Merge pull request #3779 from lammps/fix-ttm-mod-arrays
Reorder fix ttm/mod 3d arrays to be consistent with fix ttm and fix ttm/grid
This commit is contained in:
Axel Kohlmeyer
@ -1,6 +1,4 @@
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LAMMPS (24 Mar 2022)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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LAMMPS (28 Mar 2023 - Development)
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units metal
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atom_style atomic
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boundary p p p
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@ -15,7 +13,7 @@ mass 1 28.0855
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create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 basis 5 1 basis 6 1 basis 7 1 basis 8 1
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Created 8000 atoms
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using lattice units in orthogonal box = (0 0 0) to (54.309 54.309 54.309)
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create_atoms CPU = 0.001 seconds
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create_atoms CPU = 0.002 seconds
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pair_style sw
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pair_coeff * * Si.sw Si
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@ -42,12 +40,12 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- fix ttm/mod command:
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- fix ttm/mod command: doi:10.1088/0953-8984/26/47/475401, doi:10.1002/ctpp.201310025
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@article{Pisarev2014,
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author = {Pisarev, V. V. and Starikov, S. V.},
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title = {{Atomistic simulation of ion track formation in UO2.}},
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journal = {J.~Phys.:~Condens.~Matter},
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title = {Atomistic Simulation of Ion Track Formation in {UO$_2$}.},
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journal = {J.~Phys.\ Condens.\ Matter},
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volume = {26},
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number = {47},
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pages = {475401},
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@ -56,8 +54,8 @@ year = {2014}
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@article{Norman2013,
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author = {Norman, G. E. and Starikov, S. V. and Stegailov, V. V. and Saitov, I. M. and Zhilyaev, P. A.},
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title = {{Atomistic Modeling of Warm Dense Matter in the Two-Temperature State}},
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journal = {Contrib.~Plasm.~Phys.},
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title = {Atomistic Modeling of Warm Dense Matter in the Two-Temperature State},
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journal = {Contrib.\ Plasma Phys.},
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number = {2},
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volume = {53},
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pages = {129--139},
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@ -67,7 +65,7 @@ year = {2013}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Neighbor list info ...
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update every 5 steps, delay 0 steps, check yes
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update: every = 5 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 5.77118
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ghost atom cutoff = 5.77118
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@ -81,30 +79,30 @@ Neighbor list info ...
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Per MPI rank memory allocation (min/avg/max) = 4.433 | 4.433 | 4.433 Mbytes
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Step Temp TotEng f_twotemp[1] f_twotemp[2]
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0 0 -34692.79996100604 -52.79390940511979 0
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100 2.004897156140836 -34690.27961013186 -55.34997305431884 0.01301140393178354
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200 2.837118035232607 -34687.74741132015 -57.93445748841878 0.02696025968760173
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300 4.263087164947482 -34684.98084093686 -60.75945453846786 0.02175636603841567
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400 5.568003854939066 -34682.25271040963 -63.56896518300501 0.0300061848347275
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500 6.225602451570786 -34679.49948952029 -66.40897551884576 0.02768827702656702
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600 7.608847536264781 -34676.69728436362 -69.32060611557266 0.05579466731854093
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700 9.049471241531297 -34674.00093206036 -72.10055094219446 0.004335980559879027
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800 9.826796099683211 -34671.27720242751 -74.9501061086213 0.02371649678091513
