Merge pull request #3177 from akohlmey/collected-small-changes
Collected small changes and fixes
This commit is contained in:
Axel Kohlmeyer
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# COMB parameters for various elements (Si, Cu, Hf, Ti, Zr, U, O) and mixtures (their oxides and alloys)
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# Edited by Tzu-Ray Shan from MSE, Univ. FL in Apr 2010
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#
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# Elements currently available: Si, Cu, Hf, Ti, Zr, U, O
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# Oxides currently available: Si-O, Cu-O, Hf-O, Ti-O
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#
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# Si parameter set from (JG Yu, SB Sinnott, SR Phillpot, Phys. Rev. B 75 085311 2007)
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# ,and (TR Shan, BD Devine, SR Phillpot, SB Sinnott, to be sub to Phys. Rev. B)
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# O parameter set from (TR Shan, BD Devine, SB Sinnott, SR Phillpot, Phys. Rev. B 81 125328 2010)
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# Cu parameter set from (BD Devine, TR Shan, SB Sinnott, SR Phillpot, to be sub to Phys. Rev. B)
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# Hf parameter set from (TR Shan, BD Devine, SB Sinnott, SR Phillpot, Phys. Rev. B 81 125328 2010)
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# Ti parameter set from (TR Shan, SR Phillpot, SB Sinnott, in preparation)
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# U parameter set from (Y Li, TR Shan, SB Sinnott, SR Phillpot, in preparation)
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# Zr parameter set from (T Iwasaki, J. Mater. Res. 20 5 1300 2005)
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#
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# Multiple entries can be added to this file, LAMMPS reads the ones it needs
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# Only M-O are added in the potential table, using mixing rules to generate desired alloy (A-B) parameters
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# 8 entries for a desired A-B type: AAA, BBB, AAB, ABA, ABB, BAA, BBA, BBA
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# 27 entries for a system containing three elements A, B and C
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# These entries are in LAMMPS "metal" units
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#
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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
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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
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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
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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
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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
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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
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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
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#
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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
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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
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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
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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
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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
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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
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#
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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
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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
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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
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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
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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
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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
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#
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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
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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
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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
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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
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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
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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
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#
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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
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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
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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
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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
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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
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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
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#
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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
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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
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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
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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
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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
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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
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#
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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
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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
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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
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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
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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
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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
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#
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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
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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
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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
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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
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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
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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
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#
|
||||
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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -261,4 +261,4 @@ 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 recompile/reinstall all of LAMMPS.
|
||||
having to re-compile or re-install all of LAMMPS.
|
||||
|
||||
@ -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).
|
||||
|
||||
@ -143,7 +143,7 @@ control the induced charge solver and the initial values of the interface elemen
|
||||
*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 upperbound is set by *iter_max*). The second element is the RMS error.
|
||||
(of which the upper bound is set by *iter_max*). The second element is the RMS error.
|
||||
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -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.
|
||||
|
||||
@ -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
|
||||
""""""""""""""""
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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 $E 0 0 0
|
||||
run 1
|
||||
|
||||
|
||||
@ -1,75 +1,75 @@
|
||||
#needs description
|
||||
echo both
|
||||
units metal
|
||||
|
||||
variable E equal 0.1
|
||||
variable L equal 10.0
|
||||
#variable N equal 100
|
||||
variable N equal 80
|
||||
variable T equal 1000
|
||||
variable n0 equal 0.0001
|
||||
variable dn equal 2.0*${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 $m
|
||||
|
||||
@ -1,65 +1,65 @@
|
||||
# needs description
|
||||
# DESCRIPTION: haynes-schockley
|
||||
# continuity eqn: n,t = J,x + (G-R) = D n,xx + mu (n E),x + G - 1/tau (n - n_0)
|
||||
# w/ J = D n,x + mu n phi,x
|
||||
# poisson eqn for E-field: epsilon phi,xx = -e (n - p + N_D - N_A)
|
||||
# w/ E = phi,x
|
||||
# NOTE: does not conserve electrons even with fixed E field and zero mobility
|
||||
# if J=0 --> n,x = mu/D n phi,x
|
||||
|
||||
echo both
|
||||
units metal
|
||||
|
||||
variable E equal 10.0
|
||||
variable n0 equal 0.0001
|
||||
variable dn equal 2.0*${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
|
||||
|
||||
@ -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
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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 $w
|
||||
|
||||
boundary f f f # p
|
||||
pair_style lj/cut 13.5
|
||||
read_data temp.init
|
||||
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
|
||||
mass 1 39.95
|
||||
pair_coeff 1 1 .238 3.405 13.5
|
||||
group internal region mdInternal
|
||||
|
||||
