.5
read_data uniform_exchange_init.data
orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215)
1 by 1 by 1 processor grid
3456 atoms
3456 velocities
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
3456 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
# ID part keywords nx ny nz region
fix_modify AtC fem create mesh 4 1 1 feRegion p p p
# fix a temperature
fix_modify AtC transfer fix temperature all 20.0
fix_modify AtC transfer 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 transfer thermal control rescale 13
run 500
Memory usage per processor = 21.0377 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 35.8006 on 1 procs for 500 steps with 3456 atoms
Pair time (%) = 15.2531 (42.6057)
Neigh time (%) = 6.75833 (18.8777)
Comm time (%) = 0.191267 (0.534258)
Outpt time (%) = 0.0041759 (0.0116643)
Other time (%) = 13.5937 (37.9707)
Nlocal: 3456 ave 3456 max 3456 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 17500 ave 17500 max 17500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.15129e+06 ave 1.15129e+06 max 1.15129e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 2.30259e+06 ave 2.30259e+06 max 2.30259e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2302588
Ave neighs/atom = 666.258
Neighbor list builds = 50
Dangerous builds = 0
# relax
fix_modify AtC transfer output uniform_exchangeFE 100 text
fix_modify AtC transfer atomic_output uniform_exchangeMD 10000
fix_modify AtC transfer filter type exponential
fix_modify AtC transfer filter scale 5.0e2
fix_modify AtC transfer filter on
fix_modify AtC transfer unfix temperature all
fix_modify AtC transfer unfix electron_temperature all
fix_modify AtC transfer thermal control flux
# run with FE
run 5000
Memory usage per processor = 21.4955 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 19.4659 19.964127 29.843272
530 -6578.0632 19.385557 19.929008 29.765503
540 -6576.7688 19.408522 19.894578 29.688066
550 -6577.5441 19.634386 19.875758 29.611022
560 -6580.0311 20.033795 19.890374 29.53457
570 -6582.692 20.453287 19.943612 29.459004
580 -6584.4988 20.792547 20.027892 29.384591
590 -6584.8106 20.986314 20.129173 29.311509
600 -6583.0642 20.973001 20.22873 29.239803
610 -6579.3187 20.764598 20.306625 29.16936
620 -6575.2098 20.510316 20.35374 29.099949
630 -6571.8246 20.325666 20.375584 29.031339
640 -6569.5494 20.242631 20.383183 28.96337
650 -6568.5339 20.279067 20.388293 28.895976
660 -6569.1807 20.481137 20.404722 28.82919
670 -6571.8804 20.888192 20.449466 28.763169
680 -6575.8853 21.427508 20.536803 28.698198
690 -6578.9633 21.878185 20.664173 28.634605
700 -6578.9118 22.022484 20.807267 28.572603
710 -6575.3784 21.818747 20.931312 28.51215
720 -6570.6353 21.492481 21.01549 28.452979
730 -6567.3963 21.301197 21.066664 28.39478
740 -6566.2643 21.309502 21.105617 28.337373
750 -6566.5396 21.457094 21.149722 28.280738
760 -6567.3538 21.656064 21.206898 28.224948
770 -6568.3366 21.872173 21.278393 28.170108
780 -6569.7079 22.127021 21.365289 28.116326
790 -6571.8911 22.460621 21.472163 28.063731
800 -6573.915 22.778464 21.601239 28.012488
810 -6573.25 22.83355 21.736318 27.962706
820 -6568.3888 22.472517 21.841822 27.914274
830 -6561.7617 21.926658 21.890085 27.866811
840 -6557.7119 21.622644 21.892222 27.81988
850 -6557.6644 21.705712 21.886316 27.773274
860 -6559.1067 21.938106 21.89967 27.727064
870 -6558.3139 21.958478 21.924594 27.681388
880 -6555.286 21.753082 21.935245 27.636218
890 -6553.5069 21.670608 21.929199 27.591405
900 -6554.6754 21.873951 21.93129 27.546912
910 -6557.3535 22.227866 21.961833 27.502902
920 -6559.804 22.562976 22.023052 27.459614
930 -6561.1035 22.79027 22.104812 27.417244
940 -6561.0754 22.886975 22.193563 27.375888
950 -6559.6583 22.843876 22.275637 27.335535
960 -6557.4925 22.726414 22.340854 27.296074
970 -6556.6435 22.735242 22.393663 27.257372
980 -6558.3713 22.994521 22.455738 27.219413
990 -6560.8396 23.325967 22.542517 27.182345
1000 -6561.3932 23.466884 22.643974 27.146328
1010 -6558.92 23.310436 22.73347 27.111357
1020 -6554.7313 22.97887 22.788548 27.077224
1030 -6551.9728 22.778205 22.811405 27.043641
1040 -6552.7121 22.918294 22.830752 27.010464
1050 -6555.4107 23.25518 22.874224 26.977793
1060 -6557.2332 23.507029 22.942583 26.945836
1070 -6557.3475 23.592787 23.019287 26.914715
1080 -6556.597 23.589643 23.091387 26.884426
1090 -6555.4951 23.548501 23.154448 26.854904
1100 -6553.7313 23.441062 23.204214 26.826055
1110 -6551.9517 23.328444 23.237874 26.797754
1120 -6551.0782 23.301201 23.26207 26.769892
1130 -6550.2773 23.281684 23.282808 26.742424
1140 -6549.0221 23.216408 23.297021 26.715309
1150 -6547.9388 23.165837 23.304079 26.688486
1160 -6547.5388 23.17981 23.308483 26.661913
1170 -6549.0771 23.386392 23.322795 26.635614
1180 -6552.9501 23.82246 23.368332 26.609757
1190 -6556.3527 24.216018 23.451529 26.584629
1200 -6556.0233 24.248394 23.546626 26.56043
1210 -6551.6739 23.885282 23.613811 26.53707
1220 -6546.3396 23.413349 23.631352 26.51421
1230 -6543.8694 23.214363 23.6148 26.491499
1240 -6545.2248 23.388954 23.601111 26.468824
1250 -6548.9978 23.804744 23.619657 26.446347
1260 -6552.0331 24.153528 23.675151 26.42436
1270 -6551.2447 24.130608 23.740189 26.403048
1280 -6546.9419 23.761466 23.776739 26.382311
1290 -6543.2504 23.442367 23.773669 26.361846
1300 -6544.0697 23.560897 23.762296 26.341452
1310 -6548.1889 24.00497 23.783494 26.321251
1320 -6550.8691 24.316793 23.840927 26.301545
1330 -6550.16 24.296091 23.904741 26.282495
1340 -6547.5804 24.091397 23.948993 26.264021
1350 -6545.5875 23.937081 23.970706 26.245937
1360 -6545.7935 23.992778 23.986105 26.228124
1370 -6547.9636 24.244836 24.016755 26.210627
1380 -6550.0271 24.487949 24.069589 26.193606
1390 -6550.748 24.602181 24.133807 26.177193
1400 -6549.5567 24.526748 24.193782 26.161407
1410 -6545.7348 24.189059 24.226461 26.146114
1420 -6541.8049 23.835117 24.220739 26.131029
1430 -6539.7085 23.656302 24.19082 26.115899
1440 -6539.9557 23.705239 24.158333 26.100628
1450 -6542.6224 23.996103 24.146799 26.085297
1460 -6546.255 24.386388 24.170746 26.070146
1470 -6548.5015 24.643846 24.224187 26.055442
1480 -6547.7415 24.610745 24.281882 26.04131
1490 -6545.2911 24.406159 24.319952 26.027667
1500 -6544.0033 24.31102 24.33879 26.014338
1510 -6545.1817 24.454182 24.359724 26.001255
1520 -6546.9716 24.656688 24.397463 25.988511
1530 -6547.337 24.722103 24.444177 25.976212
1540 -6546.4396 24.665666 24.485712 25.964361
1550 -6544.6031 24.515493 24.513107 25.952873
1560 -6542.0417 24.286541 24.519007 25.941602
1570 -6539.924 24.098546 24.503746 25.93037
1580 -6539.2427 24.051084 24.479094 25.919055
1590 -6540.47 24.188563 24.461792 25.907656
1600 -6543.5268 24.510003 24.469289 25.896308
1610 -6546.3182 24.810245 24.508235 25.885248
1620 -6544.9543 24.707464 24.552878 25.874633
1630 -6539.6863 24.213642 24.560345 25.864314
1640 -6535.4885 23.822162 24.521524 25.853923
1650 -6535.6525 23.850915 24.471296 25.84323
1660 -6537.9998 24.099209 24.442787 25.83231
1670 -6540.151 24.332665 24.440284 25.821366
1680 -6542.4466 24.584801 24.460451 25.810588
1690 -6544.8542 24.849339 24.503996 25.800154
1700 -6546.292 25.0213 24.564184 25.790224
1710 -6546.4347 25.065675 24.628133 25.780869
1720 -6545.9648 25.0447 24.685966 25.772068
1730 -6545.5871 25.030591 24.73665 25.763758
1740 -6544.4505 24.941938 24.77843 25.755877
1750 -6541.6713 24.688734 24.79902 25.748305
1760 -6539.0289 24.44345 24.7918 25.74083
1770 -6539.3176 24.483553 24.775655 25.733299
1780 -6542.0848 24.765189 24.779816 25.725774
1790 -6543.1928 24.886643 24.805158 25.718447
1800 -6540.1609 24.605257 24.818215 25.711348
1810 -6535.7937 24.186873 24.792665 25.704246
1820 -6534.2421 24.039421 24.74188 25.696869
1830 -6536.6369 24.282841 24.703222 25.689179
1840 -6539.9801 24.624823 24.700101 25.681396
1850 -6540.2476 24.668839 24.715536 25.673753
1860 -6538.3668 24.504144 24.720045 25.666255
1870 -6537.6209 24.445697 24.712456 25.658791
1880 -6538.6438 24.561109 24.709858 25.651336
1890 -6539.466 24.660384 24.719506 25.643975
1900 -6538.9182 24.624177 24.730114 25.636761
1910 -6538.628 24.614154 24.735921 25.629663
1920 -6540.1221 24.775356 24.749034 25.622688
1930 -6542.452 25.023854 24.78218 25.615953
1940 -6543.3431 25.134236 24.830292 25.609607
1950 -6541.5193 24.976983 24.869936 25.603669
1960 -6539.1628 24.760981 24.885117 25.597985
1970 -6539.2823 24.783512 24.889791 25.592402