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900 11.8609224958918 -34668.35091308811 -77.98544170794551 0.004658649791374929
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1000 13.88037467640968 -34665.35025858006 -81.16445160194114 0.07684078334464739
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Loop time of 4.85247 on 1 procs for 1000 steps with 8000 atoms
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100 2.004897156140836 -34690.27961013186 -55.3499730543189 0.01301140393178352
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200 2.837118035232607 -34687.74741132015 -57.93445748841876 0.02696025968760173
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300 4.263087164947482 -34684.98084093686 -60.75945453846793 0.02175636603841567
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400 5.568003854939066 -34682.25271040963 -63.56896518300499 0.03000618483472749
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500 6.225602451570786 -34679.49948952029 -66.40897551884574 0.02768827702656703
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600 7.608847536264781 -34676.69728436362 -69.32060611557282 0.05579466731854091
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700 9.049471241531297 -34674.00093206036 -72.10055094219462 0.004335980559879032
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800 9.826796099683211 -34671.27720242751 -74.95010610862134 0.02371649678091515
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900 11.8609224958918 -34668.35091308811 -77.98544170794545 0.004658649791374908
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1000 13.88037467640968 -34665.35025858006 -81.16445160194111 0.07684078334464743
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Loop time of 2.48942 on 1 procs for 1000 steps with 8000 atoms
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Performance: 1.781 ns/day, 13.479 hours/ns, 206.081 timesteps/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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Performance: 3.471 ns/day, 6.915 hours/ns, 401.700 timesteps/s, 3.214 Matom-step/s
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100.0% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 4.1286 | 4.1286 | 4.1286 | 0.0 | 85.08
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Pair | 2.126 | 2.126 | 2.126 | 0.0 | 85.40
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.030972 | 0.030972 | 0.030972 | 0.0 | 0.64
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Output | 0.0026351 | 0.0026351 | 0.0026351 | 0.0 | 0.05
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Modify | 0.67848 | 0.67848 | 0.67848 | 0.0 | 13.98
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Other | | 0.01182 | | | 0.24
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Comm | 0.016147 | 0.016147 | 0.016147 | 0.0 | 0.65
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Output | 0.0013116 | 0.0013116 | 0.0013116 | 0.0 | 0.05
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Modify | 0.33864 | 0.33864 | 0.33864 | 0.0 | 13.60
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Other | | 0.007318 | | | 0.29
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Nlocal: 8000 ave 8000 max 8000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -119,4 +117,4 @@ Total # of neighbors = 272000
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Ave neighs/atom = 34
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:04
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Total wall time: 0:00:02
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@ -1,6 +1,5 @@
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LAMMPS (24 Mar 2022)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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LAMMPS (28 Mar 2023 - Development)
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WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:531)
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units metal
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atom_style atomic
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boundary p p p
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@ -15,7 +14,7 @@ mass 1 28.0855
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create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 basis 5 1 basis 6 1 basis 7 1 basis 8 1
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Created 8000 atoms
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using lattice units in orthogonal box = (0 0 0) to (54.309 54.309 54.309)
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create_atoms CPU = 0.000 seconds
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create_atoms CPU = 0.001 seconds
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pair_style sw
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pair_coeff * * Si.sw Si
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@ -42,12 +41,12 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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||||
|
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Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix ttm/mod command:
|
||||
- fix ttm/mod command: doi:10.1088/0953-8984/26/47/475401, doi:10.1002/ctpp.201310025
|
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@article{Pisarev2014,
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author = {Pisarev, V. V. and Starikov, S. V.},
