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Axel Kohlmeyer
2022-03-23 04:47:52 -04:00
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# COMB parameters for various elements (Si, Cu, Hf, Ti, Zr, U, O) and mixtures (their oxides and alloys)
# Edited by Tzu-Ray Shan from MSE, Univ. FL in Apr 2010
#
# Elements currently available: Si, Cu, Hf, Ti, Zr, U, O
# Oxides currently available: Si-O, Cu-O, Hf-O, Ti-O
#
# Si parameter set from (JG Yu, SB Sinnott, SR Phillpot, Phys. Rev. B 75 085311 2007)
# ,and (TR Shan, BD Devine, SR Phillpot, SB Sinnott, to be sub to Phys. Rev. B)
# O parameter set from (TR Shan, BD Devine, SB Sinnott, SR Phillpot, Phys. Rev. B 81 125328 2010)
# Cu parameter set from (BD Devine, TR Shan, SB Sinnott, SR Phillpot, to be sub to Phys. Rev. B)
# Hf parameter set from (TR Shan, BD Devine, SB Sinnott, SR Phillpot, Phys. Rev. B 81 125328 2010)
# Ti parameter set from (TR Shan, SR Phillpot, SB Sinnott, in preparation)
# U parameter set from (Y Li, TR Shan, SB Sinnott, SR Phillpot, in preparation)
# Zr parameter set from (T Iwasaki, J. Mater. Res. 20 5 1300 2005)
#
# Multiple entries can be added to this file, LAMMPS reads the ones it needs
# Only M-O are added in the potential table, using mixing rules to generate desired alloy (A-B) parameters
# 8 entries for a desired A-B type: AAA, BBB, AAB, ABA, ABB, BAA, BBA, BBA
# 27 entries for a system containing three elements A, B and C
# These entries are in LAMMPS "metal" units
#
Hf Hf Hf 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.90 0.10 2.069563 2.069563 707.53 707.53 0 0 0.008 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12 0.0
Ti Ti Ti 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 3.40 0.10 2.082408 2.082408 546.386 546.386 0 0 0.0084 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 2.46820415900968 0 0.151351003255176 0 0.873685 0.392632 0.392632 1.78349 1.78349 12 0.0
O O O 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.8 0.2 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0.0
Cu Cu Cu 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.95 0.05 2.794608 2.794608 952.693 952.693 0.077 0.0095 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12 -2.0
Si Si Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.90 0.10 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0.0
Zr Zr Zr 1 0 1 0 1 0 0.929 0.929 39.9454 39.9454 3.8 0.31 1.857 1.857 382.6 382.6 0 0 0 0 0 0 1 1 1 1 -4 4 1.64 -1.5 -4 4 1.64 -1.5 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12 0.0
U U U 1 0 1 0 4.346966 0.77617 0.832 0.832 162.6 162.6 3.9 0.15 1.835 1.835 795.6 795.6 0 0 0 0 0 0 1 1 1 1 -4 4 2 -2 -4 4 2 -2 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12 0.0
#
Si O O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.25 2.4799 5.36 1830.8 3326.69 0 0 0 109.47 0.3122 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
O Si Si 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 2.80 0.25 5.36 2.4799 3326.69 1830.8 0 0 0 143.73 2.6 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0
Si O Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.25 2.4799 5.36 1830.8 3326.69 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
O Si O 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 3.20 0.25 5.36 2.4799 3326.69 1830.8 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0
Si Si O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.80 0.25 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0
O O Si 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.80 0.25 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0
#
Si Cu Cu 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.681711 471.18 146.987 2.70 0.10 2.4799 2.794608 1830.8 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -6 2 0.1677645 -0.161007 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 0.72571 2.999911 0.274649 12 0
Cu Si Si 1 0 1 0 1 0.140835 1.681711 1.7322 146.987 471.18 2.70 0.10 2.794608 2.4799 952.693 1830.8 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 1.651725 -1.658949 0 5.946437 0 0 0 0.454784 0.72571 -0.499378 0.274649 2.999911 12 0
Si Cu Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.681711 471.18 146.987 2.70 0.10 2.4799 2.794608 1830.8 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -6 2 0.1677645 -0.161007 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 0.72571 2.999911 0.274649 12 0
Cu Si Cu 1 0 1 0 1 0.140835 1.681711 1.7322 146.987 471.18 2.70 0.10 2.794608 2.4799 952.693 1830.8 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 1.651725 -1.658949 0 5.946437 0 0 0 0.454784 0.72571 -0.499378 0.274649 2.999911 12 0
Si Si Cu 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.70 0.10 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0
Cu Cu Si 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.70 0.10 2.794608 2.794608 952.693 952.693 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12 0
#
Si O Cu 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.10 2.4799 5.36 1830.8 3326.69 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
Cu O Si 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.40 0.10 2.794608 5.36 952.693 3326.69 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12 0
Si Cu O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.681711 471.18 146.987 2.70 0.10 2.4799 2.794608 1830.8 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -6 2 0.1677645 -0.161007 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 0.72571 2.999911 0.274649 12 0
Cu Si O 1 0 1 0 1 0.140835 1.681711 1.7322 146.987 471.18 2.70 0.10 2.794608 2.4799 952.693 1830.8 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 1.651725 -1.658949 0 5.946437 0 0 0 0.454784 0.72571 -0.499378 0.274649 2.999911 12 0
O Si Cu 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 2.80 0.10 5.36 2.4799 3326.69 1830.8 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0
O Cu Si 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.40 0.10 5.36 2.794608 3326.69 952.693 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12 0
#
Cu O O 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.40 0.110 2.794608 5.36 952.693 3326.69 0 0 0 360 3.0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12 -1.0
O Cu Cu 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.40 0.110 5.36 2.794608 3326.69 952.693 0 0 0 109.47 2.98 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12 0
Cu O Cu 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.40 0.110 2.794608 5.36 952.693 3326.69 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12 0
O Cu O 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.40 0.110 5.36 2.794608 3326.69 952.693 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12 0
Cu Cu O 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.90 0.05 2.794608 2.794608 952.693 952.693 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12 0
O O Cu 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.80 0.20 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0
#
Si Hf Hf 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 0.959614 471.18 55.9421 3.26 0.15 2.4799 2.069563 1830.8 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 0.26152 -0.25918 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.92875 2.999911 4.83958 12 0
Hf Si Si 1 0 1 0 1.011011 0.046511 0.959614 1.7322 55.9421 471.18 3.26 0.15 2.069563 2.4799 707.53 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 1.651725 -1.658949 0 3.13952 0 0.00941 0 0.719131 -3.92875 -0.499378 4.83958 2.999911 12 0
Si Hf Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 0.959614 471.18 55.9421 3.26 0.15 2.4799 2.069563 1830.8 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 0.26152 -0.25918 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.92875 2.999911 4.83958 12 0
Hf Si Hf 1 0 1 0 1.011011 0.046511 0.959614 1.7322 55.9421 471.18 3.26 0.15 2.069563 2.4799 707.53 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 1.651725 -1.658949 0 3.13952 0 0.00941 0 0.719131 -3.92875 -0.499378 4.83958 2.999911 12 0
Si Si Hf 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 3.26 0.15 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0
Hf Hf Si 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.26 0.15 2.069563 2.069563 707.53 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.13952 0 0.00941 0 0.719131 -3.92875 -3.92875 4.83958 4.83958 12 0
#
Si O Hf 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 3.196 0.21 2.4799 5.36 1830.8 3326.69 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
Hf O Si 1 0 1 0 1.011011 0.046511 0.959614 2.68 55.9421 260.893 3.196 0.21 2.069563 5.36 707.53 3326.69 0 0 0 0 0 0.14 1 1 1 1 -4 4 0.26152 -0.25918 -1.8349 5.5046 0.00148 -0.00112 0 3.13952 0 0.00941 0 0.719131 -3.92875 -3.922011 4.83958 0.971086 12 0.16
Si Hf O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 0.959614 471.18 55.9421 3.26 0.15 2.4799 2.069563 1830.8 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 0.26152 -0.25918 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.92875 2.999911 4.83958 12 0
Hf Si O 1 0 1 0 1.011011 0.046511 0.959614 1.7322 55.9421 471.18 3.26 0.15 2.069563 2.4799 707.53 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 1.651725 -1.658949 0 3.13952 0 0.00941 0 0.719131 -3.92875 -0.499378 4.83958 2.999911 12 0
O Si Hf 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 3.196 0.21 5.36 2.4799 3326.69 1830.8 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0
O Hf Si 1 6.6 1 -0.229 1 2 2.68 0.959614 260.893 55.9421 3.196 0.21 5.36 2.069563 3326.69 707.53 0 0 0 0 0 0.14 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 0.26152 -0.25918 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.92875 0.971086 4.83958 12 0.16
#
Hf O O 1 0 1 0 1.011011 0.046511 0.959614 2.68 55.9421 260.893 3.29 0.12 2.069563 5.36 707.53 3326.69 0 0 0 0 0 0.14 1 1 1 1 -4 4 0.26152 -0.25918 -1.8349 5.5046 0.00148 -0.00112 0 3.13952 0 0.00941 0 0.679131 -3.92875 -3.922011 4.83958 0.971086 12 0.30
O Hf Hf 1 6.6 1 -0.229 1 2 2.68 0.959614 260.893 55.9421 3.29 0.12 5.36 2.069563 3326.69 707.53 0 0 0 0 0 0.14 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 0.26152 -0.25918 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.92875 0.971086 4.83958 12 0.30
Hf O Hf 1 0 1 0 1.011011 0.046511 0.959614 2.68 55.9421 260.893 3.29 0.12 2.069563 5.36 707.53 3326.69 0 0 0 0 0 0.14 1 1 1 1 -4 4 0.26152 -0.25918 -1.8349 5.5046 0.00148 -0.00112 0 3.13952 0 0.00941 0 0.679131 -3.92875 -3.922011 4.83958 0.971086 12 0.30
O Hf O 1 6.6 1 -0.229 1 2 2.68 0.959614 260.893 55.9421 3.29 0.12 5.36 2.069563 3326.69 707.53 0 0 0 0 0 0.14 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 0.26152 -0.25918 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.92875 0.971086 4.83958 12 0.30
Hf Hf O 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.29 0.12 2.069563 2.069563 707.53 707.53 0 0 0 0 0 0.0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.13952 0 0.00941 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12 0.30
O O Hf 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 3.29 0.12 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0.0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0.30
#
Ti O O 1 0 1 0 1.255016 0.089078 1.226342 2.68 99.3916 260.893 3.25 0.10 2.082408 5.36 546.386 3326.69 0 0 0 90 0.403105 8.45 0.088406 0.969934 0.296577 1.326746 -4 4 2.508854 -2.511416 -1.8349 5.5046 0.00148 -0.00112 0 1.943430774 0 0.254695274 0 0.873685 0.392632 -3.922011 1.78349 0.971086 12 0.0
O Ti Ti 1 6.6 1 -0.229 1 2 2.68 1.226342 260.893 99.3916 3.25 0.10 5.36 2.082408 3326.69 546.386 0 0 0 130.54 0.202777 8.45 0.088406 0.969934 0.296577 1.326746 -1.8349 5.5046 0.00148 -0.00112 -4 4 2.508854 -2.511416 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.392632 0.971086 1.78349 12 0.0
Ti O Ti 1 0 1 0 1.255016 0.089078 1.226342 2.68 99.3916 260.893 3.25 0.10 2.082408 5.36 546.386 3326.69 0 0 0 0 0 8.45 0.088406 0.969934 0.296577 1.326746 -4 4 2.508854 -2.511416 -1.8349 5.5046 0.00148 -0.00112 0 1.943430774 0 0.254695274 0 0.873685 0.392632 -3.922011 1.78349 0.971086 12 0.0
O Ti O 1 6.6 1 -0.229 1 2 2.68 1.226342 260.893 99.3916 3.25 0.10 5.36 2.082408 3326.69 546.386 0 0 0 0 0 8.45 0.088406 0.969934 0.296577 1.326746 -1.8349 5.5046 0.00148 -0.00112 -4 4 2.508854 -2.511416 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.392632 0.971086 1.78349 12 0.0
Ti Ti O 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 3.25 0.10 2.082408 2.082408 546.386 546.386 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.392632 1.78349 1.78349 12 0.0
O O Ti 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.80 0.20 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0.0
#
Ti Cu Cu 1 0 1 0 1.255016 0.089078 1.226342 1.681711 99.3916 146.987 3.40 0.15 2.082408 2.794608 546.386 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -6 2 0.1677645 -0.161007 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.72571 1.78349 0.274649 12 0
Cu Ti Ti 1 0 1 0 1 0.140835 1.681711 1.226342 146.987 99.3916 3.40 0.15 2.794608 2.082408 952.693 546.386 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 2.508854 -2.511416 0 5.946437 0 0 0 0.454784 0.72571 0.392632 0.274649 1.78349 12 0
Ti Cu Ti 1 0 1 0 1.255016 0.089078 1.226342 1.681711 99.3916 146.987 3.40 0.15 2.082408 2.794608 546.386 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -6 2 0.1677645 -0.161007 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.72571 1.78349 0.274649 12 0
Cu Ti Cu 1 0 1 0 1 0.140835 1.681711 1.226342 146.987 99.3916 3.40 0.15 2.794608 2.082408 952.693 546.386 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 2.508854 -2.511416 0 5.946437 0 0 0 0.454784 0.72571 0.392632 0.274649 1.78349 12 0
Ti Ti Cu 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 3.40 0.10 2.082408 2.082408 546.386 546.386 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.392632 1.78349 1.78349 12 0
Cu Cu Ti 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.90 0.05 2.794608 2.794608 952.693 952.693 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12 0
#
Ti O Cu 1 0 1 0 1.255016 0.089078 1.226342 2.68 99.3916 260.893 3.25 0.10 2.082408 5.36 546.386 3326.69 0 0 0 0 0 8.45 0.088406 0.969934 0.296577 1.326746 -4 4 2.508854 -2.511416 -1.8349 5.5046 0.00148 -0.00112 0 1.943430774 0 0.254695274 0 0.873685 0.392632 -3.922011 1.78349 0.971086 12 0
Cu O Ti 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.40 0.10 2.794608 5.36 952.693 3326.69 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12 0
Ti Cu O 1 0 1 0 1.255016 0.089078 1.226342 1.681711 99.3916 146.987 3.40 0.15 2.082408 2.794608 546.386 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -6 2 0.1677645 -0.161007 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.72571 1.78349 0.274649 12 0
Cu Ti O 1 0 1 0 1 0.140835 1.681711 1.226342 146.987 99.3916 3.40 0.15 2.794608 2.082408 952.693 546.386 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 2.508854 -2.511416 0 5.946437 0 0 0 0.454784 0.72571 0.392632 0.274649 1.78349 12 0
O Ti Cu 1 6.6 1 -0.229 1 2 2.68 1.226342 260.893 99.3916 3.25 0.10 5.36 2.082408 3326.69 546.386 0 0 0 0 0 8.45 0.088406 0.969934 0.296577 1.326746 -1.8349 5.5046 0.00148 -0.00112 -4 4 2.508854 -2.511416 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.392632 0.971086 1.78349 12 0
O Cu Ti 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.40 0.10 5.36 2.794608 3326.69 952.693 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12 0
# COMB parameters for various elements (Si, Cu, Hf, Ti, Zr, U, O) and mixtures (their oxides and alloys)
# Edited by Tzu-Ray Shan from MSE, Univ. FL in Apr 2010
#
# Elements currently available: Si, Cu, Hf, Ti, Zr, U, O
# Oxides currently available: Si-O, Cu-O, Hf-O, Ti-O
#
# Si parameter set from (JG Yu, SB Sinnott, SR Phillpot, Phys. Rev. B 75 085311 2007)
# ,and (TR Shan, BD Devine, SR Phillpot, SB Sinnott, to be sub to Phys. Rev. B)
# O parameter set from (TR Shan, BD Devine, SB Sinnott, SR Phillpot, Phys. Rev. B 81 125328 2010)
# Cu parameter set from (BD Devine, TR Shan, SB Sinnott, SR Phillpot, to be sub to Phys. Rev. B)
# Hf parameter set from (TR Shan, BD Devine, SB Sinnott, SR Phillpot, Phys. Rev. B 81 125328 2010)
# Ti parameter set from (TR Shan, SR Phillpot, SB Sinnott, in preparation)
# U parameter set from (Y Li, TR Shan, SB Sinnott, SR Phillpot, in preparation)
# Zr parameter set from (T Iwasaki, J. Mater. Res. 20 5 1300 2005)
#
# Multiple entries can be added to this file, LAMMPS reads the ones it needs
# Only M-O are added in the potential table, using mixing rules to generate desired alloy (A-B) parameters
# 8 entries for a desired A-B type: AAA, BBB, AAB, ABA, ABB, BAA, BBA, BBA
# 27 entries for a system containing three elements A, B and C
# These entries are in LAMMPS "metal" units
#
Hf Hf Hf 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.90 0.10 2.069563 2.069563 707.53 707.53 0 0 0.008 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12 0.0
Ti Ti Ti 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 3.40 0.10 2.082408 2.082408 546.386 546.386 0 0 0.0084 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 2.46820415900968 0 0.151351003255176 0 0.873685 0.392632 0.392632 1.78349 1.78349 12 0.0
O O O 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.8 0.2 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0.0
Cu Cu Cu 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.95 0.05 2.794608 2.794608 952.693 952.693 0.077 0.0095 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12 -2.0
Si Si Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.90 0.10 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0.0
Zr Zr Zr 1 0 1 0 1 0 0.929 0.929 39.9454 39.9454 3.8 0.31 1.857 1.857 382.6 382.6 0 0 0 0 0 0 1 1 1 1 -4 4 1.64 -1.5 -4 4 1.64 -1.5 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12 0.0
U U U 1 0 1 0 4.346966 0.77617 0.832 0.832 162.6 162.6 3.9 0.15 1.835 1.835 795.6 795.6 0 0 0 0 0 0 1 1 1 1 -4 4 2 -2 -4 4 2 -2 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12 0.0
#
Si O O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.25 2.4799 5.36 1830.8 3326.69 0 0 0 109.47 0.3122 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
O Si Si 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 2.80 0.25 5.36 2.4799 3326.69 1830.8 0 0 0 143.73 2.6 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0
Si O Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.25 2.4799 5.36 1830.8 3326.69 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
O Si O 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 3.20 0.25 5.36 2.4799 3326.69 1830.8 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0
Si Si O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.80 0.25 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0
O O Si 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.80 0.25 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0
#
Si Cu Cu 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.681711 471.18 146.987 2.70 0.10 2.4799 2.794608 1830.8 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -6 2 0.1677645 -0.161007 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 0.72571 2.999911 0.274649 12 0
Cu Si Si 1 0 1 0 1 0.140835 1.681711 1.7322 146.987 471.18 2.70 0.10 2.794608 2.4799 952.693 1830.8 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 1.651725 -1.658949 0 5.946437 0 0 0 0.454784 0.72571 -0.499378 0.274649 2.999911 12 0
Si Cu Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.681711 471.18 146.987 2.70 0.10 2.4799 2.794608 1830.8 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -6 2 0.1677645 -0.161007 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 0.72571 2.999911 0.274649 12 0
Cu Si Cu 1 0 1 0 1 0.140835 1.681711 1.7322 146.987 471.18 2.70 0.10 2.794608 2.4799 952.693 1830.8 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 1.651725 -1.658949 0 5.946437 0 0 0 0.454784 0.72571 -0.499378 0.274649 2.999911 12 0
Si Si Cu 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.70 0.10 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0
Cu Cu Si 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.70 0.10 2.794608 2.794608 952.693 952.693 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12 0
#
Si O Cu 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.10 2.4799 5.36 1830.8 3326.69 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
Cu O Si 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.40 0.10 2.794608 5.36 952.693 3326.69 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12 0
Si Cu O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.681711 471.18 146.987 2.70 0.10 2.4799 2.794608 1830.8 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -6 2 0.1677645 -0.161007 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 0.72571 2.999911 0.274649 12 0
Cu Si O 1 0 1 0 1 0.140835 1.681711 1.7322 146.987 471.18 2.70 0.10 2.794608 2.4799 952.693 1830.8 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 1.651725 -1.658949 0 5.946437 0 0 0 0.454784 0.72571 -0.499378 0.274649 2.999911 12 0
O Si Cu 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 2.80 0.10 5.36 2.4799 3326.69 1830.8 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0
O Cu Si 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.40 0.10 5.36 2.794608 3326.69 952.693 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12 0
#
Cu O O 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.40 0.110 2.794608 5.36 952.693 3326.69 0 0 0 360 3.0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12 -1.0
O Cu Cu 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.40 0.110 5.36 2.794608 3326.69 952.693 0 0 0 109.47 2.98 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12 0
Cu O Cu 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.40 0.110 2.794608 5.36 952.693 3326.69 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12 0
O Cu O 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.40 0.110 5.36 2.794608 3326.69 952.693 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12 0
Cu Cu O 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.90 0.05 2.794608 2.794608 952.693 952.693 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12 0
O O Cu 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.80 0.20 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0
#
Si Hf Hf 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 0.959614 471.18 55.9421 3.26 0.15 2.4799 2.069563 1830.8 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 0.26152 -0.25918 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.92875 2.999911 4.83958 12 0
Hf Si Si 1 0 1 0 1.011011 0.046511 0.959614 1.7322 55.9421 471.18 3.26 0.15 2.069563 2.4799 707.53 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 1.651725 -1.658949 0 3.13952 0 0.00941 0 0.719131 -3.92875 -0.499378 4.83958 2.999911 12 0
Si Hf Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 0.959614 471.18 55.9421 3.26 0.15 2.4799 2.069563 1830.8 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 0.26152 -0.25918 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.92875 2.999911 4.83958 12 0
Hf Si Hf 1 0 1 0 1.011011 0.046511 0.959614 1.7322 55.9421 471.18 3.26 0.15 2.069563 2.4799 707.53 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 1.651725 -1.658949 0 3.13952 0 0.00941 0 0.719131 -3.92875 -0.499378 4.83958 2.999911 12 0
Si Si Hf 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 3.26 0.15 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0
Hf Hf Si 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.26 0.15 2.069563 2.069563 707.53 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.13952 0 0.00941 0 0.719131 -3.92875 -3.92875 4.83958 4.83958 12 0
#
Si O Hf 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 3.196 0.21 2.4799 5.36 1830.8 3326.69 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
Hf O Si 1 0 1 0 1.011011 0.046511 0.959614 2.68 55.9421 260.893 3.196 0.21 2.069563 5.36 707.53 3326.69 0 0 0 0 0 0.14 1 1 1 1 -4 4 0.26152 -0.25918 -1.8349 5.5046 0.00148 -0.00112 0 3.13952 0 0.00941 0 0.719131 -3.92875 -3.922011 4.83958 0.971086 12 0.16
Si Hf O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 0.959614 471.18 55.9421 3.26 0.15 2.4799 2.069563 1830.8 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 0.26152 -0.25918 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.92875 2.999911 4.83958 12 0
Hf Si O 1 0 1 0 1.011011 0.046511 0.959614 1.7322 55.9421 471.18 3.26 0.15 2.069563 2.4799 707.53 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 1.651725 -1.658949 0 3.13952 0 0.00941 0 0.719131 -3.92875 -0.499378 4.83958 2.999911 12 0
O Si Hf 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 3.196 0.21 5.36 2.4799 3326.69 1830.8 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0
O Hf Si 1 6.6 1 -0.229 1 2 2.68 0.959614 260.893 55.9421 3.196 0.21 5.36 2.069563 3326.69 707.53 0 0 0 0 0 0.14 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 0.26152 -0.25918 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.92875 0.971086 4.83958 12 0.16
#
Hf O O 1 0 1 0 1.011011 0.046511 0.959614 2.68 55.9421 260.893 3.29 0.12 2.069563 5.36 707.53 3326.69 0 0 0 0 0 0.14 1 1 1 1 -4 4 0.26152 -0.25918 -1.8349 5.5046 0.00148 -0.00112 0 3.13952 0 0.00941 0 0.679131 -3.92875 -3.922011 4.83958 0.971086 12 0.30
O Hf Hf 1 6.6 1 -0.229 1 2 2.68 0.959614 260.893 55.9421 3.29 0.12 5.36 2.069563 3326.69 707.53 0 0 0 0 0 0.14 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 0.26152 -0.25918 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.92875 0.971086 4.83958 12 0.30
Hf O Hf 1 0 1 0 1.011011 0.046511 0.959614 2.68 55.9421 260.893 3.29 0.12 2.069563 5.36 707.53 3326.69 0 0 0 0 0 0.14 1 1 1 1 -4 4 0.26152 -0.25918 -1.8349 5.5046 0.00148 -0.00112 0 3.13952 0 0.00941 0 0.679131 -3.92875 -3.922011 4.83958 0.971086 12 0.30
O Hf O 1 6.6 1 -0.229 1 2 2.68 0.959614 260.893 55.9421 3.29 0.12 5.36 2.069563 3326.69 707.53 0 0 0 0 0 0.14 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 0.26152 -0.25918 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.92875 0.971086 4.83958 12 0.30
Hf Hf O 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.29 0.12 2.069563 2.069563 707.53 707.53 0 0 0 0 0 0.0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.13952 0 0.00941 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12 0.30
O O Hf 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 3.29 0.12 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0.0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0.30
#
Ti O O 1 0 1 0 1.255016 0.089078 1.226342 2.68 99.3916 260.893 3.25 0.10 2.082408 5.36 546.386 3326.69 0 0 0 90 0.403105 8.45 0.088406 0.969934 0.296577 1.326746 -4 4 2.508854 -2.511416 -1.8349 5.5046 0.00148 -0.00112 0 1.943430774 0 0.254695274 0 0.873685 0.392632 -3.922011 1.78349 0.971086 12 0.0
O Ti Ti 1 6.6 1 -0.229 1 2 2.68 1.226342 260.893 99.3916 3.25 0.10 5.36 2.082408 3326.69 546.386 0 0 0 130.54 0.202777 8.45 0.088406 0.969934 0.296577 1.326746 -1.8349 5.5046 0.00148 -0.00112 -4 4 2.508854 -2.511416 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.392632 0.971086 1.78349 12 0.0
Ti O Ti 1 0 1 0 1.255016 0.089078 1.226342 2.68 99.3916 260.893 3.25 0.10 2.082408 5.36 546.386 3326.69 0 0 0 0 0 8.45 0.088406 0.969934 0.296577 1.326746 -4 4 2.508854 -2.511416 -1.8349 5.5046 0.00148 -0.00112 0 1.943430774 0 0.254695274 0 0.873685 0.392632 -3.922011 1.78349 0.971086 12 0.0
O Ti O 1 6.6 1 -0.229 1 2 2.68 1.226342 260.893 99.3916 3.25 0.10 5.36 2.082408 3326.69 546.386 0 0 0 0 0 8.45 0.088406 0.969934 0.296577 1.326746 -1.8349 5.5046 0.00148 -0.00112 -4 4 2.508854 -2.511416 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.392632 0.971086 1.78349 12 0.0
Ti Ti O 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 3.25 0.10 2.082408 2.082408 546.386 546.386 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.392632 1.78349 1.78349 12 0.0
O O Ti 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.80 0.20 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0.0
#
Ti Cu Cu 1 0 1 0 1.255016 0.089078 1.226342 1.681711 99.3916 146.987 3.40 0.15 2.082408 2.794608 546.386 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -6 2 0.1677645 -0.161007 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.72571 1.78349 0.274649 12 0
Cu Ti Ti 1 0 1 0 1 0.140835 1.681711 1.226342 146.987 99.3916 3.40 0.15 2.794608 2.082408 952.693 546.386 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 2.508854 -2.511416 0 5.946437 0 0 0 0.454784 0.72571 0.392632 0.274649 1.78349 12 0
Ti Cu Ti 1 0 1 0 1.255016 0.089078 1.226342 1.681711 99.3916 146.987 3.40 0.15 2.082408 2.794608 546.386 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -6 2 0.1677645 -0.161007 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.72571 1.78349 0.274649 12 0
Cu Ti Cu 1 0 1 0 1 0.140835 1.681711 1.226342 146.987 99.3916 3.40 0.15 2.794608 2.082408 952.693 546.386 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 2.508854 -2.511416 0 5.946437 0 0 0 0.454784 0.72571 0.392632 0.274649 1.78349 12 0
Ti Ti Cu 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 3.40 0.10 2.082408 2.082408 546.386 546.386 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.392632 1.78349 1.78349 12 0
Cu Cu Ti 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.90 0.05 2.794608 2.794608 952.693 952.693 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12 0
#
Ti O Cu 1 0 1 0 1.255016 0.089078 1.226342 2.68 99.3916 260.893 3.25 0.10 2.082408 5.36 546.386 3326.69 0 0 0 0 0 8.45 0.088406 0.969934 0.296577 1.326746 -4 4 2.508854 -2.511416 -1.8349 5.5046 0.00148 -0.00112 0 1.943430774 0 0.254695274 0 0.873685 0.392632 -3.922011 1.78349 0.971086 12 0
Cu O Ti 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.40 0.10 2.794608 5.36 952.693 3326.69 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12 0
Ti Cu O 1 0 1 0 1.255016 0.089078 1.226342 1.681711 99.3916 146.987 3.40 0.15 2.082408 2.794608 546.386 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -6 2 0.1677645 -0.161007 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.72571 1.78349 0.274649 12 0
Cu Ti O 1 0 1 0 1 0.140835 1.681711 1.226342 146.987 99.3916 3.40 0.15 2.794608 2.082408 952.693 546.386 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 2.508854 -2.511416 0 5.946437 0 0 0 0.454784 0.72571 0.392632 0.274649 1.78349 12 0
O Ti Cu 1 6.6 1 -0.229 1 2 2.68 1.226342 260.893 99.3916 3.25 0.10 5.36 2.082408 3326.69 546.386 0 0 0 0 0 8.45 0.088406 0.969934 0.296577 1.326746 -1.8349 5.5046 0.00148 -0.00112 -4 4 2.508854 -2.511416 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.392632 0.971086 1.78349 12 0
O Cu Ti 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.40 0.10 5.36 2.794608 3326.69 952.693 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12 0

10
cmake/Modules/Packages/GPU.cmake
View File

@ -30,7 +30,15 @@ file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
if(GPU_API STREQUAL "CUDA")
find_package(CUDA REQUIRED)
find_package(CUDA QUIET)
# augment search path for CUDA toolkit libraries to include the stub versions. Needed to find libcuda.so on machines without a CUDA driver installation
if(CUDA_FOUND)
set(CMAKE_LIBRARY_PATH "${CUDA_TOOLKIT_ROOT_DIR}/lib64/stubs;${CUDA_TOOLKIT_ROOT_DIR}/lib/stubs;${CUDA_TOOLKIT_ROOT_DIR}/lib64;${CUDA_TOOLKIT_ROOT_DIR}/lib;${CMAKE_LIBRARY_PATH}")
find_package(CUDA REQUIRED)
else()
message(FATAL_ERROR "CUDA Toolkit not found")
endif()
find_program(BIN2C bin2c)
if(NOT BIN2C)
message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")

1
cmake/Modules/Packages/ML-QUIP.cmake
View File

@ -51,6 +51,7 @@ if(DOWNLOAD_QUIP)
GIT_TAG origin/public
GIT_SHALLOW YES
GIT_PROGRESS YES
GIT_SUBMODULES "src/fox;src/GAP"
PATCH_COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_BINARY_DIR}/quip.config <SOURCE_DIR>/arch/Makefile.lammps
CONFIGURE_COMMAND env QUIP_ARCH=lammps make config
BUILD_COMMAND env QUIP_ARCH=lammps make libquip