fix AtC internal atc two_temperature Ar_ttm.mat
|
||||
fix_modify AtC mesh read gaussianIC2d_hex20_uniform.mesh
|
||||
fix_modify AtC output gaussianIC2d_hex20_uniformFE 10 full_text
|
||||
|
||||
fix_modify AtC initial temperature all 20.0
|
||||
# NOTE this is only gaussian in x
|
||||
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
|
||||
fix_modify AtC fix temperature 11 20.0
|
||||
fix_modify AtC fix temperature 12 20.0
|
||||
fix_modify AtC control thermal flux
|
||||
fix_modify AtC extrinsic exchange on
|
||||
fix_modify AtC extrinsic electron_integration explicit 10
|
||||
|
||||
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
|
||||
timestep 1.0
|
||||
thermo 10
|
||||
run 100
|
||||
|
||||
@ -1,37 +1,37 @@
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
variable L equal 12
|
||||
variable l2 equal 6
|
||||
variable l equal 4
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region mdInternal block -$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 $w
|
||||
|
||||
boundary f f f # p
|
||||
pair_style lj/cut 13.5
|
||||
read_data temp.init
|
||||
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
|
||||
mass 1 39.95
|
||||
pair_coeff 1 1 .238 3.405 13.5
|
||||
group internal region mdInternal
|
||||
|
||||
fix AtC internal atc two_temperature Ar_ttm.mat
|
||||
fix_modify AtC mesh read gaussianIC2d_hex27_uniform.mesh
|
||||
fix_modify AtC output gaussianIC2d_hex27_uniformFE 10 full_text
|
||||
|
||||
fix_modify AtC initial temperature all 20.0
|
||||
# NOTE this is only gaussian in x
|
||||
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
|
||||
fix_modify AtC fix temperature 11 20.0
|
||||
fix_modify AtC fix temperature 12 20.0
|
||||
fix_modify AtC control thermal flux
|
||||
fix_modify AtC extrinsic exchange on
|
||||
fix_modify AtC extrinsic electron_integration explicit 10
|
||||
|
||||
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
|
||||
timestep 1.0
|
||||
thermo 10
|
||||
run 100
|
||||
|
||||
@ -1,40 +1,40 @@
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
variable L equal 12
|
||||
variable l2 equal 6
|
||||
variable l equal 4
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region mdInternal block -$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 $w
|
||||
|
||||
boundary f f f # p
|
||||
pair_style lj/cut 13.5
|
||||
read_data temp.init
|
||||
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
|
||||
mass 1 39.95
|
||||
pair_coeff 1 1 .238 3.405 13.5
|
||||
group internal region mdInternal
|
||||
|
||||
fix AtC internal atc two_temperature Ar_ttm.mat
|
||||
fix_modify AtC mesh read gaussianIC2d_tet.mesh
|
||||
#fix_modify AtC mesh read gaussianIC2d_tet.exo
|
||||
fix_modify AtC mesh write parsed_gaussianIC2d_tet.mesh
|
||||
fix_modify AtC mesh output parsed_gaussianIC2d_tetMESH
|
||||
fix_modify AtC output gaussianIC2d_tetFE 10 full_text
|
||||
|
||||
fix_modify AtC initial temperature all 20.0
|
||||
# NOTE this is only gaussian in x
|
||||
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
|
||||
fix_modify AtC fix temperature 11 20.0
|
||||
fix_modify AtC fix temperature 12 20.0
|
||||
fix_modify AtC control thermal flux
|
||||
fix_modify AtC extrinsic exchange on
|
||||
fix_modify AtC extrinsic electron_integration explicit 10
|
||||
|
||||
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
|
||||
timestep 1.0
|
||||
thermo 10
|
||||
run 100
|
||||
|
||||
@ -1,32 +1,32 @@
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
# correct mass density = 1.0120
|
||||
# NOTE the mesh is not currently periodic, so the density estimate is off by a factor of 2
|
||||
|
||||
variable L equal 6
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region BOX block -$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 $w
|
||||
|
||||
boundary f f p
|
||||
create_box 1 BOX
|
||||
create_atoms 1 region BOX
|
||||
mass 1 39.95
|
||||
pair_style lj/cut 13.5
|
||||
pair_coeff 1 1 .238 3.405 13.5
|
||||
group internal region BOX
|
||||
|
||||
fix AtC internal atc hardy
|
||||
fix_modify AtC kernel quartic_cylinder 5.0
|
||||
fix_modify AtC mesh read gaussianIC2d_hex.mesh
|
||||
fix_modify AtC fields add mass_density
|
||||
fix_modify AtC output kernel2d_hexFE 1 full_text binary
|
||||
#dump CONFIG all custom 1 kernel2d_hexMD.dmp id type x y z
|
||||
|
||||
thermo_style custom step cpu temp
|
||||
timestep 0.0
|
||||
thermo 1
|
||||
run 2
|
||||
|
||||
@ -1,28 +1,28 @@
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
variable L equal 6
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region BOX block -$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 $w
|
||||
|
||||
boundary f f p
|
||||
create_box 1 BOX
|
||||
create_atoms 1 region BOX
|
||||
mass 1 39.95
|
||||
pair_style lj/cut 13.5
|
||||
pair_coeff 1 1 .238 3.405 13.5
|
||||
group internal region BOX
|
||||
|
||||
fix AtC internal atc hardy
|
||||
fix_modify AtC kernel quartic_sphere 5.0
|
||||
fix_modify AtC mesh read gaussianIC2d_tet.mesh
|
||||
fix_modify AtC fields add mass_density
|
||||
fix_modify AtC output kernel2d_tetFE 1 full_text binary
|
||||
|
||||
thermo_style custom step cpu temp
|
||||
timestep 0.0
|
||||
thermo 1
|
||||
run 2
|
||||
|
||||
@ -1,29 +1,29 @@
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
variable L equal 6
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region BOX block -$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
|
||||
|
||||
@ -1,101 +1,101 @@
|
||||
# this input can be used to generate the benchmark for in.gaussianIC2d_hex_uniform
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
variable l equal 8
|
||||
variable g equal 2
|
||||
variable lg equal $l+$g
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
boundary f f f
|
||||
|
||||
# region to create atoms
|
||||
region bigCyl cylinder z 0. 0. ${lg} -$w $w
|
||||
region offsetPlane block -${lg} $g -${lg} ${lg} -$w $w
|
||||
region mdRegion intersect 2 bigCyl offsetPlane
|
||||
#create_box 1 mdRegion
|
||||
pair_style lj/cut 13.5
|
||||
read_data semicircle.init
|
||||
|
||||
# region for internal atoms
|
||||
region mdInternalCyl cylinder z 0. 0. $l -$w $w
|
||||
region leftHalfPlane block INF 0. INF INF INF INF
|
||||
region mdInternal intersect 2 mdInternalCyl leftHalfPlane
|
||||
|
||||
# region for coupling ghosts
|
||||
region rightHalfPlane block 0. INF INF INF INF INF
|
||||
region mdGhost union 2 rightHalfPlane mdInternal side out
|
||||
|
||||
#create_atoms 1 region mdRegion
|
||||
#create_atoms 1 region mdInternal
|
||||
#create_atoms 2 region mdGhost
|
||||
#region outerGhost intersect 2 rightHalfPlane mdRegion
|
||||
#create_atoms 3 region outerGhost
|
||||
|
||||
#pair_style lj/cut 13.5
|
||||
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 region mdGhost
|
||||
#velocity internal create 40 102486 mom yes rot yes dist gaussian
|
||||
#write_restart semicircle_init.rst
|
||||
|
||||
# ATC commands
|
||||
fix AtC internal atc thermal Ar_ttm.mat
|
||||
fix_modify AtC boundary ghost
|
||||
fix_modify AtC mesh read semicircle.mesh f f p
|
||||
fix_modify AtC mesh nodeset_to_elementset 2 hole min
|
||||
fix_modify AtC internal_quadrature off
|
||||
fix_modify AtC time_integration fractional_step
|
||||
|
||||
# initial conditions
|
||||
fix_modify AtC fix temperature all 20.
|
||||
fix_modify AtC control thermal rescale 10
|
||||
fix_modify AtC control tolerance 1.e-14 # tolerance needed to produce consistent parallel and serial results
|
||||
|
||||
# initial output
|
||||
#fix_modify AtC mesh output semicircle_mesh
|
||||
#fix_modify AtC output semicircle_init 100 text binary
|
||||
#dump D1 all atom 100 semicircle_init.dmp
|
||||
|
||||
# run
|
||||
timestep 5.0
|
||||
thermo 100
|
||||
run 500
|
||||
|
||||
# boundary conditions
|
||||
fix_modify AtC unfix temperature all
|
||||
fix_modify AtC fix temperature 1 20.
|
||||
fix_modify AtC control thermal flux
|
||||
fix_modify AtC control localized_lambda on
|
||||
|
||||
# NOTE appears to be a problem with the temporal ramp function
|
||||
variable delta_t equal 1000*5.
|
||||
fix_modify AtC source temperature hole temporal_ramp 0. 0.0000000001 ${delta_t}
|
||||
|
||||
# equilibrate filter
|
||||
fix_modify AtC filter type exponential
|
||||
fix_modify AtC filter scale 1000.
|
||||
fix_modify AtC filter on
|
||||
|
||||
# equilibration output
|
||||
fix_modify AtC output semicircleFE 100 full_text #binary
|
||||
#undump D1
|
||||
#dump D1 all atom 100 semicircle_equil.dmp
|
||||
|
||||
# run
|
||||
fix_modify AtC reset_time 0.
|
||||
reset_timestep 0
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
# heat source
|
||||
# NOTE second run omitted as it causes diffs in parallel execution after just one timestep, not sure why
|
||||
#fix_modify AtC source temperature hole 0.0000000001
|
||||
#fix_modify AtC output semicircleFE 1 full_text #binary
|
||||
#undump D1
|
||||
#dump D1 all atom 100 semicircle.dmp
|
||||
#run 1#000
|
||||
# this input can be used to generate the benchmark for in.gaussianIC2d_hex_uniform
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
variable l equal 8
|
||||
variable g equal 2
|
||||
variable lg equal $l+$g
|
||||
variable w equal 2
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
boundary f f f
|
||||
|
||||
# region to create atoms
|
||||
region bigCyl cylinder z 0. 0. ${lg} -$w $w
|
||||
region offsetPlane block -${lg} $g -${lg} ${lg} -$w $w
|
||||
region mdRegion intersect 2 bigCyl offsetPlane
|
||||
#create_box 1 mdRegion
|
||||
pair_style lj/cut 13.5
|
||||
read_data semicircle.init
|
||||
|
||||
# region for internal atoms
|
||||
region mdInternalCyl cylinder z 0. 0. $l -$w $w
|
||||
region leftHalfPlane block INF 0. INF INF INF INF
|
||||
region mdInternal intersect 2 mdInternalCyl leftHalfPlane
|
||||
|
||||
# region for coupling ghosts
|
||||
region rightHalfPlane block 0. INF INF INF INF INF
|
||||
region mdGhost union 2 rightHalfPlane mdInternal side out
|
||||
|
||||
#create_atoms 1 region mdRegion
|
||||
#create_atoms 1 region mdInternal
|
||||
#create_atoms 2 region mdGhost
|
||||
#region outerGhost intersect 2 rightHalfPlane mdRegion
|
||||
#create_atoms 3 region outerGhost
|
||||
|
||||
#pair_style lj/cut 13.5
|
||||
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 region mdGhost
|
||||
#velocity internal create 40 102486 mom yes rot yes dist gaussian
|
||||
#write_restart semicircle_init.rst
|
||||
|
||||
# ATC commands
|
||||
fix AtC internal atc thermal Ar_ttm.mat
|
||||
fix_modify AtC boundary ghost
|
||||
fix_modify AtC mesh read semicircle.mesh f f p
|
||||
fix_modify AtC mesh nodeset_to_elementset 2 hole min
|
||||
fix_modify AtC internal_quadrature off
|
||||
fix_modify AtC time_integration fractional_step
|
||||
|
||||
# initial conditions
|
||||
fix_modify AtC fix temperature all 20.