|
||||
title = {{Atomistic simulation of ion track formation in UO2.}},
|
||||
journal = {J.~Phys.:~Condens.~Matter},
|
||||
title = {Atomistic Simulation of Ion Track Formation in {UO$_2$}.},
|
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journal = {J.~Phys.\ Condens.\ Matter},
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volume = {26},
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number = {47},
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pages = {475401},
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@ -56,8 +55,8 @@ year = {2014}
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@article{Norman2013,
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author = {Norman, G. E. and Starikov, S. V. and Stegailov, V. V. and Saitov, I. M. and Zhilyaev, P. A.},
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title = {{Atomistic Modeling of Warm Dense Matter in the Two-Temperature State}},
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journal = {Contrib.~Plasm.~Phys.},
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title = {Atomistic Modeling of Warm Dense Matter in the Two-Temperature State},
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journal = {Contrib.\ Plasma Phys.},
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number = {2},
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volume = {53},
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pages = {129--139},
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@ -67,7 +66,7 @@ year = {2013}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Neighbor list info ...
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update every 5 steps, delay 0 steps, check yes
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update: every = 5 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 5.77118
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ghost atom cutoff = 5.77118
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@ -81,30 +80,30 @@ Neighbor list info ...
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Per MPI rank memory allocation (min/avg/max) = 3.436 | 3.436 | 3.436 Mbytes
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Step Temp TotEng f_twotemp[1] f_twotemp[2]
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0 0 -34692.79996100361 -52.79390940511979 0
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100 1.852689977101411 -34690.49204900486 -55.14271612882062 0.027261886765771
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200 2.735750477179192 -34688.11139028054 -57.57110998717796 0.03387986355513582
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300 3.931848271449558 -34685.54667417785 -60.18684521127226 0.02261256315262404
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400 5.462009198576365 -34682.74455105668 -63.05420336037231 0.002402241637719583
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500 6.267811692893873 -34679.96493887379 -65.93304222280049 0.02448378880218699
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600 7.21148216150661 -34677.41455784726 -68.58391420045932 0.04114045759945373
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700 8.84660534187052 -34674.40610468235 -71.68798344296847 0.0237298402743454
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800 10.1748456457686 -34671.08749605772 -75.11943618276236 0.007538225788030298
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900 11.27479036162859 -34668.4118066423 -77.92921692176769 0.02537529314475071
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1000 13.26881394868076 -34665.56617589539 -80.91544540266329 0.03112665440209921
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Loop time of 1.60214 on 4 procs for 1000 steps with 8000 atoms
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100 1.852689977101411 -34690.49204900486 -55.14271612882064 0.02726188676577098
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200 2.735750477179192 -34688.11139028054 -57.57110998717798 0.03387986355513584
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300 3.931848271449558 -34685.54667417785 -60.18684521127231 0.02261256315262403
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400 5.462009198576365 -34682.74455105668 -63.05420336037233 0.002402241637719578
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500 6.267811692893873 -34679.96493887379 -65.93304222280051 0.02448378880218699
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600 7.21148216150661 -34677.41455784726 -68.58391420045926 0.04114045759945374
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700 8.84660534187052 -34674.40610468235 -71.68798344296859 0.02372984027434538
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800 10.1748456457686 -34671.08749605772 -75.11943618276216 0.007538225788030307
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900 11.27479036162859 -34668.4118066423 -77.92921692176756 0.02537529314475071
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1000 13.26881394868076 -34665.56617589539 -80.91544540266317 0.03112665440209921
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Loop time of 0.995347 on 4 procs for 1000 steps with 8000 atoms
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Performance: 5.393 ns/day, 4.450 hours/ns, 624.165 timesteps/s