18
doc/src/Build_settings.rst
View File

@ -4,15 +4,15 @@ Optional build settings
LAMMPS can be built with several optional settings. Each sub-section
explain how to do this for building both with CMake and make.
* :ref:`C++11 standard compliance <cxx11>` when building all of LAMMPS
* :ref:`FFT library <fft>` for use with the :doc:`kspace_style pppm <kspace_style>` command
* :ref:`Size of LAMMPS integer types <size>`
* :ref:`Read or write compressed files <gzip>`
* :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command
* :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command
* :ref:`Memory allocation alignment <align>`
* :ref:`Workaround for long long integers <longlong>`
* :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library
* `C++11 standard compliance`_ when building all of LAMMPS
* `FFT library`_ for use with the :doc:`kspace_style pppm <kspace_style>` command
* `Size of LAMMPS integer types and size limits`_
* `Read or write compressed files`_
* `Output of JPG, PNG, and move files` via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
* `Memory allocation alignment`_
* `Workaround for long long integers`_
* `Exception handling when using LAMMPS as a library`_ to capture errors
* `Trigger selected floating-point exceptions`_
----------

6
doc/src/Commands_compute.rst
View File

@ -142,11 +142,11 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`sph/t/atom <compute_sph_t_atom>`
* :doc:`spin <compute_spin>`
* :doc:`stress/atom <compute_stress_atom>`
* :doc:`stress/cartesian <compute_stress_cartesian>`
* :doc:`stress/cylinder <compute_stress_cartesian>`
* :doc:`stress/cartesian <compute_stress_profile>`
* :doc:`stress/cylinder <compute_stress_profile>`
* :doc:`stress/mop <compute_stress_mop>`
* :doc:`stress/mop/profile <compute_stress_mop>`
* :doc:`stress/spherical <compute_stress_cartesian>`
* :doc:`stress/spherical <compute_stress_profile>`
* :doc:`stress/tally <compute_tally>`
* :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`
* :doc:`temp (k) <compute_temp>`

2
doc/src/Commands_fix.rst
View File

@ -98,8 +98,6 @@ OPT.
* :doc:`latte <fix_latte>`
* :doc:`lb/fluid <fix_lb_fluid>`
* :doc:`lb/momentum <fix_lb_momentum>`
* :doc:`lb/pc <fix_lb_pc>`
* :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`
* :doc:`lb/viscous <fix_lb_viscous>`
* :doc:`lineforce <fix_lineforce>`
* :doc:`manifoldforce <fix_manifoldforce>`

175
doc/src/Developer_notes.rst
View File

@ -7,6 +7,15 @@ typically document what a variable stores, what a small section of
code does, or what a function does and its input/outputs. The topics
on this page are intended to document code functionality at a higher level.
Available topics are:
- `Reading and parsing of text and text files`_
- `Requesting and accessing neighbor lists`_
- `Fix contributions to instantaneous energy, virial, and cumulative energy`_
- `KSpace PPPM FFT grids`_
----
Reading and parsing of text and text files
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -25,18 +34,17 @@ following benefits:
- transparent support for translating unsupported UTF-8 characters to their ASCII equivalents
(the text-to-value conversion functions **only** accept ASCII characters)
In most cases (e.g. potential files) the same data is needed on all
MPI ranks. Then it is best to do the reading and parsing only on MPI
rank 0, and communicate the data later with one or more
``MPI_Bcast()`` calls. For reading generic text and potential
parameter files the custom classes :cpp:class:`TextFileReader
<LAMMPS_NS::TextFileReader>` and :cpp:class:`PotentialFileReader
<LAMMPS_NS::PotentialFileReader>` are available. They allow reading
the file as individual lines for which they can return a tokenizer
class (see below) for parsing the line. Or they can return blocks of
numbers as a vector directly. The documentation on `File reader
classes <file-reader-classes>`_ contains an example for a typical
case.
In most cases (e.g. potential files) the same data is needed on all MPI
ranks. Then it is best to do the reading and parsing only on MPI rank
0, and communicate the data later with one or more ``MPI_Bcast()``
calls. For reading generic text and potential parameter files the
custom classes :cpp:class:`TextFileReader <LAMMPS_NS::TextFileReader>`
and :cpp:class:`PotentialFileReader <LAMMPS_NS::PotentialFileReader>`
are available. They allow reading the file as individual lines for which
they can return a tokenizer class (see below) for parsing the line. Or
they can return blocks of numbers as a vector directly. The
documentation on :ref:`File reader classes <file-reader-classes>`
contains an example for a typical case.
When reading per-atom data, the data on each line of the file usually
needs to include an atom ID so it can be associated with a particular
@ -65,6 +73,149 @@ when converting "12.5", while the ValueTokenizer class will throw an
:cpp:func:`ValueTokenizer::next_int()
<LAMMPS_NS::ValueTokenizer::next_int>` is called on the same string.
Requesting and accessing neighbor lists
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
LAMMPS uses Verlet-style neighbor lists to avoid having to loop over
*all* pairs of *all* atoms when computing pairwise properties with a
cutoff (e.g. pairwise forces or radial distribution functions). There
are three main algorithms that can be selected by the :doc:`neighbor
command <neighbor>`: `bin` (the default, uses binning to achieve linear
scaling with system size), `nsq` (without binning, quadratic scaling),
`multi` (with binning, optimized for varying cutoffs or polydisperse
granular particles). In addition to how the neighbor lists are
constructed a number of different variants of neighbor lists need to be
created (e.g. "full" or "half") for different purposes and styles and
those may be required in every time step ("perpetual") or on some steps
("occasional").
The neighbor list creation is managed by the ``Neighbor`` class.
Individual classes can obtain a neighbor list by creating an instance of
a ``NeighRequest`` class which is stored in a list inside the
``Neighbor`` class. The ``Neighbor`` class will then analyze the
various requests and apply optimizations where neighbor lists that have
the same settings will be created only once and then copied, or a list
may be constructed by processing a neighbor list from a different
request that is a superset of the requested list. The neighbor list
build is then :doc:`processed in parallel <Developer_par_neigh>`.
The most commonly required neighbor list is a so-called "half" neighbor
list, where each pair of atoms is listed only once (except when the
:doc:`newton command setting <newton>` for pair is off; in that case
pairs straddling sub-domains or periodic boundaries will be listed twice).
Thus these are the default settings when a neighbor list request is created in:
.. code-block:: C++
void Pair::init_style()
{
neighbor->add_request(this);
}
void Pair::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
The ``this`` pointer argument is required so the neighbor list code can
access the requesting class instance to store the assembled neighbor
list with that instance by calling its ``init_list()`` member function.
The optional second argument (omitted here) contains a bitmask of flags
that determines the kind of neighbor list requested. The default value
used here asks for a perpetual "half" neighbor list.
Non-default values of the second argument need to be used to adjust a
neighbor list request to the specific needs of a style an additional
request flag is needed. The :doc:`tersoff <pair_tersoff>` pair style,
for example, needs a "full" neighbor list:
.. code-block:: C++
void PairTersoff::init_style()
{
// [...]
neighbor->add_request(this, NeighConst::REQ_FULL);
}
When a pair style supports r-RESPA time integration with different cutoff regions,
the request flag may depend on the corresponding r-RESPA settings. Here an example
from pair style lj/cut:
.. code-block:: C++
void PairLJCut::init_style()
{
int list_style = NeighConst::REQ_DEFAULT;
if (update->whichflag == 1 && utils::strmatch(update->integrate_style, "^respa")) {
auto respa = (Respa *) update->integrate;
if (respa->level_inner >= 0) list_style = NeighConst::REQ_RESPA_INOUT;
if (respa->level_middle >= 0) list_style = NeighConst::REQ_RESPA_ALL;
}
neighbor->add_request(this, list_style);
// [...]
}
Granular pair styles need neighbor lists based on particle sizes and not cutoff
and also may require to have the list of previous neighbors available ("history").
For example with:
.. code-block:: C++
if (use_history) neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_HISTORY);
else neighbor->add_request(this, NeighConst::REQ_SIZE);
In case a class would need to make multiple neighbor list requests with different
settings each request can set an id which is then used in the corresponding
``init_list()`` function to assign it to the suitable pointer variable. This is
done for example by the :doc:`pair style meam <pair_meam>`:
.. code-block:: C++
void PairMEAM::init_style()
{
// [...]
neighbor->add_request(this, NeighConst::REQ_FULL)->set_id(1);
neighbor->add_request(this)->set_id(2);
}
void PairMEAM::init_list(int id, NeighList *ptr)
{
if (id == 1) listfull = ptr;
else if (id == 2) listhalf = ptr;
}
Fixes may require a neighbor list that is only build occasionally (or
just once) and this can also be indicated by a flag. As an example here
is the request from the ``FixPeriNeigh`` class which is created
internally by :doc:`Peridynamics pair styles <pair_peri>`:
.. code-block:: C++
neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
It is also possible to request a neighbor list that uses a different cutoff
than what is usually inferred from the pair style settings (largest cutoff of
all pair styles plus neighbor list skin). The following is used in the
:doc:`compute rdf <compute_rdf>` command implementation:
.. code-block:: C++
if (cutflag)
neighbor->add_request(this, NeighConst::REQ_OCCASIONAL)->set_cutoff(mycutneigh);
else
neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);
The neighbor list request function has a slightly different set of arguments
when created by a command style. In this case the neighbor list is
*always* an occasional neighbor list, so that flag is not needed. However
for printing the neighbor list summary the name of the requesting command
should be set. Below is the request from the :doc:`delete atoms <delete_atoms>`
command:
.. code-block:: C++
neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);
Fix contributions to instantaneous energy, virial, and cumulative energy
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

6
doc/src/Developer_org.rst
View File

@ -252,12 +252,6 @@ follows:
- The Timer class logs timing information, output at the end
of a run.
.. TODO section on "Spatial decomposition and parallel operations"
.. diagram of 3d processor grid, brick vs. tiled. local vs. ghost
.. atoms, 6-way communication with pack/unpack functions,
.. PBC as part of the communication, forward and reverse communication
.. rendezvous communication, ring communication.
.. TODO section on "Fixes, Computes, and Variables"
.. how and when data is computed and provided and how it is
.. referenced. flags in Fix/Compute/Variable classes tell

49
doc/src/Developer_plugins.rst
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@ -8,11 +8,20 @@ without recompiling LAMMPS. The functionality for this and the
Plugins use the operating system's capability to load dynamic shared
object (DSO) files in a way similar shared libraries and then reference
specific functions in those DSOs. Any DSO file with plugins has to include
an initialization function with a specific name, "lammpsplugin_init", that
has to follow specific rules described below. When loading the DSO with
the "plugin" command, this function is looked up and called and will then
register the contained plugin(s) with LAMMPS.
specific functions in those DSOs. Any DSO file with plugins has to
include an initialization function with a specific name,
"lammpsplugin_init", that has to follow specific rules described below.
When loading the DSO with the "plugin" command, this function is looked
up and called and will then register the contained plugin(s) with
LAMMPS.
When the environment variable ``LAMMPS_PLUGIN_PATH`` is set, then LAMMPS
will search the directory (or directories) listed in this path for files
with names that end in ``plugin.so`` (e.g. ``helloplugin.so``) and will
try to load the contained plugins automatically at start-up. For
plugins that are loaded this way, the behavior of LAMMPS should be
identical to a binary where the corresponding code was compiled in
statically as a package.
From the programmer perspective this can work because of the object
oriented design of LAMMPS where all pair style commands are derived from
@ -65,19 +74,18 @@ Members of ``lammpsplugin_t``
* - handle
- Pointer to the open DSO file handle
Only one of the three alternate creator entries can be used at a time
and which of those is determined by the style of plugin. The
"creator.v1" element is for factory functions of supported styles
computing forces (i.e. command, pair, bond, angle, dihedral, or
improper styles) and the function takes as single argument the pointer
to the LAMMPS instance. The factory function is cast to the
``lammpsplugin_factory1`` type before assignment. The "creator.v2"
element is for factory functions creating an instance of a fix, compute,
or region style and takes three arguments: a pointer to the LAMMPS
instance, an integer with the length of the argument list and a ``char
**`` pointer to the list of arguments. The factory function pointer
needs to be cast to the ``lammpsplugin_factory2`` type before
assignment.
Only one of the two alternate creator entries can be used at a time and
which of those is determined by the style of plugin. The "creator.v1"
element is for factory functions of supported styles computing forces
(i.e. pair, bond, angle, dihedral, or improper styles) or command styles
and the function takes as single argument the pointer to the LAMMPS
instance. The factory function is cast to the ``lammpsplugin_factory1``
type before assignment. The "creator.v2" element is for factory
functions creating an instance of a fix, compute, or region style and
takes three arguments: a pointer to the LAMMPS instance, an integer with
the length of the argument list and a ``char **`` pointer to the list of
arguments. The factory function pointer needs to be cast to the
``lammpsplugin_factory2`` type before assignment.
Pair style example
^^^^^^^^^^^^^^^^^^
@ -249,3 +257,8 @@ by ``#ifdef PAIR_CLASS`` is not needed, since the mapping of the class
name to the style name is done by the plugin registration function with
the information from the ``lammpsplugin_t`` struct. It may be included
in case the new code is intended to be later included in LAMMPS directly.
A plugin may be registered under an existing style name. In that case
the plugin will override the existing code. This can be used to modify
the behavior of existing styles or to debug new versions of them without
having to re-compile or re-install all of LAMMPS.

2
doc/src/Developer_utils.rst
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@ -396,7 +396,7 @@ A typical code segment would look like this:
----------
.. file-reader-classes:
.. _file-reader-classes:
File reader classes
-------------------

55
doc/src/Howto_structured_data.rst
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@ -21,7 +21,8 @@ YAML
print """---
timestep: $(step)
pe: $(pe)
ke: $(ke)""" file current_state.yaml screen no
ke: $(ke)
...""" file current_state.yaml screen no
.. code-block:: yaml
:caption: current_state.yaml
@ -51,6 +52,58 @@ JSON
"ke": 2.4962152903997174569
}
YAML format thermo_style output
===============================
.. versionadded:: 24Mar2022
LAMMPS supports the thermo style "yaml" and for "custom" style
thermodynamic output the format can be changed to YAML with
:doc:`thermo_modify line yaml <thermo_modify>`. This will produce a
block of output in a compact YAML format - one "document" per run - of
the following style:
.. code-block:: yaml
---
keywords: [Step, Temp, E_pair, E_mol, TotEng, Press, ]
data:
- [100, 0.757453103239935, -5.7585054860159, 0, -4.62236133677021, 0.207261053624721, ]
- [110, 0.759322359337036, -5.7614668389562, 0, -4.62251889318624, 0.194314975399602, ]
- [120, 0.759372342462676, -5.76149365656489, 0, -4.62247073844943, 0.191600048851267, ]
- [130, 0.756833027516501, -5.75777334823494, 0, -4.62255928350835, 0.208792327853067, ]
...
This data can be extracted and parsed from a log file using python with:
.. code-block:: python
import re, yaml
docs = ""
with open("log.lammps") as f:
for line in f:
m = re.search(r"^(keywords:.*$|data:$|---$|\.\.\.$| - \[.*\]$)", line)
if m: docs += m.group(0) + '\n'
thermo = list(yaml.load_all(docs, Loader=yaml.SafeLoader))
print("Number of runs: ", len(thermo))
print(thermo[1]['keywords'][4], ' = ', thermo[1]['data'][2][4])
After loading the YAML data, `thermo` is a list containing a dictionary
for each "run" where the tag "keywords" maps to the list of thermo
header strings and the tag "data" has a list of lists where the outer
list represents the lines of output and the inner list the values of the
columns matching the header keywords for that step. The second print()
command for example will print the header string for the fifth keyword
of the second run and the corresponding value for the third output line
of that run:
.. parsed-literal::
Number of runs: 2
TotEng = -4.62140097780047
Writing continuous data during a simulation
===========================================

3
doc/src/Install_git.rst
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@ -165,5 +165,4 @@ changed. How to do this depends on the build system you are using.
URL "git@github.com:lammps/lammps.git".
The LAMMPS GitHub project is currently managed by Axel Kohlmeyer
(Temple U, akohlmey at gmail.com) and Richard Berger (Temple U,
richard.berger at temple.edu).
(Temple U, akohlmey at gmail.com).

67
doc/src/Modify_thermo.rst
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@ -1,27 +1,54 @@
Thermodynamic output options
============================
There is one class that computes and prints thermodynamic information
to the screen and log file; see the file thermo.cpp.
The ``Thermo`` class computes and prints thermodynamic information to
the screen and log file; see the files ``thermo.cpp`` and ``thermo.h``.
There are two styles defined in thermo.cpp: "one" and "multi". There
is also a flexible "custom" style which allows the user to explicitly
list keywords for quantities to print when thermodynamic info is
output. See the :doc:`thermo_style <thermo_style>` command for a list
of defined quantities.
There are four styles defined in ``thermo.cpp``: "one", "multi", "yaml",
and "custom". The "custom" style allows the user to explicitly list
keywords for individual quantities to print when thermodynamic output is
generated. The others have a fixed list of keywords. See the
:doc:`thermo_style <thermo_style>` command for a list of available
quantities. The formatting of the "custom" style defaults to the "one"
style, but can be adapted using :doc:`thermo_modify line <thermo_modify>`.
The thermo styles (one, multi, etc) are simply lists of keywords.
Adding a new style thus only requires defining a new list of keywords.
Search for the word "customize" with references to "thermo style" in
thermo.cpp to see the two locations where code will need to be added.
The thermo styles (one, multi, etc) are defined by lists of keywords
with associated formats for integer and floating point numbers and
identified but an enumerator constant. Adding a new style thus mostly
requires defining a new list of keywords and the associated formats and
then inserting the required output processing where the enumerators are
identified. Search for the word "CUSTOMIZATION" with references to
"thermo style" in the ``thermo.cpp`` file to see the locations where
code will need to be added. The member function ``Thermo::header()``
prints output at the very beginning of a thermodynamic output block and
can be used to print column headers or other front matter. The member
function ``Thermo::footer()`` prints output at the end of a
thermodynamic output block. The formatting of the output is done by
assembling a "line" (which may span multiple lines if the style inserts
newline characters ("\n" as in the "multi" style).
New keywords can also be added to thermo.cpp to compute new quantities
for output. Search for the word "customize" with references to
"keyword" in thermo.cpp to see the several locations where code will
need to be added.
New thermodynamic keywords can also be added to ``thermo.cpp`` to
compute new quantities for output. Search for the word "CUSTOMIZATION"
with references to "keyword" in ``thermo.cpp`` to see the several
locations where code will need to be added. Effectively, you need to
define a member function that computes the property, add an if statement
in ``Thermo::parse_fields()`` where the corresponding header string for
the keyword and the function pointer is registered by calling the
``Thermo::addfield()`` method, and add an if statement in
``Thermo::evaluate_keyword()`` which is called from the ``Variable``
class when a thermo keyword is encountered.
Note that the :doc:`thermo_style custom <thermo_style>` command already allows
for thermo output of quantities calculated by :doc:`fixes <fix>`,
:doc:`computes <compute>`, and :doc:`variables <variable>`. Thus, it may
be simpler to compute what you wish via one of those constructs, than
by adding a new keyword to the thermo command.
.. note::
The third argument to ``Thermo::addfield()`` is a flag indicating
whether the function for the keyword computes a floating point
(FLOAT), regular integer (INT), or big integer (BIGINT) value. This
information is used for formatting the thermodynamic output. Inside
the function the result must then be stored either in the ``dvalue``,
``ivalue`` or ``bivalue`` member variable, respectively.
Since the :doc:`thermo_style custom <thermo_style>` command allows to
use output of quantities calculated by :doc:`fixes <fix>`,
:doc:`computes <compute>`, and :doc:`variables <variable>`, it may often
be simpler to compute what you wish via one of those constructs, rather
than by adding a new keyword to the thermo_style command.

19
doc/src/Modify_variable.rst
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@ -1,8 +1,8 @@
Variable options
================
There is one class that computes and stores :doc:`variable <variable>`
information in LAMMPS; see the file variable.cpp. The value
The ``Variable`` class computes and stores :doc:`variable <variable>`
information in LAMMPS; see the file ``variable.cpp``. The value
associated with a variable can be periodically printed to the screen
via the :doc:`print <print>`, :doc:`fix print <fix_print>`, or
:doc:`thermo_style custom <thermo_style>` commands. Variables of style
@ -19,21 +19,22 @@ of arguments:
compute values = c_mytemp[0], c_thermo_press[3], ...
Adding keywords for the :doc:`thermo_style custom <thermo_style>`
command (which can then be accessed by variables) is discussed on the
:doc:`Modify thermo <Modify_thermo>` doc page.
command (which can then be accessed by variables) is discussed in the
:doc:`Modify thermo <Modify_thermo>` documentation.
Adding a new math function of one or two arguments can be done by
editing one section of the Variable::evaluate() method. Search for
editing one section of the ``Variable::evaluate()`` method. Search for
the word "customize" to find the appropriate location.
Adding a new group function can be done by editing one section of the
Variable::evaluate() method. Search for the word "customize" to find
the appropriate location. You may need to add a new method to the
Group class as well (see the group.cpp file).
``Variable::evaluate()`` method. Search for the word "customize" to
find the appropriate location. You may need to add a new method to the
Group class as well (see the ``group.cpp`` file).
Accessing a new atom-based vector can be done by editing one section
of the Variable::evaluate() method. Search for the word "customize"
to find the appropriate location.
Adding new :doc:`compute styles <compute>` (whose calculated values can
then be accessed by variables) is discussed on the :doc:`Modify compute <Modify_compute>` doc page.
then be accessed by variables) is discussed in the :doc:`Modify compute
<Modify_compute>` documentation.

7
doc/src/Packages_details.rst
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@ -9,7 +9,7 @@ gives links to documentation, example scripts, and pictures/movies (if
available) that illustrate use of the package.
The majority of packages can be included in a LAMMPS build with a
single setting (``-D PGK_<NAME>=on`` for CMake) or command
single setting (``-D PKG_<NAME>=on`` for CMake) or command
(``make yes-<name>`` for make). See the :doc:`Build package <Build_package>`
page for more info. A few packages may require additional steps;
this is indicated in the descriptions below. The :doc:`Build extras <Build_extras>`
@ -2154,6 +2154,11 @@ A :doc:`plugin <plugin>` command that can load and unload several
kind of styles in LAMMPS from shared object files at runtime without
having to recompile and relink LAMMPS.
When the environment variable ``LAMMPS_PLUGIN_PATH`` is set, then LAMMPS
will search the directory (or directories) listed in this path for files
with names that end in ``plugin.so`` (e.g. ``helloplugin.so``) and will
try to load the contained plugins automatically at start-up.
**Authors:** Axel Kohlmeyer (Temple U)
**Supporting info:**

2
doc/src/Python_install.rst
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@ -187,7 +187,7 @@ folder that the dynamic loader searches or inside of the installed
folders are searched by default by Python or the LAMMPS Python
package.
.. versionchanged:: TBD
.. versionchanged:: 24Mar2022
.. note::

6
doc/src/compute.rst
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@ -288,11 +288,11 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`sph/t/atom <compute_sph_t_atom>` - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms
* :doc:`spin <compute_spin>` - magnetic quantities for a system of atoms having spins
* :doc:`stress/atom <compute_stress_atom>` - stress tensor for each atom
* :doc:`stress/cartesian <compute_stress_cartesian>` - stress tensor in cartesian coordinates
* :doc:`stress/cylinder <compute_stress_cartesian>` - stress tensor in cylindrical coordinates
* :doc:`stress/cartesian <compute_stress_profile>` - stress tensor in cartesian coordinates
* :doc:`stress/cylinder <compute_stress_profile>` - stress tensor in cylindrical coordinates
* :doc:`stress/mop <compute_stress_mop>` - normal components of the local stress tensor using the method of planes
* :doc:`stress/mop/profile <compute_stress_mop>` - profile of the normal components of the local stress tensor using the method of planes
* :doc:`stress/spherical <compute_stress_cartesian>` - stress tensor in spherical coordinates
* :doc:`stress/spherical <compute_stress_profile>` - stress tensor in spherical coordinates
* :doc:`stress/tally <compute_tally>` - stress between two groups of atoms via the tally callback mechanism
* :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>` - per-atom chemical concentration of a specified species for each tDPD particle
* :doc:`temp <compute_temp>` - temperature of group of atoms

9
doc/src/compute_momentum.rst
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@ -23,11 +23,10 @@ Examples
Description
"""""""""""
Define a computation that calculates the translational momentum
of a group of particles.
The momentum of each particles is computed as m v, where m and v are
the mass and velocity of the particle.
Define a computation that calculates the translational momentum *p*
of a group of particles. It is computed as the sum :math:`\vec{p} = \sum_i m_i \cdot \vec{v}_i`
over all particles in the compute group, where *m* and *v* are
the mass and velocity vector of the particle, respectively.
Output info
"""""""""""

26
doc/src/compute_sna_atom.rst
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@ -33,7 +33,7 @@ Syntax
* R_1, R_2,... = list of cutoff radii, one for each type (distance units)
* w_1, w_2,... = list of neighbor weights, one for each type
* zero or more keyword/value pairs may be appended
* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag*
* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag*
.. parsed-literal::
@ -59,6 +59,9 @@ Syntax
*bikflag* value = *0* or *1* (only implemented for compute snap)
*0* = per-atom bispectrum descriptors are summed over atoms
*1* = per-atom bispectrum descriptors are not summed over atoms
*switchinnerflag* values = *rinnerlist* *drinnerlist*
*rinnerlist* = *ntypes* values of rinner (distance units)
*drinnerlist* = *ntypes* values of drinner (distance units)
Examples
""""""""
@ -70,6 +73,7 @@ Examples
compute vb all sna/atom 1.4 0.95 6 2.0 1.0
compute snap all snap 1.4 0.95 6 2.0 1.0
compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 chem 2 0 1
compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 switchinnerflag 1.1 1.3 0.5 0.6
Description
"""""""""""
@ -308,6 +312,26 @@ the resulting bispectrum rows are :math:`B_{i,k}` instead of just
:math:`B_k`. In this case, the entries in the final column for these rows
are set to zero.
The keyword *switchinnerflag* activates an additional radial switching
function similar to :math:`f_c(r)` above, but acting to switch off
smoothly contributions from neighbor atoms at short separation distances.
This is useful when SNAP is used in combination with a simple
repulsive potential. The keyword is followed by the *ntypes*
values for :math:`r_{inner}` and the *ntypes*
values for :math:`\Delta r_{inner}`. For a neighbor atom at
distance :math:`r`, its contribution is scaled by a multiplicative
factor :math:`f_{inner}(r)` defined as follows:
.. math::
= & 0, r \leq r_{inner} \\
f_{inner}(r) = & \frac{1}{2}(1 - \cos(\pi \frac{r-r_{inner}}{\Delta r_{inner}})), r_{inner} < r \leq r_{inner} + \Delta r_{inner} \\
= & 1, r > r_{inner} + \Delta r_{inner}
The values of :math:`r_{inner}` and :math:`\Delta r_{inner}` are
the arithmetic means of the values for the central atom of type I
and the neighbor atom of type J.
.. note::
If you have a bonded system, then the settings of :doc:`special_bonds

4
doc/src/compute_stress_mop.rst
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@ -73,7 +73,7 @@ command, since those are contributions to the global system pressure.
NOTE 3: The local stress profile generated by compute *stress/mop/profile*
is similar to that obtained by compute
:doc:`stress/cartesian <compute_stress_cartesian>`.
:doc:`stress/cartesian <compute_stress_profile>`.
A key difference
is that compute *stress/mop/profile* considers particles
crossing a set of planes,
@ -122,7 +122,7 @@ intra-molecular interactions, and long range (kspace) interactions.
Related commands
""""""""""""""""
:doc:`compute stress/atom <compute_stress_atom>`, :doc:`compute pressure <compute_pressure>`, :doc:`compute stress/cartesian <compute_stress_cartesian>`, :doc:`compute stress/cylinder <compute_stress_cartesian>`, :doc:`compute stress/spherical <compute_stress_cartesian>`
:doc:`compute stress/atom <compute_stress_atom>`, :doc:`compute pressure <compute_pressure>`, :doc:`compute stress/cartesian <compute_stress_profile>`, :doc:`compute stress/cylinder <compute_stress_profile>`, :doc:`compute stress/spherical <compute_stress_profile>`
Default
"""""""

0
doc/src/compute_stress_cartesian.rst → doc/src/compute_stress_profile.rst
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60
doc/src/compute_tally.rst
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@ -31,7 +31,7 @@ Syntax
compute ID group-ID style group2-ID
* ID, group-ID are documented in :doc:`compute <compute>` command
* style = *force/tally* or *heat/flux/tally* or *heat/flux/virial/tally* or * or *pe/tally* or *pe/mol/tally* or *stress/tally*
* style = *force/tally* or *heat/flux/tally* or *heat/flux/virial/tally* or *pe/tally* or *pe/mol/tally* or *stress/tally*
* group2-ID = group ID of second (or same) group
Examples
@ -61,7 +61,7 @@ mechanism. Compute *pe/mol/tally* is one such style, that can
- through using this mechanism - separately tally intermolecular
and intramolecular energies. Something that would otherwise be
impossible without integrating this as a core functionality into
the based classes of LAMMPS.
the base classes of LAMMPS.
----------
@ -148,30 +148,38 @@ pairwise property computations.
Output info
"""""""""""
Compute *pe/tally* calculates a global scalar (the energy) and a per
atom scalar (the contributions of the single atom to the global
scalar). Compute *pe/mol/tally* calculates a global 4-element vector
containing (in this order): *evdwl* and *ecoul* for intramolecular pairs
and *evdwl* and *ecoul* for intermolecular pairs. Since molecules are
identified by their molecule IDs, the partitioning does not have to be
related to molecules, but the energies are tallied into the respective
slots depending on whether the molecule IDs of a pair are the same or
different. Compute *force/tally* calculates a global scalar (the force
magnitude) and a per atom 3-element vector (force contribution from
each atom). Compute *stress/tally* calculates a global scalar
(average of the diagonal elements of the stress tensor) and a per atom
vector (the 6 elements of stress tensor contributions from the
individual atom). As in :doc:`compute heat/flux <compute_heat_flux>`,
compute *heat/flux/tally* calculates a global vector of length 6,
where the first 3 components are the :math:`x`, :math:`y`, :math:`z`
components of the full heat flow vector,
and the next 3 components are the corresponding components
of just the convective portion of the flow, i.e. the
first term in the equation for :math:`\mathbf{Q}`.
Compute *heat/flux/virial/tally* calculates a global scalar (heat flow)
and a per atom 3-element vector
(contribution to the force acting over atoms in the first group
from individual atoms in both groups).
- Compute *pe/tally* calculates a global scalar (the energy) and a per
atom scalar (the contributions of the single atom to the global
scalar).
- Compute *pe/mol/tally* calculates a global 4-element vector containing
(in this order): *evdwl* and *ecoul* for intramolecular pairs and
*evdwl* and *ecoul* for intermolecular pairs. Since molecules are
identified by their molecule IDs, the partitioning does not have to be
related to molecules, but the energies are tallied into the respective
slots depending on whether the molecule IDs of a pair are the same or
different.
- Compute *force/tally* calculates a global scalar (the force magnitude)
and a per atom 3-element vector (force contribution from each atom).
- Compute *stress/tally* calculates a global scalar
(average of the diagonal elements of the stress tensor) and a per atom
vector (the 6 elements of stress tensor contributions from the
individual atom).
- As in :doc:`compute heat/flux <compute_heat_flux>`,
compute *heat/flux/tally* calculates a global vector of length 6,
where the first 3 components are the :math:`x`, :math:`y`, :math:`z`
components of the full heat flow vector,
and the next 3 components are the corresponding components
of just the convective portion of the flow, i.e. the
first term in the equation for :math:`\mathbf{Q}`.
- Compute *heat/flux/virial/tally* calculates a global scalar (heat flow)
and a per atom 3-element vector
(contribution to the force acting over atoms in the first group
from individual atoms in both groups).
Both the scalar and vector values calculated by this compute are
"extensive".

