fix file reader bug and add ttm/mod example
This commit is contained in:
Axel Kohlmeyer
@ -214,7 +214,7 @@ generate an error. LAMMPS will check if a "UNITS:" tag is in the first
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line and stop with an error, if there is a mismatch with the current
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line and stop with an error, if there is a mismatch with the current
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units used.
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units used.
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..note::
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.. note::
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The electronic temperature at each grid point must be a non-zero
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The electronic temperature at each grid point must be a non-zero
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positive value, both initially, and as the temperature evovles over
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positive value, both initially, and as the temperature evovles over
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1
examples/ttm/Si.sw
Symbolic link
1
examples/ttm/Si.sw
Symbolic link
@ -0,0 +1 @@
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../../potentials/Si.sw
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44
examples/ttm/Si.ttm_mod
Normal file
44
examples/ttm/Si.ttm_mod
Normal file
@ -0,0 +1,44 @@
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a_0, energy/(temperature*electron) units
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-0.00012899
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a_1, energy/(temperature^2*electron) units
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-0.0000000293276
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a_2, energy/(temperature^3*electron) units
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-0.0000229991
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a_3, energy/(temperature^4*electron) units
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-0.000000927036
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a_4, energy/(temperature^5*electron) units
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-0.0000011747
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C_0, energy/(temperature*electron) units
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0.000129
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A, 1/temperature units
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0.180501
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rho_e, electrons/volume units
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0.05
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D_e, length^2/time units
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20000
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gamma_p, mass/time units
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39.235
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gamma_s, mass/time units
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24.443
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v_0, length/time units
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79.76
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I_0, energy/(time*length^2) units
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0
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lsurface, electron grid units (positive integer)
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0
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rsurface, electron grid units (positive integer)
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1
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l_skin, length units
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1
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tau, time units
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0
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B, dimensionless
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0
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lambda, length units
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0
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n_ion, ions/volume units
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0.05
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surface_movement: 0 to disable tracking of surface motion, 1 to enable
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0
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T_e_min, temperature units
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0
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29
examples/ttm/in.ttm.mod
Normal file
29
examples/ttm/in.ttm.mod
Normal file
@ -0,0 +1,29 @@
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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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lattice diamond 5.4309
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region box block 0 10 0 10 0 10
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create_box 1 box
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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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pair_style sw
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pair_coeff * * Si.sw Si
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neighbor 2.0 bin
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neigh_modify every 5 delay 0 check yes
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fix 1 all nve
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fix twotemp all ttm/mod 1354684 Si.ttm_mod 10 10 10 set 1000.0 # outfile 100 T_out.txt
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compute pe all pe/atom