1980 -6540.7963 24.942943 24.90599 25.586942
1990 -6540.3741 24.91461 24.927471 25.581689
2000 -6538.1889 24.712386 24.933358 25.576588
2010 -6536.9679 24.602664 24.922546 25.571493
2020 -6537.5036 24.6615 24.912017 25.566344
2030 -6538.3282 24.752621 24.910662 25.561191
2040 -6539.0384 24.830601 24.917315 25.556104
2050 -6539.3726 24.877446 24.92958 25.551136
2060 -6538.5177 24.805175 24.939349 25.546301
2070 -6536.9777 24.663065 24.936466 25.541529
2080 -6536.0953 24.583463 24.923169 25.536721
2090 -6535.7139 24.554377 24.906814 25.531831
2100 -6535.4232 24.532482 24.889552 25.526846
2110 -6535.7906 24.576113 24.874652 25.52177
2120 -6537.4405 24.750456 24.871846 25.516662
2130 -6540.6254 25.071774 24.893787 25.511671
2140 -6543.8757 25.408101 24.946696 25.507027
2150 -6544.8455 25.519155 25.016043 25.502922
2160 -6542.465 25.303874 25.07216 25.499358
2170 -6538.0696 24.881733 25.089735 25.496107
2180 -6534.4995 24.537126 25.067709 25.492839
2190 -6533.6381 24.451523 25.02814 25.48933
2200 -6535.3207 24.617318 24.998296 25.485564
2210 -6537.6097 24.846562 24.99231 25.481694
2220 -6538.0545 24.899867 25.000682 25.477883
2230 -6536.3515 24.740221 25.00117 25.474147
2240 -6534.7208 24.587268 24.984642 25.470368
2250 -6535.237 24.647545 24.965848 25.466464
2260 -6537.1641 24.843312 24.96326 25.462507
2270 -6538.6557 24.998812 24.978116 25.45864
2280 -6539.5707 25.09882 25.003003 25.454967
2290 -6540.1337 25.165772 25.033386 25.451545
2300 -6539.6374 25.12831 25.06263 25.448391
2310 -6537.488 24.929215 25.076593 25.445435
2320 -6535.5588 24.744551 25.069274 25.442517
2330 -6535.6453 24.756559 25.054735 25.439519
2340 -6537.6865 24.96228 25.053928 25.436478
2350 -6539.5064 25.147711 25.073603 25.433547
2360 -6538.9785 25.104764 25.097982 25.43083
2370 -6535.9938 24.81954 25.10214 25.428252
2380 -6533.2946 24.560341 25.077546 25.425598
2390 -6533.5869 24.593174 25.045104 25.422718
2400 -6536.8933 24.921555 25.035318 25.419686
2410 -6541.0746 25.338331 25.064543 25.416767
2420 -6542.5816 25.499512 25.119582 25.414232
2430 -6540.063 25.264983 25.162836 25.412124
2440 -6536.9576 24.968222 25.172898 25.410228
2450 -6536.951 24.969345 25.168211 25.408342
2460 -6539.4419 25.214921 25.179043 25.406486
2470 -6541.1806 25.392515 25.210842 25.404828
2480 -6540.4123 25.324658 25.243707 25.403453
2490 -6538.0804 25.101896 25.257565 25.402274
2500 -6535.6554 24.867152 25.247508 25.401108
2510 -6534.4717 24.74523 25.221069 25.399792
2520 -6535.4275 24.836527 25.196548 25.398274
2530 -6538.0484 25.091527 25.192681 25.396655
2540 -6539.9593 25.283759 25.212446 25.395127
2550 -6538.2499 25.119889 25.23125 25.393786
2560 -6533.5145 24.658368 25.214545 25.392466
2570 -6530.2956 24.339786 25.159637 25.390847
2580 -6531.6565 24.468597 25.102613 25.38877
2590 -6536.4187 24.933447 25.083292 25.386406
2600 -6540.3305 25.323643 25.109487 25.384115
2610 -6539.7078 25.278653 25.148619 25.382134
2620 -6535.3812 24.864243 25.15787 25.380367
2630 -6531.6571 24.503504 25.126242 25.378503
2640 -6532.1378 24.548061 25.083352 25.376328
2650 -6536.513 24.978713 25.07096 25.373943
2660 -6541.0671 25.432831 25.105063 25.371683
2670 -6542.5346 25.593366 25.164578 25.369841
2680 -6541.3055 25.487926 25.218359 25.368472
2690 -6539.0338 25.274683 25.250359 25.367447
2700 -6536.932 25.070102 25.258694 25.366577
2710 -6536.337 25.014184 25.253661 25.36571
2720 -6537.5684 25.134734 25.25396 25.364822
2730 -6538.7522 25.254801 25.267149 25.364002
2740 -6538.738 25.257133 25.284427 25.363317
2750 -6538.1195 25.200206 25.296109 25.362752
2760 -6538.4498 25.232579 25.305125 25.362266
2770 -6539.4182 25.327904 25.320942 25.36188
2780 -6539.5018 25.338481 25.340332 25.361643
2790 -6539.179 25.307551 25.355836 25.361546
2800 -6538.7423 25.263215 25.36689 25.361552
2810 -6536.8564 25.077086 25.366095 25.361603
2820 -6533.8447 24.780923 25.340443 25.361545
2830 -6532.5021 24.64363 25.295434 25.36119
2840 -6533.9931 24.78317 25.25683 25.360494
2850 -6536.148 24.990655 25.241027 25.359597
2860 -6536.449 25.01986 25.237977 25.358651
2870 -6535.2997 24.91021 25.22919 25.357671
2880 -6534.3565 24.818339 25.211284 25.356589
2890 -6533.5574 24.737242 25.187118 25.355347
2900 -6533.454 24.730052 25.160421 25.353908
2910 -6535.0653 24.887773 25.144195 25.352305
2920 -6537.6792 25.149129 25.150698 25.350682
2930 -6540.0654 25.391995 25.18162 25.349231
2940 -6540.3661 25.43401 25.223084 25.348094
2950 -6539.3637 25.343507 25.255387 25.34726
2960 -6539.8616 25.396878 25.28256 25.346653
2970 -6540.7425 25.489455 25.316564 25.346293
2980 -6539.5572 25.379366 25.346386 25.346198
2990 -6536.6805 25.103907 25.352834 25.346246
3000 -6534.4652 24.884149 25.333822 25.346228
3010 -6534.1671 24.849993 25.305501 25.346008
3020 -6534.8623 24.914856 25.283048 25.345587
3030 -6535.6612 24.993225 25.26938 25.34503
3040 -6537.6493 25.186591 25.269652 25.344424
3050 -6539.9926 25.42064 25.292463 25.343922
3060 -6539.7826 25.40483 25.323614 25.343656
3070 -6537.5109 25.184227 25.337514 25.343575
3080 -6535.6456 24.998436 25.329887 25.343505
3090 -6534.5985 24.892705 25.309812 25.343317
3100 -6534.1432 24.842631 25.284758 25.342947
3110 -6533.9749 24.823894 25.259178 25.342378
3120 -6534.0254 24.824242 25.235123 25.341619
3130 -6535.3169 24.949861 25.218498 25.3407
3140 -6538.8237 25.296996 25.227751 25.339758
3150 -6541.5395 25.569606 25.268148 25.339038
3160 -6541.2883 25.553386 25.315141 25.33869
3170 -6539.7281 25.40703 25.347478 25.338656
3180 -6538.5967 25.297385 25.364213 25.338806
3190 -6537.7425 25.2129 25.371095 25.339041
3200 -6535.9467 25.035124 25.365116 25.339279
3210 -6533.3 24.773082 25.337727 25.339378
3220 -6530.6338 24.504815 25.287305 25.339161
3230 -6529.1331 24.349645 25.220879 25.338472
3240 -6530.1991 24.446533 25.158679 25.337268
3250 -6534.3024 24.844155 25.127479 25.335701
3260 -6539.5426 25.358505 25.145934 25.334112
3270 -6541.5921 25.569557 25.198132 25.332851
3280 -6539.6223 25.390844 25.243112 25.332003
3290 -6537.2113 25.16368 25.261615 25.3314
3300 -6536.1615 25.065082 25.263657 25.330867
3310 -6535.8385 25.034668 25.260387 25.330326
3320 -6535.6703 25.021271 25.255639 25.329756
3330 -6535.8095 25.03327 25.251102 25.329153
3340 -6536.2748 25.082314 25.250386 25.328534
3350 -6536.6 25.112787 25.253728 25.327932
3360 -6536.7488 25.130726 25.258572 25.32737
3370 -6537.3855 25.194718 25.2668 25.326861
3380 -6538.1563 25.270292 25.281642 25.326449
3390 -6538.3249 25.290401 25.299512 25.326175
3400 -6537.5034 25.213493 25.313081 25.32603
3410 -6535.2381 24.99426 25.310262 25.325931
3420 -6533.2319 24.794828 25.286114 25.325714
3430 -6533.3393 24.798837 25.255413 25.325267
3440 -6535.4422 25.003549 25.239243 25.324633
3450 -6537.9943 25.254931 25.248171 25.323985
3460 -6538.7605 25.331471 25.272125 25.323491
3470 -6537.7503 25.233915 25.290464 25.323175
3480 -6537.0843 25.169627 25.298439 25.322956
3490 -6537.1112 25.170227 25.303272 25.322785
3500 -6537.7611 25.234727 25.310985 25.322661
3510 -6538.2408 25.283019 25.324602 25.322626
3520 -6536.8595 25.147213 25.332621 25.322686
3530 -6533.7188 24.83662 25.316807 25.322715
3540 -6530.7734 24.540788 25.272188 25.322492
3550 -6529.7444 24.433842 25.212795 25.321842
3560 -6531.3469 24.584517 25.162556 25.320754
3570 -6534.0579 24.848326 25.13945 25.319392
3580 -6535.2761 24.97031 25.13723 25.317962
3590 -6535.1081 24.963418 25.138825 25.31655
3600 -6534.7802 24.93572 25.138272 25.315153
3610 -6534.3909 24.90361 25.134511 25.313748
3620 -6535.3477 25.002897 25.133519 25.312329
3630 -6538.679 25.334465 25.154688 25.310995
3640 -6541.4791 25.616476 25.20632 25.309976
3650 -6539.778 25.460697 25.258053 25.3094
3660 -6535.1377 25.010006 25.271211 25.309084
3670 -6532.6338 24.765372 25.247769 25.308698
3680 -6534.3079 24.929933 25.225526 25.30811
3690 -6537.9993 25.294817 25.233913 25.307474
3700 -6540.3433 25.529579 25.271624 25.307047
3710 -6539.9411 25.49804 25.313231 25.306955
3720 -6539.2002 25.430008 25.34382 25.307142
3730 -6539.2664 25.436451 25.369625 25.307543
3740 -6538.5567 25.365851 25.39078 25.308129
3750 -6536.2916 25.143204 25.395047 25.308812
3760 -6533.7851 24.891501 25.374724 25.309416
3770 -6532.7643 24.783967 25.339286 25.30978
3780 -6533.4489 24.842155 25.306126 25.309862
3790 -6535.0135 24.991419 25.287313 25.30974
3800 -6535.4923 25.037885 25.280918 25.309534
3810 -6533.5853 24.848268 25.266669 25.309259