|
||||
fix_modify AtC control thermal rescale 10
|
||||
fix_modify AtC control tolerance 1.e-14 # tolerance needed to produce consistent parallel and serial results
|
||||
|
||||
# initial output
|
||||
#fix_modify AtC mesh output semicircle_mesh
|
||||
#fix_modify AtC output semicircle_init 100 text binary
|
||||
#dump D1 all atom 100 semicircle_init.dmp
|
||||
|
||||
# run
|
||||
timestep 5.0
|
||||
thermo 100
|
||||
run 500
|
||||
|
||||
# boundary conditions
|
||||
fix_modify AtC unfix temperature all
|
||||
fix_modify AtC fix temperature 1 20.
|
||||
fix_modify AtC control thermal flux
|
||||
fix_modify AtC control localized_lambda on
|
||||
|
||||
# NOTE appears to be a problem with the temporal ramp function
|
||||
variable delta_t equal 1000*5.
|
||||
fix_modify AtC source temperature hole temporal_ramp 0. 0.0000000001 ${delta_t}
|
||||
|
||||
# equilibrate filter
|
||||
fix_modify AtC filter type exponential
|
||||
fix_modify AtC filter scale 1000.
|
||||
fix_modify AtC filter on
|
||||
|
||||
# equilibration output
|
||||
fix_modify AtC output semicircleFE 100 full_text #binary
|
||||
#undump D1
|
||||
#dump D1 all atom 100 semicircle_equil.dmp
|
||||
|
||||
# run
|
||||
fix_modify AtC reset_time 0.
|
||||
reset_timestep 0
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
# heat source
|
||||
# NOTE second run omitted as it causes diffs in parallel execution after just one timestep, not sure why
|
||||
#fix_modify AtC source temperature hole 0.0000000001
|
||||
#fix_modify AtC output semicircleFE 1 full_text #binary
|
||||
#undump D1
|
||||
#dump D1 all atom 100 semicircle.dmp
|
||||
#run 1#000
|
||||
|
||||
@ -1,56 +1,56 @@
|
||||
# needs description
|
||||
#AtC thermal Coupling
|
||||
#
|
||||
echo both
|
||||
|
||||
units real
|
||||
atom_style atomic
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region feRegion block -10 10 -1 1 -1 1
|
||||
boundary f p p
|
||||
create_box 1 feRegion
|
||||
mass 1 39.95 # need to keep this
|
||||
atom_modify sort 0 1
|
||||
region dummyRegion block -100 -99 -1 1 -1 1
|
||||
group dummy region dummyRegion
|
||||
|
||||
# ID group atc PhysicsType ParameterFile
|
||||
fix AtC dummy atc thermal Ar_thermal.mat
|
||||
timestep 5.0
|
||||
|
||||
# ID part keywords nx ny nz region
|
||||
fix_modify AtC mesh create 10 1 1 feRegion f p p
|
||||
|
||||
# fix end temperatures and an internal source
|
||||
fix_modify AtC initial temperature all 20.0
|
||||
fix_modify AtC source temperature all 0.0000000000632
|
||||
fix_modify AtC mesh create_nodeset lbc -10.1 -9.9 -INF INF -INF INF
|
||||
fix_modify AtC mesh create_nodeset rbc 9.9 10.1 -INF INF -INF INF
|
||||
fix_modify AtC fix temperature lbc 20.
|
||||
fix_modify AtC fix temperature rbc 20.
|
||||
|
||||
fix_modify AtC mesh create_elementset middle -4.1 4.1 -INF INF -INF INF
|
||||
fix_modify AtC material middle Ar2
|
||||
|
||||
thermo_style custom step cpu f_AtC[1] f_AtC[2]
|
||||
fix_modify AtC output no_atomsFE 1000 text binary
|
||||
thermo 100
|
||||
run 10000
|
||||
|
||||
|
||||
fix_modify AtC remove_source temperature all
|
||||
fix_modify AtC unfix temperature rbc
|
||||
|
||||
fix_modify AtC fix temperature all 20.
|
||||
run 1
|
||||
fix_modify AtC unfix temperature all
|
||||
reset_timestep 0
|
||||
|
||||
# fix one end temperature and the a source at the other
|
||||
fix_modify AtC fix temperature lbc 20.
|
||||
fix_modify AtC mesh create_faceset rbcFace plane x 10.0
|
||||
fix_modify AtC fix_flux temperature rbcFace 0.000000001
|
||||
|
||||
fix_modify AtC output no_atoms_flux_FE 1000 text binary # NOTE not used
|
||||
thermo 100
|
||||
run 10000
|
||||
# needs description
|
||||
#AtC thermal Coupling
|
||||
#
|
||||
echo both
|
||||
|
||||
units real
|
||||
atom_style atomic
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region feRegion block -10 10 -1 1 -1 1
|
||||
boundary f p p
|
||||
create_box 1 feRegion
|
||||
mass 1 39.95 # need to keep this
|
||||
atom_modify sort 0 1
|
||||
region dummyRegion block -100 -99 -1 1 -1 1
|
||||
group dummy region dummyRegion
|
||||
|
||||
# ID group atc PhysicsType ParameterFile
|
||||
fix AtC dummy atc thermal Ar_thermal.mat
|
||||
timestep 5.0
|
||||
|
||||
# ID part keywords nx ny nz region
|
||||
fix_modify AtC mesh create 10 1 1 feRegion f p p
|
||||
|
||||
# fix end temperatures and an internal source
|
||||
fix_modify AtC initial temperature all 20.0
|
||||
fix_modify AtC source temperature all 0.0000000000632
|
||||
fix_modify AtC mesh create_nodeset lbc -10.1 -9.9 -INF INF -INF INF
|
||||
fix_modify AtC mesh create_nodeset rbc 9.9 10.1 -INF INF -INF INF
|
||||
fix_modify AtC fix temperature lbc 20.
|
||||
fix_modify AtC fix temperature rbc 20.
|
||||
|
||||
fix_modify AtC mesh create_elementset middle -4.1 4.1 -INF INF -INF INF
|
||||
fix_modify AtC material middle Ar2
|
||||
|
||||
thermo_style custom step cpu f_AtC[1] f_AtC[2]
|
||||
fix_modify AtC output no_atomsFE 1000 text binary
|
||||
thermo 100
|
||||
run 10000
|
||||
|
||||
|
||||
fix_modify AtC remove_source temperature all
|
||||
fix_modify AtC unfix temperature rbc
|
||||
|
||||
fix_modify AtC fix temperature all 20.
|
||||
run 1
|
||||
fix_modify AtC unfix temperature all
|
||||
reset_timestep 0
|
||||
|
||||
# fix one end temperature and the a source at the other
|
||||
fix_modify AtC fix temperature lbc 20.