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compute ke all ke/atom
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timestep 0.0001
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thermo 100
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thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
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thermo_modify format float "%20.16g"
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run 1000
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122
examples/ttm/log.20Apr22.ttm.mod.g++.1
Normal file
122
examples/ttm/log.20Apr22.ttm.mod.g++.1
Normal file
@ -0,0 +1,122 @@
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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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units metal
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atom_style atomic
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boundary p p p
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lattice diamond 5.4309
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Lattice spacing in x,y,z = 5.4309 5.4309 5.4309
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region box block 0 10 0 10 0 10
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create_box 1 box
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Created orthogonal box = (0 0 0) to (54.309 54.309 54.309)
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1 by 1 by 1 MPI processor grid
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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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pair_style sw
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pair_coeff * * Si.sw Si
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Reading sw potential file Si.sw with DATE: 2007-06-11
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neighbor 2.0 bin
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neigh_modify every 5 delay 0 check yes
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fix 1 all nve
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fix twotemp all ttm/mod 1354684 Si.ttm_mod 10 10 10 set 1000.0 # outfile 100 T_out.txt
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compute pe all pe/atom
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compute ke all ke/atom
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timestep 0.0001
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thermo 100
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thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
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thermo_modify format float "%20.16g"
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run 1000
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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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@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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volume = {26},
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number = {47},
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pages = {475401},
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year = {2014}
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}
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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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number = {2},
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volume = {53},
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pages = {129--139},
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year = {2013}
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}
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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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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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binsize = 2.88559, bins = 19 19 19
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair sw, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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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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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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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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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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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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Nghost: 6725 ave 6725 max 6725 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 272000 ave 272000 max 272000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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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122
examples/ttm/log.20Apr22.ttm.mod.g++.4
Normal file
122
examples/ttm/log.20Apr22.ttm.mod.g++.4
Normal file
@ -0,0 +1,122 @@
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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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units metal
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atom_style atomic
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boundary p p p
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lattice diamond 5.4309
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Lattice spacing in x,y,z = 5.4309 5.4309 5.4309
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region box block 0 10 0 10 0 10
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create_box 1 box
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Created orthogonal box = (0 0 0) to (54.309 54.309 54.309)