3820 -6531.8583 24.678119 25.233693 25.30879
3830 -6533.6311 24.850013 25.204527 25.30806
3840 -6538.3299 25.310761 25.211531 25.307247
3850 -6542.574 25.73673 25.262558 25.306692
3860 -6542.5857 25.748011 25.329936 25.306642
3870 -6537.0829 25.215826 25.361756 25.307001
3880 -6532.1817 24.735668 25.336047 25.307348
3890 -6534.4809 24.953451 25.302546 25.30741
3900 -6540.4701 25.539887 25.318158 25.307401
3910 -6542.9599 25.792473 25.374044 25.307717
3920 -6540.5413 25.561212 25.421677 25.308463
3930 -6536.3122 25.147316 25.430381 25.309418
3940 -6533.6221 24.879512 25.404882 25.310273
3950 -6533.3474 24.842024 25.369272 25.310862
3960 -6533.7666 24.874337 25.338585 25.311184
3970 -6533.6879 24.863079 25.311849 25.311283
3980 -6533.244 24.816284 25.284335 25.311169
3990 -6533.259 24.815347 25.256556 25.310836
4000 -6534.5517 24.939522 25.237776 25.310319
4010 -6536.0789 25.091987 25.235683 25.30973
4020 -6535.8844 25.078138 25.240131 25.309169
4030 -6535.3555 25.02731 25.238437 25.308623
4040 -6537.1013 25.197763 25.243021 25.308079
4050 -6539.6199 25.449006 25.270042 25.307671
4060 -6540.3986 25.531772 25.310327 25.307547
4070 -6539.5084 25.451784 25.34529 25.307728
4080 -6538.1577 25.324203 25.365895 25.308122
4090 -6537.5593 25.267095 25.37547 25.308621
4100 -6537.8475 25.293 25.383723 25.309181
4110 -6537.8872 25.295676 25.393196 25.309808
4120 -6537.2622 25.231835 25.398449 25.310491
4130 -6536.0501 25.111078 25.394152 25.311171
4140 -6534.4892 24.954586 25.376477 25.311756
4150 -6533.6538 24.868587 25.348298 25.312146
4160 -6534.5523 24.956357 25.323523 25.312315
4170 -6536.6395 25.157201 25.316528 25.312359
4180 -6538.3119 25.320029 25.328083 25.312432
4190 -6538.8911 25.376999 25.348713 25.312642
4200 -6537.9572 25.290203 25.365223 25.313004
4210 -6536.7709 25.173775 25.368577 25.313437
4220 -6537.2691 25.220268 25.368689 25.313867
4230 -6538.2886 25.321535 25.377853 25.314331
4240 -6537.9491 25.287644 25.38953 25.314884
4250 -6536.1194 25.109123 25.388466 25.315478
4260 -6534.3985 24.937074 25.3697 25.31598
4270 -6533.6519 24.858538 25.341305 25.316282
4280 -6533.8806 24.875393 25.312936 25.316353
4290 -6535.9379 25.072139 25.297539 25.316245
4300 -6539.6662 25.437267 25.31242 25.316139
4310 -6541.739 25.643241 25.355427 25.316286
4320 -6539.0241 25.382742 25.389952 25.316764
4330 -6533.5044 24.842688 25.378465 25.317324
4340 -6529.9373 24.486837 25.323472 25.317585
4350 -6530.4701 24.528733 25.260973 25.317353
4360 -6533.7894 24.845446 25.224514 25.316729
4370 -6537.5183 25.209526 25.225723 25.315986
4380 -6539.6412 25.425416 25.254686 25.315391
4390 -6539.0509 25.374158 25.28781 25.315063
4400 -6536.1206 25.091171 25.299323 25.314919
4410 -6533.9567 24.879583 25.283889 25.314741
4420 -6534.7145 24.951514 25.264894 25.31441
4430 -6536.2656 25.104852 25.261386 25.313996
4440 -6536.1346 25.092331 25.264813 25.313599
4450 -6534.8926 24.974094 25.259499 25.3132
4460 -6535.057 24.9926 25.249055 25.31273
4470 -6537.3839 25.220723 25.253033 25.312232
4480 -6540.2277 25.503923 25.282586 25.311879
4490 -6541.8456 25.669268 25.331215 25.311852
4500 -6541.091 25.601424 25.378769 25.312218
4510 -6538.9713 25.39624 25.406706 25.312877
4520 -6537.3013 25.233013 25.413671 25.313655
4530 -6536.8398 25.183688 25.410637 25.31443
4540 -6536.3536 25.132267 25.404731 25.315164
4550 -6534.3097 24.929694 25.386713 25.315802
4560 -6531.8407 24.683308 25.34745 25.316203
4570 -6530.9144 24.583408 25.294813 25.316223
4580 -6532.7912 24.75696 25.252108 25.315855
4590 -6535.7514 25.045266 25.238033 25.315274
4600 -6537.6363 25.229728 25.248103 25.3147
4610 -6537.792 25.251127 25.266171 25.314255
4620 -6536.3983 25.117623 25.276005 25.313929
4630 -6534.5672 24.939853 25.268776 25.313611
4640 -6533.4331 24.828261 25.24834 25.313176
4650 -6533.8103 24.863909 25.226376 25.312567
4660 -6536.1182 25.089611 25.219959 25.311847
4670 -6539.7174 25.446333 25.243392 25.311204
4680 -6542.3279 25.710054 25.295851 25.310885
4690 -6541.4186 25.631483 25.351201 25.311017
4700 -6537.8829 25.288876 25.377928 25.311473
4710 -6534.4499 24.950975 25.368312 25.311974
4720 -6532.1278 24.715487 25.333007 25.312276
4730 -6530.8911 24.58177 25.283963 25.312232
4740 -6531.2701 24.611996 25.234939 25.311792
4750 -6533.3482 24.810093 25.202985 25.311035
4760 -6535.5974 25.03102 25.195283 25.310138
4770 -6536.9532 25.166885 25.204967 25.30927
4780 -6537.7181 25.248615 25.223325 25.308526
4790 -6537.6447 25.247517 25.244092 25.307948
4800 -6536.6577 25.153281 25.256841 25.307508
4810 -6536.8034 25.168748 25.263785 25.307139
4820 -6538.3174 25.317178 25.279721 25.306859
4830 -6538.9558 25.381122 25.305443 25.306755
4840 -6537.7898 25.268152 25.325142 25.306839
4850 -6535.7991 25.075013 25.32706 25.307004
4860 -6534.1303 24.911139 25.311502 25.307103
4870 -6532.9988 24.800685 25.284748 25.307027
4880 -6532.8016 24.778236 25.254157 25.306719
4890 -6533.9121 24.885926 25.231314 25.306198
4900 -6535.7463 25.064522 25.225147 25.305571
4910 -6537.8798 25.273809 25.238247 25.304983
4920 -6539.1951 25.406749 25.267581 25.30458
4930 -6537.4521 25.240192 25.291972 25.304408
4940 -6533.9081 24.894588 25.285942 25.304306
4950 -6532.7343 24.778079 25.25729 25.304043
4960 -6534.5236 24.952741 25.237351 25.303576
4970 -6536.2977 25.126322 25.23785 25.303047
4980 -6536.9578 25.194672 25.248843 25.302579
4990 -6537.1578 25.217257 25.262555 25.302215
5000 -6536.8376 25.187791 25.274576 25.301959
5010 -6536.1979 25.125233 25.280363 25.301773
5020 -6535.9038 25.097062 25.281288 25.30161
5030 -6535.5094 25.058244 25.27963 25.301446
5040 -6534.6382 24.970893 25.27155 25.301245
5050 -6534.2083 24.93028 25.257573 25.300953
5060 -6534.8051 24.98816 25.246427 25.300559
5070 -6535.6238 25.068136 25.243858 25.300117
5080 -6535.8714 25.093069 25.246352 25.299685
5090 -6535.9431 25.101267 25.249454 25.299279
5100 -6536.3657 25.142361 25.254857 25.298908
5110 -6536.449 25.153818 25.262675 25.298596
5120 -6536.2916 25.142934 25.268877 25.298342
5130 -6537.05 25.216595 25.277483 25.298143
5140 -6537.9504 25.307283 25.294484 25.298049
5150 -6537.5766 25.271706 25.31233 25.298102
5160 -6536.315 25.15146 25.319554 25.298254
5170 -6535.9252 25.114151 25.317923 25.298416
5180 -6536.4797 25.166993 25.31887 25.29857
5190 -6536.1179 25.131359 25.321011 25.298741
5200 -6534.9205 25.015122 25.314483 25.298895
5210 -6534.1764 24.937389 25.298688 25.298953
5220 -6534.5271 24.971833 25.282929 25.298879
5230 -6535.3186 25.047102 25.27495 25.298714
5240 -6535.931 25.108114 25.273958 25.298519
5250 -6536.9152 25.207036 25.280381 25.298348
5260 -6538.4517 25.35902 25.298595 25.298277
5270 -6539.799 25.494651 25.329407 25.298406
5280 -6539.8898 25.50717 25.36441 25.298803
5290 -6538.0805 25.333627 25.38759 25.299432
5300 -6535.0967 25.042437 25.384621 25.300131
5310 -6533.658 24.896665 25.359622 25.300693
5320 -6535.3136 25.053548 25.339646 25.301057
5330 -6537.5652 25.272894 25.342373 25.301359
5340 -6537.8096 25.296812 25.356373 25.301742
5350 -6535.8769 25.106667 25.359182 25.302196
5360 -6533.9006 24.911229 25.341371 25.302578
5370 -6533.6917 24.885202 25.315233 25.302769
5380 -6535.1639 25.02472 25.298247 25.302783
5390 -6536.8588 25.192813 25.299422 25.302742
5400 -6536.3923 25.145895 25.306382 25.30275
5410 -6534.0169 24.912716 25.296709 25.302752
5420 -6532.4609 24.759441 25.268064 25.302588
5430 -6533.6554 24.873377 25.240966 25.302189
5440 -6537.273 25.226778 25.241142 25.301685
5450 -6540.52 25.548422 25.275716 25.301341
5460 -6540.7994 25.581781 25.323131 25.301347
5470 -6538.9727 25.411283 25.356422 25.301676
5480 -6538.026 25.32227 25.372919 25.302184
5490 -6538.1542 25.336104 25.386457 25.302798
5500 -6536.874 25.212637 25.393998 25.303497
Loop time of 478.494 on 1 procs for 5000 steps with 3456 atoms
Pair time (%) = 152.419 (31.8539)
Neigh time (%) = 67.4687 (14.1002)
Comm time (%) = 1.95807 (0.409215)
Outpt time (%) = 0.0418682 (0.00875)
Other time (%) = 256.606 (53.6279)
Nlocal: 3456 ave 3456 max 3456 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 17500 ave 17500 max 17500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.15063e+06 ave 1.15063e+06 max 1.15063e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 2.30127e+06 ave 2.30127e+06 max 2.30127e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2301266
Ave neighs/atom = 665.876
Neighbor list builds = 500
Dangerous builds = 0