|
||||
fix_modify AtC mesh create_faceset rbcFace plane x 10.0
|
||||
fix_modify AtC fix_flux temperature rbcFace 0.000000001
|
||||
|
||||
fix_modify AtC output no_atoms_flux_FE 1000 text binary # NOTE not used
|
||||
thermo 100
|
||||
run 10000
|
||||
|
||||
@ -1,87 +1,87 @@
|
||||
# needs description
|
||||
#AtC Two temperature Coupling
|
||||
# DESCRIPTION:
|
||||
# delete elements from the mesh
|
||||
# heating and then relaxation
|
||||
|
||||
echo both
|
||||
units metal
|
||||
variable INF equal 1000
|
||||
|
||||
variable T equal 20
|
||||
|
||||
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
|
||||
#create_atoms 1 region MD
|
||||
#group internal region FREE
|
||||
#mass 1 39.95
|
||||
#read_data cutout.data
|
||||
#pair_coeff * * .238 3.405 13.5
|
||||
#velocity internal create 40 87287 mom yes loop geom
|
||||
#fix NVE internal nve
|
||||
#thermo 100
|
||||
#dump CONFIG all atom 100 cutout.dump
|
||||
##run 1000
|
||||
#unfix NVE
|
||||
#write_restart cutout.rst
|
||||
|
||||
pair_style lj/cut 13.5
|
||||
read_data cutout.init
|
||||
group internal region FREE
|
||||
group ghost subtract all internal
|
||||
|
||||
timestep 0.002
|
||||
thermo 20
|
||||
|
||||
# allow initial state to relax
|
||||
fix NVT internal nvt temp $T $T 10 drag 0.2
|
||||
fix RESCALE internal temp/rescale 25 $T $T 0.05 1.0
|
||||
run 200
|
||||
unfix RESCALE
|
||||
run 800
|
||||
unfix NVT
|
||||
|
||||
# ID group atc PhysicsType ParameterFile
|
||||
fix AtC internal atc two_temperature Ar_ttm.mat
|
||||
|
||||
# ID part keywords nx ny nz region
|
||||
fix_modify AtC mesh create 8 6 1 FE f f p
|
||||
|
||||
fix_modify AtC mesh create_elementset wire -4 4 -INF 0 -INF INF
|
||||
fix_modify AtC mesh create_nodeset gap -4 4 -0 INF -INF INF
|
||||
fix_modify AtC mesh create_elementset gap -4 4 -0 INF -INF INF
|
||||
fix_modify AtC mesh delete_elements gap
|
||||
|
||||
fix_modify AtC mesh create_faceset bndy box -4 4 -INF 0 -INF INF
|
||||
fix_modify AtC control thermal flux faceset bndy
|
||||
|
||||
# fix a temperature
|
||||
fix_modify AtC initial temperature all 20.0
|
||||
fix_modify AtC initial electron_temperature all 30.0
|
||||
fix_modify AtC initial temperature gap 0.0
|
||||
|
||||
# relaxation
|
||||
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4]
|
||||
fix_modify AtC output cutoutFE 10 text
|
||||
fix_modify AtC extrinsic electron_integration implicit
|
||||
|
||||
# heating
|
||||
fix_modify AtC mesh create_nodeset lbc -8 -8 -INF INF -INF INF
|
||||
fix_modify AtC mesh create_nodeset rbc 8 8 -INF INF -INF INF
|
||||
fix_modify AtC fix electron_temperature lbc 20.
|
||||
fix_modify AtC fix electron_temperature rbc 20.
|
||||
fix_modify AtC source electron_temperature wire 0.001
|
||||
run 200
|
||||
|
||||
# relaxation
|
||||
fix_modify AtC remove_source electron_temperature wire
|
||||
run 200
|
||||
# needs description
|
||||
#AtC Two temperature Coupling
|
||||
# DESCRIPTION:
|
||||
# delete elements from the mesh
|
||||
# heating and then relaxation
|
||||
|
||||
echo both
|
||||
units metal
|
||||
variable INF equal 1000
|
||||
|
||||
variable T equal 20
|
||||
|
||||
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
|
||||
#create_atoms 1 region MD
|
||||
#group internal region FREE
|
||||
#mass 1 39.95
|
||||
#read_data cutout.data
|
||||
#pair_coeff * * .238 3.405 13.5
|
||||
#velocity internal create 40 87287 mom yes loop geom
|
||||
#fix NVE internal nve
|
||||
#thermo 100
|
||||
#dump CONFIG all atom 100 cutout.dump
|
||||
##run 1000
|
||||
#unfix NVE
|
||||
#write_restart cutout.rst
|
||||
|
||||
pair_style lj/cut 13.5
|
||||
read_data cutout.init
|
||||
group internal region FREE
|
||||
group ghost subtract all internal
|
||||
|
||||
timestep 0.002
|
||||
thermo 20
|
||||
|
||||
# allow initial state to relax
|
||||
fix NVT internal nvt temp $T $T 10 drag 0.2
|
||||
fix RESCALE internal temp/rescale 25 $T $T 0.05 1.0
|
||||
run 200
|
||||
unfix RESCALE
|
||||
run 800
|
||||
unfix NVT
|
||||
|
||||
# ID group atc PhysicsType ParameterFile
|
||||
fix AtC internal atc two_temperature Ar_ttm.mat
|
||||
|
||||
# ID part keywords nx ny nz region
|
||||
fix_modify AtC mesh create 8 6 1 FE f f p
|
||||
|
||||
fix_modify AtC mesh create_elementset wire -4 4 -INF 0 -INF INF
|
||||
fix_modify AtC mesh create_nodeset gap -4 4 -0 INF -INF INF
|
||||
fix_modify AtC mesh create_elementset gap -4 4 -0 INF -INF INF
|
||||
fix_modify AtC mesh delete_elements gap
|
||||
|
||||
fix_modify AtC mesh create_faceset bndy box -4 4 -INF 0 -INF INF
|
||||
fix_modify AtC control thermal flux faceset bndy
|
||||
|
||||
# fix a temperature
|
||||
fix_modify AtC initial temperature all 20.0
|
||||
fix_modify AtC initial electron_temperature all 30.0
|
||||
fix_modify AtC initial temperature gap 0.0
|
||||
|
||||
# relaxation
|
||||
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4]
|
||||
fix_modify AtC output cutoutFE 10 text
|
||||
fix_modify AtC extrinsic electron_integration implicit
|
||||
|
||||
# heating
|
||||
fix_modify AtC mesh create_nodeset lbc -8 -8 -INF INF -INF INF
|
||||
fix_modify AtC mesh create_nodeset rbc 8 8 -INF INF -INF INF
|
||||
fix_modify AtC fix electron_temperature lbc 20.
|
||||
fix_modify AtC fix electron_temperature rbc 20.
|
||||
fix_modify AtC source electron_temperature wire 0.001
|
||||
run 200
|
||||
|
||||
# relaxation
|
||||
fix_modify AtC remove_source electron_temperature wire
|
||||
run 200
|
||||
|
||||
@ -1,94 +1,94 @@
|
||||
#AtC Two temperature Coupling
|
||||
# DESCRIPTION:
|
||||
# full overlap of MD and FE regions w/ free ends & lateral periodic bcs
|
||||
# initial gaussian electron temperature profile and uniform phonon temperature
|
||||
# results in fast exchange followed by slower diffusion and finally relaxation
|
||||
# to equilibrium
|
||||
#
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
# create domain
|
||||
#lattice type reduced density rho* = 4*(sigma/a)^3,
|
||||
# where N = 4 for fcc,
|
||||
# s = 3.405 A (Wagner)
|
||||
# a = 5.25 A (Ashcroft & Mermin, p. 70)
|
||||
# to create restart :
|
||||
# write_restart temp.bin
|
||||
# then : restart2data temp.bin temp.init
|
||||
#if {restart}
|
||||
boundary f p p
|
||||
pair_style lj/cut 13.5
|
||||
read_data temp.init
|
||||
#endif
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region feRegion block -10 10 -3 3 -3 3
|
||||
region mdRegion block -12 12 -3 3 -3 3
|
||||
region mdInternal block -10 10 -3 3 -3 3
|
||||
|
||||
|
||||
# create atoms, NOTE commented out for restart
|
||||
#if !{restart}
|
||||
#boundary f p p
|
||||
#create_box 1 mdRegion
|
||||
#create_atoms 1 region mdRegion
|
||||
#mass 1 39.95
|
||||
#pair_style lj/cut 13.5
|
||||
#pair_coeff 1 1 .238 3.405 13.5
|
||||
#velocity internal create 40 87287 mom yes loop geom
|
||||
#endif
|
||||
|
||||
# specify interal/ghost atoms
|
||||
group internal region mdInternal
|
||||
# do not define ghosts if outside fe region
|
||||
#group ghost subtract all internal
|
||||
|
||||
neighbor 5. bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
# ID group atc PhysicsType ParameterFile
|
||||
fix AtC internal atc two_temperature Ar_ttm.mat
|
||||
|
||||
# ID part keywords nx ny nz region
|
||||
fix_modify AtC mesh create 10 1 1 feRegion f p p
|
||||
|
||||
# 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
|
||||
#timestep 0.1
|
||||
thermo 10
|
||||
#if !{restart}
|
||||
#run 1000
|
||||
#endif
|
||||
|
||||
# write restart file (for atoms)
|
||||
#if !{restart}
|
||||
#write_restart gaussianT0.dat
|
||||
#endif
|
||||
|
||||
#output
|
||||
fix_modify AtC output gaussianIC_ttmFE 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 400
|
||||
#AtC Two temperature Coupling
|
||||
# DESCRIPTION:
|
||||
# full overlap of MD and FE regions w/ free ends & lateral periodic bcs
|
||||
# initial gaussian electron temperature profile and uniform phonon temperature
|
||||
# results in fast exchange followed by slower diffusion and finally relaxation
|
||||
# to equilibrium
|
||||
#
|
||||
echo both
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
# create domain
|
||||
#lattice type reduced density rho* = 4*(sigma/a)^3,
|
||||
# where N = 4 for fcc,
|
||||
# s = 3.405 A (Wagner)
|
||||
# a = 5.25 A (Ashcroft & Mermin, p. 70)
|
||||
# to create restart :
|
||||
# write_restart temp.bin
|
||||
# then : restart2data temp.bin temp.init
|
||||
#if {restart}
|
||||
boundary f p p
|
||||
pair_style lj/cut 13.5
|
||||
read_data temp.init
|
||||
#endif
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region feRegion block -10 10 -3 3 -3 3
|
||||
region mdRegion block -12 12 -3 3 -3 3
|
||||
region mdInternal block -10 10 -3 3 -3 3
|
||||
|
||||
|
||||
# create atoms, NOTE commented out for restart
|
||||
#if !{restart}
|
||||
#boundary f p p
|
||||
#create_box 1 mdRegion
|
||||
#create_atoms 1 region mdRegion
|
||||
#mass 1 39.95
|
||||
#pair_style lj/cut 13.5
|
||||
#pair_coeff 1 1 .238 3.405 13.5
|
||||
#velocity internal create 40 87287 mom yes loop geom
|
||||
#endif
|
||||
|
||||
# specify interal/ghost atoms
|
||||
group internal region mdInternal
|
||||
# do not define ghosts if outside fe region
|
||||
#group ghost subtract all internal
|
||||
|
||||
neighbor 5. bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
# ID group atc PhysicsType ParameterFile
|
||||
fix AtC internal atc two_temperature Ar_ttm.mat
|
||||
|
||||
# ID part keywords nx ny nz region
|
||||
fix_modify AtC mesh create 10 1 1 feRegion f p p
|
||||
|
||||
# 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
|
||||
#timestep 0.1
|
||||
thermo 10
|
||||
#if !{restart}
|
||||
#run 1000
|
||||
#endif
|
||||
|
||||
# write restart file (for atoms)
|
||||
#if !{restart}
|
||||
#write_restart gaussianT0.dat
|
||||
#endif
|
||||
|
||||
#output
|
||||
fix_modify AtC output gaussianIC_ttmFE 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 400