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1 by 2 by 2 MPI processor grid
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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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pair_style sw
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pair_coeff * * Si.sw Si
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Reading sw potential file Si.sw with DATE: 2007-06-11
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neighbor 2.0 bin
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neigh_modify every 5 delay 0 check yes
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fix 1 all nve
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fix twotemp all ttm/mod 1354684 Si.ttm_mod 10 10 10 set 1000.0 # outfile 100 T_out.txt
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compute pe all pe/atom
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compute ke all ke/atom
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timestep 0.0001
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thermo 100
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thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
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thermo_modify format float "%20.16g"
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run 1000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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||||||
|
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||||||
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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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||||||
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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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volume = {26},
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number = {47},
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pages = {475401},
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year = {2014}
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}
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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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number = {2},
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volume = {53},
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pages = {129--139},
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year = {2013}
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}
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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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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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binsize = 2.88559, bins = 19 19 19
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair sw, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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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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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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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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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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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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Nghost: 3165 ave 3165 max 3165 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 68000 ave 68000 max 68000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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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: 0:00:01
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||||||
@ -435,121 +435,146 @@ void FixTTMMod::reset_dt()
|
|||||||
|
|
||||||
void FixTTMMod::read_parameters(const std::string &filename)
|
void FixTTMMod::read_parameters(const std::string &filename)
|
||||||
{
|
{
|
||||||
try {
|
if (comm->me == 0) {
|
||||||
PotentialFileReader reader(lmp, filename, "ttm/mod parameter");
|
|
||||||
|
|
||||||
// C0 (metal)
|
try {
|
||||||
|
PotentialFileReader reader(lmp, filename, "ttm/mod parameter");
|
||||||
|
|
||||||
reader.next_line();
|
// C0 (metal)
|
||||||
esheat_0 = reader.next_values(1).next_double();
|
|
||||||
|
|
||||||
// C1 (metal*10^3)
|
reader.next_line();
|
||||||
|
esheat_0 = reader.next_values(1).next_double();
|
||||||
|
|
||||||
reader.next_line();
|
// C1 (metal*10^3)
|
||||||
esheat_1 = reader.next_values(1).next_double();
|
|
||||||
|
|
||||||
// C2 (metal*10^6)
|
reader.next_line();
|
||||||
|
esheat_1 = reader.next_values(1).next_double();
|
||||||
|
|
||||||
reader.next_line();
|
// C2 (metal*10^6)
|
||||||
esheat_2 = reader.next_values(1).next_double();
|
|
||||||
|
|
||||||
// C3 (metal*10^9)
|
reader.next_line();
|
||||||
|
esheat_2 = reader.next_values(1).next_double();
|
||||||
|
|
||||||
reader.next_line();
|
// C3 (metal*10^9)
|
||||||
esheat_3 = reader.next_values(1).next_double();
|
|
||||||
|
|
||||||
// C4 (metal*10^12)
|
reader.next_line();
|
||||||
|
esheat_3 = reader.next_values(1).next_double();
|
||||||
|
|
||||||
reader.next_line();
|
// C4 (metal*10^12)
|
||||||
esheat_4 = reader.next_values(1).next_double();
|
|
||||||
|
|
||||||
// C_limit
|
reader.next_line();
|
||||||
|
esheat_4 = reader.next_values(1).next_double();
|
||||||
|
|
||||||
reader.next_line();
|
// C_limit
|
||||||
C_limit = reader.next_values(1).next_double();
|
|
||||||
|
|
||||||
// Temperature damping factor
|
reader.next_line();
|
||||||
|
C_limit = reader.next_values(1).next_double();
|
||||||
|
|
||||||
reader.next_line();
|
// Temperature damping factor
|
||||||