2
doc/src/fix.rst
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@ -241,8 +241,6 @@ accelerated styles exist.
* :doc:`latte <fix_latte>` - wrapper on LATTE density-functional tight-binding code
* :doc:`lb/fluid <fix_lb_fluid>` -
* :doc:`lb/momentum <fix_lb_momentum>` -
* :doc:`lb/pc <fix_lb_pc>` -
* :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` -
* :doc:`lb/viscous <fix_lb_viscous>` -
* :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
* :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization

2
doc/src/fix_gcmc.rst
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@ -451,7 +451,7 @@ well in parallel. Currently, molecule translations and rotations
are not supported with more than one MPI process.
It is still possible to do parallel molecule exchange without
translation and rotation moves by setting MC moves to zero
and/or by using mcmoves keyword with *Pmoltrans*=*Pmolrotate*=0.
and/or by using the *mcmoves* keyword with *Pmoltrans* = *Pmolrotate* = 0 .
When using fix gcmc in combination with fix shake or fix rigid,

453
doc/src/fix_lb_fluid.rst
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@ -12,55 +12,65 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command
* lb/fluid = style name of this fix command
* nevery = update the lattice-Boltzmann fluid every this many timesteps
* LBtype = 1 to use the standard finite difference LB integrator,
2 to use the LB integrator of :ref:`Ollila et al. <Ollila>`
* nevery = update the lattice-Boltzmann fluid every this many timesteps (should normally be 1)
* viscosity = the fluid viscosity (units of mass/(time\*length)).
* density = the fluid density.
* zero or more keyword/value pairs may be appended
* keyword = *setArea* or *setGamma* or *scaleGamma* or *dx* or *dm* or *a0* or *noise* or *calcforce* or *trilinear* or *D3Q19* or *read_restart* or *write_restart* or *zwall_velocity* or *bodyforce* or *printfluid*
* keyword = *dx* or *dm* or *noise* or *stencil* or *read_restart* or *write_restart* or *zwall_velocity* or *pressurebcx* or *bodyforce* or *D3Q19* or *dumpxdmf* or *dof* or *scaleGamma* or *a0* or *npits* or *wp* or *sw*
.. parsed-literal::
*setArea* values = type node_area
type = atom type (1-N)
node_area = portion of the surface area of the composite object associated with the particular atom type (used when the force coupling constant is set by default).
*setGamma* values = gamma
gamma = user set value for the force coupling constant.
*scaleGamma* values = type gammaFactor
type = atom type (1-N)
gammaFactor = factor to scale the *setGamma* gamma value by, for the specified atom type.
*dx* values = dx_LB = the lattice spacing.
*dm* values = dm_LB = the lattice-Boltzmann mass unit.
*a0* values = a_0_real = the square of the speed of sound in the fluid.
*noise* values = Temperature seed
Temperature = fluid temperature.
seed = random number generator seed (positive integer)
*calcforce* values = N forcegroup-ID
N = output the force and torque every N timesteps
forcegroup-ID = ID of the particle group to calculate the force and torque of
*trilinear* values = none (used to switch from the default Peskin interpolation stencil to the trilinear stencil).
*D3Q19* values = none (used to switch from the default D3Q15, 15 velocity lattice, to the D3Q19, 19 velocity lattice).
*stencil* values = 2 (trilinear stencil, the default), 3 (3-point immersed boundary stencil), or 4 (4-point Keys' interpolation stencil)
*read_restart* values = restart file = name of the restart file to use to restart a fluid run.
*write_restart* values = N = write a restart file every N MD timesteps.
*zwall_velocity* values = velocity_bottom velocity_top = velocities along the y-direction of the bottom and top walls (located at z=zmin and z=zmax).
*pressurebcx* values = pgradav = imposes a pressure jump at the (periodic) x-boundary of pgradav*Lx*1000.
*bodyforce* values = bodyforcex bodyforcey bodyforcez = the x,y and z components of a constant body force added to the fluid.
*printfluid* values = N = print the fluid density and velocity at each grid point every N timesteps.
*D3Q19* values = none (used to switch from the default D3Q15, 15 velocity lattice, to the D3Q19, 19 velocity lattice).
*dumpxdmf* values = N file timeI
N = output the force and torque every N timesteps
file = output file name
timeI = 1 (use simulation time to index xdmf file), 0 (use output frame number to index xdmf file)
*dof* values = dof = specify the number of degrees of freedom for temperature calculation
*scaleGamma* values = type gammaFactor
type = atom type (1-N)
gammaFactor = factor to scale the *setGamma* gamma value by, for the specified atom type.
*a0* values = a_0_real = the square of the speed of sound in the fluid.
*npits* values = npits h_p l_p l_pp l_e
npits = number of pit regions
h_p = z-height of pit regions (floor to bottom of slit)
l_p = x-length of pit regions
l_pp = x-length of slit regions between consecutive pits
l_e = x-length of slit regions at ends
*wp* values = w_p = y-width of slit regions (defaults to full width if not present or if sw active)
*sw* values = none (turns on y-sidewalls (in xz plane) if npits option active)
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all lb/fluid 1 2 1.0 1.0 setGamma 13.0 dx 4.0 dm 10.0 calcforce sphere1
fix 1 all lb/fluid 1 1 1.0 0.0009982071 setArea 1 1.144592082 dx 2.0 dm 0.3 trilinear noise 300.0 8979873
fix 1 all lb/fluid 1 1.0 0.0009982071 dx 1.2 dm 0.001
fix 1 all lb/fluid 1 1.0 0.0009982071 dx 1.2 dm 0.001 noise 300.0 2761
fix 1 all lb/fluid 1 1.0 1.0 dx 4.0 dm 10.0 dumpxdmf 500 fflow 0 pressurebcx 0.01 npits 2 20 40 5 0 wp 30
Description
"""""""""""
Implement a lattice-Boltzmann fluid on a uniform mesh covering the LAMMPS
simulation domain. The MD particles described by *group-ID* apply a velocity
dependent force to the fluid.
.. versionchanged:: 24Mar2022
Implement a lattice-Boltzmann fluid on a uniform mesh covering the
LAMMPS simulation domain. Note that this fix was updated in 2022 and is
not backward compatible with the previous version. If you need the
previous version, please download an older version of LAMMPS. The MD
particles described by *group-ID* apply a velocity dependent force to
the fluid.
The lattice-Boltzmann algorithm solves for the fluid motion governed by
the Navier Stokes equations,
@ -86,28 +96,23 @@ respectively. Here, we have implemented
\sigma_{\alpha \beta} = -P_{\alpha \beta} = -\rho a_0 \delta_{\alpha \beta}
with :math:`a_0` set to :math:`\frac{1}{3} \frac{dx}{dt}^2` by default.
You should not normally need to change this default.
The algorithm involves tracking the time evolution of a set of partial
distribution functions which evolve according to a velocity
discretized version of the Boltzmann equation,
distribution functions which evolve according to a velocity discretized
version of the Boltzmann equation,
.. math::
\left(\partial_t + e_{i\alpha}\partial_{\alpha}\right)f_i = -\frac{1}{\tau}\left(f_i - f_i^{eq}\right) + W_i
where the first term on the right hand side represents a single time
relaxation towards the equilibrium distribution function, and :math:`\tau` is a
parameter physically related to the viscosity. On a technical note,
we have implemented a 15 velocity model (D3Q15) as default; however,
the user can switch to a 19 velocity model (D3Q19) through the use of
the *D3Q19* keyword. This fix provides the user with the choice of
two algorithms to solve this equation, through the specification of
the keyword *LBtype*\ . If *LBtype* is set equal to 1, the standard
finite difference LB integrator is used. If *LBtype* is set equal to
2, the algorithm of :ref:`Ollila et al. <Ollila>` is used.
Physical variables are then defined in terms of moments of the distribution
functions,
relaxation towards the equilibrium distribution function, and
:math:`\tau` is a parameter physically related to the viscosity. On a
technical note, we have implemented a 15 velocity model (D3Q15) as
default; however, the user can switch to a 19 velocity model (D3Q19)
through the use of the *D3Q19* keyword. Physical variables are then
defined in terms of moments of the distribution functions,
.. math::
@ -115,7 +120,7 @@ functions,
\rho u_{\alpha} = & \displaystyle\sum\limits_{i} f_i e_{i\alpha}
Full details of the lattice-Boltzmann algorithm used can be found in
:ref:`Mackay et al. <fluid-Mackay>`.
:ref:`Denniston et al. <fluid-Denniston>`.
The fluid is coupled to the MD particles described by *group-ID* through
a velocity dependent force. The contribution to the fluid force on a
@ -127,92 +132,66 @@ calculated as:
{\bf F}_{j \alpha} = \gamma \left({\bf v}_n - {\bf u}_f \right) \zeta_{j\alpha}
where :math:`\mathbf{v}_n` is the velocity of the MD particle,
:math:`\mathbf{u}_f` is the fluid
velocity interpolated to the particle location, and :math:`\gamma` is the force
coupling constant. :math:`\zeta` is a weight assigned to the grid point,
obtained by distributing the particle to the nearest lattice sites.
For this, the user has the choice between a trilinear stencil, which
provides a support of 8 lattice sites, or the immersed boundary method
Peskin stencil, which provides a support of 64 lattice sites. While
the Peskin stencil is seen to provide more stable results, the
trilinear stencil may be better suited for simulation of objects close
to walls, due to its smaller support. Therefore, by default, the
Peskin stencil is used; however the user may switch to the trilinear
stencil by specifying the keyword, *trilinear*\ .
:math:`\mathbf{u}_f` is the fluid velocity interpolated to the particle
location, and :math:`\gamma` is the force coupling constant. This
force, as with most forces in LAMMPS, and hence the velocities, are
calculated at the half-time step. :math:`\zeta` is a weight assigned to
the grid point, obtained by distributing the particle to the nearest
lattice sites.
By default, the force coupling constant, :math:`\gamma`, is calculated
The force coupling constant, :math:`\gamma`, is calculated
according to
.. math::
\gamma = \frac{2m_um_v}{m_u+m_v}\left(\frac{1}{\Delta t_{collision}}\right)
\gamma = \frac{2m_um_v}{m_u+m_v}\left(\frac{1}{\Delta t}\right)
Here, :math:`m_v` is the mass of the MD particle, :math:`m_u` is a
representative fluid mass at the particle location, and :math:`\Delta
t_{collision}` is a collision time, chosen such that
:math:`\frac{\tau}{\Delta t_{collision}} = 1` (see :ref:`Mackay and
Denniston <Mackay2>` for full details). In order to calculate :math:`m_u`,
the fluid density is interpolated to the MD particle location, and
multiplied by a volume, node_area * :math:`dx_{LB}`, where node_area
represents the portion of the surface area of the composite object
associated with a given MD particle. By default, node_area is set
equal to :math:`dx_{LB}^2`; however specific values for given atom types
can be set using the *setArea* keyword.
The user also has the option of specifying their own value for the
force coupling constant, for all the MD particles associated with the
fix, through the use of the *setGamma* keyword. This may be useful
when modelling porous particles. See :ref:`Mackay et al. <fluid-Mackay>` for a
detailed description of the method by which the user can choose an
appropriate :math:`\gamma` value.
representative fluid mass at the particle location, and :math:`\Delta t`
is the time step. The fluid mass :math:`m_u` that the MD particle
interacts with is calculated internally. This coupling is chosen to
constrain the particle and associated fluid velocity to match at the end
of the time step. As with other constraints, such as :doc:`shake
<fix_shake>`, this constraint can remove degrees of freedom from the
simulation which are accounted for internally in the algorithm.
.. note::
while this fix applies the force of the particles on the fluid,
it does not apply the force of the fluid to the particles. When the
force coupling constant is set using the default method, there is only
one option to include this hydrodynamic force on the particles, and
that is through the use of the :doc:`lb/viscous <fix_lb_viscous>` fix.
This fix adds the hydrodynamic force to the total force acting on the
particles, after which any of the built-in LAMMPS integrators can be
used to integrate the particle motion. However, if the user specifies
their own value for the force coupling constant, as mentioned in
:ref:`Mackay et al. <fluid-Mackay>`, the built-in LAMMPS integrators may prove to
be unstable. Therefore, we have included our own integrators
:doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`, and
:doc:`fix lb/pc <fix_lb_pc>`, to solve for the particle motion in these
cases. These integrators should not be used with the
:doc:`lb/viscous <fix_lb_viscous>` fix, as they add hydrodynamic forces
to the particles directly. In addition, they can not be used if the
force coupling constant has been set the default way.
.. note::
if the force coupling constant is set using the default method,
and the :doc:`lb/viscous <fix_lb_viscous>` fix is NOT used to add the
While this fix applies the force of the particles on the fluid, it
does not apply the force of the fluid to the particles. There is
only one option to include this hydrodynamic force on the particles,
and that is through the use of the :doc:`lb/viscous <fix_lb_viscous>`
fix. This fix adds the hydrodynamic force to the total force acting
on the particles, after which any of the built-in LAMMPS integrators
can be used to integrate the particle motion. If the
:doc:`lb/viscous <fix_lb_viscous>` fix is NOT used to add the
hydrodynamic force to the total force acting on the particles, this
physically corresponds to a situation in which an infinitely massive
particle is moving through the fluid (since collisions between the
particle and the fluid do not act to change the particle's velocity).
Therefore, the user should set the mass of the particle to be
significantly larger than the mass of the fluid at the particle
location, in order to approximate an infinitely massive particle (see
the dragforce test run for an example).
In this case, setting *scaleGamma* to -1 for the corresponding
particle type will explicitly take this limit (of infinite particle
mass) in computing the force coupling for the fluid force.
----------
Inside the fix, parameters are scaled by the lattice-Boltzmann
Physical parameters describing the fluid are specified through
*viscosity* and *density*. These parameters should all be given in
terms of the mass, distance, and time units chosen for the main LAMMPS
run, as they are scaled by the LB timestep, lattice spacing, and mass
unit, inside the fix.
The *dx* keyword allows the user to specify a value for the LB grid
spacing and the *dm* keyword allows the user to specify the LB mass
unit. Inside the fix, parameters are scaled by the lattice-Boltzmann
timestep, :math:`dt_{LB}`, grid spacing, :math:`dx_{LB}`, and mass unit,
:math:`dm_{LB}`. :math:`dt_{LB}` is set equal to
:math:`\mathrm{nevery}\cdot dt_{MD}`, where :math:`dt_{MD}` is the MD timestep.
By default,
:math:`dm_{LB}` is set equal to 1.0, and :math:`dx_{LB}` is chosen so that
:math:`\frac{\tau}{dt} = \frac{3\eta dt}{\rho dx^2}` is approximately equal to 1.
However, the user has the option of specifying their own values for
:math:`dm_{LB}`, and :math:`dx_{LB}`, by using
the optional keywords *dm*, and *dx* respectively.
:math:`\mathrm{nevery}\cdot dt_{MD}`, where :math:`dt_{MD}` is the MD
timestep. By default, :math:`dm_{LB}` is set equal to 1.0, and
:math:`dx_{LB}` is chosen so that :math:`\frac{\tau}{dt} = \frac{3\eta
dt}{\rho dx^2}` is approximately equal to 1.
.. note::
.. note::
Care must be taken when choosing both a value for :math:`dx_{LB}`,
and a simulation domain size. This fix uses the same subdivision of
@ -223,74 +202,27 @@ the optional keywords *dm*, and *dx* respectively.
with equal lengths in all dimensions, and the default value for
:math:`dx_{LB}` is used, this will automatically be satisfied.
Physical parameters describing the fluid are specified through
*viscosity*, *density*, and *a0*\ . If the force coupling constant is
set the default way, the surface area associated with the MD particles
is specified using the *setArea* keyword. If the user chooses to
specify a value for the force coupling constant, this is set using the
*setGamma* keyword. These parameters should all be given in terms of
the mass, distance, and time units chosen for the main LAMMPS run, as
they are scaled by the LB timestep, lattice spacing, and mass unit,
inside the fix.
----------
The *setArea* keyword allows the user to associate a surface area with
a given atom type. For example if a spherical composite object of
radius R is represented as a spherical shell of N evenly distributed
MD particles, all of the same type, the surface area per particle
associated with that atom type should be set equal to :math:`\frac{4\pi R^2}{N}`.
This keyword should only be used if the force coupling constant,
:math:`\gamma`, is set the default way.
The *setGamma* keyword allows the user to specify their own value for
the force coupling constant, :math:`\gamma`, instead of using the default
value.
The *scaleGamma* keyword should be used in conjunction with the
*setGamma* keyword, when the user wishes to specify different :math:`\gamma`
values for different atom types. This keyword allows the user to
scale the *setGamma* :math:`\gamma` value by a factor, gammaFactor,
for a given atom type.
The *dx* keyword allows the user to specify a value for the LB grid
spacing.
The *dm* keyword allows the user to specify the LB mass unit.
If the *a0* keyword is used, the value specified is used for the
square of the speed of sound in the fluid. If this keyword is not
present, the speed of sound squared is set equal to
:math:`\frac{1}{3}\left(\frac{dx_{LB}}{dt_{LB}}\right)^2`.
Setting :math:`a0 > (\frac{dx_{LB}}{dt_{LB}})^2` is not allowed,
as this may lead to instabilities.
If the *noise* keyword is used, followed by a positive temperature
value, and a positive integer random number seed, a thermal
lattice-Boltzmann algorithm is used. If *LBtype* is set equal to 1
(i.e. the standard LB integrator is chosen), the thermal LB algorithm
of :ref:`Adhikari et al. <Adhikari>` is used; however if *LBtype* is set
equal to 2 both the LB integrator, and thermal LB algorithm described
in :ref:`Ollila et al. <Ollila>` are used.
value, and a positive integer random number seed, the thermal LB algorithm
of :ref:`Adhikari et al. <Adhikari>` is used.
If the *calcforce* keyword is used, both the fluid force and torque
acting on the specified particle group are printed to the screen every
N timesteps.
If the keyword *stencil* is used, the value sets the number of
interpolation points used in each direction. For this, the user has the
choice between a trilinear stencil (*stencil* 2), which provides a
support of 8 lattice sites, or the 3-point immersed boundary method
stencil (*stencil* 3), which provides a support of 27 lattice sites, or
the 4-point Keys' interpolation stencil (stencil 4), which provides a
support of 64 lattice sites. The trilinear stencil is the default as it
is better suited for simulation of objects close to walls or other
objects, due to its smaller support. The 3-point stencil provides
smoother motion of the lattice and is suitable for particles not likely
to be to close to walls or other objects.
If the keyword *trilinear* is used, the trilinear stencil is used to
interpolate the particle nodes onto the fluid mesh. By default, the
immersed boundary method, Peskin stencil is used. Both of these
interpolation methods are described in :ref:`Mackay et al. <fluid-Mackay>`.
If the keyword *D3Q19* is used, the 19 velocity (D3Q19) lattice is
used by the lattice-Boltzmann algorithm. By default, the 15 velocity
(D3Q15) lattice is used.
If the keyword *write_restart* is used, followed by a positive
integer, N, a binary restart file is printed every N LB timesteps.
This restart file only contains information about the fluid.
Therefore, a LAMMPS restart file should also be written in order to
print out full details of the simulation.
If the keyword *write_restart* is used, followed by a positive integer,
N, a binary restart file is printed every N LB timesteps. This restart
file only contains information about the fluid. Therefore, a LAMMPS
restart file should also be written in order to print out full details
of the simulation.
.. note::
@ -308,19 +240,100 @@ conditions in the z-direction. If fixed boundary conditions are
present in the z-direction, and this keyword is not used, the walls
are assumed to be stationary.
If the *pressurebcx* keyword is used, a pressure jump (implemented by a
step jump in density) is imposed at the (periodic) x-boundary. The
value set specifies what would be the resulting equilibrium average
pressure gradient in the x-direction if the system had a constant
cross-section (i.e. resistance to flow). It is converted to a pressure
jump by multiplication by the system size in the x-direction. As this
value should normally be quite small, it is also assumed to be scaled
by 1000.
If the *bodyforce* keyword is used, a constant body force is added to
the fluid, defined by it's x, y and z components.
If the *printfluid* keyword is used, followed by a positive integer, N,
the fluid densities and velocities at each lattice site are printed to the
screen every N timesteps.
If the keyword *D3Q19* is used, the 19 velocity (D3Q19) lattice is
used by the lattice-Boltzmann algorithm. By default, the 15 velocity
(D3Q15) lattice is used.
If the *dumpxdmf* keyword is used, followed by a positive integer, N,
and a file name, the fluid densities and velocities at each lattice site
are output to an xdmf file every N timesteps. This is a binary file
format that can be read by visualization packages such as `Paraview
<https://www.paraview.org/>`_ . The xdmf file format contains a time
index for each frame dump and the value timeI = 1 uses simulation time
while 0 uses the output frame number to index xdmf file. The later can
be useful if the :doc:`dump vtk <dump_vtk>` command is used to output
the particle positions at the same timesteps and you want to visualize
both the fluid and particle data together in `Paraview
<https://www.paraview.org/>`_ .
The *scaleGamma* keyword allows the user to scale the :math:`\gamma`
value by a factor, gammaFactor, for a given atom type. Setting
*scaleGamma* to -1 for the corresponding particle type will explicitly
take the limit of infinite particle mass in computing the force coupling
for the fluid force (see note above).
If the *a0* keyword is used, the value specified is used for the square
of the speed of sound in the fluid. If this keyword is not present, the
speed of sound squared is set equal to
:math:`\frac{1}{3}\left(\frac{dx_{LB}}{dt_{LB}}\right)^2`. Setting
:math:`a0 > (\frac{dx_{LB}}{dt_{LB}})^2` is not allowed, as this may
lead to instabilities. As the speed of sound should usually be much
larger than any fluid velocity of interest, its value does not normally
have a significant impact on the results. As such, it is usually best
to use the default for this option.
The *npits* keyword (followed by integer arguments: npits, h_p, l_p,
l_pp, l_e) sets the fluid domain to the pits geometry. These arguments
should only be used if you actually want something more complex than a
rectangular/cubic geometry. The npits value sets the number of pits
regions (arranged along x). The remaining arguments are sizes measured
in multiples of dx_lb: h_p is the z-height of the pit regions, l_p is
the x-length of the pit regions, l_pp is the length of the region
between consecutive pits (referred to as a "slit" region), and l_e is
the x-length of the slit regions at each end of the channel. The pit
geometry must fill the system in the x-direction but can be longer, in
which case it is truncated (which enables asymmetric entrance/exit end
sections). The additional *wp* keyword allows the width (in
y-direction) of the pit to be specified (the default is full width) and
the *sw* keyword indicates that there should be sidewalls in the
y-direction (default is periodic in y-direction). These parameters are
illustrated below::
Sideview (in xz plane) of pit geometry:
______________________________________________________________________
slit slit slit ^
|
<---le---><---------lp-------><---lpp---><-------lp--------><---le---> hs = (Nbz-1) - hp
|
__________ __________ __________ v
| | | | ^ z
| | | | | |
| pit | | pit | hp +-x
| | | | |
|__________________| |__________________| v
Endview (in yz plane) of pit geometry (no sw so wp is active):
_____________________
^
|
hs
|
_____________________ v
| | ^
| | | z
|<---wp--->| hp |
| | | +-y
|__________| v
----------
For further details, as well as descriptions and results of several
test runs, see :ref:`Mackay et al. <fluid-Mackay>`. Please include a citation to
this paper if the lb_fluid fix is used in work contributing to
published research.
For further details, as well as descriptions and results of several test
runs, see :ref:`Denniston et al. <fluid-Denniston>`. Please include a
citation to this paper if the lb_fluid fix is used in work contributing
to published research.
----------
@ -333,68 +346,77 @@ binary restart files, if requested, independent of the main LAMMPS
is written to the main LAMMPS :doc:`binary restart files <restart>`.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
access by various :doc:`output commands <Howto_output>`. No parameter
of this fix can be used with the *start/stop* keywords of the
:doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
fix.
The fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the current
temperature of the group of particles described by *group-ID* along with
the fluid constrained to move with them. The temperature is computed via
the kinetic energy of the group and fluid constrained to move with them
and the total number of degrees of freedom (calculated internally). If
the particles are not integrated independently (such as via :doc:`fix
NVE <fix_nve>`) but have additional constraints imposed on them (such as
via integration using :doc:`fix rigid <fix_rigid>`) the degrees of
freedom removed from these additional constraints will not be properly
accounted for. In this case, the user can specify the total degrees of
freedom independently using the *dof* keyword.
The fix also computes a global array of values which can be accessed by
various :doc:`output commands <Howto_output>`. There are 5 entries in
the array. The first entry is the temperature of the fluid, the second
entry is the total mass of the fluid plus particles, the third through
fifth entries give the x, y, and z total momentum of the fluid plus
particles.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` page for more info.
was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This fix can only be used with an orthogonal simulation domain.
Walls have only been implemented in the z-direction. Therefore, the
boundary conditions, as specified via the main LAMMPS boundary command
must be periodic for x and y, and either fixed or periodic for z.
Shrink-wrapped boundary conditions are not permitted with this fix.
The boundary conditions for the fluid are specified independently to the
particles. However, these should normally be specified consistently via
the main LAMMPS :doc:`boundary <boundary>` command (p p p, p p f, and p
f f are the only consistent possibilities). Shrink-wrapped boundary
conditions are not permitted with this fix.
This fix must be used before any of :doc:`fix lb/viscous <fix_lb_viscous>`, :doc:`fix lb/momentum <fix_lb_momentum>`, :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`, and/ or :doc:`fix lb/pc <fix_lb_pc>` , as the fluid needs to be initialized before
any of these routines try to access its properties. In addition, in
order for the hydrodynamic forces to be added to the particles, this
fix must be used in conjunction with the
:doc:`lb/viscous <fix_lb_viscous>` fix if the force coupling constant is
set by default, or either the :doc:`lb/viscous <fix_lb_viscous>` fix or
one of the :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` or
:doc:`lb/pc <fix_lb_pc>` integrators, if the user chooses to specify
their own value for the force coupling constant.
This fix must be used before any of :doc:`fix lb/viscous
<fix_lb_viscous>` and :doc:`fix lb/momentum <fix_lb_momentum>` as the
fluid needs to be initialized before any of these routines try to access
its properties. In addition, in order for the hydrodynamic forces to be
added to the particles, this fix must be used in conjunction with the
:doc:`lb/viscous <fix_lb_viscous>` fix.
This fix needs to be used in conjunction with a standard LAMMPS
integrator such as :doc:`fix NVE <fix_nve>` or :doc:`fix rigid
<fix_rigid>`.
Related commands
""""""""""""""""
:doc:`fix lb/viscous <fix_lb_viscous>`, :doc:`fix lb/momentum <fix_lb_momentum>`, :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`, :doc:`fix lb/pc <fix_lb_pc>`
:doc:`fix lb/viscous <fix_lb_viscous>`, :doc:`fix lb/momentum <fix_lb_momentum>`
Default
"""""""
By default, the force coupling constant is set according to
.. math::
\gamma = \frac{2m_um_v}{m_u+m_v}\left(\frac{1}{\Delta t_{collision}}\right)
and an area of :math:`dx_{LB}^2` per node, used to calculate the fluid mass at
the particle node location, is assumed.
*dx* is chosen such that :math:`\frac{\tau}{dt_{LB}} =
\frac{3\eta dt_{LB}}{\rho dx_{LB}^2}` is approximately equal to 1.
*dx* is chosen such that :math:`\frac{\tau}{dt_{LB}} = \frac{3\eta dt_{LB}}{\rho dx_{LB}^2}` is approximately equal to 1.
*dm* is set equal to 1.0.
*a0* is set equal to :math:`\frac{1}{3}\left(\frac{dx_{LB}}{dt_{LB}}\right)^2`.
The Peskin stencil is used as the default interpolation method.
The trilinear stencil is used as the default interpolation method.
The D3Q15 lattice is used for the lattice-Boltzmann algorithm.
If walls are present, they are assumed to be stationary.
----------
.. _Ollila:
.. _fluid-Denniston:
**(Ollila et al.)** Ollila, S.T.T., Denniston, C., Karttunen, M., and Ala-Nissila, T., Fluctuating lattice-Boltzmann model for complex fluids, J. Chem. Phys. 134 (2011) 064902.
.. _fluid-Mackay:
**(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.
**(Denniston et al.)** Denniston, C., Afrasiabian, N., Cole-Andre, M.G., Mackay, F. E., Ollila, S.T.T., and Whitehead, T., LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 275 (2022) `108318 <https://doi.org/10.1016/j.cpc.2022.108318>`_ .
.. _Mackay2:
@ -403,3 +425,4 @@ If walls are present, they are assumed to be stationary.
.. _Adhikari:
**(Adhikari et al.)** Adhikari, R., Stratford, K., Cates, M. E., and Wagner, A. J., Fluctuating lattice Boltzmann, Europhys. Lett. 71 (2005) 473-479.

2
doc/src/fix_lb_momentum.rst
View File

@ -38,7 +38,7 @@ lattice-Boltzmann fluid is present.
Zero the total linear momentum of the system, including both the atoms
specified by group-ID and the lattice-Boltzmann fluid every nevery
timesteps. This is accomplished by adjusting the particle velocities
timesteps. If there are no atoms specified by group-ID only the fluid momentum is affected. This is accomplished by adjusting the particle velocities
and the fluid velocities at each lattice site.
.. note::

65
doc/src/fix_lb_pc.rst
View File

@ -1,65 +0,0 @@
.. index:: fix lb/pc
fix lb/pc command
=================
Syntax
""""""
.. parsed-literal::
fix ID group-ID lb/pc
* ID, group-ID are documented in the :doc:`fix <fix>` command
* lb/pc = style name of this fix command
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all lb/pc
Description
"""""""""""
Update the positions and velocities of the individual particles
described by *group-ID*, experiencing velocity-dependent hydrodynamic
forces, using the integration algorithm described in :ref:`Mackay et al. <Mackay1>`. This integration algorithm should only be used if a
user-specified value for the force-coupling constant used in :doc:`fix lb/fluid <fix_lb_fluid>` has been set; do not use this integration
algorithm if the force coupling constant has been set by default.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` page for more info.
Can only be used if a lattice-Boltzmann fluid has been created via the
:doc:`fix lb/fluid <fix_lb_fluid>` command, and must come after this
command.
Related commands
""""""""""""""""
:doc:`fix lb/fluid <fix_lb_fluid>` :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`
Default
"""""""
none.
----------
.. _Mackay1:
**(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.