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99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
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Performance: 8.680 ns/day, 2.765 hours/ns, 1004.675 timesteps/s, 8.037 Matom-step/s
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97.9% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 1.0424 | 1.0558 | 1.0696 | 1.0 | 65.90
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Pair | 0.65351 | 0.6616 | 0.66783 | 0.8 | 66.47
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.05072 | 0.063773 | 0.079458 | 4.9 | 3.98
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Output | 0.0024362 | 0.0024703 | 0.0025297 | 0.1 | 0.15
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Modify | 0.47018 | 0.47332 | 0.48004 | 0.6 | 29.54
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Other | | 0.006786 | | | 0.42
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Comm | 0.041606 | 0.048314 | 0.056589 | 2.9 | 4.85
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Output | 0.0014609 | 0.0014742 | 0.0014968 | 0.0 | 0.15
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Modify | 0.27934 | 0.28016 | 0.28089 | 0.1 | 28.15
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Other | | 0.003798 | | | 0.38
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Nlocal: 2000 ave 2000 max 2000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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@ -75,10 +75,8 @@ static constexpr double SHIFT = 0.0;
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FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg),
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random(nullptr), nsum(nullptr), nsum_all(nullptr),
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gfactor1(nullptr), gfactor2(nullptr), ratio(nullptr), flangevin(nullptr),
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T_electron(nullptr), T_electron_old(nullptr), sum_vsq(nullptr), sum_mass_vsq(nullptr),
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sum_vsq_all(nullptr), sum_mass_vsq_all(nullptr), net_energy_transfer(nullptr),
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random(nullptr), gfactor1(nullptr), gfactor2(nullptr), ratio(nullptr), flangevin(nullptr),
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T_electron(nullptr), T_electron_old(nullptr), net_energy_transfer(nullptr),
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net_energy_transfer_all(nullptr)
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{
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if (lmp->citeme) lmp->citeme->add(cite_fix_ttm_mod);
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@ -167,20 +165,14 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
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// allocate 3d grid variables
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memory->create(nsum,nxgrid,nygrid,nzgrid,"ttm/mod:nsum");
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memory->create(nsum_all,nxgrid,nygrid,nzgrid,"ttm/mod:nsum_all");
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memory->create(sum_vsq,nxgrid,nygrid,nzgrid,"ttm/mod:sum_vsq");
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memory->create(sum_mass_vsq,nxgrid,nygrid,nzgrid,"ttm/mod:sum_mass_vsq");
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memory->create(sum_vsq_all,nxgrid,nygrid,nzgrid,"ttm/mod:sum_vsq_all");
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memory->create(sum_mass_vsq_all,nxgrid,nygrid,nzgrid,
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"ttm/mod:sum_mass_vsq_all");
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memory->create(T_electron_old,nxgrid,nygrid,nzgrid,"ttm/mod:T_electron_old");
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memory->create(T_electron_first,nxgrid,nygrid,nzgrid,"ttm/mod:T_electron_first");
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memory->create(T_electron,nxgrid,nygrid,nzgrid,"ttm/mod:T_electron");
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memory->create(net_energy_transfer,nxgrid,nygrid,nzgrid,
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memory->create(T_electron_old,nzgrid,nygrid,nxgrid,"ttm/mod:T_electron_old");
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memory->create(T_electron_first,nzgrid,nygrid,nxgrid,"ttm/mod:T_electron_first");
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memory->create(T_electron,nzgrid,nygrid,nxgrid,"ttm/mod:T_electron");
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memory->create(net_energy_transfer,nzgrid,nygrid,nxgrid,
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"ttm/mod:net_energy_transfer");
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memory->create(net_energy_transfer_all,nxgrid,nygrid,nzgrid,
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memory->create(net_energy_transfer_all,nzgrid,nygrid,nxgrid,
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"ttm/mod:net_energy_transfer_all");
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flangevin = nullptr;
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grow_arrays(atom->nmax);
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@ -203,10 +195,10 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
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// initialize electron temperatures on grid
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int ix,iy,iz;