|
||||
|
||||
@ -1,61 +1,61 @@
|
||||
# needs description
|
||||
#AtC Two temperature Coupling
|
||||
# DESCRIPTION:
|
||||
# no atoms and FE regions with periodic boundary conditions.
|
||||
# heating and then relaxation
|
||||
|
||||
echo both
|
||||
#units real
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region simRegion block -14 14 -3 3 -3 3
|
||||
region feRegion block -12 12 -3 3 -3 3
|
||||
|
||||
# need to create atoms or lammps throws an error
|
||||
region mdRegion block -12 12 -3 3 -3 3
|
||||
boundary f p p
|
||||
create_box 1 mdRegion
|
||||
mass 1 39.95 # need to keep this
|
||||
atom_modify sort 0 1
|
||||
region dummyRegion block -100 -99 -1 1 -1 1
|
||||
group dummy region dummyRegion
|
||||
|
||||
# ID group atc PhysicsType ParameterFile
|
||||
fix AtC dummy atc two_temperature Cu_ttm.mat
|
||||
timestep 0.002
|
||||
thermo 20
|
||||
|
||||
# ID part keywords nx ny nz region
|
||||
fix_modify AtC mesh create 12 1 1 feRegion f p p
|
||||
|
||||
# fix a temperature
|
||||
fix_modify AtC initial temperature all 20.0
|
||||
#fix_modify AtC initial electron_temperature all 30.0
|
||||
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
|
||||
|
||||
# relaxation
|
||||
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4]
|
||||
fix_modify AtC output no_atomsFE 10 text
|
||||
#fix_modify AtC extrinsic electron_integration subcycle 100
|
||||
fix_modify AtC extrinsic electron_integration implicit
|
||||
run 400
|
||||
|
||||
# heating
|
||||
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
|
||||
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
|
||||
fix_modify AtC fix electron_temperature lbc 20.
|
||||
fix_modify AtC fix electron_temperature rbc 20.
|
||||
#fix_modify AtC extrinsic exchange off
|
||||
#fix_modify AtC fix temperature lbc 20.
|
||||
#fix_modify AtC fix temperature rbc 20.
|
||||
#fix_modify AtC extrinsic electron_integration lockstep
|
||||
#fix_modify AtC source electron_temperature all 1000.0
|
||||
fix_modify AtC source electron_temperature all 0.521981
|
||||
run 400
|
||||
|
||||
# relaxation
|
||||
fix_modify AtC remove_source electron_temperature all
|
||||
run 400
|
||||
# needs description
|
||||
#AtC Two temperature Coupling
|
||||
# DESCRIPTION:
|
||||
# no atoms and FE regions with periodic boundary conditions.
|
||||
# heating and then relaxation
|
||||
|
||||
echo both
|
||||
#units real
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
region simRegion block -14 14 -3 3 -3 3
|
||||
region feRegion block -12 12 -3 3 -3 3
|
||||
|
||||
# need to create atoms or lammps throws an error
|
||||
region mdRegion block -12 12 -3 3 -3 3
|
||||
boundary f p p
|
||||
create_box 1 mdRegion
|
||||
mass 1 39.95 # need to keep this
|
||||
atom_modify sort 0 1
|
||||
region dummyRegion block -100 -99 -1 1 -1 1
|
||||
group dummy region dummyRegion
|
||||
|
||||
# ID group atc PhysicsType ParameterFile
|
||||
fix AtC dummy atc two_temperature Cu_ttm.mat
|
||||
timestep 0.002
|
||||
thermo 20
|
||||
|
||||
# ID part keywords nx ny nz region
|
||||
fix_modify AtC mesh create 12 1 1 feRegion f p p
|
||||
|
||||
# fix a temperature
|
||||
fix_modify AtC initial temperature all 20.0
|
||||
#fix_modify AtC initial electron_temperature all 30.0
|
||||
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
|
||||
|
||||
# relaxation
|
||||
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4]
|
||||
fix_modify AtC output no_atomsFE 10 text
|
||||
#fix_modify AtC extrinsic electron_integration subcycle 100
|
||||
fix_modify AtC extrinsic electron_integration implicit
|
||||
run 400
|
||||
|
||||
# heating
|
||||
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
|
||||
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
|
||||
fix_modify AtC fix electron_temperature lbc 20.
|
||||
fix_modify AtC fix electron_temperature rbc 20.
|
||||
#fix_modify AtC extrinsic exchange off
|
||||
#fix_modify AtC fix temperature lbc 20.
|
||||
#fix_modify AtC fix temperature rbc 20.