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# 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
Memory usage per processor = 12.6012 Mbytes
Step CPU PotEng TotEng Temp AtC[1] AtC[2]
0 0 -4406.6687 -4200.7544 29.995658 206.60693 20
100 4.374239 -4258.7421 -4155.7253 15.006513 206.60693 20
200 8.7224889 -4317.7651 -4214.7483 15.006513 206.60693 20
300 13.107087 -4308.7092 -4205.6924 15.006513 206.60693 20
400 17.471487 -4305.0489 -4202.0322 15.006513 206.60693 20
Loop time of 17.4723 on 1 procs for 400 steps with 2304 atoms
Pair time (%) = 7.26201 (41.563)
Neigh time (%) = 3.21221 (18.3845)
Comm time (%) = 0.0692339 (0.396249)
Outpt time (%) = 0.0033679 (0.0192756)
Other time (%) = 6.92549 (39.637)
Nlocal: 2304 ave 2304 max 2304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8512 ave 8512 max 8512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708396 ave 708396 max 708396 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.41679e+06 ave 1.41679e+06 max 1.41679e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1416792
Ave neighs/atom = 614.927
Neighbor list builds = 40
Dangerous builds = 0
# change thermostat
fix_modify AtC transfer output uniform_heatingFE 100 text
fix_modify AtC transfer unfix temperature all
fix_modify AtC transfer thermal control flux
# fix boundary
fix_modify AtC mesh create_nodeset lbc -6.1 -5.9 -12 12 -12 12
fix_modify AtC transfer fix temperature lbc 20.
fix_modify AtC mesh create_nodeset rbc 5.9 6.1 -12 12 -12 12
fix_modify AtC transfer fix temperature rbc 20.
# add source
fix_modify AtC transfer internal_quadrature on
#fix_modify AtC transfer source temperature all 0.01
fix_modify AtC transfer source temperature all 6.3363e-10
# run with FE
reset_timestep 0
run 1000
Memory usage per processor = 12.8301 Mbytes
Step CPU PotEng TotEng Temp AtC[1] AtC[2]
0 0 -4305.0489 -4202.0322 15.006513 206.60693 20
100 4.999783 -4284.0298 -4161.843 17.799024 245.0222 23.187441
200 10.004533 -4271.7421 -4126.3033 21.186144 291.62708 27.054401
300 14.997962 -4252.1549 -4092.7431 23.221608 319.6337 29.378203
400 19.994763 -4243.1541 -4066.5034 25.732803 354.18694 32.245199
500 24.995776 -4220.6621 -4038.0194 26.605674 366.2029 33.242202
600 30.001314 -4216.5541 -4017.5256 28.992598 399.04557 35.967267
700 35.011217 -4214.2511 -3996.8157 31.673926 435.9421 39.028694
800 40.015315 -4198.8979 -3978.4057 32.119215 442.05328 39.535758
900 45.030258 -4186.3755 -3963.2872 32.497398 447.23921 39.966052
1000 50.05034 -4182.9374 -3949.4046 34.018854 468.17469 41.703138
Loop time of 50.0512 on 1 procs for 1000 steps with 2304 atoms
Pair time (%) = 18.1533 (36.2694)
Neigh time (%) = 8.00558 (15.9948)
Comm time (%) = 0.15968 (0.319034)
Outpt time (%) = 0.00851512 (0.0170128)
Other time (%) = 23.7241 (47.3998)
Nlocal: 2304 ave 2304 max 2304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8512 ave 8512 max 8512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 703501 ave 703501 max 703501 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.407e+06 ave 1.407e+06 max 1.407e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1407002
Ave neighs/atom = 610.678
Neighbor list builds = 100
Dangerous builds = 0