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for (ix = 0; ix < nxgrid; ix++)
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for (iz = 0; iz < nzgrid; iz++)
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for (iy = 0; iy < nygrid; iy++)
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for (iz = 0; iz < nzgrid; iz++)
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T_electron[ix][iy][iz] = tinit;
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for (ix = 0; ix < nxgrid; ix++)
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T_electron[iz][iy][ix] = tinit;
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// if specified, read initial electron temperatures from file
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@ -221,18 +213,13 @@ FixTTMMod::~FixTTMMod()
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delete[] gfactor1;
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delete[] gfactor2;
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memory->destroy(nsum);
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memory->destroy(nsum_all);
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memory->destroy(sum_vsq);
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memory->destroy(sum_mass_vsq);
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memory->destroy(sum_vsq_all);
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memory->destroy(sum_mass_vsq_all);
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memory->destroy(T_electron_first);
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memory->destroy(T_electron_old);
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memory->destroy(T_electron);
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memory->destroy(flangevin);
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memory->destroy(net_energy_transfer);
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memory->destroy(net_energy_transfer_all);
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memory->destroy(flangevin);
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}
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/* ---------------------------------------------------------------------- */
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@ -265,10 +252,10 @@ void FixTTMMod::init()
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sqrt(24.0*force->boltz*gamma_p/update->dt/force->mvv2e) / force->ftm2v;
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}
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for (int ix = 0; ix < nxgrid; ix++)
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for (int iz = 0; iz < nzgrid; iz++)
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for (int iy = 0; iy < nygrid; iy++)
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for (int iz = 0; iz < nzgrid; iz++)
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net_energy_transfer_all[ix][iy][iz] = 0;
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for (int ix = 0; ix < nxgrid; ix++)
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net_energy_transfer_all[iz][iy][ix] = 0;
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if (utils::strmatch(update->integrate_style,"^respa"))
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nlevels_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels;
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@ -320,10 +307,10 @@ void FixTTMMod::post_force(int /*vflag*/)
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while (iy < 0) iy += nygrid;
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while (iz < 0) iz += nzgrid;
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if (T_electron[ix][iy][iz] < 0)
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if (T_electron[iz][iy][ix] < 0)
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error->all(FLERR,"Electronic temperature dropped below zero");
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double tsqrt = sqrt(T_electron[ix][iy][iz]);
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double tsqrt = sqrt(T_electron[iz][iy][ix]);
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gamma1 = gfactor1[type[i]];
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double vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
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@ -342,20 +329,14 @@ void FixTTMMod::post_force(int /*vflag*/)
|
||||
if (right_x == nxgrid) right_x = 0;
|
||||
if (right_y == nygrid) right_y = 0;
|
||||
if (right_z == nzgrid) right_z = 0;
|
||||
int left_x = ix - 1;
|
||||
int left_y = iy - 1;
|
||||
int left_z = iz - 1;
|
||||
if (left_x == -1) left_x = nxgrid - 1;
|
||||
if (left_y == -1) left_y = nygrid - 1;
|
||||
if (left_z == -1) left_z = nzgrid - 1;
|
||||
double T_i = T_electron[ix][iy][iz];
|
||||
double T_ir = T_electron[right_x][iy][iz];
|
||||
double T_iu = T_electron[ix][right_y][iz];
|
||||
double T_if = T_electron[ix][iy][right_z];
|
||||
double C_i = el_properties(T_electron[ix][iy][iz]).el_heat_capacity;
|
||||
double C_ir = el_properties(T_electron[right_x][iy][iz]).el_heat_capacity;
|
||||
double C_iu = el_properties(T_electron[ix][right_y][iz]).el_heat_capacity;
|
||||
double C_if = el_properties(T_electron[ix][iy][right_z]).el_heat_capacity;
|
||||
double T_i = T_electron[iz][iy][ix];
|
||||
double T_ir = T_electron[iz][iy][right_x];