|
||||
#fix_modify AtC extrinsic electron_integration lockstep
|
||||
#fix_modify AtC source electron_temperature all 1000.0
|
||||
fix_modify AtC source electron_temperature all 0.521981
|
||||
run 400
|
||||
|
||||
# relaxation
|
||||
fix_modify AtC remove_source electron_temperature all
|
||||
run 400
|
||||
|
||||
@ -1,66 +1,66 @@
|
||||
#AtC Two temperature Coupling
|
||||
# DESCRIPTION:
|
||||
# full overlap of MD and FE regions with full periodic boundary conditions.
|
||||
# initial electron and phonon temperatures are different and then allowed to
|
||||
# relax.
|
||||
#
|
||||
|
||||
units real
|
||||
atom_style atomic
|
||||
boundary p p p
|
||||
|
||||
# create domain
|
||||
#lattice type reduced density rho* = 4*(sigma/a)^3,
|
||||
# where N = 4 for fcc,
|
||||
# s = 3.405 A (Wagner)
|
||||
# a = 5.25 A (Ashcroft & Mermin, p. 70)
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
|
||||
pair_style lj/cut 13.5
|
||||
|
||||
read_data uniform_exchange.init
|
||||
|
||||
region simRegion block -12 12 -3 3 -3 3
|
||||
region feRegion block -12 12 -3 3 -3 3
|
||||
|
||||
# create atoms
|
||||
region mdRegion block -12 12 -3 3 -3 3
|
||||
|
||||
# specify interal/ghost atoms
|
||||
region mdInternal block -12 12 -3 3 -3 3
|
||||
group internal region mdInternal
|
||||
|
||||
neighbor 5. bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
# ID group atc PhysicsType ParameterFile
|
||||
fix AtC internal atc two_temperature Ar_ttm.mat
|
||||
|
||||
# ID part keywords nx ny nz region
|
||||
fix_modify AtC mesh create 4 1 1 feRegion p p p
|
||||
|
||||
# fix a temperature
|
||||
fix_modify AtC fix temperature all 20.0
|
||||
fix_modify AtC fix electron_temperature all 30.0
|
||||
|
||||
timestep 5.0
|
||||
|
||||
# output
|
||||
thermo_style custom step pe temp f_AtC[2] f_AtC[4]
|
||||
thermo 10
|
||||
|
||||
# equilibrate MD field
|
||||
fix_modify AtC control thermal rescale 13
|
||||
run 500
|
||||
|
||||
# relax
|
||||
fix_modify AtC output uniform_exchangeFE 100 text
|
||||
fix_modify AtC filter type exponential
|
||||
fix_modify AtC filter scale 5.0e2
|
||||
fix_modify AtC filter on
|
||||
fix_modify AtC unfix temperature all
|
||||
fix_modify AtC unfix electron_temperature all
|
||||
fix_modify AtC control thermal flux
|
||||
|
||||
# run with FE
|
||||
run 5000
|
||||
#AtC Two temperature Coupling
|
||||
# DESCRIPTION:
|
||||
# full overlap of MD and FE regions with full periodic boundary conditions.
|
||||
# initial electron and phonon temperatures are different and then allowed to
|
||||
# relax.
|
||||
#
|
||||
|
||||
units real
|
||||
atom_style atomic
|
||||
boundary p p p
|
||||
|
||||
# create domain
|
||||
#lattice type reduced density rho* = 4*(sigma/a)^3,
|
||||
# where N = 4 for fcc,
|
||||
# s = 3.405 A (Wagner)
|
||||
# a = 5.25 A (Ashcroft & Mermin, p. 70)
|
||||
lattice fcc 5.405 origin 0.25 0.25 0.25
|
||||
|
||||
pair_style lj/cut 13.5
|
||||
|
||||
read_data uniform_exchange.init
|
||||
|
||||
region simRegion block -12 12 -3 3 -3 3
|
||||
region feRegion block -12 12 -3 3 -3 3
|
||||
|
||||
# create atoms
|
||||
region mdRegion block -12 12 -3 3 -3 3
|
||||
|
||||
# specify interal/ghost atoms
|
||||
region mdInternal block -12 12 -3 3 -3 3
|
||||
group internal region mdInternal
|
||||
|
||||
neighbor 5. bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
# ID group atc PhysicsType ParameterFile
|
||||
fix AtC internal atc two_temperature Ar_ttm.mat
|
||||
|
||||
# ID part keywords nx ny nz region
|
||||
fix_modify AtC mesh create 4 1 1 feRegion p p p
|
||||
|
||||
# fix a temperature
|
||||
fix_modify AtC fix temperature all 20.0
|
||||
fix_modify AtC fix electron_temperature all 30.0
|
||||
|
||||
timestep 5.0
|
||||
|
||||
# output
|
||||
thermo_style custom step pe temp f_AtC[2] f_AtC[4]
|
||||
thermo 10
|
||||
|
||||
# equilibrate MD field
|
||||
fix_modify AtC control thermal rescale 13
|
||||
run 500
|
||||
|
||||
# relax
|
||||
fix_modify AtC output uniform_exchangeFE 100 text
|
||||
fix_modify AtC filter type exponential
|
||||
fix_modify AtC filter scale 5.0e2
|
||||
fix_modify AtC filter on
|
||||
fix_modify AtC unfix temperature all
|
||||
fix_modify AtC unfix electron_temperature all
|
||||
fix_modify AtC control thermal flux
|
||||
|
||||
# run with FE
|
||||
run 5000
|
||||
|
||||
@ -1,119 +1,119 @@
|
||||
Created by AJB
|
||||
|
||||
102 atoms
|
||||
3 atom types
|
||||
|
||||
-500.0 500.0 xlo xhi
|
||||
-500.0 500.0 ylo yhi
|
||||
-500.0 500.0 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 12.01070 # C nuclei
|
||||
2 1.000794 # H nuclei
|
||||
3 1.000000 # electron
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 6.00 0 0.000000 0.223271 2.836177 0.99547
|
||||
2 1 6.00 0 0.000000 -0.611326 1.278041 3.303884
|
||||
3 1 6.00 0 0.000000 -0.645795 -1.544681 2.608294
|
||||
4 1 6.00 0 0.000000 -2.509122 -1.980433 0.419368
|
||||
5 1 6.00 0 0.000000 -1.674732 -0.422977 -1.889518
|
||||
6 1 6.00 0 0.000000 -1.640226 2.39965 -1.193097
|
||||
7 1 6.00 0 0.000000 2.018681 -2.373515 1.79163
|
||||
8 1 6.00 0 0.000000 2.887596 2.006776 0.178976
|
||||
9 1 6.00 0 0.000000 0.98999 -1.251962 -2.705445
|
||||
10 1 6.00 0 0.000000 2.853997 -0.815965 -0.517029
|
||||
11 2 1.00 0 0.000000 -3.029741 -0.739677 -3.479893
|
||||
12 2 1.00 0 0.000000 -4.456466 -1.425024 1.003463
|
||||
13 2 1.00 0 0.000000 -2.581253 -4.027951 -0.074795
|
||||
14 2 1.00 0 0.000000 -1.252983 -2.67657 4.28622
|
||||
15 2 1.00 0 0.000000 -2.524731 1.891635 3.93955
|
||||
16 2 1.00 0 0.000000 0.703394 1.61118 4.917143
|
||||
17 2 1.00 0 0.000000 0.247516 4.887701 1.501501
|
||||
18 2 1.00 0 0.000000 2.027034 -4.428006 1.321731
|
||||
19 2 1.00 0 0.000000 3.379737 -2.105382 3.378244
|
||||
20 2 1.00 0 0.000000 4.790758 -1.418428 -1.109855
|
||||
21 2 1.00 0 0.000000 -1.077541 3.552194 -2.865467
|
||||
22 2 1.00 0 0.000000 -3.572149 3.033181 -0.63782
|
||||
23 2 1.00 0 0.000000 1.599389 -0.164293 -4.40463