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LAMMPS (7 Jul 2009)
log consistency.log
units metal
atom_style atomic
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
region mdRegion block 0 $L -3 3 -3 3
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 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
Setting up minimization ...
Memory usage per processor = 2.60694 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 0.0242112 on 1 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
Iterations, force evaluations = 1 2
Pair time (%) = 0.023643 (97.6533)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000159502 (0.658795)
Outpt time (%) = 0 (0)
Other time (%) = 0.000408649 (1.68786)
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
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
# 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
# displace atoms
# NOTE we need to figure out how to output post minimize w/o a "run"
# or try to interface with "dump"
# this is fine, no integrator is being used
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 = 4.47614 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 0.226753 on 1 procs for 1 steps with 2304 atoms
Pair time (%) = 0.00827098 (3.64757)
Neigh time (%) = 0 (0)
Comm time (%) = 9.60827e-05 (0.0423733)
Outpt time (%) = 6.10352e-05 (0.026917)
Other time (%) = 0.218325 (96.2831)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
Neighbor list builds = 0
Dangerous builds = 0
# increment
variable n equal 10
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"
#displace_box all x delta 0 $s units lattice
displace_box all x scale 1.001
System init for displace_box ...
Displacing box ...
minimize 1.e-10 1.e-10 100000 1000000
WARNING: Resetting reneighboring criteria during minimization
Setting up minimization ...
Memory usage per processor = 5.46796 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 0.0246379 on 1 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
Iterations, force evaluations = 1 2
Pair time (%) = 0.0240541 (97.6301)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000166893 (0.677382)
Outpt time (%) = 0 (0)
Other time (%) = 0.000416994 (1.69249)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
Neighbor list builds = 0
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 = 4.55243 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 0.119391 on 1 procs for 1 steps with 2304 atoms
Pair time (%) = 0.00807405 (6.76269)
Neigh time (%) = 0 (0)
Comm time (%) = 5.38826e-05 (0.0451312)
Outpt time (%) = 5.60284e-05 (0.0469285)
Other time (%) = 0.111207 (93.1452)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
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"
#displace_box all x delta 0 $s units lattice
displace_box all x scale 1.001
System init for displace_box ...
Displacing box ...
minimize 1.e-10 1.e-10 100000 1000000
WARNING: Resetting reneighboring criteria during minimization
Setting up minimization ...
Memory usage per processor = 5.46796 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 0.024636 on 1 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 = 1.32585e-12 7.30748e-13
Force max component initial, final = 8.13585e-14 2.95606e-14
Final line search alpha, max atom move = 1 2.95606e-14
Iterations, force evaluations = 1 2
Pair time (%) = 0.024039 (97.5767)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00015974 (0.648402)
Outpt time (%) = 0 (0)
Other time (%) = 0.00043726 (1.77488)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
Neighbor list builds = 0
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 = 4.55243 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 0.120375 on 1 procs for 1 steps with 2304 atoms
Pair time (%) = 0.00805187 (6.689)
Neigh time (%) = 0 (0)
Comm time (%) = 5.29289e-05 (0.0439701)
Outpt time (%) = 6.10352e-05 (0.0507042)
Other time (%) = 0.112209 (93.2163)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
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"
#displace_box all x delta 0 $s units lattice
displace_box all x scale 1.001
System init for displace_box ...
Displacing box ...
minimize 1.e-10 1.e-10 100000 1000000
WARNING: Resetting reneighboring criteria during minimization
Setting up minimization ...
Memory usage per processor = 5.46796 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 0.0247059 on 1 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 = 1.94102e-12 7.61581e-13
Force max component initial, final = 1.05763e-13 5.39187e-14
Final line search alpha, max atom move = 1 5.39187e-14
Iterations, force evaluations = 1 2
Pair time (%) = 0.024051 (97.3491)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000176191 (0.713155)
Outpt time (%) = 0 (0)
Other time (%) = 0.000478745 (1.93778)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
Neighbor list builds = 0
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 = 4.55243 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 0.120042 on 1 procs for 1 steps with 2304 atoms
Pair time (%) = 0.0080452 (6.70198)
Neigh time (%) = 0 (0)
Comm time (%) = 5.36442e-05 (0.0446878)
Outpt time (%) = 7.9155e-05 (0.0659393)
Other time (%) = 0.111864 (93.1874)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
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"
#displace_box all x delta 0 $s units lattice
displace_box all x scale 1.001
System init for displace_box ...
Displacing box ...
minimize 1.e-10 1.e-10 100000 1000000
WARNING: Resetting reneighboring criteria during minimization
Setting up minimization ...
Memory usage per processor = 5.46796 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 0.0245981 on 1 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 = 1.08269e-12 5.81022e-13
Force max component initial, final = 8.02492e-14 2.99639e-14
Final line search alpha, max atom move = 1 2.99639e-14
Iterations, force evaluations = 1 2
Pair time (%) = 0.0240219 (97.6573)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000160217 (0.65134)
Outpt time (%) = 0 (0)
Other time (%) = 0.00041604 (1.69135)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
Neighbor list builds = 0
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 = 4.55243 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 0.120122 on 1 procs for 1 steps with 2304 atoms
Pair time (%) = 0.00808311 (6.72908)
Neigh time (%) = 0 (0)
Comm time (%) = 5.50747e-05 (0.045849)
Outpt time (%) = 5.79357e-05 (0.0482307)
Other time (%) = 0.111926 (93.1768)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
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"
#displace_box all x delta 0 $s units lattice
displace_box all x scale 1.001
System init for displace_box ...
Displacing box ...
minimize 1.e-10 1.e-10 100000 1000000
WARNING: Resetting reneighboring criteria during minimization
Setting up minimization ...
Memory usage per processor = 5.46796 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 0.024632 on 1 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 = 1.1313e-12 7.82853e-13
Force max component initial, final = 8.02778e-14 5.43714e-14
Final line search alpha, max atom move = 1 5.43714e-14
Iterations, force evaluations = 1 2
Pair time (%) = 0.0240543 (97.6547)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000161648 (0.656252)
Outpt time (%) = 0 (0)
Other time (%) = 0.00041604 (1.68903)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
Neighbor list builds = 0
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 = 4.55243 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 0.120206 on 1 procs for 1 steps with 2304 atoms
Pair time (%) = 0.00806189 (6.70672)
Neigh time (%) = 0 (0)
Comm time (%) = 5.4121e-05 (0.0450235)
Outpt time (%) = 5.6982e-05 (0.0474036)
Other time (%) = 0.112033 (93.2009)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
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"
#displace_box all x delta 0 $s units lattice
displace_box all x scale 1.001
System init for displace_box ...
Displacing box ...
minimize 1.e-10 1.e-10 100000 1000000
WARNING: Resetting reneighboring criteria during minimization
Setting up minimization ...
Memory usage per processor = 5.46796 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 0.024919 on 1 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 = 1.14021e-12 6.70937e-13
Force max component initial, final = 8.01356e-14 2.94677e-14
Final line search alpha, max atom move = 1 2.94677e-14
Iterations, force evaluations = 1 2
Pair time (%) = 0.024272 (97.4033)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000189066 (0.758721)
Outpt time (%) = 0 (0)
Other time (%) = 0.000458002 (1.83796)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
Neighbor list builds = 0
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 = 4.55243 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 0.121576 on 1 procs for 1 steps with 2304 atoms
Pair time (%) = 0.00806904 (6.63703)
Neigh time (%) = 0 (0)
Comm time (%) = 5.38826e-05 (0.0443201)
Outpt time (%) = 6.41346e-05 (0.0527526)
Other time (%) = 0.113389 (93.2659)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
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"
#displace_box all x delta 0 $s units lattice
displace_box all x scale 1.001
System init for displace_box ...
Displacing box ...
minimize 1.e-10 1.e-10 100000 1000000
WARNING: Resetting reneighboring criteria during minimization
Setting up minimization ...
Memory usage per processor = 5.46796 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 0.0250602 on 1 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 = 1.08631e-12 6.99247e-13
Force max component initial, final = 5.57783e-14 3.60094e-14
Final line search alpha, max atom move = 1 3.60094e-14
Iterations, force evaluations = 1 2
Pair time (%) = 0.0243783 (97.279)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000192642 (0.768718)
Outpt time (%) = 0 (0)
Other time (%) = 0.000489235 (1.95224)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
Neighbor list builds = 0
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 = 4.55243 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 0.120006 on 1 procs for 1 steps with 2304 atoms
Pair time (%) = 0.00805497 (6.71215)
Neigh time (%) = 0 (0)
Comm time (%) = 5.4121e-05 (0.0450987)
Outpt time (%) = 6.19888e-05 (0.0516548)
Other time (%) = 0.111835 (93.1911)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
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"
#displace_box all x delta 0 $s units lattice
displace_box all x scale 1.001
System init for displace_box ...
Displacing box ...
minimize 1.e-10 1.e-10 100000 1000000
WARNING: Resetting reneighboring criteria during minimization
Setting up minimization ...
Memory usage per processor = 5.46796 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 0.0249629 on 1 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 = 2.06136e-12 1.22509e-12
Force max component initial, final = 1.0524e-13 5.42014e-14
Final line search alpha, max atom move = 1 5.42014e-14
Iterations, force evaluations = 1 2
Pair time (%) = 0.0242603 (97.1853)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000189781 (0.760253)
Outpt time (%) = 0 (0)
Other time (%) = 0.000512838 (2.0544)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
Neighbor list builds = 0
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 = 4.55243 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 0.119222 on 1 procs for 1 steps with 2304 atoms
Pair time (%) = 0.00806999 (6.76888)
Neigh time (%) = 0 (0)
Comm time (%) = 5.4121e-05 (0.0453952)
Outpt time (%) = 5.4121e-05 (0.0453952)
Other time (%) = 0.111044 (93.1403)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
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"
#displace_box all x delta 0 $s units lattice
displace_box all x scale 1.001
System init for displace_box ...
Displacing box ...
minimize 1.e-10 1.e-10 100000 1000000
WARNING: Resetting reneighboring criteria during minimization
Setting up minimization ...
Memory usage per processor = 5.46796 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 0.024843 on 1 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 = 1.42303e-12 6.1217e-13
Force max component initial, final = 1.02033e-13 3.68872e-14
Final line search alpha, max atom move = 1 3.68872e-14
Iterations, force evaluations = 1 2
Pair time (%) = 0.02426 (97.6535)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000159025 (0.640121)
Outpt time (%) = 0 (0)
Other time (%) = 0.000423908 (1.70635)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
Neighbor list builds = 0
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 = 4.55243 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 0.120457 on 1 procs for 1 steps with 2304 atoms
Pair time (%) = 0.008075 (6.70363)
Neigh time (%) = 0 (0)
Comm time (%) = 5.36442e-05 (0.0445338)
Outpt time (%) = 6.07967e-05 (0.0504717)
Other time (%) = 0.112268 (93.2014)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
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"
#displace_box all x delta 0 $s units lattice
displace_box all x scale 1.001
System init for displace_box ...
Displacing box ...
minimize 1.e-10 1.e-10 100000 1000000
WARNING: Resetting reneighboring criteria during minimization
Setting up minimization ...
Memory usage per processor = 5.46796 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 0.024864 on 1 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 = 1.51105e-12 7.3975e-13
Force max component initial, final = 1.02474e-13 5.17997e-14
Final line search alpha, max atom move = 1 5.17997e-14
Iterations, force evaluations = 1 2
Pair time (%) = 0.0242813 (97.6565)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00016427 (0.660677)
Outpt time (%) = 0 (0)
Other time (%) = 0.000418425 (1.68286)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
Neighbor list builds = 0
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 = 4.55243 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 0.120968 on 1 procs for 1 steps with 2304 atoms
Pair time (%) = 0.00806904 (6.67039)
Neigh time (%) = 0 (0)
Comm time (%) = 5.31673e-05 (0.0439515)
Outpt time (%) = 5.6982e-05 (0.047105)
Other time (%) = 0.112789 (93.2386)
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
Total # of neighbors = 124416
Ave neighs/atom = 54
Neighbor list builds = 0
Dangerous builds = 0
next i
jump in.consistency loop_i