167
doc/src/fix_lb_rigid_pc_sphere.rst
View File

@ -1,167 +0,0 @@
.. index:: fix lb/rigid/pc/sphere
fix lb/rigid/pc/sphere command
==============================
Syntax
""""""
.. parsed-literal::
fix ID group-ID lb/rigid/pc/sphere bodystyle args keyword values ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* lb/rigid/pc/sphere = style name of this fix command
* bodystyle = *single* or *molecule* or *group*
.. parsed-literal::
*single* args = none
*molecule* args = none
*group* args = N groupID1 groupID2 ...
N = # of groups
* zero or more keyword/value pairs may be appended
* keyword = *force* or *torque* or *innerNodes*
.. parsed-literal::
*force* values = M xflag yflag zflag
M = which rigid body from 1-Nbody (see asterisk form below)
xflag,yflag,zflag = off/on if component of center-of-mass force is active
*torque* values = M xflag yflag zflag
M = which rigid body from 1-Nbody (see asterisk form below)
xflag,yflag,zflag = off/on if component of center-of-mass torque is active
*innerNodes* values = innergroup-ID
innergroup-ID = ID of the atom group which does not experience a hydrodynamic force from the lattice-Boltzmann fluid
Examples
""""""""
.. code-block:: LAMMPS
fix 1 spheres lb/rigid/pc/sphere
fix 1 all lb/rigid/pc/sphere force 1 0 0 innerNodes ForceAtoms
Description
"""""""""""
This fix is based on the :doc:`fix rigid <fix_rigid>` command, and was
created to be used in place of that fix, to integrate the equations of
motion of spherical rigid bodies when a lattice-Boltzmann fluid is
present with a user-specified value of the force-coupling constant.
The fix uses the integration algorithm described in :ref:`Mackay et
al. <Mackay>` to update the positions, velocities, and orientations of
a set of spherical rigid bodies experiencing velocity dependent
hydrodynamic forces. The spherical bodies are assumed to rotate as
solid, uniform density spheres, with moments of inertia calculated
using the combined sum of the masses of all the constituent particles
(which are assumed to be point particles).
----------
By default, all of the atoms that this fix acts on experience a
hydrodynamic force due to the presence of the lattice-Boltzmann fluid.
However, the *innerNodes* keyword allows the user to specify atoms
belonging to a rigid object which do not interact with the
lattice-Boltzmann fluid (i.e. these atoms do not feel a hydrodynamic
force from the lattice-Boltzmann fluid). This can be used to
distinguish between atoms on the surface of a non-porous object, and
those on the inside.
This feature can be used, for example, when implementing a hard sphere
interaction between two spherical objects. Instead of interactions
occurring between the particles on the surfaces of the two spheres, it
is desirable simply to place an atom at the center of each sphere,
which does not contribute to the hydrodynamic force, and have these
central atoms interact with one another.
----------
Apart from the features described above, this fix is very similar to
the rigid fix (although it includes fewer optional arguments, and
assumes the constituent atoms are point particles); see
:doc:`fix rigid <fix_rigid>` for a complete documentation.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about the *rigid* and *rigid/nve* fixes are written to
:doc:`binary restart files <restart>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the added forces on atoms to
both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
Similar to the :doc:`fix rigid <fix_rigid>` command: The rigid fix
computes a global scalar which can be accessed by various :doc:`output
commands <Howto_output>`. The scalar value calculated by these fixes
is "intensive". The scalar is the current temperature of the
collection of rigid bodies. This is averaged over all rigid bodies
and their translational and rotational degrees of freedom. The
translational energy of a rigid body is 1/2 m v\^2, where m = total
mass of the body and v = the velocity of its center of mass. The
rotational energy of a rigid body is 1/2 I w\^2, where I = the moment
of inertia tensor of the body and w = its angular velocity. Degrees
of freedom constrained by the *force* and *torque* keywords are
removed from this calculation.
All of these fixes compute a global array of values which can be
accessed by various :doc:`output commands <Howto_output>`. The number
of rows in the array is equal to the number of rigid bodies. The
number of columns is 15. Thus for each rigid body, 15 values are
stored: the xyz coords of the center of mass (COM), the xyz components
of the COM velocity, the xyz components of the force acting on the
COM, the xyz components of the torque acting on the COM, and the xyz
image flags of the COM, which have the same meaning as image flags for
atom positions (see the "dump" command). The force and torque values
in the array are not affected by the *force* and *torque* keywords in
the fix rigid command; they reflect values before any changes are made
by those keywords.
The ordering of the rigid bodies (by row in the array) is as follows.
For the *single* keyword there is just one rigid body. For the
*molecule* keyword, the bodies are ordered by ascending molecule ID.
For the *group* keyword, the list of group IDs determines the ordering
of bodies.
The array values calculated by these fixes are "intensive", meaning
they are independent of the number of atoms in the simulation.
No parameter of these fixes can be used with the *start/stop* keywords
of the :doc:`run <run>` command. These fixes are not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Can only be used if a lattice-Boltzmann fluid has been created via the
:doc:`fix lb/fluid <fix_lb_fluid>` command, and must come after this
command. Should only be used if the force coupling constant used in
:doc:`fix lb/fluid <fix_lb_fluid>` has been set by the user; this
integration fix cannot be used if the force coupling constant is set
by default.
Related commands
""""""""""""""""
:doc:`fix lb/fluid <fix_lb_fluid>`, :doc:`fix lb/pc <fix_lb_pc>`
Default
"""""""
The defaults are force \* on on on, and torque \* on on on.
----------
.. _Mackay:
**(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.

30
doc/src/fix_lb_viscous.rst
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@ -25,27 +25,14 @@ Description
This fix is similar to the :doc:`fix viscous <fix_viscous>` command, and
is to be used in place of that command when a lattice-Boltzmann fluid
is present, and the user wishes to integrate the particle motion using
one of the built in LAMMPS integrators.
is present using the :doc:`fix lb/fluid <fix_lb_fluid>`. This should be used in conjunction with one of the built-in LAMMPS integrators, such as :doc:`fix NVE <fix_nve>` or :doc:`fix rigid <fix_rigid>`.
This fix adds a force, F = - Gamma\*(velocity-fluid_velocity), to each
atom, where Gamma is the force coupling constant described in the :doc:`fix lb/fluid <fix_lb_fluid>` command (which applies an equal and
opposite force to the fluid).
.. note::
This fix should only be used in conjunction with one of the
built in LAMMPS integrators; it should not be used with the :doc:`fix lb/pc <fix_lb_pc>` or :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` integrators, which
already include the hydrodynamic forces. These latter fixes should
only be used if the force coupling constant has been set by the user
(instead of using the default value); if the default force coupling
value is used, then this fix provides the only method for adding the
hydrodynamic forces to the particles.
This fix adds a viscous force to each atom to cause it move with the same velocity as the fluid (an equal and opposite force is applied to the fluid via :doc:`fix lb/fluid <fix_lb_fluid>`). When :doc:`fix lb/fluid <fix_lb_fluid>` is called with the noise option, the atoms will also experience random forces which will thermalize them to the same temperature as the fluid. In this way, the combination of this fix with :doc:`fix lb/fluid <fix_lb_fluid>` and a LAMMPS integrator like :doc:`fix NVE <fix_nve>` is analogous to :doc:`fix langevin <fix_langevin>` except here the fluid is explicit. The temperature of the particles can be monitored via the scalar output of :doc:`fix lb/fluid <fix_lb_fluid>`.
----------
For further details, as well as descriptions and results of several
test runs, see :ref:`Mackay et al. <Mackay3>`. Please include a citation to
For details of this fix, as well as descriptions and results of several
test runs, see :ref:`Denniston et al. <fluid-Denniston2>`. Please include a citation to
this paper if this fix is used in work contributing to published
research.
@ -78,14 +65,11 @@ Can only be used if a lattice-Boltzmann fluid has been created via the
:doc:`fix lb/fluid <fix_lb_fluid>` command, and must come after this
command.
This fix should not be used if either the :doc:`fix lb/pc <fix_lb_pc>`
or :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` integrator is
used.
Related commands
""""""""""""""""
:doc:`fix lb/fluid <fix_lb_fluid>`, :doc:`fix lb/pc <fix_lb_pc>`, :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`
:doc:`fix lb/fluid <fix_lb_fluid>`
Default
"""""""
@ -94,6 +78,6 @@ none
----------
.. _Mackay3:
.. _fluid-Denniston2:
**(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.
**(Denniston et al.)** Denniston, C., Afrasiabian, N., Cole-Andre, M.G., Mackay, F. E., Ollila, S.T.T., and Whitehead, T., LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 275 (2022) `108318 <https://doi.org/10.1016/j.cpc.2022.108318>`_ .

81
doc/src/fix_polarize.rst
View File

@ -21,7 +21,7 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command
* style = *polarize/bem/gmres* or *polarize/bem/icc* or *polarize/functional*
* Nevery = this fixed is invoked every this many timesteps
* tolerance = the tolerance for the iterative solver to stop
* tolerance = the relative tolerance for the iterative solver to stop
Examples
@ -45,10 +45,45 @@ Description
"""""""""""
These fixes compute induced charges at the interface between two
impermeable media with different dielectric constants.
impermeable media with different dielectric constants. The interfaces
need to be discretized into vertices, each representing a boundary element.
The vertices are treated as if they were regular atoms or particles.
:doc:`atom_style dielectric <atom_style>` should be used since it defines
the additional properties of each interface particle such as
interface normal vectors, element areas, and local dielectric mismatch.
These fixes also require the use of :doc:`pair_style <pair_style>` and
:doc:`kspace_style <kspace_style>` with the *dielectric* suffix.
At every time step, given a configuration of the physical charges in the system
(such as atoms and charged particles) these fixes compute and update
the charge of the interface particles. The interfaces are allowed to move
during the simulation with appropriate time integrators (for example,
with :doc:`fix_rigid <fix_rigid>`).
There are some example scripts for using this fix
with LAMMPS in the examples/PACKAGES/dielectric directory.
Consider an interface between two media: one with dielectric constant
of 78 (water), the other of 4 (silica). The interface is discretized
into 2000 boundary elements, each represented by an interface particle. Suppose that
each interface particle has a normal unit vector pointing from the silica medium to water.
The dielectric difference along the normal vector is then 78 - 4 = 74,
the mean dielectric value is (78 + 4) / 2 = 41. Each boundary element
also has its area and the local mean curvature (which is used by these fixes
for computing a correction term in the local electric field).
To model charged interfaces, the interface particle will have a non-zero charge value,
coming from its area and surface charge density.
For non-interface particles such as atoms and charged particles,
the interface normal vectors, element area, and dielectric mismatch are
irrelevant. Their local dielectric value is used to rescale their actual charge
when computing the Coulombic interactions. For instance, for a cation carrying
a charge of +2 (in charge unit) in an implicit solvent with dielectric constant of 40
would have actual charge of +2, and a local dielectric constant value of 40.
It is assumed that the particles cannot pass through the interface during the simulation
so that its local dielectric constant value does not change.
There are some example scripts for using these fixes
with LAMMPS in the ``examples/PACKAGES/dielectric directory``. The README file
therein contains specific details on the system setup. Note that the example data files
show the additional fields (columns) needed for :doc:`atom_style dielectric <atom_style>`
beyond the conventional fields *id*, *mol*, *type*, *q*, *x*, *y*, and *z*.
----------
@ -75,12 +110,41 @@ as described in :ref:`(Barros) <Barros>` to solve :math:`\sigma_b`.
Fix *polarize/bem/icc* employs the successive over-relaxation algorithm
as described in :ref:`(Tyagi) <Tyagi>` to solve :math:`\sigma_b`.
Fix *polarize/functional* ...
The iterative solvers would terminate either when the maximum relative change
in the induced charges in consecutive iterations is below the set tolerance,
or when the number of iterations reaches *iter_max* (see below).
Fix *polarize/functional* employs the energy functional variation approach
as described in :ref:`(Jadhao) <Jadhao>` to solve :math:`\sigma_b`.
More details on the implementation of these fixes and their recommended use
are described in :ref:`(NguyenTD) <NguyenTD>`.
Restart, fix_modify, output, run start/stop, minimize info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
...
No information about this fix is written to :doc:`binary restart files <restart>`.
The :doc:`fix_modify <fix_modify>` command provides certain options to
control the induced charge solver and the initial values of the interface elements:
.. parsed-literal::
*itr_max* arg
arg = maximum number of iterations for convergence
*dielectrics* ediff emean epsilon area charge
ediff = dielectric difference
emean = dielectric mean
epsilon = local dielectric value
aree = element area
charge = real interface charge
*polarize/bem/gmres* or *polarize/bem/icc* compute a global 2-element vector
which can be accessed by various :doc:`output commands <Howto_output>`.
The first element is the number of iterations when the solver terminates
(of which the upper bound is set by *iter_max*). The second element is the RMS error.
Restrictions
""""""""""""
@ -94,12 +158,15 @@ KSPACE package is installed. See the :doc:`Build package
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`fix polarize <fix_polarize>`, :doc:`read_data <read_data>`,
:doc:`pair_style lj/cut/coul/long/dielectric <pair_dielectric>`,
:doc:`kspace_style pppm/dielectric <kspace_style>`,
:doc:`compute efield/atom <compute_efield_atom>`
Default
"""""""
None.
*iter_max* = 20
----------

82
doc/src/pair_python.rst
View File

@ -20,6 +20,9 @@ Examples
pair_style python 2.5
pair_coeff * * py_pot.LJCutMelt lj
pair_style python 10.0
pair_coeff * * py_pot.HarmonicCut A B
pair_style hybrid/overlay coul/long 12.0 python 12.0
pair_coeff * * coul/long
pair_coeff * * python py_pot.LJCutSPCE OW NULL
@ -159,23 +162,82 @@ Following the *LJCutMelt* example, here are the two functions:
to be multiplied by delta x, delta y, and delta z to conveniently obtain
the three components of the force vector between these two atoms.
Below is a more complex example using *real* units and defines an interaction
equivalent to:
.. code-block:: LAMMPS
units real
pair_style harmonic/cut
pair_coeff 1 1 0.2 9.0
pair_coeff 2 2 0.4 9.0
This uses the default geometric mixing. The equivalent input with pair
style *python* is:
.. code-block:: LAMMPS
units real
pair_style python 10.0
pair_coeff * * py_pot.Harmonic A B
Note that while for pair style *harmonic/cut* the cutoff is implicitly
set to the minimum of the harmonic potential, for pair style python a
global cutoff must be set and it must be equal or larger to the implicit
cutoff of the potential in python, which has to explicitly return zero
force and energy beyond the cutoff. Also, the mixed parameters have to
be explicitly provided. The corresponding python code is:
.. code-block:: python
class Harmonic(LAMMPSPairPotential):
def __init__(self):
super(Harmonic,self).__init__()
self.units = 'real'
# set coeffs: K, r0
self.coeff = {'A' : {'A' : (0.2,9.0),
'B' : (math.sqrt(0.2*0.4),9.0)},
'B' : {'A' : (math.sqrt(0.2*0.4),9.0),
'B' : (0.4,9.0)}}
def compute_force(self,rsq,itype,jtype):
coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
r = math.sqrt(rsq)
delta = coeff[1]-r
if (r < coeff[1]):
return 2.0*delta*coeff[0]/r
else:
return 0.0
def compute_energy(self,rsq,itype,jtype):
coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
r = math.sqrt(rsq)
delta = coeff[1]-r
if (r < coeff[1]):
return delta*delta*coeff[0]
else:
return 0.0
----------
.. note::
.. admonition:: Performance Impact
:class: note
The evaluation of scripted python code will slow down the
computation pairwise interactions quite significantly. However, this
can be largely worked around through using the python pair style not
for the actual simulation, but to generate tabulated potentials on the
fly using the :doc:`pair_write <pair_write>` command. Please see below
for an example LAMMPS input of how to build a table file:
The evaluation of scripted python code will slow down the computation
of pairwise interactions quite significantly. However, this performance
penalty can be worked around through using the python pair style not
for the actual simulation, but to generate tabulated potentials using
the :doc:`pair_write <pair_write>` command. This will also enable
GPU or multi-thread acceleration through the GPU, KOKKOS, or OPENMP
package versions of the *table* pair style. Please see below for a
LAMMPS input example demonstrating how to build a table file:
.. code-block:: LAMMPS
pair_style python 2.5
pair_coeff * * py_pot.LJCutMelt lj
shell rm -f melt.table
pair_write 1 1 2000 rsq 0.01 2.5 lj1_lj2.table lj
shell rm -f lj.table
pair_write 1 1 2000 rsq 0.01 2.5 lj.table lj
Note that it is strongly recommended to try to **delete** the potential
table file before generating it. Since the *pair_write* command will
@ -190,7 +252,7 @@ to be assigned to the LAMMPS atom types like this:
.. code-block:: LAMMPS
pair_style table linear 2000
pair_coeff 1 1 melt.table lj
pair_coeff 1 1 lj.table lj
This can also be done for more complex systems. Please see the
*examples/python* folders for a few more examples.

14
doc/src/pair_snap.rst
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@ -135,7 +135,8 @@ with #) anywhere. Each non-blank non-comment line must contain one
keyword/value pair. The required keywords are *rcutfac* and
*twojmax*\ . Optional keywords are *rfac0*, *rmin0*,
*switchflag*, *bzeroflag*, *quadraticflag*, *chemflag*,
*bnormflag*, *wselfallflag*, *chunksize*, and *parallelthresh*\ .
*bnormflag*, *wselfallflag*, *switchinnerflag*,
*rinner*, *drinner*, *chunksize*, and *parallelthresh*\ .
The default values for these keywords are
@ -147,6 +148,7 @@ The default values for these keywords are
* *chemflag* = 0
* *bnormflag* = 0
* *wselfallflag* = 0
* *switchinnerflag* = 0
* *chunksize* = 32768
* *parallelthresh* = 8192
@ -189,6 +191,16 @@ corresponding *K*-vector of linear coefficients for element
which must equal the number of unique elements appearing in the LAMMPS
pair_coeff command, to avoid ambiguity in the number of coefficients.
The keyword *switchinnerflag* activates an additional switching function
that smoothly turns off contributions to the SNAP potential from neighbor
atoms at short separations. If *switchinnerflag* is set to 1 then
the additional keywords *rinner* and *drinner* must also be provided.
Each of these is followed by *nelements* values, where *nelements*
is the number of unique elements appearing in appearing in the LAMMPS
pair_coeff command. The element order should correspond to the order
in which elements first appear in the pair_coeff command reading from
left to right.
The keywords *chunksize* and *parallelthresh* are only applicable when
using the pair style *snap* with the KOKKOS package on GPUs and are
ignored otherwise. The *chunksize* keyword controls the number of atoms

9
doc/src/plugin.rst
View File

@ -56,6 +56,15 @@ styles and names.
The *clear* command will unload all currently loaded plugins.
.. admonition:: Automatic loading of plugins
:class: note
When the environment variable ``LAMMPS_PLUGIN_PATH`` is set, then
LAMMPS will search the directory (or directories) listed in this path
for files with names that end in ``plugin.so``
(e.g. ``helloplugin.so``) and will try to load the contained plugins
automatically at start-up.
Restrictions
""""""""""""

58
doc/src/shell.rst
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@ -20,8 +20,9 @@ Syntax
dir1,dir2 = one or more directories to create
*mv* args = old new
old = old filename
new = new filename
*rm* args = file1 file2 ...
new = new filename or destination folder
*rm* args = [-f] file1 file2 ...
-f = turn off warnings (optional)
file1,file2 = one or more filenames to delete
*rmdir* args = dir1 dir2 ...
dir1,dir2 = one or more directories to delete
@ -36,8 +37,8 @@ Examples
shell cd sub1
shell cd ..
shell mkdir tmp1 tmp2 tmp3
shell rmdir tmp1
shell mkdir tmp1 tmp2/tmp3
shell rmdir tmp1 tmp2
shell mv log.lammps hold/log.1
shell rm TMP/file1 TMP/file2
shell putenv LAMMPS_POTENTIALS=../../potentials
@ -50,34 +51,39 @@ Description
Execute a shell command. A few simple file-based shell commands are
supported directly, in Unix-style syntax. Any command not listed
above is passed as-is to the C-library system() call, which invokes
the command in a shell.
the command in a shell. To use the external executable instead of
the built-in version one needs to use a full path, for example
*/bin/rm* instead of *rm*. The built-in commands will also work
on operating systems, that do not - by default - provide the
corresponding external executables (like *mkdir* on Windows).
This is means to invoke other commands from your input script. For
example, you can move files around in preparation for the next section
of the input script. Or you can run a program that pre-processes data
for input into LAMMPS. Or you can run a program that post-processes
LAMMPS output data.
This command provides a ways to invoke custom commands or executables
from your input script. For example, you can move files around in
preparation for the next section of the input script. Or you can run a
program that pre-processes data for input into LAMMPS. Or you can run a
program that post-processes LAMMPS output data.
With the exception of *cd*, all commands, including ones invoked via a
system() call, are executed by only a single processor, so that
files/directories are not being manipulated by multiple processors.
files/directories are not being manipulated by multiple processors
concurrently which may result in unexpected errors or corrupted files.
The *cd* command executes the Unix "cd" command to change the working
directory. All subsequent LAMMPS commands that read/write files will
use the new directory. All processors execute this command.
The *cd* command changes the current working directory similar to
the ``cd`` command. All subsequent LAMMPS commands that read/write files
will use the new directory. All processors execute this command.
The *mkdir* command executes the Unix "mkdir" command to create one or
more directories.
The *mkdir* command creates directories similar to the Unix ``mkdir -p``
command. That is, it will attempt to create the entire path of
sub-directories if they do not exist yet.
The *mv* command executes the Unix "mv" command to rename a file and/or
move it to a new directory.
The *mv* command renames a file and/or moves it to a new directory.
It cannot rename files across filesystem boundaries or between drives.
The *rm* command executes the Unix "rm" command to remove one or more
files.
The *rm* command deletes file similar to the Unix ``rm`` command.
The *rmdir* command executes the Unix "rmdir" command to remove one or
more directories. A directory must be empty to be successfully
removed.
The *rmdir* command deletes directories similar to Unix ``rmdir`` command.
If a directory is not empty, its contents are also removed recursively
similar to the Unix ``rm -r`` command.
The *putenv* command defines or updates an environment variable directly.
Since this command does not pass through the shell, no shell variable
@ -107,9 +113,9 @@ with 3 arguments: file1 10 file2.
Restrictions
""""""""""""
LAMMPS does not detect errors or print warnings when any of these
commands execute. E.g. if the specified directory does not exist,
executing the *cd* command will silently do nothing.
LAMMPS will do a best effort to detect errors and print suitable
warnings, but due to the nature of delegating commands to the C-library
system() call, this is not always reliable.
Related commands
""""""""""""""""

22
doc/src/thermo.rst
View File

@ -32,18 +32,20 @@ The content and format of what is printed is controlled by the
:doc:`thermo_style <thermo_style>` and
:doc:`thermo_modify <thermo_modify>` commands.
Instead of a numeric value, N can be specified as an :doc:`equal-style variable <variable>`, which should be specified as v_name, where
name is the variable name. In this case, the variable is evaluated at
the beginning of a run to determine the next timestep at which
thermodynamic info will be written out. On that timestep, the
variable will be evaluated again to determine the next timestep, etc.
Thus the variable should return timestep values. See the stagger()
and logfreq() and stride() math functions for :doc:`equal-style variables <variable>`, as examples of useful functions to use in
this context. Other similar math functions could easily be added as
options for :doc:`equal-style variables <variable>`.
Instead of a numeric value, N can be specified as an :doc:`equal-style
variable <variable>`, which should be specified as v_name, where name is
the variable name. In this case, the variable is evaluated at the
beginning of a run to determine the next timestep at which thermodynamic
info will be written out. On that timestep, the variable will be
evaluated again to determine the next timestep, etc. Thus the variable
should return timestep values. See the stagger() and logfreq() and
stride() math functions for :doc:`equal-style variables <variable>`, as
examples of useful functions to use in this context. Other similar math
functions could easily be added as options for :doc:`equal-style
variables <variable>`.
For example, the following commands will output thermodynamic info at
timesteps 0,10,20,30,100,200,300,1000,2000,etc:
timesteps 0, 10, 20, 30, 100, 200, 300, 1000, 2000, *etc*:
.. code-block:: LAMMPS

179
doc/src/thermo_modify.rst
View File

@ -20,7 +20,7 @@ Syntax
*warn* value = *ignore* or *reset* or *default* or a number
*norm* value = *yes* or *no*
*flush* value = *yes* or *no*
*line* value = *one* or *multi*
*line* value = *one* or *multi* or *yaml*
*format* values = *line* string, *int* string, *float* string, M string, or *none*
string = C-style format string
M = integer from 1 to N, where N = # of quantities being output
@ -36,35 +36,35 @@ Examples
thermo_modify temp myTemp format 3 %15.8g
thermo_modify temp myTemp format line "%ld %g %g %15.8g"
thermo_modify line multi format float %g
themos_modify line yaml format none
Description
"""""""""""
Set options for how thermodynamic information is computed and printed
by LAMMPS.
Set options for how thermodynamic information is computed and printed by
LAMMPS.
.. note::
These options apply to the currently defined thermo style. When
These options apply to the *currently defined* thermo style. When
you specify a :doc:`thermo_style <thermo_style>` command, all
thermodynamic settings are restored to their default values, including
those previously reset by a thermo_modify command. Thus if your input
script specifies a thermo_style command, you should use the
thermo_modify command after it.
thermodynamic settings are restored to their default values,
including those previously reset by a thermo_modify command. Thus if
your input script specifies a thermo_style command, you should use
the thermo_modify command **after** it.
The *lost* keyword determines whether LAMMPS checks for lost atoms
each time it computes thermodynamics and what it does if atoms are
lost. An atom can be "lost" if it moves across a non-periodic
simulation box :doc:`boundary <boundary>` or if it moves more than a box
length outside the simulation domain (or more than a processor
sub-domain length) before reneighboring occurs. The latter case is
typically due to bad dynamics, e.g. too large a timestep or huge
forces and velocities. If the value is *ignore*, LAMMPS does not
check for lost atoms. If the value is *error* or *warn*, LAMMPS
checks and either issues an error or warning. The code will exit with
an error and continue with a warning. A warning will only be issued
once, the first time an atom is lost. This can be a useful debugging
option.
The *lost* keyword determines whether LAMMPS checks for lost atoms each
time it computes thermodynamics and what it does if atoms are lost. An
atom can be "lost" if it moves across a non-periodic simulation box
:doc:`boundary <boundary>` or if it moves more than a box length outside
the simulation domain (or more than a processor sub-domain length)
before reneighboring occurs. The latter case is typically due to bad
dynamics, e.g. too large a timestep or huge forces and velocities. If
the value is *ignore*, LAMMPS does not check for lost atoms. If the
value is *error* or *warn*, LAMMPS checks and either issues an error or
warning. The code will exit with an error and continue with a warning.
A warning will only be issued once, the first time an atom is lost.
This can be a useful debugging option.
The *lost/bond* keyword determines whether LAMMPS throws an error or
not if an atom in a bonded interaction (bond, angle, etc) cannot be
@ -109,55 +109,55 @@ will be reset to zero, and with the value *default*, the counter is
reset and the limit set to 100. An example usage of either *reset* or
*default* would be to re-enable warnings that were disabled or have
reached the limit during equilibration, where the warnings would be
acceptable while the system is still adjusting, but then change
to all warnings for the production run, where they would indicate
problems that would require a closer look at what is causing them.
acceptable while the system is still adjusting, but then change to all
warnings for the production run, where they would indicate problems that
would require a closer look at what is causing them.
The *norm* keyword determines whether various thermodynamic output
values are normalized by the number of atoms or not, depending on
whether it is set to *yes* or *no*\ . Different unit styles have
different defaults for this setting (see below). Even if *norm* is
set to *yes*, a value is only normalized if it is an "extensive"
quantity, meaning that it scales with the number of atoms in the
system. For the thermo keywords described by the page for the
:doc:`thermo_style <thermo_style>` command, all energy-related keywords
are extensive, such as *pe* or *ebond* or *enthalpy*\ . Other keywords
such as *temp* or *press* are "intensive" meaning their value is
independent (in a statistical sense) of the number of atoms in the
system and thus are never normalized. For thermodynamic output values
extracted from fixes and computes in a :doc:`thermo_style custom <thermo_style>` command, the page for the individual
:doc:`fix <fix>` or :doc:`compute <compute>` lists whether the value is
"extensive" or "intensive" and thus whether it is normalized.
Thermodynamic output values calculated by a variable formula are
assumed to be "intensive" and thus are never normalized. You can
always include a divide by the number of atoms in the variable formula
if this is not the case.
different defaults for this setting (see below). Even if *norm* is set
to *yes*, a value is only normalized if it is an "extensive" quantity,
meaning that it scales with the number of atoms in the system. For the
thermo keywords described by the page for the :doc:`thermo_style
<thermo_style>` command, all energy-related keywords are extensive, such
as *pe* or *ebond* or *enthalpy*\ . Other keywords such as *temp* or
*press* are "intensive" meaning their value is independent (in a
statistical sense) of the number of atoms in the system and thus are
never normalized. For thermodynamic output values extracted from fixes
and computes in a :doc:`thermo_style custom <thermo_style>` command, the
page for the individual :doc:`fix <fix>` or :doc:`compute <compute>`
lists whether the value is "extensive" or "intensive" and thus whether
it is normalized. Thermodynamic output values calculated by a variable
formula are assumed to be "intensive" and thus are never normalized.
You can always include a divide by the number of atoms in the variable
formula if this is not the case.
The *flush* keyword invokes a flush operation after thermodynamic info
is written to the screen and log file. This insures the output is
updated and not buffered (by the application) even if LAMMPS halts
before the simulation completes. Please note that this does not
affect buffering by the OS or devices, so you may still lose data
in case the simulation stops due to a hardware failure.
before the simulation completes. Please note that this does not affect
buffering by the OS or devices, so you may still lose data in case the
simulation stops due to a hardware failure.
The *line* keyword determines whether thermodynamics will be output as
a series of numeric values on one line or in a multi-line format with
3 quantities with text strings per line and a dashed-line header
containing the timestep and CPU time. This modify option overrides
the *one* and *multi* thermo_style settings.
The *line* keyword determines whether thermodynamics will be output as a
series of numeric values on one line ("one"), in a multi-line format
with 3 quantities with text strings per line and a dashed-line header
containing the timestep and CPU time ("multi"), or in a YAML format
block ("yaml"). This modify option overrides the *one*, *multi*, or
*yaml* thermo_style settings.
The *format* keyword can be used to change the default numeric format
of any of quantities the :doc:`thermo_style <thermo_style>` command
outputs. All the specified format strings are C-style formats,
e.g. as used by the C/C++ printf() command. The *line* keyword takes
a single argument which is the format string for the entire line of
thermo output, with N fields, which you must enclose in quotes if it
is more than one field. The *int* and *float* keywords take a single
format argument and are applied to all integer or floating-point
quantities output. The setting for *M string* also takes a single
format argument which is used for the Mth value output in each line,
e.g. the fifth column is output in high precision for "format 5
%20.15g".
The *format* keyword can be used to change the default numeric format of
any of quantities the :doc:`thermo_style <thermo_style>` command
outputs. All the specified format strings are C-style formats, e.g. as
used by the C/C++ printf() command. The *line* keyword takes a single
argument which is the format string for the entire line of thermo
output, with N fields, which you must enclose in quotes if it is more
than one field. The *int* and *float* keywords take a single format
argument and are applied to all integer or floating-point quantities
output. The setting for *M string* also takes a single format argument
which is used for the Mth value output in each line, e.g. the fifth
column is output in high precision for "format 5 %20.15g".
The *format* keyword can be used multiple times. The precedence is
that for each value in a line of output, the *M* format (if specified)
@ -168,46 +168,46 @@ settings, reverting all values to their default format.
.. note::
The thermo output values *step* and *atoms* are stored
internally as 8-byte signed integers, rather than the usual 4-byte
signed integers. When specifying the *format int* option you can use
a "%d"-style format identifier in the format string and LAMMPS will
convert this to the corresponding 8-byte form when it is applied to
those keywords. However, when specifying the *line* option or *format
M string* option for *step* and *natoms*, you should specify a format
The thermo output values *step* and *atoms* are stored internally as
8-byte signed integers, rather than the usual 4-byte signed integers.
When specifying the *format int* option you can use a "%d"-style
format identifier in the format string and LAMMPS will convert this
to the corresponding 8-byte form when it is applied to those
keywords. However, when specifying the *line* option or *format M
string* option for *step* and *natoms*, you should specify a format
string appropriate for an 8-byte signed integer, e.g. one with "%ld".
The *temp* keyword is used to determine how thermodynamic temperature
is calculated, which is used by all thermo quantities that require a
The *temp* keyword is used to determine how thermodynamic temperature is
calculated, which is used by all thermo quantities that require a
temperature ("temp", "press", "ke", "etotal", "enthalpy", "pxx", etc).
The specified compute ID must have been previously defined by the user
via the :doc:`compute <compute>` command and it must be a style of
compute that calculates a temperature. As described in the
:doc:`thermo_style <thermo_style>` command, thermo output uses a default
compute for temperature with ID = *thermo_temp*. This option allows
the user to override the default.
compute for temperature with ID = *thermo_temp*. This option allows the
user to override the default.
The *press* keyword is used to determine how thermodynamic pressure is
calculated, which is used by all thermo quantities that require a
pressure ("press", "enthalpy", "pxx", etc). The specified compute ID
must have been previously defined by the user via the
:doc:`compute <compute>` command and it must be a style of compute that
calculates a pressure. As described in the
:doc:`thermo_style <thermo_style>` command, thermo output uses a default
compute for pressure with ID = *thermo_press*. This option allows the
user to override the default.
must have been previously defined by the user via the :doc:`compute
<compute>` command and it must be a style of compute that calculates a
pressure. As described in the :doc:`thermo_style <thermo_style>`
command, thermo output uses a default compute for pressure with ID =
*thermo_press*. This option allows the user to override the default.
.. note::
If both the *temp* and *press* keywords are used in a single
thermo_modify command (or in two separate commands), then the order in
which the keywords are specified is important. Note that a :doc:`pressure compute <compute_pressure>` defines its own temperature compute as
an argument when it is specified. The *temp* keyword will override
this (for the pressure compute being used by thermodynamics), but only
if the *temp* keyword comes after the *press* keyword. If the *temp*
keyword comes before the *press* keyword, then the new pressure
compute specified by the *press* keyword will be unaffected by the
*temp* setting.
thermo_modify command (or in two separate commands), then the order
in which the keywords are specified is important. Note that a
:doc:`pressure compute <compute_pressure>` defines its own
temperature compute as an argument when it is specified. The *temp*
keyword will override this (for the pressure compute being used by
thermodynamics), but only if the *temp* keyword comes after the
*press* keyword. If the *temp* keyword comes before the *press*
keyword, then the new pressure compute specified by the *press*
keyword will be unaffected by the *temp* setting.
Restrictions
""""""""""""
@ -225,7 +225,8 @@ The option defaults are lost = error, warn = 100, norm = yes for unit
style of *lj*, norm = no for unit style of *real* and *metal*,
flush = no, and temp/press = compute IDs defined by thermo_style.
The defaults for the line and format options depend on the thermo
style. For styles "one" and "custom", the line and format defaults
are "one", "%8d", and "%12.8g". For style "multi", the line and
format defaults are "multi", "%8d", and "%14.4f".
The defaults for the line and format options depend on the thermo style.
For styles "one" and "custom", the line and format defaults are "one",
"%10d", and "%12.8g". For style "multi", the line and format defaults
are "multi", "%14d", and "%14.4f". For style "yaml", the line and format
defaults are "%d" and "%.15g".