|
||||
double T_iu = T_electron[iz][right_y][ix];
|
||||
double T_if = T_electron[right_z][iy][ix];
|
||||
double C_i = el_properties(T_electron[iz][iy][ix]).el_heat_capacity;
|
||||
double C_ir = el_properties(T_electron[iz][iy][right_x]).el_heat_capacity;
|
||||
double C_iu = el_properties(T_electron[iz][right_y][ix]).el_heat_capacity;
|
||||
double C_if = el_properties(T_electron[right_z][iy][ix]).el_heat_capacity;
|
||||
double diff_x = (x_at - x_surf)*(x_at - x_surf);
|
||||
diff_x = pow(diff_x,0.5);
|
||||
double len_factor = diff_x/(diff_x+free_path);
|
||||
@ -587,7 +568,7 @@ void FixTTMMod::read_electron_temperatures(const std::string &filename)
|
||||
if (comm->me == 0) {
|
||||
|
||||
int ***T_initial_set;
|
||||
memory->create(T_initial_set,nxgrid,nygrid,nzgrid,"ttm/mod:T_initial_set");
|
||||
memory->create(T_initial_set,nzgrid,nygrid,nxgrid,"ttm/mod:T_initial_set");
|
||||
memset(&T_initial_set[0][0][0],0,ngridtotal*sizeof(int));
|
||||
|
||||
// read initial electron temperature values from file
|
||||
@ -614,8 +595,8 @@ void FixTTMMod::read_electron_temperatures(const std::string &filename)
|
||||
if (T_tmp < 0.0)
|
||||
throw TokenizerException("Fix ttm electron temperatures must be > 0.0","");
|
||||
|
||||
T_electron[ix][iy][iz] = T_tmp;
|
||||
T_initial_set[ix][iy][iz] = 1;
|
||||
T_electron[iz][iy][ix] = T_tmp;
|
||||
T_initial_set[iz][iy][ix] = 1;
|
||||
}
|
||||
} catch (std::exception &e) {
|
||||
error->one(FLERR, e.what());
|
||||
@ -626,7 +607,7 @@ void FixTTMMod::read_electron_temperatures(const std::string &filename)
|
||||
for (int iz = 0; iz < nzgrid; iz++)
|
||||
for (int iy = 0; iy < nygrid; iy++)
|
||||
for (int ix = 0; ix < nxgrid; ix++)
|
||||
if (T_initial_set[ix][iy][iz] == 0)
|
||||
if (T_initial_set[iz][iy][ix] == 0)
|
||||
error->all(FLERR,"Fix ttm/mod infile did not set all temperatures");
|
||||
|
||||
memory->destroy(T_initial_set);
|
||||
@ -656,9 +637,9 @@ void FixTTMMod::write_electron_temperatures(const std::string &filename)
|
||||
for (ix = 0; ix < nxgrid; ix++)
|
||||
for (iy = 0; iy < nygrid; iy++)
|
||||
for (iz = 0; iz < nzgrid; iz++) {
|
||||
if (movsur == 1 && T_electron[ix][iy][iz] == 0.0)
|
||||
T_electron[ix][iy][iz] = electron_temperature_min;
|
||||
fprintf(fp,"%d %d %d %20.16g\n",ix+1,iy+1,iz+1,T_electron[ix][iy][iz]);
|
||||
if (movsur == 1 && T_electron[iz][iy][ix] == 0.0)
|
||||
T_electron[iz][iy][ix] = electron_temperature_min;
|
||||
fprintf(fp,"%d %d %d %20.16g\n",ix+1,iy+1,iz+1,T_electron[iz][iy][ix]);
|
||||
}
|
||||
|
||||
fclose(fp);
|
||||
@ -678,6 +659,9 @@ el_heat_capacity_thermal_conductivity FixTTMMod::el_properties(double T_e)
|
||||
properties.el_thermal_conductivity = el_th_diff*properties.el_heat_capacity; // thermal conductivity
|
||||
return properties;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double FixTTMMod::el_sp_heat_integral(double T_e)
|
||||
{
|
||||
double T_temp = T_e/1000.0, T_reduced = T_damp*T_temp;
|
||||
@ -700,20 +684,21 @@ void FixTTMMod::end_of_step()
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
if (movsur == 1) {
|
||||
for (int ix = 0; ix < nxgrid; ix++)
|
||||
for (int iz = 0; iz < nzgrid; iz++)
|
||||
for (int iy = 0; iy < nygrid; iy++)
|
||||
for (int iz = 0; iz < nzgrid; iz++) {
|
||||
double TTT = T_electron[ix][iy][iz];
|
||||
for (int ix = 0; ix < nxgrid; ix++) {
|
||||
double TTT = T_electron[iz][iy][ix];
|
||||
if (TTT > 0) {
|
||||
if (ix < t_surface_l)
|
||||
t_surface_l = ix;
|
||||
}
|
||||
}
|
||||
}
|
||||
for (int ix = 0; ix < nxgrid; ix++)
|
||||
|
||||
for (int iz = 0; iz < nzgrid; iz++)
|
||||
for (int iy = 0; iy < nygrid; iy++)
|
||||
for (int iz = 0; iz < nzgrid; iz++)
|
||||
net_energy_transfer[ix][iy][iz] = 0;
|
||||
for (int ix = 0; ix < nxgrid; ix++)
|
||||
net_energy_transfer[iz][iy][ix] = 0;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
@ -731,7 +716,7 @@ void FixTTMMod::end_of_step()
|
||||
while (iz < 0) iz += nzgrid;
|
||||
if (ix >= t_surface_l) {
|
||||
if (ix < surface_r)
|
||||
net_energy_transfer[ix][iy][iz] +=
|
||||
net_energy_transfer[iz][iy][ix] +=
|
||||
(flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
|
||||
flangevin[i][2]*v[i][2]);
|
||||
}
|
||||
@ -747,18 +732,16 @@ void FixTTMMod::end_of_step()
|
||||
double del_vol = dx*dy*dz;
|
||||
double el_specific_heat = 0.0;
|
||||
double el_thermal_conductivity = el_properties(electron_temperature_min).el_thermal_conductivity;
|
||||
for (int ix = 0; ix < nxgrid; ix++)
|
||||
|
||||
for (int iz = 0; iz < nzgrid; iz++)
|
||||
for (int iy = 0; iy < nygrid; iy++)
|
||||
for (int iz = 0; iz < nzgrid; iz++)
|
||||
{
|
||||
if (el_properties(T_electron[ix][iy][iz]).el_thermal_conductivity > el_thermal_conductivity)
|
||||
el_thermal_conductivity = el_properties(T_electron[ix][iy][iz]).el_thermal_conductivity;
|
||||
if (el_specific_heat > 0.0)
|
||||
{
|
||||
if ((T_electron[ix][iy][iz] > 0.0) && (el_properties(T_electron[ix][iy][iz]).el_heat_capacity < el_specific_heat))
|
||||
el_specific_heat = el_properties(T_electron[ix][iy][iz]).el_heat_capacity;
|
||||
}
|
||||
else if (T_electron[ix][iy][iz] > 0.0) el_specific_heat = el_properties(T_electron[ix][iy][iz]).el_heat_capacity;
|
||||
for (int ix = 0; ix < nxgrid; ix++) {
|
||||
if (el_properties(T_electron[iz][iy][ix]).el_thermal_conductivity > el_thermal_conductivity)
|
||||
el_thermal_conductivity = el_properties(T_electron[iz][iy][ix]).el_thermal_conductivity;