2767
examples/USER/atc/hardy/eam_kernel_convergence.screen Normal file
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70
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LAMMPS (7 Jul 2009)
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 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
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 = 8.29119 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 0.0510271 on 1 procs for 1 steps with 4896 atoms
Pair time (%) = 0.0173669 (34.0347)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000237226 (0.464903)
Outpt time (%) = 0.00011301 (0.221472)
Other time (%) = 0.0333099 (65.279)
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
Total # of neighbors = 260064
Ave neighs/atom = 53.1176
Neighbor list builds = 0
Dangerous builds = 0
System init for displace_atoms ...
Displacing atoms ...
ATC:: Warning : text output can create _LARGE_ files
Setting up run ...
ATC:: conversion factor for energy/vol -> stress 1.60218e+06
ATC:: cutoff radius 4.95
Memory usage per processor = 8.52007 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 0.19337 on 1 procs for 1 steps with 4896 atoms
Pair time (%) = 0.0174251 (9.01126)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000144005 (0.0744712)
Outpt time (%) = 0.000128031 (0.0662103)
Other time (%) = 0.175673 (90.8481)
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
Total # of neighbors = 260064
Ave neighs/atom = 53.1176
Neighbor list builds = 0
Dangerous builds = 0

69
examples/USER/atc/hardy/eam_unistrain_mesh.screen Normal file
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LAMMPS (7 Jul 2009)
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 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
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 = 8.29119 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 0.0511031 on 1 procs for 1 steps with 4896 atoms
Pair time (%) = 0.017396 (34.0409)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000231981 (0.453947)
Outpt time (%) = 0.000114918 (0.224874)
Other time (%) = 0.0333602 (65.2803)
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
Total # of neighbors = 260064
Ave neighs/atom = 53.1176
Neighbor list builds = 0
Dangerous builds = 0
System init for displace_atoms ...
Displacing atoms ...
ATC:: Warning : text output can create _LARGE_ files
Setting up run ...
ATC:: conversion factor for energy/vol -> stress 1.60218e+06
ATC:: cutoff radius 4.95
Memory usage per processor = 8.52007 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 0.253512 on 1 procs for 1 steps with 4896 atoms
Pair time (%) = 0.017252 (6.80518)
Neigh time (%) = 0 (0)
Comm time (%) = 8.2016e-05 (0.0323519)
Outpt time (%) = 0.000113964 (0.0449541)
Other time (%) = 0.236064 (93.1175)
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
Total # of neighbors = 260064
Ave neighs/atom = 53.1176
Neighbor list builds = 0
Dangerous builds = 0