32
doc/src/thermo_style.rst
View File

@ -10,13 +10,14 @@ Syntax
thermo_style style args
* style = *one* or *multi* or *custom*
* style = *one* or *multi* *yaml* or *custom*
* args = list of arguments for a particular style
.. parsed-literal::
*one* args = none
*multi* args = none
*yaml* args = none
*custom* args = list of keywords
possible keywords = step, elapsed, elaplong, dt, time,
cpu, tpcpu, spcpu, cpuremain, part, timeremain,
@ -92,6 +93,8 @@ Examples
.. code-block:: LAMMPS
thermo_style multi
thermo_style yaml
thermo_style one
thermo_style custom step temp pe etotal press vol
thermo_style custom step temp etotal c_myTemp v_abc
thermo_style custom step temp etotal c_myTemp[*] v_abc
@ -99,18 +102,35 @@ Examples
Description
"""""""""""
Set the style and content for printing thermodynamic data to the
screen and log file.
Set the style and content for printing thermodynamic data to the screen
and log files.
Style *one* prints a one-line summary of thermodynamic info that is
the equivalent of "thermo_style custom step temp epair emol etotal
press". The line contains only numeric values.
Style *one* prints a single line of thermodynamic info that is the
equivalent of "thermo_style custom step temp epair emol etotal press".
The line contains only numeric values.
Style *multi* prints a multiple-line listing of thermodynamic info
that is the equivalent of "thermo_style custom etotal ke temp pe ebond
eangle edihed eimp evdwl ecoul elong press". The listing contains
numeric values and a string ID for each quantity.
.. versionadded:: 24Mar2022
Style *yaml* is similar to style *one* but prints the output in `YAML
<https://yaml.org/>`_ format which can be easily read by a variety of
script languages and data handling packages. Since LAMMPS may print
other output before, after, or in between thermodynamic output, the
YAML format content needs to be separated from the rest. All YAML
format thermodynamic output can be matched with a regular expression
and can thus be extracted with commands like ``egrep`` as follows:
.. code-block:: sh
egrep '^(keywords:|data:$|---$|\.\.\.$| - \[)' log.lammps > log.yaml
Information about processing such YAML files is in the :doc:`structured
data output howto <Howto_structured_data>`.
Style *custom* is the most general setting and allows you to specify
which of the keywords listed above you want printed on each
thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are

41
doc/utils/sphinx-config/_themes/lammps_theme/__init__.py
View File

@ -5,13 +5,18 @@ From https://github.com/ryan-roemer/sphinx-bootstrap-theme.
"""
from os import path
from sys import version_info as python_version
import sphinx
from sphinx import version_info as sphinx_version
from sphinx.locale import _
from sphinx.util.logging import getLogger
__version__ = '0.5.0'
__version__ = '1.0.0'
__version_full__ = __version__
logger = getLogger(__name__)
def get_html_theme_path():
"""Return list of HTML theme paths."""
@ -19,16 +24,40 @@ def get_html_theme_path():
return cur_dir
def config_initiated(app, config):
theme_options = config.html_theme_options or {}
if theme_options.get('canonical_url'):
logger.warning(
_('The canonical_url option is deprecated, use the html_baseurl option from Sphinx instead.')
)
# See http://www.sphinx-doc.org/en/stable/theming.html#distribute-your-theme-as-a-python-package
def setup(app):
if sphinx.version_info >= (1, 6, 0):
# Register the theme that can be referenced without adding a theme path
app.add_html_theme('sphinx_rtd_theme', path.abspath(path.dirname(__file__)))
if python_version[0] < 3:
logger.warning("Python 2 is deprecated with sphinx_rtd_theme, update to Python 3")
app.require_sphinx('1.6')
if sphinx_version <= (2, 0, 0):
logger.warning("Sphinx 1.x is deprecated with sphinx_rtd_theme, update to Sphinx 2.x or greater")
if not app.config.html_experimental_html5_writer:
logger.warning("'html4_writer' is deprecated with sphinx_rtd_theme")
else:
if app.config.html4_writer:
logger.warning("'html4_writer' is deprecated with sphinx_rtd_theme")
if sphinx.version_info >= (1, 8, 0):
# Register the theme that can be referenced without adding a theme path
app.add_html_theme('lammps_theme', path.abspath(path.dirname(__file__)))
if sphinx_version >= (1, 8, 0):
# Add Sphinx message catalog for newer versions of Sphinx
# See http://www.sphinx-doc.org/en/master/extdev/appapi.html#sphinx.application.Sphinx.add_message_catalog
rtd_locale_path = path.join(path.abspath(path.dirname(__file__)), 'locale')
app.add_message_catalog('sphinx', rtd_locale_path)
app.connect('config-inited', config_initiated)
# sphinx emits the permalink icon for headers, so choose one more in keeping with our theme
if sphinx_version >= (3, 5, 0):
app.config.html_permalinks_icon = "\uf0c1"
else:
app.config.html_add_permalinks = "\uf0c1"
return {'parallel_read_safe': True, 'parallel_write_safe': True}

115
doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html
View File

@ -1,86 +1,79 @@
{# Support for Sphinx 1.3+ page_source_suffix, but don't break old builds. #}
{%- if meta is defined and meta is not none %}
{%- set check_meta = True %}
{%- else %}
{%- set check_meta = False %}
{%- endif %}
{% if page_source_suffix %}
{% set suffix = page_source_suffix %}
{% else %}
{% set suffix = source_suffix %}
{% endif %}
{%- if check_meta and 'github_url' in meta %}
{%- set display_github = True %}
{%- endif %}
{% if meta is defined and meta is not none %}
{% set check_meta = True %}
{% else %}
{% set check_meta = False %}
{% endif %}
{%- if check_meta and 'bitbucket_url' in meta %}
{%- set display_bitbucket = True %}
{%- endif %}
{% if check_meta and 'github_url' in meta %}
{% set display_github = True %}
{% endif %}
{%- if check_meta and 'gitlab_url' in meta %}
{%- set display_gitlab = True %}
{%- endif %}
{% if check_meta and 'bitbucket_url' in meta %}
{% set display_bitbucket = True %}
{% endif %}
{% if check_meta and 'gitlab_url' in meta %}
{% set display_gitlab = True %}
{% endif %}
{% set display_vcs_links = display_vcs_links if display_vcs_links is defined else True %}
<div role="navigation" aria-label="breadcrumbs navigation">
{%- set display_vcs_links = display_vcs_links if display_vcs_links is defined else True %}
{#- Translators: This is an ARIA section label for page links, including previous/next page link and links to GitHub/GitLab/etc. -#}
<div role="navigation" aria-label="{{ _('Page navigation') }}">
<ul class="wy-breadcrumbs">
{% block breadcrumbs %}
{%- block breadcrumbs %}
<li><a href="{{ pathto(master_doc) }}" class="icon icon-home"></a> &raquo;</li>
{% for doc in parents %}
{%- for doc in parents %}
<li><a href="{{ doc.link|e }}">{{ doc.title }}</a> &raquo;</li>
{% endfor %}
{%- endfor %}
<li>{{ title }}</li>
{% endblock %}
{% block breadcrumbs_aside %}
{%- endblock %}
{%- block breadcrumbs_aside %}
<li class="wy-breadcrumbs-aside">
{% if hasdoc(pagename) and display_vcs_links %}
{% if display_github %}
{% if check_meta and 'github_url' in meta %}
{%- if hasdoc(pagename) and display_vcs_links %}
{%- if display_github %}
{%- if check_meta and 'github_url' in meta %}
<!-- User defined GitHub URL -->
<a href="{{ meta['github_url'] }}" class="fa fa-github"> {{ _('Edit on GitHub') }}</a>
{% else %}
<a href="https://{{ github_host|default("github.com") }}/{{ github_user }}/{{ github_repo }}/{{ theme_vcs_pageview_mode|default("blob") }}/{{ github_version }}{{ conf_py_path }}{{ pagename }}{{ suffix }}" class="fa fa-github"> {{ _('Edit on GitHub') }}</a>
{% endif %}
{% elif display_bitbucket %}
{% if check_meta and 'bitbucket_url' in meta %}
{%- else %}
<a href="https://{{ github_host|default("github.com") }}/{{ github_user }}/{{ github_repo }}/{{ theme_vcs_pageview_mode or "blob" }}/{{ github_version }}{{ conf_py_path }}{{ pagename }}{{ page_source_suffix }}" class="fa fa-github"> {{ _('Edit on GitHub') }}</a>
{%- endif %}
{%- elif display_bitbucket %}
{%- if check_meta and 'bitbucket_url' in meta %}
<!-- User defined Bitbucket URL -->
<a href="{{ meta['bitbucket_url'] }}" class="fa fa-bitbucket"> {{ _('Edit on Bitbucket') }}</a>
{% else %}
<a href="https://bitbucket.org/{{ bitbucket_user }}/{{ bitbucket_repo }}/src/{{ bitbucket_version}}{{ conf_py_path }}{{ pagename }}{{ suffix }}?mode={{ theme_vcs_pageview_mode|default("view") }}" class="fa fa-bitbucket"> {{ _('Edit on Bitbucket') }}</a>
{% endif %}
{% elif display_gitlab %}
{% if check_meta and 'gitlab_url' in meta %}
{%- else %}
<a href="https://bitbucket.org/{{ bitbucket_user }}/{{ bitbucket_repo }}/src/{{ bitbucket_version}}{{ conf_py_path }}{{ pagename }}{{ page_source_suffix }}?mode={{ theme_vcs_pageview_mode or "view" }}" class="fa fa-bitbucket"> {{ _('Edit on Bitbucket') }}</a>
{%- endif %}
{%- elif display_gitlab %}
{%- if check_meta and 'gitlab_url' in meta %}
<!-- User defined GitLab URL -->
<a href="{{ meta['gitlab_url'] }}" class="fa fa-gitlab"> {{ _('Edit on GitLab') }}</a>
{% else %}
<a href="https://{{ gitlab_host|default("gitlab.com") }}/{{ gitlab_user }}/{{ gitlab_repo }}/{{ theme_vcs_pageview_mode|default("blob") }}/{{ gitlab_version }}{{ conf_py_path }}{{ pagename }}{{ suffix }}" class="fa fa-gitlab"> {{ _('Edit on GitLab') }}</a>
{% endif %}
{% elif show_source and source_url_prefix %}
<a href="{{ source_url_prefix }}{{ pagename }}{{ suffix }}">{{ _('View page source') }}</a>
{% elif show_source and has_source and sourcename %}
{%- else %}
<a href="https://{{ gitlab_host|default("gitlab.com") }}/{{ gitlab_user }}/{{ gitlab_repo }}/{{ theme_vcs_pageview_mode or "blob" }}/{{ gitlab_version }}{{ conf_py_path }}{{ pagename }}{{ page_source_suffix }}" class="fa fa-gitlab"> {{ _('Edit on GitLab') }}</a>
{%- endif %}
{%- elif show_source and source_url_prefix %}
<a href="{{ source_url_prefix }}{{ pagename }}{{ page_source_suffix }}">{{ _('View page source') }}</a>
{%- elif show_source and has_source and sourcename %}
<a href="{{ pathto('_sources/' + sourcename, true)|e }}" rel="nofollow"> {{ _('View page source') }}</a>
{% endif %}
{%- endif %}
<a href="https://www.lammps.org">Website</a>
<a href="Commands_all.html">Commands</a>
{% endif %}
{%- endif %}
</li>
{% endblock %}
{%- endblock %}
</ul>
{% if (theme_prev_next_buttons_location == 'top' or theme_prev_next_buttons_location == 'both') and (next or prev) %}
<div class="rst-breadcrumbs-buttons" role="navigation" aria-label="breadcrumb navigation">
{% if next %}
<a href="{{ next.link|e }}" class="btn btn-neutral float-right" title="{{ next.title|striptags|e }}" accesskey="n">{{ _('Next') }} <span class="fa fa-arrow-circle-right"></span></a>
{% endif %}
{% if prev %}
<a href="{{ prev.link|e }}" class="btn btn-neutral float-left" title="{{ prev.title|striptags|e }}" accesskey="p"><span class="fa fa-arrow-circle-left"></span> {{ _('Previous') }}</a>
{% endif %}
{%- if (theme_prev_next_buttons_location == 'top' or theme_prev_next_buttons_location == 'both') and (next or prev) %}
{#- Translators: This is an ARIA section label for sequential page links, such as previous and next page links. -#}
<div class="rst-breadcrumbs-buttons" role="navigation" aria-label="{{ _('Sequential page navigation') }}">
{%- if prev %}
<a href="{{ prev.link|e }}" class="btn btn-neutral float-left" title="{{ prev.title|striptags|e }}" accesskey="p"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> {{ _('Previous') }}</a>
{%- endif %}
{%- if next %}
<a href="{{ next.link|e }}" class="btn btn-neutral float-right" title="{{ next.title|striptags|e }}" accesskey="n">{{ _('Next') }} <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
{%- endif %}
</div>
{% endif %}
{%- endif %}
<hr/>
</div>

61
doc/utils/sphinx-config/_themes/lammps_theme/footer.html
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@ -1,60 +1,61 @@
<footer>
{% if (theme_prev_next_buttons_location == 'bottom' or theme_prev_next_buttons_location == 'both') and (next or prev) %}
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
{% if next %}
<a href="{{ next.link|e }}" class="btn btn-neutral float-right" title="{{ next.title|striptags|e }}" accesskey="n" rel="next">{{ _('Next') }} <span class="fa fa-arrow-circle-right"></span></a>
{% endif %}
{% if prev %}
<a href="{{ prev.link|e }}" class="btn btn-neutral float-left" title="{{ prev.title|striptags|e }}" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> {{ _('Previous') }}</a>
{% endif %}
{%- if (theme_prev_next_buttons_location == 'bottom' or theme_prev_next_buttons_location == 'both') and (next or prev) %}
{#- Translators: This is an ARIA section label for the footer section of the page. -#}
<div class="rst-footer-buttons" role="navigation" aria-label="{{ _('Footer') }}">
{%- if prev %}
<a href="{{ prev.link|e }}" class="btn btn-neutral float-left" title="{{ prev.title|striptags|e }}" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> {{ _('Previous') }}</a>
{%- endif %}
{%- if next %}
<a href="{{ next.link|e }}" class="btn btn-neutral float-right" title="{{ next.title|striptags|e }}" accesskey="n" rel="next">{{ _('Next') }} <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
{%- endif %}
</div>
{% endif %}
{%- endif %}
<hr/>
<div role="contentinfo">
{%- block contentinfo %}
<p>
{%- if show_copyright %}
{%- if hasdoc('copyright') %}
{% set path = pathto('copyright') %}
{% set copyright = copyright|e %}
&copy; <a href="{{ path }}">{% trans %}Copyright{% endtrans %}</a> {{ copyright }}
{%- trans path=pathto('copyright'), copyright=copyright|e %}&#169; <a href="{{ path }}">Copyright</a> {{ copyright }}.{% endtrans %}
{%- else %}
{% set copyright = copyright|e %}
&copy; {% trans %}Copyright{% endtrans %} {{ copyright }}
{%- trans copyright=copyright|e %}&#169; Copyright {{ copyright }}.{% endtrans %}
{%- endif %}
{%- endif %}
{%- if build_id and build_url %}
<span class="build">
{# Translators: Build is a noun, not a verb #}
{% trans %}Build{% endtrans %}
{#- Translators: Build is a noun, not a verb -#}
{%- trans %}Build{% endtrans -%}
<a href="{{ build_url }}">{{ build_id }}</a>.
</span>
{%- elif commit %}
<span class="commit">
{# Translators: the phrase "revision" comes from Git, referring to a commit #}
{% trans %}Revision{% endtrans %} <code>{{ commit }}</code>.
</span>
{%- elif last_updated %}
<span class="lastupdated">
{% trans last_updated=last_updated|e %}Last updated on {{ last_updated }}.{% endtrans %}
{#- Translators: the phrase "revision" comes from Git, referring to a commit #}
{%- trans %}Revision{% endtrans %} <code>{{ commit }}</code>.
</span>
{%- endif %}
{%- if last_updated %}
<span class="lastupdated">
{%- trans last_updated=last_updated|e %}Last updated on {{ last_updated }}.{% endtrans %}
</span>
{%- endif -%}
</p>
{%- endblock %}
</div>
{%- if show_sphinx %}
{% set sphinx_web = '<a href="https://www.sphinx-doc.org/">Sphinx</a>' %}
{% set readthedocs_web = '<a href="https://readthedocs.org">Read the Docs</a>' %}
{# Translators: the variable "sphinx_web" is a link to the Sphinx project documentation with the text "Sphinx" #}
{% trans sphinx_web=sphinx_web, readthedocs_web=readthedocs_web %}Built with {{ sphinx_web }} using a{% endtrans %}
{# Translators: "theme" refers to a theme for Sphinx, which alters the appearance of the generated documenation #}
{% if show_sphinx %}
{%- set sphinx_web = '<a href="https://www.sphinx-doc.org/">Sphinx</a>' %}
{%- set readthedocs_web = '<a href="https://readthedocs.org">Read the Docs</a>' %}
{#- Translators: the variable "sphinx_web" is a link to the Sphinx project documentation with the text "Sphinx" #}
{%- trans sphinx_web=sphinx_web, readthedocs_web=readthedocs_web %}Built with {{ sphinx_web }} using a{% endtrans %}
{#- Translators: "theme" refers to a theme for Sphinx, which alters the appearance of the generated documenation #}
<a href="https://github.com/readthedocs/sphinx_rtd_theme">{% trans %}theme{% endtrans %}</a>
{# Translators: this is always used as "provided by Read the Docs", and should not imply Read the Docs is an author of the generated documentation. #}
{#- Translators: this is always used as "provided by Read the Docs", and should not imply Read the Docs is an author of the generated documentation. #}
{% trans %}provided by {{ readthedocs_web }}{% endtrans %}.
{%- endif %}
{% endif %}
{%- block extrafooter %} {% endblock %}

187
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View File

@ -7,44 +7,59 @@
{%- set titlesuffix = "" %}
{%- endif %}
{%- set lang_attr = 'en' if language == None else (language | replace('_', '-')) %}
{%- set sphinx_writer = 'writer-html5' if html5_doctype else 'writer-html4' %}
{%- set sphinx_writer = 'writer-html5' if html5_doctype else 'writer-html4' -%}
{# Build sphinx_version_info tuple from sphinx_version string in pure Jinja #}
{%- set (_ver_major, _ver_minor, _ver_bugfix) = sphinx_version.split('.') | map('int') -%}
{%- set sphinx_version_info = (_ver_major, _ver_minor, _ver_bugfix) -%}
<!DOCTYPE html>
<html class="{{ sphinx_writer }}" lang="{{ lang_attr }}" >
<head>
<meta charset="utf-8">
{{ metatags }}
<meta name="viewport" content="width=device-width, initial-scale=1.0">
{% block htmltitle %}
<meta charset="utf-8" />
{{- metatags }}
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
{%- block htmltitle %}
<title>{{ title|striptags|e }}{{ titlesuffix }}</title>
{% endblock %}
{%- endblock -%}
{# CSS #}
<link rel="stylesheet" href="{{ pathto('_static/' + style, 1) }}" type="text/css" />
<link rel="stylesheet" href="{{ pathto('_static/pygments.css', 1) }}" type="text/css" />
{#- CSS #}
{%- if sphinx_version_info < (4, 0) -%}
<link rel="stylesheet" href="{{ pathto('_static/' + style, 1) }}" type="text/css" />
<link rel="stylesheet" href="{{ pathto('_static/pygments.css', 1) }}" type="text/css" />
{%- endif %}
{%- for css in css_files %}
{%- if css|attr("rel") %}
<link rel="{{ css.rel }}" href="{{ pathto(css.filename, 1) }}" type="text/css"{% if css.title is not none %} title="{{ css.title }}"{% endif %} />
<link rel="{{ css.rel }}" href="{{ pathto(css.filename, 1) }}" type="text/css"{% if css.title is not none %} title="{{ css.title }}"{% endif %} />
{%- else %}
<link rel="stylesheet" href="{{ pathto(css, 1) }}" type="text/css" />
<link rel="stylesheet" href="{{ pathto(css, 1) }}" type="text/css" />
{%- endif %}
{%- endfor %}
{%- for cssfile in extra_css_files %}
<link rel="stylesheet" href="{{ pathto(cssfile, 1) }}" type="text/css" />
{%- endfor %}
{%- endfor -%}
{# FAVICON #}
{% if favicon %}
{#- FAVICON #}
{%- if favicon %}
{%- if sphinx_version_info < (4, 0) -%}
<link rel="shortcut icon" href="{{ pathto('_static/' + favicon, 1) }}"/>
{% endif %}
{%- else %}
<link rel="shortcut icon" href="{{ favicon_url }}"/>
{%- endif %}
{%- endif -%}
{#- CANONICAL URL (deprecated) #}
{%- if theme_canonical_url and not pageurl %}
<link rel="canonical" href="{{ theme_canonical_url }}{{ pagename }}.html"/>
{%- endif -%}
{#- CANONICAL URL #}
{%- if pageurl %}
<link rel="canonical" href="{{ pageurl|e }}" />
{%- endif -%}
{# JAVASCRIPTS #}
{#- JAVASCRIPTS #}
{%- block scripts %}
<!--[if lt IE 9]>
<script src="{{ pathto('_static/js/html5shiv.min.js', 1) }}"></script>
@ -55,13 +70,15 @@
{%- if not embedded %}
{# XXX Sphinx 1.8.0 made this an external js-file, quick fix until we refactor the template to inherert more blocks directly from sphinx #}
{% if sphinx_version >= "1.8.0" %}
<script type="text/javascript" id="documentation_options" data-url_root="{{ pathto('', 1) }}" src="{{ pathto('_static/documentation_options.js', 1) }}"></script>
{%- if sphinx_version_info >= (1, 8) -%}
{%- if sphinx_version_info < (4, 0) -%}
<script id="documentation_options" data-url_root="{{ url_root }}" src="{{ pathto('_static/documentation_options.js', 1) }}"></script>
{%- endif -%}
{%- for scriptfile in script_files %}
{{ js_tag(scriptfile) }}
{%- endfor %}
{% else %}
<script type="text/javascript">
{%- else %}
<script>
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'{{ url_root }}',
VERSION:'{{ release|e }}',
@ -73,12 +90,12 @@
};
</script>
{%- for scriptfile in script_files %}
<script type="text/javascript" src="{{ pathto(scriptfile, 1) }}"></script>
<script src="{{ pathto(scriptfile, 1) }}"></script>
{%- endfor %}
{% endif %}
<script type="text/javascript" src="{{ pathto('_static/js/theme.js', 1) }}"></script>
{%- endif %}
<script src="{{ pathto('_static/js/theme.js', 1) }}"></script>
{# OPENSEARCH #}
{#- OPENSEARCH #}
{%- if use_opensearch %}
<link rel="search" type="application/opensearchdescription+xml"
title="{% trans docstitle=docstitle|e %}Search within {{ docstitle }}{% endtrans %}"
@ -112,126 +129,124 @@
<body class="wy-body-for-nav">
{% block extrabody %} {% endblock %}
{%- block extrabody %} {% endblock %}
<div class="wy-grid-for-nav">
{# SIDE NAV, TOGGLES ON MOBILE #}
{#- SIDE NAV, TOGGLES ON MOBILE #}
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" {% if theme_style_nav_header_background %} style="background: {{theme_style_nav_header_background}}" {% endif %}>
{% block sidebartitle %}
{%- block sidebartitle %}
{% if logo and theme_logo_only %}
{%- if logo and theme_logo_only %}
<a href="{{ pathto(master_doc) }}">
{% else %}
{%- else %}
<a href="{{ pathto(master_doc) }}" class="icon icon-home"> {{ project }}
{% endif %}
{%- endif %}
{% if logo %}
{# Not strictly valid HTML, but it's the only way to display/scale
it properly, without weird scripting or heaps of work
{%- if logo %}
{#- Not strictly valid HTML, but it's the only way to display/scale
it properly, without weird scripting or heaps of work
#}
{%- if sphinx_version_info < (4, 0) -%}
<img src="{{ pathto('_static/' + logo, 1) }}" class="logo" alt="{{ _('Logo') }}"/>
{% endif %}
{%- else %}
<img src="{{ logo_url }}" class="logo" alt="{{ _('Logo') }}"/>
{%- endif %}
{%- endif %}
</a>
{% if theme_display_version %}
{%- if theme_display_version %}
<div class="lammps_version">Version: <b>{{ current_version }}</b></div>
<div class="lammps_release">git info: {{ release }}</div>
{% endif %}
{%- endif %}
{% include "searchbox.html" %}
{%- include "searchbox.html" %}
{% endblock %}
{%- endblock %}
</div>
{% block navigation %}
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
{% block menu %}
{#
The singlehtml builder doesn't handle this toctree call when the
toctree is empty. Skip building this for now.
#}
{% if 'singlehtml' not in builder %}
{% set global_toc = toctree(maxdepth=theme_navigation_depth|int,
collapse=theme_collapse_navigation|tobool,
includehidden=theme_includehidden|tobool,
titles_only=theme_titles_only|tobool) %}
{% endif %}
{% if global_toc %}
{{ global_toc }}
{% else %}
{%- block navigation %}
{#- Translators: This is an ARIA section label for the main navigation menu -#}
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="{{ _('Navigation menu') }}">
{%- block menu %}
{%- set toctree = toctree(maxdepth=theme_navigation_depth|int,
collapse=theme_collapse_navigation|tobool,
includehidden=theme_includehidden|tobool,
titles_only=theme_titles_only|tobool) %}
{%- if toctree %}
{{ toctree }}
{%- else %}
<!-- Local TOC -->
<div class="local-toc">{{ toc }}</div>
{% endif %}
{% endblock %}
{%- endif %}
{%- endblock %}
</div>
{% endblock %}
{%- endblock %}
</div>
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
{# MOBILE NAV, TRIGGLES SIDE NAV ON TOGGLE #}
<nav class="wy-nav-top" aria-label="top navigation">
{% block mobile_nav %}
{#- MOBILE NAV, TRIGGLES SIDE NAV ON TOGGLE #}
{#- Translators: This is an ARIA section label for the navigation menu that is visible when viewing the page on mobile devices -#}
<nav class="wy-nav-top" aria-label="{{ _('Mobile navigation menu') }}" {% if theme_style_nav_header_background %} style="background: {{theme_style_nav_header_background}}" {% endif %}>
{%- block mobile_nav %}
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="{{ pathto(master_doc) }}">{{ project }}</a>
{% endblock %}
{%- endblock %}
</nav>
<div class="wy-nav-content">
{%- block content %}
{% if theme_style_external_links|tobool %}
{%- if theme_style_external_links|tobool %}
<div class="rst-content style-external-links">
{% else %}
{%- else %}
<div class="rst-content">
{% endif %}
{%- endif %}
{% include "breadcrumbs.html" %}
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
{%- block document %}
<div itemprop="articleBody">
{% block body %}{% endblock %}
{% block body %}{% endblock %}
</div>
{% if self.comments()|trim %}
<div class="articleComments">
{% block comments %}{% endblock %}
</div>
{% endif%}
{%- if self.comments()|trim %}
<div class="articleComments">
{%- block comments %}{% endblock %}
</div>
{%- endif%}
</div>
{%- endblock %}
{% include "footer.html" %}
</div>
{%- endblock %}
</div>
</section>
</div>
{% include "versions.html" %}
{% include "versions.html" -%}
<script type="text/javascript">
<script>
jQuery(function () {
SphinxRtdTheme.Navigation.enable({{ 'true' if theme_sticky_navigation|tobool else 'false' }});
});
</script>
{# Do not conflict with RTD insertion of analytics script #}
{% if not READTHEDOCS %}
{% if theme_analytics_id %}
{#- Do not conflict with RTD insertion of analytics script #}
{%- if not READTHEDOCS %}
{%- if theme_analytics_id %}
<!-- Theme Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id={{ theme_analytics_id }}"></script>
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
ga('create', '{{ theme_analytics_id }}', 'auto');
ga('send', 'pageview');
gtag('config', '{{ theme_analytics_id }}', {
'anonymize_ip': {{ 'true' if theme_analytics_anonymize_ip|tobool else 'false' }},
});
</script>
{% endif %}
{% endif %}
{%- endif %}
{%- endif %}
{%- block footer %} {% endblock %}