|
||||
24 2 1.00 0 0.000000 0.980069 -3.286423 -3.255167
|
||||
25 2 1.00 0 0.000000 4.264224 2.353276 1.736734
|
||||
26 2 1.00 0 0.000000 3.530575 3.152347 -1.469016
|
||||
27 3 0.00 1 0.332948 0.223271 2.836177 0.99547
|
||||
28 3 0.00 -1 0.332948 0.223271 2.836177 0.99547
|
||||
29 3 0.00 1 0.332948 -0.611326 1.278041 3.303884
|
||||
30 3 0.00 -1 0.332948 -0.611326 1.278041 3.303884
|
||||
31 3 0.00 1 0.332948 -0.645795 -1.544681 2.608294
|
||||
32 3 0.00 -1 0.332948 -0.645795 -1.544681 2.608294
|
||||
33 3 0.00 1 0.332948 -2.509122 -1.980433 0.419368
|
||||
34 3 0.00 -1 0.332948 -2.509122 -1.980433 0.419368
|
||||
35 3 0.00 1 0.332948 -1.674732 -0.422977 -1.889518
|
||||
36 3 0.00 -1 0.332948 -1.674732 -0.422977 -1.889518
|
||||
37 3 0.00 1 0.332948 -1.640226 2.39965 -1.193097
|
||||
38 3 0.00 -1 0.332948 -1.640226 2.39965 -1.193097
|
||||
39 3 0.00 1 0.332948 2.018681 -2.373515 1.79163
|
||||
40 3 0.00 -1 0.332948 2.018681 -2.373515 1.79163
|
||||
41 3 0.00 1 0.332948 2.887596 2.006776 0.178976
|
||||
42 3 0.00 -1 0.332948 2.887596 2.006776 0.178976
|
||||
43 3 0.00 1 0.332948 0.98999 -1.251962 -2.705445
|
||||
44 3 0.00 -1 0.332948 0.98999 -1.251962 -2.705445
|
||||
45 3 0.00 1 0.332948 2.853997 -0.815965 -0.517029
|
||||
46 3 0.00 -1 0.332948 2.853997 -0.815965 -0.517029
|
||||
47 3 0.00 1 1.258000 -0.194028 2.057109 2.149677
|
||||
48 3 0.00 -1 1.258000 -0.194028 2.057109 2.149677
|
||||
49 3 0.00 1 1.258000 -0.628561 -0.13332 2.956089
|
||||
50 3 0.00 -1 1.258000 -0.628561 -0.13332 2.956089
|
||||
51 3 0.00 1 1.258000 -1.577458 -1.762557 1.513831
|
||||
52 3 0.00 -1 1.258000 -1.577458 -1.762557 1.513831
|
||||
53 3 0.00 1 1.258000 -2.091927 -1.201705 -0.735075
|
||||
54 3 0.00 -1 1.258000 -2.091927 -1.201705 -0.735075
|
||||
55 3 0.00 1 1.258000 -0.708477 2.617913 -0.098814
|
||||
56 3 0.00 -1 1.258000 -0.708477 2.617913 -0.098814
|
||||
57 3 0.00 1 1.258000 -1.657479 0.988336 -1.541308
|
||||
58 3 0.00 -1 1.258000 -1.657479 0.988336 -1.541308
|
||||
59 3 0.00 1 1.258000 0.686443 -1.959098 2.199962
|
||||
60 3 0.00 -1 1.258000 0.686443 -1.959098 2.199962
|
||||
61 3 0.00 1 1.258000 1.555434 2.421476 0.587223
|
||||
62 3 0.00 -1 1.258000 1.555434 2.421476 0.587223
|
||||
63 3 0.00 1 1.258000 -0.342371 -0.83747 -2.297482
|
||||
64 3 0.00 -1 1.258000 -0.342371 -0.83747 -2.297482
|
||||
65 3 0.00 1 1.258000 2.436339 -1.59474 0.637301
|
||||
66 3 0.00 -1 1.258000 2.436339 -1.59474 0.637301
|
||||
67 3 0.00 1 1.258000 2.870796 0.595405 -0.169027
|
||||
68 3 0.00 -1 1.258000 2.870796 0.595405 -0.169027
|
||||
69 3 0.00 1 1.258000 1.921993 -1.033964 -1.611237
|
||||
70 3 0.00 -1 1.258000 1.921993 -1.033964 -1.611237
|
||||
71 3 0.00 1 1.543000 -2.632724 -0.646884 -3.013913
|
||||
72 3 0.00 -1 1.543000 -2.632724 -0.646884 -3.013913
|
||||
73 3 0.00 1 1.543000 -3.885894 -1.587759 0.832324
|
||||
74 3 0.00 -1 1.543000 -3.885894 -1.587759 0.832324
|
||||
75 3 0.00 1 1.543000 -2.560118 -3.428028 0.069995
|
||||
76 3 0.00 -1 1.543000 -2.560118 -3.428028 0.069995
|
||||
77 3 0.00 1 1.543000 -1.075077 -2.344927 3.794588
|
||||
78 3 0.00 -1 1.543000 -1.075077 -2.344927 3.794588
|
||||
79 3 0.00 1 1.543000 -1.964103 1.711852 3.7533
|
||||
80 3 0.00 -1 1.543000 -1.964103 1.711852 3.7533
|
||||
81 3 0.00 1 1.543000 0.318181 1.513571 4.444458
|
||||
82 3 0.00 -1 1.543000 0.318181 1.513571 4.444458
|
||||
83 3 0.00 1 1.543000 0.240412 4.286604 1.353234
|
||||
84 3 0.00 -1 1.543000 0.240412 4.286604 1.353234
|
||||
85 3 0.00 1 1.543000 2.024586 -3.82604 1.459412
|
||||
86 3 0.00 -1 1.543000 2.024586 -3.82604 1.459412
|
||||
87 3 0.00 1 1.543000 2.980948 -2.183945 2.913367
|
||||
88 3 0.00 -1 1.543000 2.980948 -2.183945 2.913367
|
||||
89 3 0.00 1 1.543000 4.223287 -1.241907 -0.936157
|
||||
90 3 0.00 -1 1.543000 4.223287 -1.241907 -0.936157
|
||||
91 3 0.00 1 1.543000 -1.242407 3.214498 -2.375463
|
||||
92 3 0.00 -1 1.543000 -1.242407 3.214498 -2.375463
|
||||
93 3 0.00 1 1.543000 -3.006096 2.847556 -0.800517
|
||||
94 3 0.00 -1 1.543000 -3.006096 2.847556 -0.800517
|
||||
95 3 0.00 1 1.543000 1.420835 -0.48298 -3.906769
|
||||
96 3 0.00 -1 1.543000 1.420835 -0.48298 -3.906769
|
||||
97 3 0.00 1 1.543000 0.982976 -2.690326 -3.094098
|
||||
98 3 0.00 -1 1.543000 0.982976 -2.690326 -3.094098
|
||||
99 3 0.00 1 1.543000 3.860872 2.251751 1.280311
|
||||
100 3 0.00 -1 1.543000 3.860872 2.251751 1.280311
|
||||
101 3 0.00 1 1.543000 3.342182 2.816694 -0.986155
|
||||
102 3 0.00 -1 1.543000 3.342182 2.816694 -0.986155
|
||||
Created by AJB
|
||||
|
||||
102 atoms
|
||||
3 atom types
|
||||
|
||||
-500.0 500.0 xlo xhi
|
||||
-500.0 500.0 ylo yhi
|
||||
-500.0 500.0 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 12.01070 # C nuclei
|
||||
2 1.000794 # H nuclei
|
||||
3 1.000000 # electron
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 6.00 0 0.000000 0.223271 2.836177 0.99547
|
||||
2 1 6.00 0 0.000000 -0.611326 1.278041 3.303884
|
||||
3 1 6.00 0 0.000000 -0.645795 -1.544681 2.608294
|
||||
4 1 6.00 0 0.000000 -2.509122 -1.980433 0.419368
|
||||
5 1 6.00 0 0.000000 -1.674732 -0.422977 -1.889518
|
||||
6 1 6.00 0 0.000000 -1.640226 2.39965 -1.193097
|
||||
7 1 6.00 0 0.000000 2.018681 -2.373515 1.79163
|
||||
8 1 6.00 0 0.000000 2.887596 2.006776 0.178976
|
||||
9 1 6.00 0 0.000000 0.98999 -1.251962 -2.705445
|
||||
10 1 6.00 0 0.000000 2.853997 -0.815965 -0.517029
|
||||
11 2 1.00 0 0.000000 -3.029741 -0.739677 -3.479893
|
||||
12 2 1.00 0 0.000000 -4.456466 -1.425024 1.003463
|
||||
13 2 1.00 0 0.000000 -2.581253 -4.027951 -0.074795
|
||||
14 2 1.00 0 0.000000 -1.252983 -2.67657 4.28622
|
||||
15 2 1.00 0 0.000000 -2.524731 1.891635 3.93955
|
||||
16 2 1.00 0 0.000000 0.703394 1.61118 4.917143
|
||||
17 2 1.00 0 0.000000 0.247516 4.887701 1.501501
|
||||
18 2 1.00 0 0.000000 2.027034 -4.428006 1.321731
|
||||
19 2 1.00 0 0.000000 3.379737 -2.105382 3.378244
|
||||