70
examples/USER/atc/hardy/eam_unistrain_qcylinder.screen Normal file
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LAMMPS (7 Jul 2009)
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 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
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 = 8.29119 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 0.0510561 on 1 procs for 1 steps with 4896 atoms
Pair time (%) = 0.017345 (33.9723)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000228167 (0.446893)
Outpt time (%) = 0.000115156 (0.225548)
Other time (%) = 0.0333679 (65.3552)
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
Total # of neighbors = 260064
Ave neighs/atom = 53.1176
Neighbor list builds = 0
Dangerous builds = 0
System init for displace_atoms ...
Displacing atoms ...
ATC:: Warning : text output can create _LARGE_ files
Setting up run ...
ATC:: conversion factor for energy/vol -> stress 1.60218e+06
ATC:: cutoff radius 4.95
Memory usage per processor = 8.52007 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 0.204668 on 1 procs for 1 steps with 4896 atoms
Pair time (%) = 0.017287 (8.44637)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000152111 (0.0743209)
Outpt time (%) = 0.000106096 (0.0518382)
Other time (%) = 0.187123 (91.4275)
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
Total # of neighbors = 260064
Ave neighs/atom = 53.1176
Neighbor list builds = 0
Dangerous builds = 0

70
examples/USER/atc/hardy/eam_unistrain_qsphere.screen Normal file
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LAMMPS (7 Jul 2009)
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 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
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 = 8.29119 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 0.0511951 on 1 procs for 1 steps with 4896 atoms
Pair time (%) = 0.0174079 (34.003)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00023222 (0.453597)
Outpt time (%) = 0.000113964 (0.222607)
Other time (%) = 0.0334411 (65.3208)
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
Total # of neighbors = 260064
Ave neighs/atom = 53.1176
Neighbor list builds = 0
Dangerous builds = 0
System init for displace_atoms ...
Displacing atoms ...
ATC:: Warning : text output can create _LARGE_ files
Setting up run ...
ATC:: conversion factor for energy/vol -> stress 1.60218e+06
ATC:: cutoff radius 4.95
Memory usage per processor = 8.52007 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 0.188848 on 1 procs for 1 steps with 4896 atoms
Pair time (%) = 0.0172491 (9.13386)
Neigh time (%) = 0 (0)
Comm time (%) = 8.29697e-05 (0.0439346)
Outpt time (%) = 0.000128031 (0.0677957)
Other time (%) = 0.171388 (90.7544)
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
Total # of neighbors = 260064
Ave neighs/atom = 53.1176
Neighbor list builds = 0
Dangerous builds = 0