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57
doc/utils/sphinx-config/_themes/lammps_theme/locale/de/LC_MESSAGES/sphinx.po
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@ -11,7 +11,7 @@ msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Tom Kunze <transifex.com@tomabrafix.de>, 2019\n"
"Language-Team: German (https://www.transifex.com/readthedocs/teams/101354/de/)\n"
@ -22,37 +22,32 @@ msgstr ""
"Language: de\n"
"Plural-Forms: nplurals=2; plural=(n != 1);\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Auf GitHub bearbeiten"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Auf Bitbucket bearbeiten"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Auf GitLab bearbeiten"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Quelltext anzeigen"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "Weiter"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Zurück"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "Copyright"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Weiter"
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Build"
@ -64,49 +59,53 @@ msgstr "Zuletzt aktualisiert am %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Erstellt mit %(sphinx_web)s mit einem"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "bereitgestellt von %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "%(docstitle)s durchsuchen"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Über diese Dokumentation"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Index"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Suche"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Copyright"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#: sphinx_rtd_theme/search.html:29
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "Bitte aktiviere JavaScript, um die Suchfunktion zu nutzen."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Suchergebnisse"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -119,7 +118,7 @@ msgstr ""
msgid "Search docs"
msgstr "Dokumentation durchsuchen"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versionen"
@ -135,9 +134,3 @@ msgstr "Projektübersicht"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Builds"
#~ msgid "Docs"
#~ msgstr "Dokumentation"
#~ msgid "Free document hosting provided by"
#~ msgstr "Kostenloses Dokumentationen-Hosting zur Verfügung gestellt von"

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@ -8,7 +8,7 @@ msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 15:43-0600\n"
"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
"Language: en\n"
@ -19,42 +19,64 @@ msgstr ""
"Content-Transfer-Encoding: 8bit\n"
"Generated-By: Babel 2.8.0\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#. This is an ARIA section label for page links, including previous/next page
#. link and links to GitHub/GitLab/etc.
#: sphinx_rtd_theme/breadcrumbs.html:22
msgid "Page navigation"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
#. This is an ARIA section label for sequential page links, such as previous
#. and next page links.
#: sphinx_rtd_theme/breadcrumbs.html:67
msgid "Sequential page navigation"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr ""
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr ""
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr ""
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr ""
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr ""
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr ""
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr ""
@ -65,59 +87,70 @@ msgstr ""
#. the variable "sphinx_web" is a link to the Sphinx project documentation with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr ""
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr ""
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr ""
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr ""
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr ""
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr ""
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr ""
#: sphinx_rtd_theme/layout.html:121
msgid "Documentation Home"
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr ""
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr ""
#: sphinx_rtd_theme/search.html:29
#. This is an ARIA section label for the main navigation menu
#: sphinx_rtd_theme/layout.html:173
msgid "Navigation menu"
msgstr ""
#. This is an ARIA section label for the navigation menu that is visible when
#. viewing the page on mobile devices
#: sphinx_rtd_theme/layout.html:195
msgid "Mobile navigation menu"
msgstr ""
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr ""
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr ""
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words "
"are spelled correctly and that you've selected enough categories."
@ -127,7 +160,7 @@ msgstr ""
msgid "Search docs"
msgstr ""
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr ""
@ -154,3 +187,15 @@ msgstr ""
#~ msgid "Free document hosting provided by"
#~ msgstr ""
#~ msgid "Documentation Home"
#~ msgstr ""
#~ msgid "Breadcrumbs"
#~ msgstr ""
#~ msgid "Main"
#~ msgstr ""
#~ msgid "Top"
#~ msgstr ""

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@ -6,15 +6,15 @@
#
# Translators:
# Anthony <aj@ohess.org>, 2019
# Leonardo J. Caballero G. <leonardocaballero@gmail.com>, 2020
# Radina Matic <radina.matic@gmail.com>, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Leonardo J. Caballero G. <leonardocaballero@gmail.com>, 2020\n"
"Last-Translator: Radina Matic <radina.matic@gmail.com>, 2021\n"
"Language-Team: Spanish (https://www.transifex.com/readthedocs/teams/101354/es/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
@ -23,107 +23,117 @@ msgstr ""
"Language: es\n"
"Plural-Forms: nplurals=2; plural=(n != 1);\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Editar en GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Editar en Bitbucket"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Editar en GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Ver código fuente de la página"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "Siguiente"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Anterior"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "Derechos de autor"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Siguiente"
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr "Pie de página"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">Derechos de autor</a> %(copyright)s."
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; Derechos de autor %(copyright)s."
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Construido"
msgstr "Compilación"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Revisión"
#: sphinx_rtd_theme/footer.html:41
#, python-format
msgid "Last updated on %(last_updated)s."
msgstr "Actualizado por última vez en %(last_updated)s."
msgstr "Actualizado por última vez el %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Construido con %(sphinx_web)s usando un"
msgstr "Compilado con %(sphinx_web)s usando un"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "tema"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "proporcionado por %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Buscar en %(docstitle)s"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Sobre esta documentación"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Índice"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Búsqueda"
#: sphinx_rtd_theme/layout.html:121
msgid "Documentation Home"
msgstr "Inicio de Documentación"
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Derechos de autor"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logotipo"
#: sphinx_rtd_theme/search.html:29
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr ""
"Por favor, active JavaScript para habilitar la funcionalidad de búsqueda."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Resultados de la búsqueda"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -136,7 +146,7 @@ msgstr ""
msgid "Search docs"
msgstr "Buscar documentos"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versiones"
@ -155,10 +165,4 @@ msgstr "Página de Proyecto"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Construcciones"
#~ msgid "Docs"
#~ msgstr "Documentos"
#~ msgid "Free document hosting provided by"
#~ msgstr "Alojamiento gratuito de documentos proporcionado por"
msgstr "Compilaciones"

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@ -6,15 +6,15 @@
#
# Translators:
# Anthony <aj@ohess.org>, 2020
# Ivar Smolin <okul@linux.ee>, 2020
# Ivar Smolin <okul@linux.ee>, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Ivar Smolin <okul@linux.ee>, 2020\n"
"Last-Translator: Ivar Smolin <okul@linux.ee>, 2021\n"
"Language-Team: Estonian (https://www.transifex.com/readthedocs/teams/101354/et/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
@ -23,42 +23,52 @@ msgstr ""
"Language: et\n"
"Plural-Forms: nplurals=2; plural=(n != 1);\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Muuda GitHubis"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Muuda Bitbucketis"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Muuda GitLabis"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Vaata lehe lähtekoodi"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "Järgmine"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Eelmine"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "Autoriõigus"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Järgmine"
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr "Jalus"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">Autoriõigus</a> %(copyright)s."
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; Autoriõigus %(copyright)s."
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Ehitus"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Redaktsioon"
@ -70,52 +80,59 @@ msgstr "Viimati uuendatud %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Ehitatud %(sphinx_web)s'iga,"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "kujundusteema"
#: sphinx_rtd_theme/layout.html:79
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "on loonud %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Otsi dokumendist %(docstitle)s"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Nende dokumentide kirjeldused"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Indeks"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Otsing"
#: sphinx_rtd_theme/layout.html:121
msgid "Documentation Home"
msgstr "Dokumentatsiooni kodu"
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Autoriõigus"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#: sphinx_rtd_theme/search.html:29
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "Otsimisfunktsiooni lubamiseks aktiveeri palun JavaScript"
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Otsingu tulemused"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -127,7 +144,7 @@ msgstr ""
msgid "Search docs"
msgstr "Otsi dokumente"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versioonid"
@ -147,9 +164,3 @@ msgstr "Projekti kodu"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Ehitused"
#~ msgid "Docs"
#~ msgstr "Dokumendid"
#~ msgid "Free document hosting provided by"
#~ msgstr "Dokumentatsiooni majutab tasuta"

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@ -0,0 +1,160 @@
# English translations for sphinx_rtd_theme.
# Copyright (C) 2019 ORGANIZATION
# This file is distributed under the same license as the sphinx_rtd_theme
# project.
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
# Translators:
# Anthony <aj@ohess.org>, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Anthony <aj@ohess.org>, 2021\n"
"Language-Team: Persian (Iran) (https://www.transifex.com/readthedocs/teams/101354/fa_IR/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
"Content-Transfer-Encoding: 8bit\n"
"Generated-By: Babel 2.8.0\n"
"Language: fa_IR\n"
"Plural-Forms: nplurals=2; plural=(n > 1);\n"
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "ویرایش در GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "ویرایش در Bitbucket"
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "ویرایش در GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "نمایش متن منبع صفحه"
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "پیشین"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "بعدی"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">حق انتشار</a> %(copyright)s."
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; حق انتشار%(copyright)s."
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "ساخت"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "بازبینی"
#: sphinx_rtd_theme/footer.html:41
#, python-format
msgid "Last updated on %(last_updated)s."
msgstr "آخرین بروز رسانی در %(last_updated)s ."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "ساخته شده با %(sphinx_web)s"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "پوسته"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "تهیّه شده با %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "جستجو در %(docstitle)s"
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "درباره این مستندات"
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "فهرست"
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "جستجوی"
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "کپی رایت"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "آرم"
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "لطفاً جاوا اسکریپت را فعّال کنید تا قابلیّت جستجو فعّال شود."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "نتایج جستجو"
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
msgstr ""
"جستجوی شما با هیچ سندی مطابقت نداشت. لطفاً از درستی املای واژگان مطمئن شوید."
" هم‌چنین بررسی کنید آیا به اندازه کافی دسته بندی انتخاب کرده‌اید."
#: sphinx_rtd_theme/searchbox.html:4
msgid "Search docs"
msgstr "جستجوی مستندات"
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "نگارش‌ها"
#: sphinx_rtd_theme/versions.html:17
msgid "Downloads"
msgstr "بارگیری‌ها"
#. The phrase "Read the Docs" is not translated
#: sphinx_rtd_theme/versions.html:24
msgid "On Read the Docs"
msgstr "درباره‌ی خواندن مستندات"
#: sphinx_rtd_theme/versions.html:26
msgid "Project Home"
msgstr "صفحه خانگی پروژه"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "ساخت‌ها"

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@ -5,16 +5,16 @@
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
# Translators:
# Radina Matic <radina.matic@gmail.com>, 2020
# Anthony <aj@ohess.org>, 2020
# Radina Matic <radina.matic@gmail.com>, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Anthony <aj@ohess.org>, 2020\n"
"Last-Translator: Radina Matic <radina.matic@gmail.com>, 2021\n"
"Language-Team: French (https://www.transifex.com/readthedocs/teams/101354/fr/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
@ -23,42 +23,52 @@ msgstr ""
"Language: fr\n"
"Plural-Forms: nplurals=2; plural=(n > 1);\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Éditer sur GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Éditer sur Bitbucket"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Éditer sur GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Afficher la source de la page"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "Suivant"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Précédent"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "Droits d'auteur"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Suivant"
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr "Pied de page"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">Droits d'auteur</a> %(copyright)s."
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; Droits d'auteur %(copyright)s."
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Compilation"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Révision"
@ -70,55 +80,59 @@ msgstr "Dernière mise à jour le %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Compilé avec %(sphinx_web)s en utilisant un"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "thème"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "fourni par %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Rechercher dans %(docstitle)s"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "À propos de cette documentation"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Index"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Rechercher"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Droits d'auteur"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#: sphinx_rtd_theme/search.html:29
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "Activez JavaScript pour accéder à la fonction de recherche."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Résultats de la recherche"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -131,7 +145,7 @@ msgstr ""
msgid "Search docs"
msgstr "Rechercher docs"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versions"
@ -139,6 +153,11 @@ msgstr "Versions"
msgid "Downloads"
msgstr "Téléchargements"
#. The phrase "Read the Docs" is not translated
#: sphinx_rtd_theme/versions.html:24
msgid "On Read the Docs"
msgstr "À propos de Read the Docs"
#: sphinx_rtd_theme/versions.html:26
msgid "Project Home"
msgstr "Accueil du projet"
@ -146,9 +165,3 @@ msgstr "Accueil du projet"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Compilations"
#~ msgid "Docs"
#~ msgstr "Docs"
#~ msgid "Free document hosting provided by"
#~ msgstr "Hébergement gratuit de documents fourni par"

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@ -0,0 +1,190 @@
# English translations for sphinx_rtd_theme.
# Copyright (C) 2019 ORGANIZATION
# This file is distributed under the same license as the sphinx_rtd_theme
# project.
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
# Translators:
# Anthony <aj@ohess.org>, 2021
# Maurizio Paglia <mpaglia0@gmail.com>, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Maurizio Paglia <mpaglia0@gmail.com>, 2021\n"
"Language-Team: Italian (https://www.transifex.com/readthedocs/teams/101354/it/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
"Content-Transfer-Encoding: 8bit\n"
"Generated-By: Babel 2.8.0\n"
"Language: it\n"
"Plural-Forms: nplurals=2; plural=(n != 1);\n"
#. This is an ARIA section label for page links, including previous/next page
#. link and links to GitHub/GitLab/etc.
#: sphinx_rtd_theme/breadcrumbs.html:22
msgid "Page navigation"
msgstr "Naviga tra le pagine"
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Modifica su GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Modifica su Bitbucket"
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Modifica su GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Visualizza sorgente pagina"
#. This is an ARIA section label for sequential page links, such as previous
#. and next page links.
#: sphinx_rtd_theme/breadcrumbs.html:67
msgid "Sequential page navigation"
msgstr "Naviga sequenzialmente tra le pagine"
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Precedente"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Prossimo"
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr "Piè di pagina"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; Copyright %(copyright)s."
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Rev."
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Revisione"
#: sphinx_rtd_theme/footer.html:41
#, python-format
msgid "Last updated on %(last_updated)s."
msgstr "Ultimo aggiornamento il %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Realizzato con %(sphinx_web)s e il tema"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "tema"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "fornito da %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Cerca in %(docstitle)s"
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Nota sulla documentazione"
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Indice"
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Ricerca"
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Copyright"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#. This is an ARIA section label for the main navigation menu
#: sphinx_rtd_theme/layout.html:173
msgid "Navigation menu"
msgstr "Menu di navigazione"
#. This is an ARIA section label for the navigation menu that is visible when
#. viewing the page on mobile devices
#: sphinx_rtd_theme/layout.html:195
msgid "Mobile navigation menu"
msgstr "Menu navigazione dispositivi mobili"
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "Devi attivare JavaScript per attivare la funzione di ricerca."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Risultati della ricerca"
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
msgstr ""
"La tua ricerca non ha prodotto nessun risultato. Assicurati di aver scritto "
"correttamente tutti i termini cercati e di aver selezionato sufficienti "
"categorie."
#: sphinx_rtd_theme/searchbox.html:4
msgid "Search docs"
msgstr "Cerca documenti"
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versioni"
#: sphinx_rtd_theme/versions.html:17
msgid "Downloads"
msgstr "Downloads"
#. The phrase "Read the Docs" is not translated
#: sphinx_rtd_theme/versions.html:24
msgid "On Read the Docs"
msgstr "Riguardo Read the Docs"
#: sphinx_rtd_theme/versions.html:26
msgid "Project Home"
msgstr "Home progetto"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Rev."

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@ -0,0 +1,188 @@
# English translations for sphinx_rtd_theme.
# Copyright (C) 2019 ORGANIZATION
# This file is distributed under the same license as the sphinx_rtd_theme
# project.
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
# Translators:
# Tomas Straupis, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Tomas Straupis, 2021\n"
"Language-Team: Lithuanian (https://www.transifex.com/readthedocs/teams/101354/lt/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
"Content-Transfer-Encoding: 8bit\n"
"Generated-By: Babel 2.8.0\n"
"Language: lt\n"
"Plural-Forms: nplurals=4; plural=(n % 10 == 1 && (n % 100 > 19 || n % 100 < 11) ? 0 : (n % 10 >= 2 && n % 10 <=9) && (n % 100 > 19 || n % 100 < 11) ? 1 : n % 1 != 0 ? 2: 3);\n"
#. This is an ARIA section label for page links, including previous/next page
#. link and links to GitHub/GitLab/etc.
#: sphinx_rtd_theme/breadcrumbs.html:22
msgid "Page navigation"
msgstr "Puslapių navigacija"
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Keisti GitHub'e"
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Keisti Bitbucket'e"
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Keisti GitLab'e"
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Žiūrėti puslapio šaltinį"
#. This is an ARIA section label for sequential page links, such as previous
#. and next page links.
#: sphinx_rtd_theme/breadcrumbs.html:67
msgid "Sequential page navigation"
msgstr "Puslapių navigacija iš eilės"
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Ankstesnis"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Kitas"
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr "Poraštė"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; Copyright %(copyright)s."
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Surinkimas"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Versija"
#: sphinx_rtd_theme/footer.html:41
#, python-format
msgid "Last updated on %(last_updated)s."
msgstr "Atnaujinta %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Surinkta su %(sphinx_web)s naudojant"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "temą"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "pateiktą %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Ieškoti %(docstitle)s"
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Apie šiuos dokumentus"
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Indeksas"
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Paieška"
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Autorių teisės"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#. This is an ARIA section label for the main navigation menu
#: sphinx_rtd_theme/layout.html:173
msgid "Navigation menu"
msgstr "Navigacijos meniu"
#. This is an ARIA section label for the navigation menu that is visible when
#. viewing the page on mobile devices
#: sphinx_rtd_theme/layout.html:195
msgid "Mobile navigation menu"
msgstr "Mobilios navigacijos meniu"
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "Prašome įjungti JavaScript, kad veiktų paieškos funkcionalumas."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Paieškos rezultatai"
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
msgstr ""
"Jūsų paieškai neatitiko nei vienas dokumentas. Prašome įsitikinti, kad visi "
"žodžiai parašyti teisingai ir kad parinkote pakankamai kategorijų."
#: sphinx_rtd_theme/searchbox.html:4
msgid "Search docs"
msgstr "Ieškoti dokumentuose"
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versijos"
#: sphinx_rtd_theme/versions.html:17
msgid "Downloads"
msgstr "Atsisiuntimai"
#. The phrase "Read the Docs" is not translated
#: sphinx_rtd_theme/versions.html:24
msgid "On Read the Docs"
msgstr "Apie Read the Docs"
#: sphinx_rtd_theme/versions.html:26
msgid "Project Home"
msgstr "Projekto namai"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Surinkimai"

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@ -5,15 +5,15 @@
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
# Translators:
# Jesse Tan, 2019
# Jesse Tan, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Jesse Tan, 2019\n"
"Last-Translator: Jesse Tan, 2021\n"
"Language-Team: Dutch (https://www.transifex.com/readthedocs/teams/101354/nl/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
@ -22,42 +22,64 @@ msgstr ""
"Language: nl\n"
"Plural-Forms: nplurals=2; plural=(n != 1);\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#. This is an ARIA section label for page links, including previous/next page
#. link and links to GitHub/GitLab/etc.
#: sphinx_rtd_theme/breadcrumbs.html:22
msgid "Page navigation"
msgstr "Paginanavigatie"
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Bewerk op GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Bewerk op BitBucket"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Bewerk op GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Bekijk paginabron"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "Volgende"
#. This is an ARIA section label for sequential page links, such as previous
#. and next page links.
#: sphinx_rtd_theme/breadcrumbs.html:67
msgid "Sequential page navigation"
msgstr "Navigatie voor gerelateerde pagina's"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Vorige"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "Copyright"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Volgende"
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr "Voettekst"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; Copyright %(copyright)s."
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Bouwresultaat"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Revisie"
@ -69,55 +91,70 @@ msgstr "Laatste update op %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Gebouwd met %(sphinx_web)s met een"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "thema"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "geleverd door %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Zoek binnen %(docstitle)s"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Over deze documenten"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Index"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Zoek"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Copyright"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#: sphinx_rtd_theme/search.html:29
#. This is an ARIA section label for the main navigation menu
#: sphinx_rtd_theme/layout.html:173
msgid "Navigation menu"
msgstr "Navigatiemenu"
#. This is an ARIA section label for the navigation menu that is visible when
#. viewing the page on mobile devices
#: sphinx_rtd_theme/layout.html:195
msgid "Mobile navigation menu"
msgstr "Navigatiemenu voor mobiel"
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "Zet JavaScript aan om de zoekfunctie mogelijk te maken."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Zoekresultaten"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -129,7 +166,7 @@ msgstr ""
msgid "Search docs"
msgstr "Zoek in documentatie"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versies"
@ -149,9 +186,3 @@ msgstr "Project Home"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Bouwresultaten"
#~ msgid "Docs"
#~ msgstr "Documentatie"
#~ msgid "Free document hosting provided by"
#~ msgstr "Gratis hosting voor documentatie verzorgd door"

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@ -0,0 +1,137 @@
# English translations for sphinx_rtd_theme.
# Copyright (C) 2019 ORGANIZATION
# This file is distributed under the same license as the sphinx_rtd_theme
# project.
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
# Translators:
# Michal Sniatala, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Michal Sniatala, 2021\n"
"Language-Team: Polish (https://www.transifex.com/readthedocs/teams/101354/pl/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
"Content-Transfer-Encoding: 8bit\n"
"Generated-By: Babel 2.8.0\n"
"Language: pl\n"
"Plural-Forms: nplurals=4; plural=(n==1 ? 0 : (n%10>=2 && n%10<=4) && (n%100<12 || n%100>14) ? 1 : n!=1 && (n%10>=0 && n%10<=1) || (n%10>=5 && n%10<=9) || (n%100>=12 && n%100<=14) ? 2 : 3);\n"
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Edytuj na GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Edytuj na Bitbucket"
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Edytuj na GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Zobacz źródło strony"
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Poprzedni"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Następny"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">Prawa zastrzeżone</a> %(copyright)s."
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; Prawa zastrzeżone %(copyright)s."
#: sphinx_rtd_theme/footer.html:41
#, python-format
msgid "Last updated on %(last_updated)s."
msgstr "Ostatnia aktualizacja %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Zbudowano w %(sphinx_web)s używając"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "dostarczone przez %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Szukaj w %(docstitle)s"
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "O tych dokumentach"
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Indeks"
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Szukaj"
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Prawa zastrzeżone"
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr ""
"Proszę aktywować obsługę JavaScript, aby włączyć funkcję wyszukiwania."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Wyniki wyszukiwania"
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
msgstr ""
"Nie znaleziono szukanej frazy. Upewnij się, że wszystkie słowa są napisane "
"poprawnie i że wybrałeś wystarczającą liczbę kategorii."
#: sphinx_rtd_theme/searchbox.html:4
msgid "Search docs"
msgstr "Szukaj"
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Wersje"
#: sphinx_rtd_theme/versions.html:17
msgid "Downloads"
msgstr "Pobrania"
#. The phrase "Read the Docs" is not translated
#: sphinx_rtd_theme/versions.html:24
msgid "On Read the Docs"
msgstr "Na Read the Docs"
#: sphinx_rtd_theme/versions.html:26
msgid "Project Home"
msgstr "Strona projektu"

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@ -0,0 +1,161 @@
# English translations for sphinx_rtd_theme.
# Copyright (C) 2019 ORGANIZATION
# This file is distributed under the same license as the sphinx_rtd_theme
# project.
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
# Translators:
# Ana Costa <anacosta.xl@gmail.com>, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Ana Costa <anacosta.xl@gmail.com>, 2021\n"
"Language-Team: Portuguese (https://www.transifex.com/readthedocs/teams/101354/pt/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
"Content-Transfer-Encoding: 8bit\n"
"Generated-By: Babel 2.8.0\n"
"Language: pt\n"
"Plural-Forms: nplurals=2; plural=(n != 1);\n"
#. This is an ARIA section label for page links, including previous/next page
#. link and links to GitHub/GitLab/etc.
#: sphinx_rtd_theme/breadcrumbs.html:22
msgid "Page navigation"
msgstr "Navegação da página"
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Editar no GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Editar no Bitbucket"
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Editar no GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Ver código-fonte da página"
#. This is an ARIA section label for sequential page links, such as previous
#. and next page links.
#: sphinx_rtd_theme/breadcrumbs.html:67
msgid "Sequential page navigation"
msgstr "Navegação sequencial da página"
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Anterior"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Seguinte"
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr "Rodapé"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Revisão"
#: sphinx_rtd_theme/footer.html:41
#, python-format
msgid "Last updated on %(last_updated)s."
msgstr "Última actualização em %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Compilado com %(sphinx_web)s usando um"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "tema"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "fornecido por %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Procurar em %(docstitle)s"
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Sobre estes documentos"
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Índice"
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Pesquisar"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#. This is an ARIA section label for the main navigation menu
#: sphinx_rtd_theme/layout.html:173
msgid "Navigation menu"
msgstr "Menu de navegação"
#. This is an ARIA section label for the navigation menu that is visible when
#. viewing the page on mobile devices
#: sphinx_rtd_theme/layout.html:195
msgid "Mobile navigation menu"
msgstr "Menu de navegação móvel"
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "Por favor, active o JavaScript para permitir a função de pesquisa."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Resultados de Pesquisa"
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
msgstr ""
"A sua pesquisa não encontrou nenhum documento. Por favor confirme que todas "
"as palavras estão bem escritas e que selecionou categorias suficientes."
#: sphinx_rtd_theme/searchbox.html:4
msgid "Search docs"
msgstr "Pesquisar docs"
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versões"
#: sphinx_rtd_theme/versions.html:17
msgid "Downloads"
msgstr "Transferências"
#. The phrase "Read the Docs" is not translated
#: sphinx_rtd_theme/versions.html:24
msgid "On Read the Docs"
msgstr "No Read the Docs"

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@ -5,15 +5,16 @@
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
# Translators:
# Rafael Fontenelle <rffontenelle@gmail.com>, 2020
# Rafael Fontenelle <rffontenelle@gmail.com>, 2021
# Wellington Uemura <wellingtonuemura@gmail.com>, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Rafael Fontenelle <rffontenelle@gmail.com>, 2020\n"
"Last-Translator: Wellington Uemura <wellingtonuemura@gmail.com>, 2021\n"
"Language-Team: Portuguese (Brazil) (https://www.transifex.com/readthedocs/teams/101354/pt_BR/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
@ -22,42 +23,64 @@ msgstr ""
"Language: pt_BR\n"
"Plural-Forms: nplurals=2; plural=(n > 1);\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#. This is an ARIA section label for page links, including previous/next page
#. link and links to GitHub/GitLab/etc.
#: sphinx_rtd_theme/breadcrumbs.html:22
msgid "Page navigation"
msgstr "Navegação da página"
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Editar no GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Editar no Bitbucket"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Editar no GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Ver código-fonte da página"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "Próximo"
#. This is an ARIA section label for sequential page links, such as previous
#. and next page links.
#: sphinx_rtd_theme/breadcrumbs.html:67
msgid "Sequential page navigation"
msgstr "Navegação sequencial da página"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Anterior"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "Copyright"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Próximo"
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr "Rodapé"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">Direitos autorais</a> %(copyright)s."
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; Direitos autorais %(copyright)s."
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Compilação"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Revisão"
@ -69,56 +92,71 @@ msgstr "Última atualização em %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Compilado com %(sphinx_web)s usando um"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "tema"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "fornecido por %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Pesquisar em %(docstitle)s"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Sobre esses documentos"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Índice"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Pesquisar"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Copyright"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#: sphinx_rtd_theme/search.html:29
#. This is an ARIA section label for the main navigation menu
#: sphinx_rtd_theme/layout.html:173
msgid "Navigation menu"
msgstr "Menu de navegação"
#. This is an ARIA section label for the navigation menu that is visible when
#. viewing the page on mobile devices
#: sphinx_rtd_theme/layout.html:195
msgid "Mobile navigation menu"
msgstr "Menu de navegação móvel"
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr ""
"Por favor, ative JavaScript para habilitar a funcionalidade de pesquisa."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Resultados da pesquisa"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -131,7 +169,7 @@ msgstr ""
msgid "Search docs"
msgstr "Pesquisar documentos"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versões"
@ -151,9 +189,3 @@ msgstr "Página inicial"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Compilações"
#~ msgid "Docs"
#~ msgstr "Docs"
#~ msgid "Free document hosting provided by"
#~ msgstr "Hospedagem de documentos livres fornecida por"

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@ -5,16 +5,16 @@
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
# Translators:
# Dmitry Shachnev <mitya57@gmail.com>, 2019
# lvv83 <vlozhkin83@gmail.com>, 2019
# Dmitry Shachnev <mitya57@gmail.com>, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: lvv83 <vlozhkin83@gmail.com>, 2019\n"
"Last-Translator: Dmitry Shachnev <mitya57@gmail.com>, 2021\n"
"Language-Team: Russian (https://www.transifex.com/readthedocs/teams/101354/ru/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
@ -23,42 +23,64 @@ msgstr ""
"Language: ru\n"
"Plural-Forms: nplurals=4; plural=(n%10==1 && n%100!=11 ? 0 : n%10>=2 && n%10<=4 && (n%100<12 || n%100>14) ? 1 : n%10==0 || (n%10>=5 && n%10<=9) || (n%100>=11 && n%100<=14)? 2 : 3);\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#. This is an ARIA section label for page links, including previous/next page
#. link and links to GitHub/GitLab/etc.
#: sphinx_rtd_theme/breadcrumbs.html:22
msgid "Page navigation"
msgstr "Навигация по страницам"
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Редактировать на GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Редактировать на BitBucket"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Редактировать на GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Просмотреть исходный код страницы"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "Следующая"
#. This is an ARIA section label for sequential page links, such as previous
#. and next page links.
#: sphinx_rtd_theme/breadcrumbs.html:67
msgid "Sequential page navigation"
msgstr "Навигация по соседним страницам"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Предыдущая"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "Авторские права"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Следующая"
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr "Нижняя область"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">Авторские права</a> %(copyright)s. "
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; Авторские права %(copyright)s. "
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Сборка"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Ревизия"
@ -70,55 +92,70 @@ msgstr "Последний раз обновлено %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Собрано при помощи %(sphinx_web)s с использованием"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "темы,"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "предоставленной %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Поиск в %(docstitle)s"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Об этих документах"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Алфавитный указатель"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Поиск"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Авторские права"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Логотип"
#: sphinx_rtd_theme/search.html:29
#. This is an ARIA section label for the main navigation menu
#: sphinx_rtd_theme/layout.html:173
msgid "Navigation menu"
msgstr "Меню навигации"
#. This is an ARIA section label for the navigation menu that is visible when
#. viewing the page on mobile devices
#: sphinx_rtd_theme/layout.html:195
msgid "Mobile navigation menu"
msgstr "Меню навигации для мобильных устройств"
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "Активируйте JavaScript, чтобы использовать функционал поиска."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Результаты поиска"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -130,7 +167,7 @@ msgstr ""
msgid "Search docs"
msgstr "Поиск в документации"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Версии"
@ -150,9 +187,3 @@ msgstr "Домашняя страница проекта"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Сборки"
#~ msgid "Docs"
#~ msgstr "Документация"
#~ msgid "Free document hosting provided by"
#~ msgstr "Бесплатный хостинг документов, предоставленный"