|
||||
if (el_specific_heat > 0.0) {
|
||||
if ((T_electron[iz][iy][ix] > 0.0) && (el_properties(T_electron[iz][iy][ix]).el_heat_capacity < el_specific_heat))
|
||||
el_specific_heat = el_properties(T_electron[iz][iy][ix]).el_heat_capacity;
|
||||
} else if (T_electron[iz][iy][ix] > 0.0) el_specific_heat = el_properties(T_electron[iz][iy][ix]).el_heat_capacity;
|
||||
}
|
||||
// num_inner_timesteps = # of inner steps (thermal solves)
|
||||
// required this MD step to maintain a stable explicit solve
|
||||
@ -767,17 +750,16 @@ void FixTTMMod::end_of_step()
|
||||
double inner_dt = update->dt;
|
||||
double stability_criterion = 0.0;
|
||||
|
||||
for (int ix = 0; ix < nxgrid; ix++)
|
||||
for (int iz = 0; iz < nzgrid; iz++)
|
||||
for (int iy = 0; iy < nygrid; iy++)
|
||||
for (int iz = 0; iz < nzgrid; iz++)
|
||||
T_electron_first[ix][iy][iz] =
|
||||
T_electron[ix][iy][iz];
|
||||
for (int ix = 0; ix < nxgrid; ix++)
|
||||
T_electron_first[iz][iy][ix] = T_electron[iz][iy][ix];
|
||||
|
||||
do {
|
||||
for (int ix = 0; ix < nxgrid; ix++)
|
||||
for (int iz = 0; iz < nzgrid; iz++)
|
||||
for (int iy = 0; iy < nygrid; iy++)
|
||||
for (int iz = 0; iz < nzgrid; iz++)
|
||||
T_electron[ix][iy][iz] =
|
||||
T_electron_first[ix][iy][iz];
|
||||
for (int ix = 0; ix < nxgrid; ix++)
|
||||
T_electron[iz][iy][ix] = T_electron_first[iz][iy][ix];
|
||||
|
||||
stability_criterion = 1.0 -
|
||||
2.0*inner_dt/el_specific_heat *
|
||||
@ -792,16 +774,15 @@ void FixTTMMod::end_of_step()
|
||||
error->warning(FLERR,"Too many inner timesteps in fix ttm/mod");
|
||||
for (int ith_inner_timestep = 0; ith_inner_timestep < num_inner_timesteps;
|
||||
ith_inner_timestep++) {
|
||||
for (int ix = 0; ix < nxgrid; ix++)
|
||||
for (int iz = 0; iz < nzgrid; iz++)
|
||||
for (int iy = 0; iy < nygrid; iy++)
|
||||
for (int iz = 0; iz < nzgrid; iz++)
|
||||
T_electron_old[ix][iy][iz] =
|
||||
T_electron[ix][iy][iz];
|
||||
for (int ix = 0; ix < nxgrid; ix++)
|
||||
T_electron_old[iz][iy][ix] = T_electron[iz][iy][ix];
|
||||
// compute new electron T profile
|
||||
duration = duration + inner_dt;
|
||||
for (int ix = 0; ix < nxgrid; ix++)
|
||||
for (int iz = 0; iz < nzgrid; iz++)
|
||||
for (int iy = 0; iy < nygrid; iy++)
|
||||
for (int iz = 0; iz < nzgrid; iz++) {
|
||||
for (int ix = 0; ix < nxgrid; ix++) {
|
||||
int right_x = ix + 1;
|
||||
int right_y = iy + 1;
|
||||
int right_z = iz + 1;
|
||||
@ -821,50 +802,50 @@ void FixTTMMod::end_of_step()
|
||||
if (duration < width) {
|
||||
if (ix >= t_surface_l) mult_factor = (intensity/(dx*skin_layer_d))*exp((-1.0)*(ix_d - surface_d)/skin_layer_d);
|
||||
}
|
||||
if (ix < t_surface_l) net_energy_transfer_all[ix][iy][iz] = 0.0;
|
||||
if (ix < t_surface_l) net_energy_transfer_all[iz][iy][ix] = 0.0;
|
||||
double cr_vac = 1;
|
||||
if (T_electron_old[ix][iy][iz] == 0) cr_vac = 0;
|
||||
if (T_electron_old[iz][iy][ix] == 0) cr_vac = 0;
|
||||
double cr_v_l_x = 1;
|
||||
if (T_electron_old[left_x][iy][iz] == 0) cr_v_l_x = 0;
|
||||
if (T_electron_old[iz][iy][left_x] == 0) cr_v_l_x = 0;
|
||||
double cr_v_r_x = 1;
|
||||
if (T_electron_old[right_x][iy][iz] == 0) cr_v_r_x = 0;
|
||||
if (T_electron_old[iz][iy][right_x] == 0) cr_v_r_x = 0;
|
||||
double cr_v_l_y = 1;
|
||||
if (T_electron_old[ix][left_y][iz] == 0) cr_v_l_y = 0;
|
||||
if (T_electron_old[iz][left_y][ix] == 0) cr_v_l_y = 0;
|
||||
double cr_v_r_y = 1;
|
||||
if (T_electron_old[ix][right_y][iz] == 0) cr_v_r_y = 0;
|
||||
if (T_electron_old[iz][right_y][ix] == 0) cr_v_r_y = 0;
|
||||
double cr_v_l_z = 1;
|
||||
if (T_electron_old[ix][iy][left_z] == 0) cr_v_l_z = 0;
|
||||
if (T_electron_old[left_z][iy][ix] == 0) cr_v_l_z = 0;
|
||||
double cr_v_r_z = 1;
|
||||
if (T_electron_old[ix][iy][right_z] == 0) cr_v_r_z = 0;
|
||||
if (T_electron_old[right_z][iy][ix] == 0) cr_v_r_z = 0;
|
||||
if (cr_vac != 0) {
|
||||
T_electron[ix][iy][iz] =
|
||||
T_electron_old[ix][iy][iz] +
|
||||
inner_dt/el_properties(T_electron_old[ix][iy][iz]).el_heat_capacity *
|
||||
((cr_v_r_x*el_properties(T_electron_old[ix][iy][iz]/2.0+T_electron_old[right_x][iy][iz]/2.0).el_thermal_conductivity*
|
||||
(T_electron_old[right_x][iy][iz]-T_electron_old[ix][iy][iz])/dx -
|
||||
cr_v_l_x*el_properties(T_electron_old[ix][iy][iz]/2.0+T_electron_old[left_x][iy][iz]/2.0).el_thermal_conductivity*
|
||||
(T_electron_old[ix][iy][iz]-T_electron_old[left_x][iy][iz])/dx)/dx +
|
||||
(cr_v_r_y*el_properties(T_electron_old[ix][iy][iz]/2.0+T_electron_old[ix][right_y][iz]/2.0).el_thermal_conductivity*
|
||||
(T_electron_old[ix][right_y][iz]-T_electron_old[ix][iy][iz])/dy -
|
||||
cr_v_l_y*el_properties(T_electron_old[ix][iy][iz]/2.0+T_electron_old[ix][left_y][iz]/2.0).el_thermal_conductivity*
|
||||
(T_electron_old[ix][iy][iz]-T_electron_old[ix][left_y][iz])/dy)/dy +
|
||||
(cr_v_r_z*el_properties(T_electron_old[ix][iy][iz]/2.0+T_electron_old[ix][iy][right_z]/2.0).el_thermal_conductivity*
|
||||
(T_electron_old[ix][iy][right_z]-T_electron_old[ix][iy][iz])/dz -
|
||||
cr_v_l_z*el_properties(T_electron_old[ix][iy][iz]/2.0+T_electron_old[ix][iy][left_z]/2.0).el_thermal_conductivity*
|
||||
(T_electron_old[ix][iy][iz]-T_electron_old[ix][iy][left_z])/dz)/dz);
|
||||
T_electron[ix][iy][iz]+=inner_dt/el_properties(T_electron[ix][iy][iz]).el_heat_capacity*
|
||||
T_electron[iz][iy][ix] =
|
||||
T_electron_old[iz][iy][ix] +
|
||||
inner_dt/el_properties(T_electron_old[iz][iy][ix]).el_heat_capacity *