70
examples/USER/atc/hardy/eam_unistrain_step.screen Normal file
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LAMMPS (7 Jul 2009)
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 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
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 = 8.29119 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 0.051152 on 1 procs for 1 steps with 4896 atoms
Pair time (%) = 0.017437 (34.0886)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00022912 (0.447921)
Outpt time (%) = 0.000115156 (0.225125)
Other time (%) = 0.0333707 (65.2384)
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
Total # of neighbors = 260064
Ave neighs/atom = 53.1176
Neighbor list builds = 0
Dangerous builds = 0
System init for displace_atoms ...
Displacing atoms ...
ATC:: Warning : text output can create _LARGE_ files
Setting up run ...
ATC:: conversion factor for energy/vol -> stress 1.60218e+06
ATC:: cutoff radius 4.95
Memory usage per processor = 8.52007 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 0.188943 on 1 procs for 1 steps with 4896 atoms
Pair time (%) = 0.0172651 (9.13771)
Neigh time (%) = 0 (0)
Comm time (%) = 8.4877e-05 (0.044922)
Outpt time (%) = 0.000100851 (0.0533764)
Other time (%) = 0.171492 (90.764)
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
Total # of neighbors = 260064
Ave neighs/atom = 53.1176
Neighbor list builds = 0
Dangerous builds = 0

133
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LAMMPS (7 Jul 2009)
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 -3 3 -3 3 -3 3
region feRegion block -3 3 -3 3 -3 3
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
Created orthogonal box = (-10.845 -10.845 -10.845) to (10.845 10.845 10.845)
1 by 1 by 1 processor grid
# create atoms
create_atoms 1 region mdRegion
Created 864 atoms
mass 1 63.550
# specify interal/ghost 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
# 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
# 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
log eam_volume_stretch.log
# equilibrate MD field
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 = 4.02971 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 0.00839496 on 1 procs for 1 steps with 864 atoms
Pair time (%) = 0.00306296 (36.4858)
Neigh time (%) = 0 (0)
Comm time (%) = 3.79086e-05 (0.451563)
Outpt time (%) = 3.09944e-05 (0.369203)
Other time (%) = 0.00526309 (62.6935)
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
Total # of neighbors = 46656
Ave neighs/atom = 54
Neighbor list builds = 0
Dangerous builds = 0
# stretch system
displace_box all x scale 1.001 y scale 1.001 z scale 1.001
System init for displace_box ...
Displacing box ...
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
run 1
Setting up run ...
ATC:: conversion factor for energy/vol -> stress 1.60218e+06
ATC:: cutoff radius 4.95
Memory usage per processor = 4.02971 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 0.0824161 on 1 procs for 1 steps with 864 atoms
Pair time (%) = 0.00323987 (3.93112)
Neigh time (%) = 0 (0)
Comm time (%) = 5.57899e-05 (0.0676931)
Outpt time (%) = 2.69413e-05 (0.0326894)
Other time (%) = 0.0790935 (95.9685)
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
Total # of neighbors = 46656
Ave neighs/atom = 54
Neighbor list builds = 0
Dangerous builds = 0

73
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# 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
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
# 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
# displace atoms
# NOTE we need to figure out how to output post minimize w/o a "run"
# or try to interface with "dump"
# this is fine, no integrator is being used
timestep 0.0
# initial before minimization?
run 1
# increment
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"
#displace_box all x delta 0 $s units lattice
displace_box all x scale 1.001
minimize 1.e-10 1.e-10 100000 1000000
velocity all set 0 0 0
run 1
next i
jump in.consistency loop_i

66
examples/USER/atc/hardy/in.eam_kernel_convergence Normal file
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echo both
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
region SYSTEM block -6 6 -6 6 -6 6
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
# relative to a
variable d equal 0.1
variable n equal 60
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}
# initial (1)
run 1
# increment (2)
next i
jump in.eam_kernel_convergence loop_i

64
examples/USER/atc/hardy/in.eam_unistrain_cell Normal file
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#AtC Thermal Coupling
log eam_unistrain_cell.log
units metal
atom_style atomic
# 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
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 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
# ID part keywords nx ny nz region
fix_modify AtC fem create mesh 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_cellFE 1 text tensor_components
fix_modify AtC transfer atomic_output eam_unistrain_cellMD 1
run 1

60
examples/USER/atc/hardy/in.eam_unistrain_mesh Normal file
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#AtC Thermal Coupling
log eam_unistrain_mesh.log
units metal
atom_style atomic
# 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
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 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
# ID part keywords nx ny nz region
fix_modify AtC fem create mesh 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_meshFE 1 text tensor_components
fix_modify AtC transfer atomic_output eam_unistrain_meshMD 1
run 1

66
examples/USER/atc/hardy/in.eam_unistrain_qcylinder Normal file
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#AtC Thermal Coupling
log eam_unistrain_qcylinder.log
units metal
atom_style atomic
# 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
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 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
# 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
# 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
run 1

67
examples/USER/atc/hardy/in.eam_unistrain_qsphere Normal file
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#AtC Thermal Coupling
log eam_unistrain_qsphere.log
units metal
atom_style atomic
# 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
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 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
# 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
# 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
run 1

66
examples/USER/atc/hardy/in.eam_unistrain_step Normal file
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#AtC Thermal Coupling
log eam_unistrain_step.log
units metal
atom_style atomic
# 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
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 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
# 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
# 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
run 1

66
examples/USER/atc/hardy/in.eam_volume_stretch Normal file
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#AtC Thermal Coupling
echo both
units metal
atom_style atomic
# create domain
lattice fcc 3.615 origin 0.25 0.25 0.25
region simRegion block -3 3 -3 3 -3 3
region feRegion block -3 3 -3 3 -3 3
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
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
# 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
# ID part keywords nx ny nz region
fix_modify AtC fem create mesh 2 2 2 feRegion p p p
log eam_volume_stretch.log
# equilibrate MD field
timestep 0.001
reset_timestep 0
run 1
# stretch system
displace_box all x scale 1.001 y scale 1.001 z scale 1.001
fix_modify AtC transfer output eam_volume_stretchFE 1 text tensor_components
# fix_modify AtC transfer atomic_output eam_volume_stretchMD 1 text
run 1

26
examples/USER/atc/hardy/in.nvt Normal file
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read_restart nvt.restart
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
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
thermo 100
compute_modify thermo_temp extra 0
thermo_style custom step temp etotal ke pe press
log nvt.log
timestep 4.0
reset_timestep 0
fix NVT all nvt 30 30 10 drag 0.2
run 1000