93
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@ -1,15 +1,15 @@
# Translations template for sphinx_rtd_theme.
# Copyright (C) 2020 ORGANIZATION
# Copyright (C) 2021 ORGANIZATION
# This file is distributed under the same license as the sphinx_rtd_theme
# project.
# FIRST AUTHOR <EMAIL@ADDRESS>, 2020.
# FIRST AUTHOR <EMAIL@ADDRESS>, 2021.
#
#, fuzzy
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Project-Id-Version: sphinx_rtd_theme 1.0.0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
"Language-Team: LANGUAGE <LL@li.org>\n"
@ -18,42 +18,64 @@ msgstr ""
"Content-Transfer-Encoding: 8bit\n"
"Generated-By: Babel 2.8.0\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#. This is an ARIA section label for page links, including previous/next page
#. link and links to GitHub/GitLab/etc.
#: sphinx_rtd_theme/breadcrumbs.html:22
msgid "Page navigation"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
#. This is an ARIA section label for sequential page links, such as previous
#. and next page links.
#: sphinx_rtd_theme/breadcrumbs.html:67
msgid "Sequential page navigation"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr ""
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr ""
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr ""
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr ""
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr ""
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr ""
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr ""
@ -64,59 +86,70 @@ msgstr ""
#. the variable "sphinx_web" is a link to the Sphinx project documentation with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr ""
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr ""
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr ""
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr ""
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr ""
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr ""
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr ""
#: sphinx_rtd_theme/layout.html:121
msgid "Documentation Home"
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr ""
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr ""
#: sphinx_rtd_theme/search.html:29
#. This is an ARIA section label for the main navigation menu
#: sphinx_rtd_theme/layout.html:173
msgid "Navigation menu"
msgstr ""
#. This is an ARIA section label for the navigation menu that is visible when
#. viewing the page on mobile devices
#: sphinx_rtd_theme/layout.html:195
msgid "Mobile navigation menu"
msgstr ""
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr ""
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr ""
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words "
"are spelled correctly and that you've selected enough categories."
@ -126,7 +159,7 @@ msgstr ""
msgid "Search docs"
msgstr ""
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr ""

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@ -11,7 +11,7 @@ msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Daniel Holmberg <daniel.holmberg97@gmail.com>, 2020\n"
"Language-Team: Swedish (https://www.transifex.com/readthedocs/teams/101354/sv/)\n"
@ -22,42 +22,37 @@ msgstr ""
"Language: sv\n"
"Plural-Forms: nplurals=2; plural=(n != 1);\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Editera på GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Editera på Bitbucket"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Editera på GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Visa sidkälla"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "Nästa"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Tillbaka"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "Upphovsrätt"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Nästa"
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Bygg"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Ändra"
@ -69,60 +64,60 @@ msgstr "Senast uppdaterad %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Gjord med %(sphinx_web)s med hjälp av"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "tema"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "erhållet av %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Sök i %(docstitle)s"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Om dessa dokument"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Index"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Sök"
#: sphinx_rtd_theme/layout.html:121
msgid "Documentation Home"
msgstr "Dokumentation Hem"
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Upphovsrätt"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#: sphinx_rtd_theme/search.html:29
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr ""
"Var vänlig och aktivera JavaScript för att möjliggöra sökfunktionaliteten."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Sökresultat"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -134,7 +129,7 @@ msgstr ""
msgid "Search docs"
msgstr "Sök i dokumentationen"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versioner"
@ -151,8 +146,6 @@ msgstr "På Read the Docs"
msgid "Project Home"
msgstr "Projekt Hem"
#~ msgid "Docs"
#~ msgstr "Dokumentation"
#~ msgid "Free document hosting provided by"
#~ msgstr "Gratis dokumentations hysning erhållen av"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Versioner"

BIN
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56
doc/utils/sphinx-config/_themes/lammps_theme/locale/tr/LC_MESSAGES/sphinx.po
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@ -11,7 +11,7 @@ msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: BouRock, 2020\n"
"Language-Team: Turkish (https://www.transifex.com/readthedocs/teams/101354/tr/)\n"
@ -22,42 +22,37 @@ msgstr ""
"Language: tr\n"
"Plural-Forms: nplurals=2; plural=(n > 1);\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "GitHub'da Düzenle"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Bitbucket'ta Düzenle"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "GitLab'ta Düzenle"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Sayfa kaynağını görüntüle"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "Sonraki"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Önceki"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "Telif hakkı"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Sonraki"
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Oluşturma"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Gözden geçirme"
@ -68,49 +63,53 @@ msgstr "Son olarak %(last_updated)s tarihinde güncellendi."
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "tema"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "kullanılarak %(readthedocs_web)s tarafından sağlanmasıyla oluşturuldu"
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "%(docstitle)s içinde ara"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Bu belgeler hakkında"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Dizin"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Arama"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Telif hakkı"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#: sphinx_rtd_theme/search.html:29
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr ""
"Arama işlevselliğini etkinleştirmek için lütfen JavaScript'i etkinleştirin."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Arama Sonuçları"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -122,7 +121,7 @@ msgstr ""
msgid "Search docs"
msgstr "Belgeleri arayın"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Sürümler"
@ -142,6 +141,3 @@ msgstr "Proje Ana Sayfa"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Oluşturmalar"
#~ msgid "Free document hosting provided by"
#~ msgstr "Ücretsiz belge barındırmayı sağlayan"

BIN
doc/utils/sphinx-config/_themes/lammps_theme/locale/zh_CN/LC_MESSAGES/sphinx.mo
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64
doc/utils/sphinx-config/_themes/lammps_theme/locale/zh_CN/LC_MESSAGES/sphinx.po
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@ -12,7 +12,7 @@ msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Anthony <aj@ohess.org>, 2020\n"
"Language-Team: Chinese (China) (https://www.transifex.com/readthedocs/teams/101354/zh_CN/)\n"
@ -23,40 +23,40 @@ msgstr ""
"Language: zh_CN\n"
"Plural-Forms: nplurals=1; plural=0;\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "在 GitHub 上修改"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "在 Bitbucket 上修改"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "在 GitLab 上修改"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "查看页面源码"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "下一页"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "上一页"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "版权所有"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "下一页"
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "构建"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "修订"
#: sphinx_rtd_theme/footer.html:41
#, python-format
msgid "Last updated on %(last_updated)s."
@ -65,55 +65,59 @@ msgstr "最后更新时间 %(last_updated)s。"
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "利用 %(sphinx_web)s 构建，使用了 "
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "主题"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "由 %(readthedocs_web)s开发"
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "在 %(docstitle)s中搜索"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "关于此文档"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "索引"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "搜索"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "版权所有"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#: sphinx_rtd_theme/search.html:29
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "请启用 JavaScript 以便使用搜索功能"
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "搜索结果"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -123,7 +127,7 @@ msgstr "您的搜索没有匹配到任何文档。请确保所有单词拼写正
msgid "Search docs"
msgstr "在文档中搜索"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "版本列表"
@ -143,9 +147,3 @@ msgstr "项目首页"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "构建"
#~ msgid "Docs"
#~ msgstr "文档"
#~ msgid "Free document hosting provided by"
#~ msgstr "此文档免费托管于"

4
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2
doc/utils/sphinx-config/_themes/lammps_theme/static/js/theme.js
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2
doc/utils/sphinx-config/_themes/lammps_theme/theme.conf
View File

@ -5,6 +5,7 @@ pygments_style = default
[options]
analytics_id =
analytics_anonymize_ip = False
collapse_navigation = False
sticky_navigation = False
navigation_depth = 4
@ -15,3 +16,4 @@ display_version = True
prev_next_buttons_location = both
style_external_links = True
style_nav_header_background =
vcs_pageview_mode =

7
doc/utils/sphinx-config/false_positives.txt
View File

@ -42,6 +42,7 @@ advect
advection
advects
affine
Afrasiabian
Afshar
agilio
Agilio
@ -1929,7 +1930,9 @@ Mayoral
mbt
MBytes
mc
mcmoves
McLachlan
mcmoves
md
mdf
mdi
@ -2230,6 +2233,7 @@ Nelement
Nelements
nelems
nemd
netapp
netcdf
netstat
Nettleton
@ -2294,6 +2298,7 @@ Nmin
Nmols
nn
nnodes
npits
nO
Nocedal
nocite
@ -3323,6 +3328,7 @@ THz
Tigran
Tij
Tildesley
timeI
timespan
timestamp
timestamps
@ -3663,6 +3669,7 @@ xcm
Xcm
Xcode
xCORE
xdmf
Xeon
xflag
xhi

144
examples/PACKAGES/atc/drift_diffusion/in.convective_pulse
View File

@ -1,72 +1,72 @@
# DESCRIPTION: haynes-schockley
echo both
units metal
variable V equal 5000.0
variable n0 equal 0.085
variable dn equal 2.0*${n0}
variable dt equal 0.0005
variable s equal 10
timestep ${dt}
atom_style atomic
lattice fcc 1.0
region simRegion block -50 50 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc convective_drift_diffusion Cu_cddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 100 1 1 simRegion f p p
fix_modify AtC material all Cu
fix_modify AtC mesh create_nodeset lbc -50.0 -50.0 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 50.0 50.0 -INF INF -INF INF
# fix a temperature
fix_modify AtC initial temperature all 300.0
#fix_modify AtC initial electron_temperature all 300.0
fix_modify AtC fix electron_temperature all 300.
#fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5.0 300. 300.
fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 ${dn} ${n0}
#fix_modify AtC fix electron_density all ${n0}
# isolate system:
# diffusion: dn/dx = 0
# drift : n = 0
fix_modify AtC fix electron_density lbc ${n0}
fix_modify AtC fix electron_density rbc ${n0}
fix_modify AtC fix temperature lbc 300.0
fix_modify AtC fix temperature rbc 300.0
fix_modify AtC fix electron_temperature lbc 300.0
fix_modify AtC fix electron_temperature rbc 300.0
fix_modify AtC fix electric_potential all 0.
fix_modify AtC extrinsic electron_integration implicit
# electron velocity
fix_modify AtC initial electron_velocity x all 0.
#fix_modify AtC fix electron_velocity x all 0.
fix_modify AtC initial electron_velocity y all 0.
fix_modify AtC fix electron_velocity y all 0
fix_modify AtC initial electron_velocity z all 0.
fix_modify AtC fix electron_velocity z all 0.
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output convective_pulseFE $s text binary
thermo $s
#run 100
# free electric field and allow shielding
fix_modify AtC unfix electric_potential all
fix_modify AtC fix electric_potential lbc -$V
fix_modify AtC fix electric_potential rbc 0
fix_modify AtC source electric_potential all ${n0}
fix_modify AtC extrinsic electron_integration implicit 10
run 100
# DESCRIPTION: haynes-schockley
echo both
units metal
variable V equal 5000.0
variable n0 equal 0.085
variable dn equal 2.0*${n0}
variable dt equal 0.0005
variable s equal 10
timestep ${dt}
atom_style atomic
lattice fcc 1.0
region simRegion block -50 50 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc convective_drift_diffusion Cu_cddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 100 1 1 simRegion f p p
fix_modify AtC material all Cu
fix_modify AtC mesh create_nodeset lbc -50.0 -50.0 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 50.0 50.0 -INF INF -INF INF
# fix a temperature
fix_modify AtC initial temperature all 300.0
#fix_modify AtC initial electron_temperature all 300.0
fix_modify AtC fix electron_temperature all 300.
#fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5.0 300. 300.
fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 ${dn} ${n0}
#fix_modify AtC fix electron_density all ${n0}
# isolate system:
# diffusion: dn/dx = 0
# drift : n = 0
fix_modify AtC fix electron_density lbc ${n0}
fix_modify AtC fix electron_density rbc ${n0}
fix_modify AtC fix temperature lbc 300.0
fix_modify AtC fix temperature rbc 300.0
fix_modify AtC fix electron_temperature lbc 300.0
fix_modify AtC fix electron_temperature rbc 300.0
fix_modify AtC fix electric_potential all 0.
fix_modify AtC extrinsic electron_integration implicit
# electron velocity
fix_modify AtC initial electron_velocity x all 0.
#fix_modify AtC fix electron_velocity x all 0.
fix_modify AtC initial electron_velocity y all 0.
fix_modify AtC fix electron_velocity y all 0
fix_modify AtC initial electron_velocity z all 0.
fix_modify AtC fix electron_velocity z all 0.
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output convective_pulseFE $s text binary
thermo $s
#run 100
# free electric field and allow shielding
fix_modify AtC unfix electric_potential all
fix_modify AtC fix electric_potential lbc -$V
fix_modify AtC fix electric_potential rbc 0
fix_modify AtC source electric_potential all ${n0}
fix_modify AtC extrinsic electron_integration implicit 10
run 100

132
examples/PACKAGES/atc/drift_diffusion/in.ddm_schrodinger
View File

@ -1,66 +1,66 @@
# needs description
# DESCRIPTION: haynes-schockley
# poisson eqn for E-field: epsilon phi,xx = -e (n - p + N_D - N_A)
# w/ E = phi,x
echo both
units metal
variable dt equal 0.0000001
variable s equal 1
variable L equal 10.0
variable N equal 40
variable T equal 30000.0
variable E equal 0.5
timestep ${dt}
atom_style atomic
lattice fcc 1.0
region simRegion block 0 $L 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion-schrodinger Si_ddm_schrodinger.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create $N 1 1 simRegion f p p
variable a equal $L-0.1
variable b equal $L+0.1
fix_modify AtC mesh create_nodeset lbc -0.1 0.1 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF
# ics/bcs : density consistent with wave function
fix_modify AtC initial temperature all 300.0
fix_modify AtC fix temperature all 300.0
fix_modify AtC initial electron_temperature all $T
fix_modify AtC fix electron_temperature all $T
fix_modify AtC initial electron_density all 0.0
#fix_modify AtC fix electron_density lbc 0
#fix_modify AtC fix electron_density rbc 0
fix_modify AtC initial electric_potential all 0.0
fix_modify AtC initial electron_wavefunction all 0.0
fix_modify AtC fix electron_wavefunction lbc 0
fix_modify AtC fix electron_wavefunction rbc 0
thermo $s
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output ddm_schrodingerFE $s text
fix_modify AtC extrinsic electron_integration implicit 1
fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 1 # 100
fix_modify AtC unfix electric_potential all
# ends zero
fix_modify AtC fix electric_potential lbc 0
fix_modify AtC fix electric_potential rbc 0
run 1
# ends from gradient
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 0
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 0
run 1
# needs description
# DESCRIPTION: haynes-schockley
# poisson eqn for E-field: epsilon phi,xx = -e (n - p + N_D - N_A)
# w/ E = phi,x
echo both
units metal
variable dt equal 0.0000001
variable s equal 1
variable L equal 10.0
variable N equal 40
variable T equal 30000.0
variable E equal 0.5
timestep ${dt}
atom_style atomic
lattice fcc 1.0
region simRegion block 0 $L 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion-schrodinger Si_ddm_schrodinger.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create $N 1 1 simRegion f p p
variable a equal $L-0.1
variable b equal $L+0.1
fix_modify AtC mesh create_nodeset lbc -0.1 0.1 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF
# ics/bcs : density consistent with wave function
fix_modify AtC initial temperature all 300.0
fix_modify AtC fix temperature all 300.0
fix_modify AtC initial electron_temperature all $T
fix_modify AtC fix electron_temperature all $T
fix_modify AtC initial electron_density all 0.0
#fix_modify AtC fix electron_density lbc 0
#fix_modify AtC fix electron_density rbc 0
fix_modify AtC initial electric_potential all 0.0
fix_modify AtC initial electron_wavefunction all 0.0
fix_modify AtC fix electron_wavefunction lbc 0
fix_modify AtC fix electron_wavefunction rbc 0
thermo $s
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output ddm_schrodingerFE $s text
fix_modify AtC extrinsic electron_integration implicit 1
fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 1 # 100
fix_modify AtC unfix electric_potential all
# ends zero
fix_modify AtC fix electric_potential lbc 0
fix_modify AtC fix electric_potential rbc 0
run 1
# ends from gradient
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 0
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 0
run 1

150
examples/PACKAGES/atc/drift_diffusion/in.finite_well
View File

@ -1,75 +1,75 @@
#needs description
echo both
units metal
variable E equal 0.1
variable L equal 10.0
#variable N equal 100
variable N equal 80
variable T equal 1000
variable n0 equal 0.0001
variable dn equal 2.0*${n0}
variable dt equal 0.0000001
variable s equal 1
timestep ${dt}
atom_style atomic
lattice fcc 1.0
variable a equal 0.5*$L
region simRegion block -$a $a 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion-schrodinger SiGe_ddm_schrodinger.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create $N 1 1 simRegion f p p
variable a equal 0.2*$L+0.001
fix_modify AtC mesh create_elementset well -$a $a -INF INF -INF INF
fix_modify AtC mesh create_nodeset well -$a $a -INF INF -INF INF
fix_modify AtC material well Ge
variable b equal $a-0.002
fix_modify AtC mesh create_nodeset lbc -$a -$b -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc $b $a -INF INF -INF INF
# ics/bcs
fix_modify AtC initial temperature all 300.0
fix_modify AtC fix temperature all 300.0
#
fix_modify AtC initial electron_temperature all $T
fix_modify AtC fix electron_temperature all $T
#
fix_modify AtC initial electron_density all 0.0
#fix_modify AtC fix electron_density all -0.001
#fix_modify AtC fix electron_density well 0.002
#
fix_modify AtC initial electric_potential all 0.0
#fix_modify AtC fix electric_potential lbc 0.5
#fix_modify AtC fix electric_potential rbc 0.5
fix_modify AtC fix electric_potential lbc 0.0
fix_modify AtC fix electric_potential rbc 0.0
#
fix_modify AtC initial electron_wavefunction all 0.0
fix_modify AtC fix electron_wavefunction lbc 0.0
fix_modify AtC fix electron_wavefunction rbc 0.0
thermo $s
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output finite_wellFE $s text
fix_modify AtC extrinsic electron_integration implicit 3
fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 3 # 30
variable m equal 1*$s
# (A) no field
run $m
# (B) fixed boundary field
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 1
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 1
run $m
#needs description
echo both
units metal
variable E equal 0.1
variable L equal 10.0
#variable N equal 100
variable N equal 80
variable T equal 1000
variable n0 equal 0.0001
variable dn equal 2.0*${n0}
variable dt equal 0.0000001
variable s equal 1
timestep ${dt}
atom_style atomic
lattice fcc 1.0
variable a equal 0.5*$L
region simRegion block -$a $a 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion-schrodinger SiGe_ddm_schrodinger.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create $N 1 1 simRegion f p p
variable a equal 0.2*$L+0.001
fix_modify AtC mesh create_elementset well -$a $a -INF INF -INF INF
fix_modify AtC mesh create_nodeset well -$a $a -INF INF -INF INF
fix_modify AtC material well Ge
variable b equal $a-0.002
fix_modify AtC mesh create_nodeset lbc -$a -$b -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc $b $a -INF INF -INF INF
# ics/bcs
fix_modify AtC initial temperature all 300.0
fix_modify AtC fix temperature all 300.0
#
fix_modify AtC initial electron_temperature all $T
fix_modify AtC fix electron_temperature all $T
#
fix_modify AtC initial electron_density all 0.0
#fix_modify AtC fix electron_density all -0.001
#fix_modify AtC fix electron_density well 0.002
#
fix_modify AtC initial electric_potential all 0.0
#fix_modify AtC fix electric_potential lbc 0.5
#fix_modify AtC fix electric_potential rbc 0.5
fix_modify AtC fix electric_potential lbc 0.0
fix_modify AtC fix electric_potential rbc 0.0
#
fix_modify AtC initial electron_wavefunction all 0.0
fix_modify AtC fix electron_wavefunction lbc 0.0
fix_modify AtC fix electron_wavefunction rbc 0.0
thermo $s
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output finite_wellFE $s text
fix_modify AtC extrinsic electron_integration implicit 3
fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 3 # 30
variable m equal 1*$s
# (A) no field
run $m
# (B) fixed boundary field
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 1
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 1
run $m

130
examples/PACKAGES/atc/drift_diffusion/in.no_atoms_ddm
View File

@ -1,65 +1,65 @@
# needs description
# DESCRIPTION: haynes-schockley
# continuity eqn: n,t = J,x + (G-R) = D n,xx + mu (n E),x + G - 1/tau (n - n_0)
# w/ J = D n,x + mu n phi,x
# poisson eqn for E-field: epsilon phi,xx = -e (n - p + N_D - N_A)
# w/ E = phi,x
# NOTE: does not conserve electrons even with fixed E field and zero mobility
# if J=0 --> n,x = mu/D n phi,x
echo both
units metal
variable E equal 10.0
variable n0 equal 0.0001
variable dn equal 2.0*${n0}
variable dt equal 0.0000001
timestep ${dt}
atom_style atomic
lattice fcc 1.0
region simRegion block -50 50 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion Si_ddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 100 1 1 simRegion f p p
fix_modify AtC mesh create_nodeset lbc -50.1 -49.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 49.9 50.1 -INF INF -INF INF
# fix a temperature
fix_modify AtC initial temperature all 300.0
fix_modify AtC initial electron_temperature all 300.0
fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 ${dn} ${n0}
# isolate system:
# diffusion: dn/dx = 0
# drift : n = 0
fix_modify AtC fix electron_density lbc ${n0}
fix_modify AtC fix electron_density rbc ${n0}
fix_modify AtC fix electric_potential all linear 0 0 0 $E 0 0 1
variable perm equal 0.06
variable nD equal 1.0e-4
fix_modify AtC source electric_potential all ${nD}
variable s equal 10
thermo $s
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output no_atoms_ddmFE $s text
fix_modify AtC extrinsic electron_integration implicit
run 40
# free electric field and allow shielding
fix_modify AtC unfix electric_potential all
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 1
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 1
fix_modify AtC extrinsic electron_integration implicit 10
run 40
# needs description
# DESCRIPTION: haynes-schockley
# continuity eqn: n,t = J,x + (G-R) = D n,xx + mu (n E),x + G - 1/tau (n - n_0)
# w/ J = D n,x + mu n phi,x
# poisson eqn for E-field: epsilon phi,xx = -e (n - p + N_D - N_A)
# w/ E = phi,x
# NOTE: does not conserve electrons even with fixed E field and zero mobility
# if J=0 --> n,x = mu/D n phi,x
echo both
units metal
variable E equal 10.0
variable n0 equal 0.0001
variable dn equal 2.0*${n0}
variable dt equal 0.0000001
timestep ${dt}
atom_style atomic
lattice fcc 1.0
region simRegion block -50 50 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion Si_ddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 100 1 1 simRegion f p p
fix_modify AtC mesh create_nodeset lbc -50.1 -49.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 49.9 50.1 -INF INF -INF INF
# fix a temperature
fix_modify AtC initial temperature all 300.0
fix_modify AtC initial electron_temperature all 300.0
fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 ${dn} ${n0}
# isolate system:
# diffusion: dn/dx = 0
# drift : n = 0
fix_modify AtC fix electron_density lbc ${n0}
fix_modify AtC fix electron_density rbc ${n0}
fix_modify AtC fix electric_potential all linear 0 0 0 $E 0 0 1
variable perm equal 0.06
variable nD equal 1.0e-4
fix_modify AtC source electric_potential all ${nD}
variable s equal 10
thermo $s
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output no_atoms_ddmFE $s text
fix_modify AtC extrinsic electron_integration implicit
run 40
# free electric field and allow shielding
fix_modify AtC unfix electric_potential all
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 1
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 1
fix_modify AtC extrinsic electron_integration implicit 10
run 40

158
examples/PACKAGES/atc/drift_diffusion/in.null_material_ddm
View File

@ -1,79 +1,79 @@
# needs description
#AtC drift diffusion Coupling
# DESCRIPTION:
# electric potential solved over whole domain
# all others only over the lower half
# temperature is fixed over whole domain
# NOTE the vacuum can fully masked out by making the material
# have null electron_density in Ar_ddm.mat
echo both
units metal
variable s equal 100
variable T equal 20
variable n equal 0.000004
variable tol equal 0.1
variable W equal 1000
atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25
region FE block -8 8 -6 6 0 3
region MD block -7 7 -6 0 0 3
region FREE block -4 4 -6 0 0 3
boundary f f p
# create atoms
create_box 1 FE
mass 1 39.95
atom_modify sort 0 1
timestep 0.002
thermo $s
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion Ar_ddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 4 4 1 FE f f p
variable a equal $W+${tol}
fix_modify AtC mesh create_elementset wire -$a $a -INF ${tol} -INF INF
fix_modify AtC mesh create_elementset gap -$a $a -${tol} INF -INF INF
# void is the complement of the wire nodeset
variable a equal $W-${tol}
fix_modify AtC mesh create_nodeset void -$a $a ${tol} INF -INF INF
fix_modify AtC mesh output null_material_ddmMESH binary
fix_modify AtC control thermal none
# fix a temperature
fix_modify AtC initial temperature all $T
fix_modify AtC initial electron_temperature all $T
fix_modify AtC initial electron_density all $n
fix_modify AtC initial electric_potential all 0.0
fix_modify AtC initial temperature void 0.0
fix_modify AtC initial electron_density void 0.0
fix_modify AtC initial electric_potential void 0.0
# create vacuum
fix_modify AtC material gap Vacuum
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4]
fix_modify AtC output null_material_ddmFE $s full_text binary
fix_modify AtC extrinsic electron_integration implicit
#
fix_modify AtC mesh create_nodeset lbc -8.1 -7.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 7.9 8.1 -INF INF -INF INF
fix_modify AtC fix electron_temperature lbc $T
fix_modify AtC fix electron_temperature rbc $T
fix_modify AtC fix electron_density lbc $n
fix_modify AtC fix electric_potential lbc 0.0
variable m equal $s*10
run $m
# needs description
#AtC drift diffusion Coupling
# DESCRIPTION:
# electric potential solved over whole domain
# all others only over the lower half
# temperature is fixed over whole domain
# NOTE the vacuum can fully masked out by making the material
# have null electron_density in Ar_ddm.mat
echo both
units metal
variable s equal 100
variable T equal 20
variable n equal 0.000004
variable tol equal 0.1
variable W equal 1000
atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25
region FE block -8 8 -6 6 0 3
region MD block -7 7 -6 0 0 3
region FREE block -4 4 -6 0 0 3
boundary f f p
# create atoms
create_box 1 FE
mass 1 39.95
atom_modify sort 0 1
timestep 0.002
thermo $s
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion Ar_ddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 4 4 1 FE f f p
variable a equal $W+${tol}
fix_modify AtC mesh create_elementset wire -$a $a -INF ${tol} -INF INF
fix_modify AtC mesh create_elementset gap -$a $a -${tol} INF -INF INF
# void is the complement of the wire nodeset
variable a equal $W-${tol}
fix_modify AtC mesh create_nodeset void -$a $a ${tol} INF -INF INF
fix_modify AtC mesh output null_material_ddmMESH binary
fix_modify AtC control thermal none
# fix a temperature
fix_modify AtC initial temperature all $T
fix_modify AtC initial electron_temperature all $T
fix_modify AtC initial electron_density all $n
fix_modify AtC initial electric_potential all 0.0
fix_modify AtC initial temperature void 0.0
fix_modify AtC initial electron_density void 0.0
fix_modify AtC initial electric_potential void 0.0
# create vacuum
fix_modify AtC material gap Vacuum
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4]
fix_modify AtC output null_material_ddmFE $s full_text binary
fix_modify AtC extrinsic electron_integration implicit
#
fix_modify AtC mesh create_nodeset lbc -8.1 -7.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 7.9 8.1 -INF INF -INF INF
fix_modify AtC fix electron_temperature lbc $T
fix_modify AtC fix electron_temperature rbc $T
fix_modify AtC fix electron_density lbc $n
fix_modify AtC fix electric_potential lbc 0.0
variable m equal $s*10
run $m

182
examples/PACKAGES/atc/elastic/in.bar1d
View File

@ -1,91 +1,91 @@
# needs description
#AtC Thermal Coupling
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)
lattice fcc 5.405 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region mdRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0
#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
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum glc_velocity
fix_modify AtC filter type exponential
fix_modify AtC filter scale 1000.0
fix_modify AtC filter on
# run to extension
#fix_modify AtC output bar1dFE 50 text
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1dFE 500 text
# run to equilibrium
timestep 5
thermo 100
run 10000
# needs description
#AtC Thermal Coupling
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)
lattice fcc 5.405 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region mdRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0
#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
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum glc_velocity
fix_modify AtC filter type exponential
fix_modify AtC filter scale 1000.0
fix_modify AtC filter on
# run to extension
#fix_modify AtC output bar1dFE 50 text
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1dFE 500 text
# run to equilibrium
timestep 5
thermo 100
run 10000

232
examples/PACKAGES/atc/elastic/in.bar1d_damped
View File

@ -1,116 +1,116 @@
# needs description
echo both
units metal
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)
lattice fcc 5.405 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 2 simRegion
create_atoms 1 region mdRegion
mass * 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.5
#pair_coeff * * .238 3.405 13.5
pair_coeff * * 0.010323166 3.405 13.5
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_damped.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
variable v equal 0.00000004e3
variable n equal 1000
variable dt equal 0.005
variable u equal $v*$n*${dt}
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc $v
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
fix_modify AtC boundary ghosts
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum glc_velocity
#fix_modify AtC filter type exponential
#fix_modify AtC filter scale 1.0
#fix_modify AtC filter on
# run to extension
timestep 0.005
thermo 100
thermo_style custom step cpu ke pe
run 0
variable pe0 equal pe
variable pe equal pe-${pe0}
thermo_style custom step cpu ke pe v_pe f_AtC[1] f_AtC[2] f_AtC[4] f_AtC[5]
run $n
fix_modify AtC output bar1d_dampedFE 500 text
dump CONFIG all custom 500 bar1d_damped.dmp id type x y z vx vy vz
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc $u
# run to equilibrium
thermo 100
log bar1d_damped.log
run 2000
fix_modify AtC material all cubic # M damping
run 2000
fix_modify AtC material all damped # K damping
run 2000
# ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 from Ar_CauchyBorn.mat
# real to metal 1 kcal/mol = 0.04336 eV
variable kCal2eV equal 0.04336
variable fconv equal 1./0.000103643 # NOTE old routine was doing calculations in lammps units, not atc units, so this conversion is necessary for bmark to pass
#variable k equal 1.e-3 # 7.56717*${kCal2eV} NOTE <<<
#variable k equal 0.75*0.355649e3*${kCal2eV}
variable k equal 0.5*39.95*${fconv} # NOTE it was set to above, should have been 2 above, but there was a bug so this value is here for bmark
#variable g equal 0.75*0.355649e3*${kCal2eV}
variable g equal 1.e-3*${fconv} # NOTE it should be above, but there was a bug so this value is here for bmark
variable m equal 2. #0.5*39.95
fix_modify AtC boundary_dynamics damped_harmonic $k $g $m
run 2000
# needs description
echo both
units metal
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)
lattice fcc 5.405 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 2 simRegion
create_atoms 1 region mdRegion
mass * 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.5
#pair_coeff * * .238 3.405 13.5
pair_coeff * * 0.010323166 3.405 13.5
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_damped.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
variable v equal 0.00000004e3
variable n equal 1000
variable dt equal 0.005
variable u equal $v*$n*${dt}
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc $v
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
fix_modify AtC boundary ghosts
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum glc_velocity
#fix_modify AtC filter type exponential
#fix_modify AtC filter scale 1.0
#fix_modify AtC filter on
# run to extension
timestep 0.005
thermo 100
thermo_style custom step cpu ke pe
run 0
variable pe0 equal pe
variable pe equal pe-${pe0}
thermo_style custom step cpu ke pe v_pe f_AtC[1] f_AtC[2] f_AtC[4] f_AtC[5]
run $n
fix_modify AtC output bar1d_dampedFE 500 text
dump CONFIG all custom 500 bar1d_damped.dmp id type x y z vx vy vz
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc $u
# run to equilibrium
thermo 100
log bar1d_damped.log
run 2000
fix_modify AtC material all cubic # M damping
run 2000
fix_modify AtC material all damped # K damping
run 2000
# ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 from Ar_CauchyBorn.mat
# real to metal 1 kcal/mol = 0.04336 eV
variable kCal2eV equal 0.04336
variable fconv equal 1./0.000103643 # NOTE old routine was doing calculations in lammps units, not atc units, so this conversion is necessary for bmark to pass
#variable k equal 1.e-3 # 7.56717*${kCal2eV} NOTE <<<
#variable k equal 0.75*0.355649e3*${kCal2eV}
variable k equal 0.5*39.95*${fconv} # NOTE it was set to above, should have been 2 above, but there was a bug so this value is here for bmark
#variable g equal 0.75*0.355649e3*${kCal2eV}
variable g equal 1.e-3*${fconv} # NOTE it should be above, but there was a bug so this value is here for bmark
variable m equal 2. #0.5*39.95
fix_modify AtC boundary_dynamics damped_harmonic $k $g $m
run 2000