|
||||
((cr_v_r_x*el_properties(T_electron_old[iz][iy][ix]/2.0+T_electron_old[iz][iy][right_x]/2.0).el_thermal_conductivity*
|
||||
(T_electron_old[iz][iy][right_x]-T_electron_old[iz][iy][ix])/dx -
|
||||
cr_v_l_x*el_properties(T_electron_old[iz][iy][ix]/2.0+T_electron_old[iz][iy][left_x]/2.0).el_thermal_conductivity*
|
||||
(T_electron_old[iz][iy][ix]-T_electron_old[iz][iy][left_x])/dx)/dx +
|
||||
(cr_v_r_y*el_properties(T_electron_old[iz][iy][ix]/2.0+T_electron_old[iz][right_y][ix]/2.0).el_thermal_conductivity*
|
||||
(T_electron_old[iz][right_y][ix]-T_electron_old[iz][iy][ix])/dy -
|
||||
cr_v_l_y*el_properties(T_electron_old[iz][iy][ix]/2.0+T_electron_old[iz][left_y][ix]/2.0).el_thermal_conductivity*
|
||||
(T_electron_old[iz][iy][ix]-T_electron_old[iz][left_y][ix])/dy)/dy +
|
||||
(cr_v_r_z*el_properties(T_electron_old[iz][iy][ix]/2.0+T_electron_old[right_z][iy][ix]/2.0).el_thermal_conductivity*
|
||||
(T_electron_old[right_z][iy][ix]-T_electron_old[iz][iy][ix])/dz -
|
||||
cr_v_l_z*el_properties(T_electron_old[iz][iy][ix]/2.0+T_electron_old[left_z][iy][ix]/2.0).el_thermal_conductivity*
|
||||
(T_electron_old[iz][iy][ix]-T_electron_old[left_z][iy][ix])/dz)/dz);
|
||||
T_electron[iz][iy][ix]+=inner_dt/el_properties(T_electron[iz][iy][ix]).el_heat_capacity*
|
||||
(mult_factor -
|
||||
net_energy_transfer_all[ix][iy][iz]/del_vol);
|
||||
net_energy_transfer_all[iz][iy][ix]/del_vol);
|
||||
}
|
||||
else T_electron[ix][iy][iz] =
|
||||
T_electron_old[ix][iy][iz];
|
||||
if ((T_electron[ix][iy][iz] > 0.0) && (T_electron[ix][iy][iz] < electron_temperature_min))
|
||||
T_electron[ix][iy][iz] = T_electron[ix][iy][iz] + 0.5*(electron_temperature_min - T_electron[ix][iy][iz]);
|
||||
else T_electron[iz][iy][ix] = T_electron_old[iz][iy][ix];
|
||||
|
||||
if (el_properties(T_electron[ix][iy][iz]).el_thermal_conductivity > el_thermal_conductivity)
|
||||
el_thermal_conductivity = el_properties(T_electron[ix][iy][iz]).el_thermal_conductivity;
|
||||
if ((T_electron[ix][iy][iz] > 0.0) && (el_properties(T_electron[ix][iy][iz]).el_heat_capacity < el_specific_heat))
|
||||
el_specific_heat = el_properties(T_electron[ix][iy][iz]).el_heat_capacity;
|
||||
if ((T_electron[iz][iy][ix] > 0.0) && (T_electron[iz][iy][ix] < electron_temperature_min))
|
||||
T_electron[iz][iy][ix] = T_electron[iz][iy][ix] + 0.5*(electron_temperature_min - T_electron[iz][iy][ix]);
|
||||
|
||||
if (el_properties(T_electron[iz][iy][ix]).el_thermal_conductivity > el_thermal_conductivity)
|
||||
el_thermal_conductivity = el_properties(T_electron[iz][iy][ix]).el_thermal_conductivity;
|
||||
if ((T_electron[iz][iy][ix] > 0.0) && (el_properties(T_electron[iz][iy][ix]).el_heat_capacity < el_specific_heat))
|
||||
el_specific_heat = el_properties(T_electron[iz][iy][ix]).el_heat_capacity;
|
||||
}
|
||||
}
|
||||
stability_criterion = 1.0 -
|
||||
@ -913,12 +894,11 @@ double FixTTMMod::compute_vector(int n)
|
||||
double dz = domain->zprd/nzgrid;
|
||||
double del_vol = dx*dy*dz;
|
||||
|
||||
for (int ix = 0; ix < nxgrid; ix++)
|
||||
for (int iz = 0; iz < nzgrid; iz++)
|
||||
for (int iy = 0; iy < nygrid; iy++)
|
||||
for (int iz = 0; iz < nzgrid; iz++) {
|
||||
e_energy += el_sp_heat_integral(T_electron[ix][iy][iz])*del_vol;
|
||||
transfer_energy +=
|
||||
net_energy_transfer_all[ix][iy][iz]*update->dt;
|
||||
for (int ix = 0; ix < nxgrid; ix++) {
|
||||
e_energy += el_sp_heat_integral(T_electron[iz][iy][ix])*del_vol;
|
||||
transfer_energy += net_energy_transfer_all[iz][iy][ix]*update->dt;
|
||||
}
|
||||
|
||||
if (n == 0) return e_energy;
|
||||
@ -933,7 +913,7 @@ double FixTTMMod::compute_vector(int n)
|
||||
void FixTTMMod::write_restart(FILE *fp)
|
||||
{
|
||||
double *rlist;
|
||||
memory->create(rlist,nxgrid*nygrid*nzgrid+4,"ttm/mod:rlist");
|
||||
memory->create(rlist,nzgrid*nygrid*nxgrid + 4,"ttm/mod:rlist");
|
||||
|
||||
int n = 0;
|
||||
rlist[n++] = nxgrid;
|
||||
@ -941,10 +921,10 @@ void FixTTMMod::write_restart(FILE *fp)
|
||||
rlist[n++] = nzgrid;
|
||||
rlist[n++] = seed;
|
||||
|
||||
for (int ix = 0; ix < nxgrid; ix++)
|
||||
for (int iz = 0; iz < nzgrid; iz++)
|
||||
for (int iy = 0; iy < nygrid; iy++)
|
||||
for (int iz = 0; iz < nzgrid; iz++)
|
||||
rlist[n++] = T_electron[ix][iy][iz];
|
||||
for (int ix = 0; ix < nxgrid; ix++)
|
||||
rlist[n++] = T_electron[iz][iy][ix];
|
||||
|
||||
if (comm->me == 0) {
|
||||
int size = n * sizeof(double);
|
||||
@ -982,10 +962,10 @@ void FixTTMMod::restart(char *buf)
|
||||
|
||||
// restore global frid values
|
||||
|
||||
for (int ix = 0; ix < nxgrid; ix++)
|
||||
for (int iz = 0; iz < nzgrid; iz++)
|
||||
for (int iy = 0; iy < nygrid; iy++)
|
||||
for (int iz = 0; iz < nzgrid; iz++)
|
||||
T_electron[ix][iy][iz] = rlist[n++];
|
||||
for (int ix = 0; ix < nxgrid; ix++)
|
||||
T_electron[iz][iy][ix] = rlist[n++];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
||||
@ -64,11 +64,8 @@ class FixTTMMod : public Fix {
|
||||
int nxgrid, nygrid, nzgrid;
|
||||
int ngridtotal;
|
||||
|
||||
int ***nsum, ***nsum_all;
|
||||
double *gfactor1, *gfactor2, *ratio, **flangevin;
|
||||
double ***T_electron, ***T_electron_old, ***T_electron_first;
|
||||
double ***sum_vsq, ***sum_mass_vsq;
|
||||
double ***sum_vsq_all, ***sum_mass_vsq_all;
|
||||
double ***net_energy_transfer, ***net_energy_transfer_all;
|
||||
|
||||
double gamma_p, gamma_s, v_0, v_0_sq;
|
||||
|
||||
Reference in New Issue
Block a user