T_damp = reader.next_values(1).next_double();
|
|
||||||
|
|
||||||
// rho_e
|
reader.next_line();
|
||||||
|
T_damp = reader.next_values(1).next_double();
|
||||||
|
|
||||||
reader.next_line();
|
// rho_e
|
||||||
electronic_density = reader.next_values(1).next_double();
|
|
||||||
|
|
||||||
// thermal_diffusion
|
reader.next_line();
|
||||||
|
electronic_density = reader.next_values(1).next_double();
|
||||||
|
|
||||||
reader.next_line();
|
// thermal_diffusion
|
||||||
el_th_diff = reader.next_values(1).next_double();
|
|
||||||
|
|
||||||
// gamma_p
|
reader.next_line();
|
||||||
|
el_th_diff = reader.next_values(1).next_double();
|
||||||
|
|
||||||
reader.next_line();
|
// gamma_p
|
||||||
gamma_p = reader.next_values(1).next_double();
|
|
||||||
|
|
||||||
// gamma_s
|
reader.next_line();
|
||||||
|
gamma_p = reader.next_values(1).next_double();
|
||||||
|
|
||||||
reader.next_line();
|
// gamma_s
|
||||||
gamma_s = reader.next_values(1).next_double();
|
|
||||||
|
|
||||||
// v0
|
reader.next_line();
|
||||||
|
gamma_s = reader.next_values(1).next_double();
|
||||||
|
|
||||||
reader.next_line();
|
// v0
|
||||||
v_0 = reader.next_values(1).next_double();
|
|
||||||
|
|
||||||
// average intensity of pulse (source of energy) (metal units)
|
reader.next_line();
|
||||||
|
v_0 = reader.next_values(1).next_double();
|
||||||
|
|
||||||
reader.next_line();
|
// average intensity of pulse (source of energy) (metal units)
|
||||||
intensity = reader.next_values(1).next_double();
|
|
||||||
|
|
||||||
// coordinate of 1st surface in x-direction (in box units) - constant
|
reader.next_line();
|
||||||
|
intensity = reader.next_values(1).next_double();
|
||||||
|
|
||||||
reader.next_line();
|
// coordinate of 1st surface in x-direction (in box units) - constant
|
||||||
surface_l = reader.next_values(1).next_int();
|
|
||||||
|
|
||||||
// coordinate of 2nd surface in x-direction (in box units) - constant
|
reader.next_line();
|
||||||
|
surface_l = reader.next_values(1).next_int();
|
||||||
|
|
||||||
reader.next_line();
|
// coordinate of 2nd surface in x-direction (in box units) - constant
|
||||||
surface_r = reader.next_values(1).next_int();
|
|
||||||
|
|
||||||
// skin_layer = intensity is reduced (I=I0*exp[-x/skin_layer])
|
reader.next_line();
|
||||||
|
surface_r = reader.next_values(1).next_int();
|
||||||
|
|
||||||
reader.next_line();
|
// skin_layer = intensity is reduced (I=I0*exp[-x/skin_layer])
|
||||||
skin_layer = reader.next_values(1).next_int();
|
|
||||||
|
|
||||||
// width of pulse (picoseconds)
|
reader.next_line();
|
||||||
|
skin_layer = reader.next_values(1).next_int();
|
||||||
|
|
||||||
reader.next_line();
|
// width of pulse (picoseconds)
|
||||||
width = reader.next_values(1).next_double();
|
|
||||||
|
|
||||||
// factor of electronic pressure (PF) Pe = PF*Ce*Te
|
reader.next_line();
|
||||||
|
width = reader.next_values(1).next_double();
|
||||||
|
|
||||||
reader.next_line();
|
// factor of electronic pressure (PF) Pe = PF*Ce*Te
|
||||||
pres_factor = reader.next_values(1).next_double();
|
|
||||||
|
|
||||||
// effective free path of electrons (angstrom)
|
reader.next_line();
|
||||||
|
pres_factor = reader.next_values(1).next_double();
|
||||||
|
|
||||||
reader.next_line();
|
// effective free path of electrons (angstrom)
|
||||||
free_path = reader.next_values(1).next_double();
|
|
||||||
|
|
||||||
// ionic density (ions*angstrom^{-3})
|
reader.next_line();
|
||||||
|
free_path = reader.next_values(1).next_double();
|
||||||
|
|
||||||
reader.next_line();
|
// ionic density (ions*angstrom^{-3})
|
||||||
ionic_density = reader.next_values(1).next_double();
|
|
||||||
|
|
||||||
// if movsur = 0: surface is frozen
|
reader.next_line();
|
||||||
|
ionic_density = reader.next_values(1).next_double();
|
||||||
|
|
||||||
reader.next_line();
|
// if movsur = 0: surface is frozen
|
||||||
movsur = reader.next_values(1).next_int();
|
|
||||||
|
|
||||||
// electron_temperature_min
|
reader.next_line();
|
||||||
|
movsur = reader.next_values(1).next_int();
|
||||||
|
|
||||||
reader.next_line();
|
// electron_temperature_min
|
||||||
electron_temperature_min = reader.next_values(1).next_double();
|
|
||||||
} catch (std::exception &e) {
|
reader.next_line();
|
||||||
error->one(FLERR,e.what());
|
electron_temperature_min = reader.next_values(1).next_double();
|
||||||
|
} catch (std::exception &e) {
|
||||||
|
error->one(FLERR,e.what());
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
MPI_Bcast(&esheat_0, 1, MPI_DOUBLE, 0, world);
|
||||||
|
MPI_Bcast(&esheat_1, 1, MPI_DOUBLE, 0, world);
|
||||||
|
MPI_Bcast(&esheat_2, 1, MPI_DOUBLE, 0, world);
|
||||||
|
MPI_Bcast(&esheat_3, 1, MPI_DOUBLE, 0, world);
|
||||||
|
MPI_Bcast(&esheat_4, 1, MPI_DOUBLE, 0, world);
|
||||||
|
MPI_Bcast(&C_limit, 1, MPI_DOUBLE, 0, world);
|
||||||
|
MPI_Bcast(&T_damp, 1, MPI_DOUBLE, 0, world);
|
||||||
|
MPI_Bcast(&electronic_density, 1, MPI_DOUBLE, 0, world);
|
||||||
|
MPI_Bcast(&el_th_diff, 1, MPI_DOUBLE, 0, world);
|
||||||
|
MPI_Bcast(&gamma_p, 1, MPI_DOUBLE, 0, world);
|
||||||
|
MPI_Bcast(&gamma_s, 1, MPI_DOUBLE, 0, world);
|
||||||
|
MPI_Bcast(&v_0, 1, MPI_DOUBLE, 0, world);
|
||||||
|
MPI_Bcast(&intensity, 1, MPI_DOUBLE, 0, world);
|
||||||
|
MPI_Bcast(&surface_l, 1, MPI_INT, 0, world);
|
||||||
|
MPI_Bcast(&surface_r, 1, MPI_INT, 0, world);
|
||||||
|
MPI_Bcast(&skin_layer, 1, MPI_INT, 0, world);
|
||||||
|
MPI_Bcast(&width, 1, MPI_DOUBLE, 0, world);
|
||||||
|
MPI_Bcast(&pres_factor, 1, MPI_DOUBLE, 0, world);
|
||||||
|
MPI_Bcast(&free_path, 1, MPI_DOUBLE, 0, world);
|
||||||
|
MPI_Bcast(&ionic_density, 1, MPI_DOUBLE, 0, world);
|
||||||
|
MPI_Bcast(&movsur, 1, MPI_INT, 0, world);
|
||||||
|
MPI_Bcast(&electron_temperature_min, 1, MPI_DOUBLE, 0, world);
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
|
|||||||
Reference in New Issue
Block a user