196
examples/PACKAGES/atc/elastic/in.bar1d_flux
View File

@ -1,98 +1,98 @@
# needs description
#AtC Thermal Coupling
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)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region mdRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc 0.00000004
#fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
#fix_modify AtC control lumped_lambda_solve on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
fix_modify AtC control momentum flux interpolate
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom NULL
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_fluxFE 10 text
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1d_fluxFE 500 text
# run to equilibrium
timestep 5
thermo 100
run 10000
# needs description
#AtC Thermal Coupling
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)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region mdRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc 0.00000004
#fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
#fix_modify AtC control lumped_lambda_solve on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
fix_modify AtC control momentum flux interpolate
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom NULL
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_fluxFE 10 text
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1d_fluxFE 500 text
# run to equilibrium
timestep 5
thermo 100
run 10000

198
examples/PACKAGES/atc/elastic/in.bar1d_frac_step
View File

@ -1,99 +1,99 @@
# needs description
#AtC Elastic Coupling
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)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -8 8 -3 3 -3 3
region mdRegion block -6 6 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region atomRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.5
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
fix_modify AtC time_integration fractional_step
fix_modify AtC internal_atom_integrate off
fix iNVE internal nve
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum flux interpolate
#fix_modify AtC control momentum hoover # tested in this mode
#fix_modify AtC filter type exponential
#fix_modify AtC filter scale 1000.0
#fix_modify AtC filter on
# run to extension
#fix_modify AtC output bar1d_frac_step_initFE 50 text binary
#dump D1 all atom 50 bar1d_frac_step_init.dmp
timestep 5
thermo 100
run 1000
# reset time
fix_modify AtC reset_time 0.
reset_timestep 0
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1d_frac_stepFE 500 text #binary
#fix_modify AtC output index step
#undump D1
#dump D1 all atom 500 bar1d_frac_step.dmp
# run to equilibrium
timestep 5
thermo 100
run 5000
# needs description
#AtC Elastic Coupling
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)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -8 8 -3 3 -3 3
region mdRegion block -6 6 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region atomRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.5
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
fix_modify AtC time_integration fractional_step
fix_modify AtC internal_atom_integrate off
fix iNVE internal nve
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum flux interpolate
#fix_modify AtC control momentum hoover # tested in this mode
#fix_modify AtC filter type exponential
#fix_modify AtC filter scale 1000.0
#fix_modify AtC filter on
# run to extension
#fix_modify AtC output bar1d_frac_step_initFE 50 text binary
#dump D1 all atom 50 bar1d_frac_step_init.dmp
timestep 5
thermo 100
run 1000
# reset time
fix_modify AtC reset_time 0.
reset_timestep 0
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1d_frac_stepFE 500 text #binary
#fix_modify AtC output index step
#undump D1
#dump D1 all atom 500 bar1d_frac_step.dmp
# run to equilibrium
timestep 5
thermo 100
run 5000

202
examples/PACKAGES/atc/elastic/in.bar1d_ghost_flux
View File

@ -1,101 +1,101 @@
# Computes elastic waves propagating in and out of a finite temperature region
#AtC ThermoElastic Coupling
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)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
region simRegion block -12 12 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region mdRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0, NOTE next for lines commented out for restart
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off
fix_modify AtC internal_atom_integrate off
fix iNVE internal nve
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
#fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# turn on multiscale
fix_modify AtC control momentum ghost_flux
# new boundary conditions
fix_modify AtC fix velocity x rbc 0.00000004
#fix_modify AtC output follow_ex.fe 50
#fix_modify AtC localized_lambda on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
#fix_modify AtC control momentum flux
#fix_modify AtC control momentum ghost_flux
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom NULL
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_ghost_fluxFE 500 text
#dump D1 all atom 100 bar1d_ghost_flux.dmp
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC unfix velocity x rbc
#fix_modify AtC fix displacement x rbc 0.0002
#fix_modify AtC output bar1d_fluxFE 500 text binary
# run to equilibrium
timestep 5
thermo 100
run 3000
# Computes elastic waves propagating in and out of a finite temperature region
#AtC ThermoElastic Coupling
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)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
region simRegion block -12 12 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region mdRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0, NOTE next for lines commented out for restart
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off
fix_modify AtC internal_atom_integrate off
fix iNVE internal nve
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
#fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# turn on multiscale
fix_modify AtC control momentum ghost_flux
# new boundary conditions
fix_modify AtC fix velocity x rbc 0.00000004
#fix_modify AtC output follow_ex.fe 50
#fix_modify AtC localized_lambda on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
#fix_modify AtC control momentum flux
#fix_modify AtC control momentum ghost_flux
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom NULL
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_ghost_fluxFE 500 text
#dump D1 all atom 100 bar1d_ghost_flux.dmp
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC unfix velocity x rbc
#fix_modify AtC fix displacement x rbc 0.0002
#fix_modify AtC output bar1d_fluxFE 500 text binary
# run to equilibrium
timestep 5
thermo 100
run 3000

278
examples/PACKAGES/atc/elastic/in.bar1d_thermo_elastic
View File

@ -1,139 +1,139 @@
# Computes elastic waves propagating in and out of a finite temperature region
#AtC ThermoElastic Coupling
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)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
# NOTE following 3 lines added for restart
boundary f p p
pair_style lj/cut 13.
read_data temp.init
region simRegion block -12 12 -3 3 -3 3
# create atoms, NOTE commented out for restart
#region mdRegion block -8 8 -3 3 -3 3
#boundary f p p
#region mdBox block -9 9 -3 3 -3 3
#create_box 1 mdBox
#create_atoms 1 region mdRegion
#mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0, NOTE next for lines commented out for restart
#velocity internal create 40. 87287 mom yes loop geom
#pair_style lj/cut 13.
##pair_coeff 1 1 0.010323166 3.405 13.
#pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
#write_restart tinit.dat
# zero initial momentum
fix AtC internal atc elastic Ar_thermo_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off
fix_modify AtC fix displacement x all 0.
fix_modify AtC fix displacement y all 0.
fix_modify AtC fix displacement z all 0.
fix_modify AtC fix velocity x all 0.
fix_modify AtC fix velocity y all 0.
fix_modify AtC fix velocity z all 0.
fix_modify AtC control momentum glc_velocity
#fix_modify AtC output bar1d_thermo_elastic_initializeFE 1 text #binary
timestep 0
thermo 1
run 1
unfix AtC
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc thermo_elastic Ar_thermo_elastic.mat
fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
fix_modify AtC fix temperature all 20.
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
#fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# rescale thermostat for initial atomic temperatures
fix_modify AtC control thermal rescale 10
fix_modify AtC control momentum ghost_flux
fix_modify AtC output bar1d_thermo_elasticFE 100 text #binary
timestep 5
thermo 100
run 1000
# free all nodes
#fix_modify AtC unfix displacement x all
#fix_modify AtC unfix velocity x all
fix_modify AtC unfix temperature all
# new boundary conditions
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix temperature lbc 20.
#fix_modify AtC output follow_ex.fe 50
#fix_modify AtC localized_lambda on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
#fix_modify AtC control momentum flux
#fix_modify AtC control momentum ghost_flux
fix_modify AtC control thermal flux
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom NULL
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_thermo_elasticFE 500 text
#dump D1 all custom 100 bar1d_thermo_elastic.dmp id type x y z vx vy vz
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC unfix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.0002
#fix_modify AtC output bar1d_fluxFE 500 text binary
# run to equilibrium
timestep 5
thermo 100
run 3000
# Computes elastic waves propagating in and out of a finite temperature region
#AtC ThermoElastic Coupling
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)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
# NOTE following 3 lines added for restart
boundary f p p
pair_style lj/cut 13.
read_data temp.init
region simRegion block -12 12 -3 3 -3 3
# create atoms, NOTE commented out for restart
#region mdRegion block -8 8 -3 3 -3 3
#boundary f p p
#region mdBox block -9 9 -3 3 -3 3
#create_box 1 mdBox
#create_atoms 1 region mdRegion
#mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0, NOTE next for lines commented out for restart
#velocity internal create 40. 87287 mom yes loop geom
#pair_style lj/cut 13.
##pair_coeff 1 1 0.010323166 3.405 13.
#pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
#write_restart tinit.dat
# zero initial momentum
fix AtC internal atc elastic Ar_thermo_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off
fix_modify AtC fix displacement x all 0.
fix_modify AtC fix displacement y all 0.
fix_modify AtC fix displacement z all 0.
fix_modify AtC fix velocity x all 0.
fix_modify AtC fix velocity y all 0.
fix_modify AtC fix velocity z all 0.
fix_modify AtC control momentum glc_velocity
#fix_modify AtC output bar1d_thermo_elastic_initializeFE 1 text #binary
timestep 0
thermo 1
run 1
unfix AtC
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc thermo_elastic Ar_thermo_elastic.mat
fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
fix_modify AtC fix temperature all 20.
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
#fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# rescale thermostat for initial atomic temperatures
fix_modify AtC control thermal rescale 10
fix_modify AtC control momentum ghost_flux
fix_modify AtC output bar1d_thermo_elasticFE 100 text #binary
timestep 5
thermo 100
run 1000
# free all nodes
#fix_modify AtC unfix displacement x all
#fix_modify AtC unfix velocity x all
fix_modify AtC unfix temperature all
# new boundary conditions
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix temperature lbc 20.
#fix_modify AtC output follow_ex.fe 50
#fix_modify AtC localized_lambda on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
#fix_modify AtC control momentum flux
#fix_modify AtC control momentum ghost_flux
fix_modify AtC control thermal flux
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom NULL
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_thermo_elasticFE 500 text
#dump D1 all custom 100 bar1d_thermo_elastic.dmp id type x y z vx vy vz
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC unfix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.0002
#fix_modify AtC output bar1d_fluxFE 500 text binary
# run to equilibrium
timestep 5
thermo 100
run 3000

160
examples/PACKAGES/atc/elastic/in.eam_energy
View File

@ -1,80 +1,80 @@
echo both
units metal
atom_style atomic
atom_modify map hash
boundary p p p
variable l equal 3
variable l2 equal 0.5*$l
variable L equal 10
variable L2 equal 0.5*$L
variable h equal $L
lattice fcc 4.08 origin 0.25 0.25 0.25
region BOX block -${l2} ${l2} -${L2} ${L2} -${l2} ${l2}
create_box 1 BOX
create_atoms 1 region BOX
pair_style eam
pair_coeff * * Au_u3.eam
mass * 196.97
### NOTE change to CB -linear
fix PP all atc field Au_elastic.mat
fix_modify PP mesh create 1 $h 1 BOX p f p
fix_modify PP fields add displacement velocity potential_energy cauchy_born_energy # kinetic_energy
fix_modify PP gradients add displacement
fix_modify PP set reference_potential_energy
fix_modify PP output counter step
fix_modify PP output eam_energyPP 1 text
fix ATC all atc elastic Au_elastic.mat
fix_modify ATC mesh create 1 $h 1 BOX p f p
fix_modify ATC internal_quadrature off
fix_modify ATC control momentum none
#fix_modify ATC consistent_fe_initialization on
fix_modify ATC output counter step
fix_modify ATC output eam_energyFE 1 text binary
fix_modify ATC material all Au_cubic
dump CONFIG all custom 1 eam_energy.dmp id type x y z
thermo 1
timestep 0 # 1.e-20 # 0
variable e0 equal pe
variable L0 equal ly
run 0
variable pe equal pe-${e0}
variable dL equal ly-${L0}
variable strain equal v_dL/${L0}
variable x equal y[1]
variable x2 equal y[2]
variable v equal vy[1]
thermo_style custom step etotal v_pe ke f_ATC[1] f_ATC[2] v_x v_v v_x2 ly v_dL v_strain
thermo_modify format 2 %15.8g
###############################################################################
log eam_energy.log
run 1
velocity all set 0 0.1 0 units box
fix_modify ATC fix velocity y all 0.1
run 1
velocity all set 0 0.2 0 units box
fix_modify ATC fix velocity y all 0.2
run 1
velocity all set 0 0.3 0 units box
fix_modify ATC fix velocity y all 0.3
run 1
change_box all y scale 1.01 remap
fix_modify ATC fix displacement y all linear 0 0 0 0 0.01 0 0
run 1
change_box all y scale 1.01 remap
fix_modify ATC fix displacement y all linear 0 0 0 0 0.0201 0 0
run 1
change_box all y scale 1.01 remap
fix_modify ATC fix displacement y all linear 0 0 0 0 0.030301 0 0
run 1
echo both
units metal
atom_style atomic
atom_modify map hash
boundary p p p
variable l equal 3
variable l2 equal 0.5*$l
variable L equal 10
variable L2 equal 0.5*$L
variable h equal $L
lattice fcc 4.08 origin 0.25 0.25 0.25
region BOX block -${l2} ${l2} -${L2} ${L2} -${l2} ${l2}
create_box 1 BOX
create_atoms 1 region BOX
pair_style eam
pair_coeff * * Au_u3.eam
mass * 196.97
### NOTE change to CB -linear
fix PP all atc field Au_elastic.mat
fix_modify PP mesh create 1 $h 1 BOX p f p
fix_modify PP fields add displacement velocity potential_energy cauchy_born_energy # kinetic_energy
fix_modify PP gradients add displacement
fix_modify PP set reference_potential_energy
fix_modify PP output counter step
fix_modify PP output eam_energyPP 1 text
fix ATC all atc elastic Au_elastic.mat
fix_modify ATC mesh create 1 $h 1 BOX p f p
fix_modify ATC internal_quadrature off
fix_modify ATC control momentum none
#fix_modify ATC consistent_fe_initialization on
fix_modify ATC output counter step
fix_modify ATC output eam_energyFE 1 text binary
fix_modify ATC material all Au_cubic
dump CONFIG all custom 1 eam_energy.dmp id type x y z
thermo 1
timestep 0 # 1.e-20 # 0
variable e0 equal pe
variable L0 equal ly
run 0
variable pe equal pe-${e0}
variable dL equal ly-${L0}
variable strain equal v_dL/${L0}
variable x equal y[1]
variable x2 equal y[2]
variable v equal vy[1]
thermo_style custom step etotal v_pe ke f_ATC[1] f_ATC[2] v_x v_v v_x2 ly v_dL v_strain
thermo_modify format 2 %15.8g
###############################################################################
log eam_energy.log
run 1
velocity all set 0 0.1 0 units box
fix_modify ATC fix velocity y all 0.1
run 1
velocity all set 0 0.2 0 units box
fix_modify ATC fix velocity y all 0.2
run 1
velocity all set 0 0.3 0 units box
fix_modify ATC fix velocity y all 0.3
run 1
change_box all y scale 1.01 remap
fix_modify ATC fix displacement y all linear 0 0 0 0 0.01 0 0
run 1
change_box all y scale 1.01 remap
fix_modify ATC fix displacement y all linear 0 0 0 0 0.0201 0 0
run 1
change_box all y scale 1.01 remap
fix_modify ATC fix displacement y all linear 0 0 0 0 0.030301 0 0
run 1

148
examples/PACKAGES/atc/elastic/in.electron_density
View File

@ -1,74 +1,74 @@
# needs description
echo both
units metal
# PARAMETERS-----------------------------
variable s equal 1
variable L equal 10
variable e equal 4
variable E equal 0.0001
variable V equal $E*$L
# END -----------------------------------
atom_style atomic
lattice diamond 1.0
boundary f p p
region box block -$L $L 0 1 0 1
create_box 1 box
group box region box
atom_modify sort 0 1
timestep 0.0
mass * 12.01
# coupling
### NOTE ATC: material cnt does not provide all interfaces for charge_density physics and will be treated as null
fix AtC box atc electrostatic-equilibrium CNT.mat
fix_modify AtC internal_quadrature off
#fix_modify AtC atom_weight constant internal 1.0 NOTE penultimate is a group
fix_modify AtC atom_weight constant box 1.0
fix_modify AtC omit atomic_charge
fix_modify AtC mesh create $e 1 1 box f p p
#fix_modify AtC control momentum flux
fix_modify AtC mesh create_elementset all -INF INF -INF INF -INF INF
# bcs/ics conditions
fix_modify AtC fix displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC fix velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
fix_modify AtC mesh create_nodeset lbc -10 -10 INF INF INF INF
fix_modify AtC mesh create_nodeset rbc 10 10 INF INF INF INF
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V
# run
thermo_style custom step cpu etotal ke
thermo $s
fix_modify AtC output electron_densityFE $s text
fix_modify AtC output index step
log electron_density.log
# run default material
print "default material - table linear"
run $s
# run CNT1 material
print "CNT1 material - analytical linear"
fix_modify AtC material all CNT1
run $s
# run CNT2 material
print "CNT2 material - analytical exponetial"
fix_modify AtC material all CNT2
run $s
# run CNT material
print "CNT material - table DOS"
fix_modify AtC material all CNT
#variable E equal 10*$E
#fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V
#fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V
run $s
# needs description
echo both
units metal
# PARAMETERS-----------------------------
variable s equal 1
variable L equal 10
variable e equal 4
variable E equal 0.0001
variable V equal $E*$L
# END -----------------------------------
atom_style atomic
lattice diamond 1.0
boundary f p p
region box block -$L $L 0 1 0 1
create_box 1 box
group box region box
atom_modify sort 0 1
timestep 0.0
mass * 12.01
# coupling
### NOTE ATC: material cnt does not provide all interfaces for charge_density physics and will be treated as null
fix AtC box atc electrostatic-equilibrium CNT.mat
fix_modify AtC internal_quadrature off
#fix_modify AtC atom_weight constant internal 1.0 NOTE penultimate is a group
fix_modify AtC atom_weight constant box 1.0
fix_modify AtC omit atomic_charge
fix_modify AtC mesh create $e 1 1 box f p p
#fix_modify AtC control momentum flux
fix_modify AtC mesh create_elementset all -INF INF -INF INF -INF INF
# bcs/ics conditions
fix_modify AtC fix displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC fix velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
fix_modify AtC mesh create_nodeset lbc -10 -10 INF INF INF INF
fix_modify AtC mesh create_nodeset rbc 10 10 INF INF INF INF
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V
# run
thermo_style custom step cpu etotal ke
thermo $s
fix_modify AtC output electron_densityFE $s text
fix_modify AtC output index step
log electron_density.log
# run default material
print "default material - table linear"
run $s
# run CNT1 material
print "CNT1 material - analytical linear"
fix_modify AtC material all CNT1
run $s
# run CNT2 material
print "CNT2 material - analytical exponetial"
fix_modify AtC material all CNT2
run $s
# run CNT material
print "CNT material - table DOS"
fix_modify AtC material all CNT
#variable E equal 10*$E
#fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V
#fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V
run $s

112
examples/PACKAGES/atc/mesh/in.gaussianIC1d_hex
View File

@ -1,56 +1,56 @@
echo both
units real
atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdRegion block -12 12 -3 3 -3 3
region mdInternal block -10 10 -3 3 -3 3
# create atoms
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
# specify interal/ghost atoms
group internal region mdInternal
velocity internal create 40 87287 mom yes loop geom # <<< NOTE
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
fix_modify AtC mesh read gaussianIC1d_hex.mesh
# fix a temperature
fix_modify AtC fix temperature all 20.0
fix_modify AtC initial temperature all 20.0
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC 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 control thermal rescale 10
# equilibrate MD field
timestep 5.0
thermo 10
#output
fix_modify AtC output gaussianIC1d_hexFE 10 text
# change thermostat
fix_modify AtC unfix temperature all
fix_modify AtC unfix electron_temperature all
fix_modify AtC control thermal 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 100 # 400
echo both
units real
atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdRegion block -12 12 -3 3 -3 3
region mdInternal block -10 10 -3 3 -3 3
# create atoms
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
# specify interal/ghost atoms
group internal region mdInternal
velocity internal create 40 87287 mom yes loop geom # <<< NOTE
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
fix_modify AtC mesh read gaussianIC1d_hex.mesh
# fix a temperature
fix_modify AtC fix temperature all 20.0
fix_modify AtC initial temperature all 20.0
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC 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 control thermal rescale 10
# equilibrate MD field
timestep 5.0
thermo 10
#output
fix_modify AtC output gaussianIC1d_hexFE 10 text
# change thermostat
fix_modify AtC unfix temperature all
fix_modify AtC unfix electron_temperature all
fix_modify AtC control thermal 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 100 # 400

138
examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex
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@ -1,69 +1,69 @@
echo both
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdRegion cylinder z 0. 0. ${l2} -$w $w
region mdInternal cylinder z 0. 0. $l -$w $w
boundary f f f
pair_style lj/cut 13.5
read_data circle_temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
group ghost subtract all internal
fix AtC internal atc two_temperature Ar_ttm.mat
# computational geometry
fix_modify AtC mesh read gaussianIC2d_hex.mesh
#fix_modify AtC mesh read gaussianIC2d_hex.exo
#fix_modify AtC mesh read gaussianIC2d_hex2.exo
#fix_modify AtC mesh read gaussianIC2d_hex2.mesh
fix_modify AtC mesh write parsed_gaussianIC2d_hex.mesh
fix_modify AtC mesh output gaussianIC2d_hexMESH
fix_modify AtC boundary ghost
# numerical parameters
fix_modify AtC time_integration fractional_step
fix_modify AtC internal_quadrature off
# initial conditions
fix_modify AtC fix temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
# thermostat
fix_modify AtC control thermal rescale 10
fix_modify AtC extrinsic exchange off
# run to equilibrate
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 400
# boundary conditions
fix_modify AtC unfix temperature all
fix_modify AtC unfix electron_temperature all
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
# numerical parameters
fix_modify AtC extrinsic electron_integration explicit 10
# thermostat
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
# output
fix_modify AtC output gaussianIC2d_hexFE 10 full_text binary
dump D1 all atom 10 gaussianIC2d_hex.dmp
# relax the system
run 1000
echo both
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdRegion cylinder z 0. 0. ${l2} -$w $w
region mdInternal cylinder z 0. 0. $l -$w $w
boundary f f f
pair_style lj/cut 13.5
read_data circle_temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
group ghost subtract all internal
fix AtC internal atc two_temperature Ar_ttm.mat
# computational geometry
fix_modify AtC mesh read gaussianIC2d_hex.mesh
#fix_modify AtC mesh read gaussianIC2d_hex.exo
#fix_modify AtC mesh read gaussianIC2d_hex2.exo
#fix_modify AtC mesh read gaussianIC2d_hex2.mesh
fix_modify AtC mesh write parsed_gaussianIC2d_hex.mesh
fix_modify AtC mesh output gaussianIC2d_hexMESH
fix_modify AtC boundary ghost
# numerical parameters
fix_modify AtC time_integration fractional_step
fix_modify AtC internal_quadrature off
# initial conditions
fix_modify AtC fix temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
# thermostat
fix_modify AtC control thermal rescale 10
fix_modify AtC extrinsic exchange off
# run to equilibrate
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 400
# boundary conditions
fix_modify AtC unfix temperature all
fix_modify AtC unfix electron_temperature all
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
# numerical parameters
fix_modify AtC extrinsic electron_integration explicit 10
# thermostat
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
# output
fix_modify AtC output gaussianIC2d_hexFE 10 full_text binary
dump D1 all atom 10 gaussianIC2d_hex.dmp
# relax the system
run 1000

74
examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex20_uniform
View File

@ -1,37 +1,37 @@
echo both
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdInternal block -$l $l -$l $l -$w $w
boundary f f f # p
pair_style lj/cut 13.5
read_data temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
fix AtC internal atc two_temperature Ar_ttm.mat
fix_modify AtC mesh read gaussianIC2d_hex20_uniform.mesh
fix_modify AtC output gaussianIC2d_hex20_uniformFE 10 full_text
fix_modify AtC initial temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 100
echo both
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdInternal block -$l $l -$l $l -$w $w
boundary f f f # p
pair_style lj/cut 13.5
read_data temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
fix AtC internal atc two_temperature Ar_ttm.mat
fix_modify AtC mesh read gaussianIC2d_hex20_uniform.mesh
fix_modify AtC output gaussianIC2d_hex20_uniformFE 10 full_text
fix_modify AtC initial temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 100

74
examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex27_uniform
View File

@ -1,37 +1,37 @@
echo both
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdInternal block -$l $l -$l $l -$w $w
boundary f f f # p
pair_style lj/cut 13.5
read_data temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
fix AtC internal atc two_temperature Ar_ttm.mat
fix_modify AtC mesh read gaussianIC2d_hex27_uniform.mesh
fix_modify AtC output gaussianIC2d_hex27_uniformFE 10 full_text
fix_modify AtC initial temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 100
echo both
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdInternal block -$l $l -$l $l -$w $w
boundary f f f # p
pair_style lj/cut 13.5
read_data temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
fix AtC internal atc two_temperature Ar_ttm.mat
fix_modify AtC mesh read gaussianIC2d_hex27_uniform.mesh
fix_modify AtC output gaussianIC2d_hex27_uniformFE 10 full_text
fix_modify AtC initial temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 100

80
examples/PACKAGES/atc/mesh/in.gaussianIC2d_tet
View File

@ -1,40 +1,40 @@
echo both
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdInternal block -$l $l -$l $l -$w $w
boundary f f f # p
pair_style lj/cut 13.5
read_data temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
fix AtC internal atc two_temperature Ar_ttm.mat
fix_modify AtC mesh read gaussianIC2d_tet.mesh
#fix_modify AtC mesh read gaussianIC2d_tet.exo
fix_modify AtC mesh write parsed_gaussianIC2d_tet.mesh
fix_modify AtC mesh output parsed_gaussianIC2d_tetMESH
fix_modify AtC output gaussianIC2d_tetFE 10 full_text
fix_modify AtC initial temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 100
echo both
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdInternal block -$l $l -$l $l -$w $w
boundary f f f # p
pair_style lj/cut 13.5
read_data temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
fix AtC internal atc two_temperature Ar_ttm.mat
fix_modify AtC mesh read gaussianIC2d_tet.mesh
#fix_modify AtC mesh read gaussianIC2d_tet.exo
fix_modify AtC mesh write parsed_gaussianIC2d_tet.mesh
fix_modify AtC mesh output parsed_gaussianIC2d_tetMESH
fix_modify AtC output gaussianIC2d_tetFE 10 full_text
fix_modify AtC initial temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 100

64
examples/PACKAGES/atc/mesh/in.kernel2d_hex
View File

@ -1,32 +1,32 @@
echo both
units real
atom_style atomic
# correct mass density = 1.0120
# NOTE the mesh is not currently periodic, so the density estimate is off by a factor of 2
variable L equal 6
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region BOX block -$L $L -$L $L -$w $w
boundary f f p
create_box 1 BOX
create_atoms 1 region BOX
mass 1 39.95
pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5
group internal region BOX
fix AtC internal atc hardy
fix_modify AtC kernel quartic_cylinder 5.0
fix_modify AtC mesh read gaussianIC2d_hex.mesh
fix_modify AtC fields add mass_density
fix_modify AtC output kernel2d_hexFE 1 full_text binary
#dump CONFIG all custom 1 kernel2d_hexMD.dmp id type x y z
thermo_style custom step cpu temp
timestep 0.0
thermo 1
run 2
echo both
units real
atom_style atomic
# correct mass density = 1.0120
# NOTE the mesh is not currently periodic, so the density estimate is off by a factor of 2
variable L equal 6
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region BOX block -$L $L -$L $L -$w $w
boundary f f p
create_box 1 BOX
create_atoms 1 region BOX
mass 1 39.95
pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5
group internal region BOX
fix AtC internal atc hardy
fix_modify AtC kernel quartic_cylinder 5.0
fix_modify AtC mesh read gaussianIC2d_hex.mesh
fix_modify AtC fields add mass_density
fix_modify AtC output kernel2d_hexFE 1 full_text binary
#dump CONFIG all custom 1 kernel2d_hexMD.dmp id type x y z
thermo_style custom step cpu temp
timestep 0.0
thermo 1
run 2

56
examples/PACKAGES/atc/mesh/in.kernel2d_tet
View File

@ -1,28 +1,28 @@
echo both
units real
atom_style atomic
variable L equal 6
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region BOX block -$L $L -$L $L -$w $w
boundary f f p
create_box 1 BOX
create_atoms 1 region BOX
mass 1 39.95
pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5
group internal region BOX
fix AtC internal atc hardy
fix_modify AtC kernel quartic_sphere 5.0
fix_modify AtC mesh read gaussianIC2d_tet.mesh
fix_modify AtC fields add mass_density
fix_modify AtC output kernel2d_tetFE 1 full_text binary
thermo_style custom step cpu temp
timestep 0.0
thermo 1
run 2
echo both
units real
atom_style atomic
variable L equal 6
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region BOX block -$L $L -$L $L -$w $w
boundary f f p
create_box 1 BOX
create_atoms 1 region BOX
mass 1 39.95
pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5
group internal region BOX
fix AtC internal atc hardy
fix_modify AtC kernel quartic_sphere 5.0
fix_modify AtC mesh read gaussianIC2d_tet.mesh
fix_modify AtC fields add mass_density
fix_modify AtC output kernel2d_tetFE 1 full_text binary
thermo_style custom step cpu temp
timestep 0.0
thermo 1
run 2

58
examples/PACKAGES/atc/mesh/in.mesh2d_tet
View File

@ -1,29 +1,29 @@
echo both
units real
atom_style atomic
variable L equal 6
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region BOX block -$L $L -$L $L -$w $w
boundary f f p
create_box 1 BOX
create_atoms 1 region BOX
mass 1 39.95
pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5
group internal region BOX
fix AtC internal atc field
fix_modify AtC mesh read gaussianIC2d_tet.mesh
fix_modify AtC fields add mass_density
fix_modify AtC output mesh2d_tetFE 1 full_text binary
dump CONFIG all custom 10 mesh2d_tet.dmp id type x y z
thermo_style custom step cpu temp
timestep 0.0
thermo 1
run 2
echo both
units real
atom_style atomic
variable L equal 6
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region BOX block -$L $L -$L $L -$w $w
boundary f f p
create_box 1 BOX
create_atoms 1 region BOX
mass 1 39.95
pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5
group internal region BOX
fix AtC internal atc field
fix_modify AtC mesh read gaussianIC2d_tet.mesh
fix_modify AtC fields add mass_density
fix_modify AtC output mesh2d_tetFE 1 full_text binary
dump CONFIG all custom 10 mesh2d_tet.dmp id type x y z
thermo_style custom step cpu temp
timestep 0.0
thermo 1
run 2

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