20 2 1.00 0 0.000000 4.790758 -1.418428 -1.109855
|
||||
21 2 1.00 0 0.000000 -1.077541 3.552194 -2.865467
|
||||
22 2 1.00 0 0.000000 -3.572149 3.033181 -0.63782
|
||||
23 2 1.00 0 0.000000 1.599389 -0.164293 -4.40463
|
||||
24 2 1.00 0 0.000000 0.980069 -3.286423 -3.255167
|
||||
25 2 1.00 0 0.000000 4.264224 2.353276 1.736734
|
||||
26 2 1.00 0 0.000000 3.530575 3.152347 -1.469016
|
||||
27 3 0.00 1 0.332948 0.223271 2.836177 0.99547
|
||||
28 3 0.00 -1 0.332948 0.223271 2.836177 0.99547
|
||||
29 3 0.00 1 0.332948 -0.611326 1.278041 3.303884
|
||||
30 3 0.00 -1 0.332948 -0.611326 1.278041 3.303884
|
||||
31 3 0.00 1 0.332948 -0.645795 -1.544681 2.608294
|
||||
32 3 0.00 -1 0.332948 -0.645795 -1.544681 2.608294
|
||||
33 3 0.00 1 0.332948 -2.509122 -1.980433 0.419368
|
||||
34 3 0.00 -1 0.332948 -2.509122 -1.980433 0.419368
|
||||
35 3 0.00 1 0.332948 -1.674732 -0.422977 -1.889518
|
||||
36 3 0.00 -1 0.332948 -1.674732 -0.422977 -1.889518
|
||||
37 3 0.00 1 0.332948 -1.640226 2.39965 -1.193097
|
||||
38 3 0.00 -1 0.332948 -1.640226 2.39965 -1.193097
|
||||
39 3 0.00 1 0.332948 2.018681 -2.373515 1.79163
|
||||
40 3 0.00 -1 0.332948 2.018681 -2.373515 1.79163
|
||||
41 3 0.00 1 0.332948 2.887596 2.006776 0.178976
|
||||
42 3 0.00 -1 0.332948 2.887596 2.006776 0.178976
|
||||
43 3 0.00 1 0.332948 0.98999 -1.251962 -2.705445
|
||||
44 3 0.00 -1 0.332948 0.98999 -1.251962 -2.705445
|
||||
45 3 0.00 1 0.332948 2.853997 -0.815965 -0.517029
|
||||
46 3 0.00 -1 0.332948 2.853997 -0.815965 -0.517029
|
||||
47 3 0.00 1 1.258000 -0.194028 2.057109 2.149677
|
||||
48 3 0.00 -1 1.258000 -0.194028 2.057109 2.149677
|
||||
49 3 0.00 1 1.258000 -0.628561 -0.13332 2.956089
|
||||
50 3 0.00 -1 1.258000 -0.628561 -0.13332 2.956089
|
||||
51 3 0.00 1 1.258000 -1.577458 -1.762557 1.513831
|
||||
52 3 0.00 -1 1.258000 -1.577458 -1.762557 1.513831
|
||||
53 3 0.00 1 1.258000 -2.091927 -1.201705 -0.735075
|
||||
54 3 0.00 -1 1.258000 -2.091927 -1.201705 -0.735075
|
||||
55 3 0.00 1 1.258000 -0.708477 2.617913 -0.098814
|
||||
56 3 0.00 -1 1.258000 -0.708477 2.617913 -0.098814
|
||||
57 3 0.00 1 1.258000 -1.657479 0.988336 -1.541308
|
||||
58 3 0.00 -1 1.258000 -1.657479 0.988336 -1.541308
|
||||
59 3 0.00 1 1.258000 0.686443 -1.959098 2.199962
|
||||
60 3 0.00 -1 1.258000 0.686443 -1.959098 2.199962
|
||||
61 3 0.00 1 1.258000 1.555434 2.421476 0.587223
|
||||
62 3 0.00 -1 1.258000 1.555434 2.421476 0.587223
|
||||
63 3 0.00 1 1.258000 -0.342371 -0.83747 -2.297482
|
||||
64 3 0.00 -1 1.258000 -0.342371 -0.83747 -2.297482
|
||||
65 3 0.00 1 1.258000 2.436339 -1.59474 0.637301
|
||||
66 3 0.00 -1 1.258000 2.436339 -1.59474 0.637301
|
||||
67 3 0.00 1 1.258000 2.870796 0.595405 -0.169027
|
||||
68 3 0.00 -1 1.258000 2.870796 0.595405 -0.169027
|
||||
69 3 0.00 1 1.258000 1.921993 -1.033964 -1.611237
|
||||
70 3 0.00 -1 1.258000 1.921993 -1.033964 -1.611237
|
||||
71 3 0.00 1 1.543000 -2.632724 -0.646884 -3.013913
|
||||
72 3 0.00 -1 1.543000 -2.632724 -0.646884 -3.013913
|
||||
73 3 0.00 1 1.543000 -3.885894 -1.587759 0.832324
|
||||
74 3 0.00 -1 1.543000 -3.885894 -1.587759 0.832324
|
||||
75 3 0.00 1 1.543000 -2.560118 -3.428028 0.069995
|
||||
76 3 0.00 -1 1.543000 -2.560118 -3.428028 0.069995
|
||||
77 3 0.00 1 1.543000 -1.075077 -2.344927 3.794588
|
||||
78 3 0.00 -1 1.543000 -1.075077 -2.344927 3.794588
|
||||
79 3 0.00 1 1.543000 -1.964103 1.711852 3.7533
|
||||
80 3 0.00 -1 1.543000 -1.964103 1.711852 3.7533
|
||||
81 3 0.00 1 1.543000 0.318181 1.513571 4.444458
|
||||
82 3 0.00 -1 1.543000 0.318181 1.513571 4.444458
|
||||
83 3 0.00 1 1.543000 0.240412 4.286604 1.353234
|
||||
84 3 0.00 -1 1.543000 0.240412 4.286604 1.353234
|
||||
85 3 0.00 1 1.543000 2.024586 -3.82604 1.459412
|
||||
86 3 0.00 -1 1.543000 2.024586 -3.82604 1.459412
|
||||
87 3 0.00 1 1.543000 2.980948 -2.183945 2.913367
|
||||
88 3 0.00 -1 1.543000 2.980948 -2.183945 2.913367
|
||||
89 3 0.00 1 1.543000 4.223287 -1.241907 -0.936157
|
||||
90 3 0.00 -1 1.543000 4.223287 -1.241907 -0.936157
|
||||
91 3 0.00 1 1.543000 -1.242407 3.214498 -2.375463
|
||||
92 3 0.00 -1 1.543000 -1.242407 3.214498 -2.375463
|
||||
93 3 0.00 1 1.543000 -3.006096 2.847556 -0.800517
|
||||
94 3 0.00 -1 1.543000 -3.006096 2.847556 -0.800517
|
||||
95 3 0.00 1 1.543000 1.420835 -0.48298 -3.906769
|
||||
96 3 0.00 -1 1.543000 1.420835 -0.48298 -3.906769
|
||||
97 3 0.00 1 1.543000 0.982976 -2.690326 -3.094098
|
||||
98 3 0.00 -1 1.543000 0.982976 -2.690326 -3.094098
|
||||
99 3 0.00 1 1.543000 3.860872 2.251751 1.280311
|
||||
100 3 0.00 -1 1.543000 3.860872 2.251751 1.280311
|
||||
101 3 0.00 1 1.543000 3.342182 2.816694 -0.986155
|
||||
102 3 0.00 -1 1.543000 3.342182 2.816694 -0.986155
|
||||
|
||||
@ -1,118 +1,118 @@
|
||||
Created by AJB
|
||||
|
||||
101 atoms
|
||||
3 atom types
|
||||
|
||||
-50.0 50.0 xlo xhi
|
||||
-50.0 50.0 ylo yhi
|
||||
-50.0 50.0 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 12.01070 # C nuclei
|
||||
2 1.000794 # H nuclei
|
||||
3 1.000000 # electron
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 6.00 0 0.000000 0.224230 2.918607 1.015812
|
||||
2 1 6.00 0 0.000000 -0.634450 1.314460 3.390303
|
||||
3 1 6.00 0 0.000000 -0.670162 -1.590173 2.675707
|
||||
4 1 6.00 0 0.000000 -2.586695 -2.037708 0.422846
|
||||
5 1 6.00 0 0.000000 -1.729127 -0.435706 -1.953488
|
||||
6 1 6.00 0 0.000000 -1.692867 2.468206 -1.236000
|
||||
7 1 6.00 0 0.000000 2.071281 -2.442011 1.834504
|
||||
8 1 6.00 0 0.000000 2.965108 2.063979 0.175607
|
||||
9 1 6.00 0 0.000000 1.013015 -1.288254 -2.791737
|
||||
10 1 6.00 0 0.000000 2.931847 -0.840220 -0.540904
|
||||
11 2 1.00 0 0.000000 -3.237070 -0.788493 -3.724286
|
||||
12 2 1.00 0 0.000000 -4.691469 -1.429253 1.056080
|
||||
13 2 1.00 0 0.000000 -2.657034 -4.253233 -0.113602
|
||||
14 2 1.00 0 0.000000 -1.345725 -2.850372 4.543752
|
||||
15 2 1.00 0 0.000000 -2.707861 1.976434 4.071194
|
||||
16 2 1.00 0 0.000000 0.794230 1.672161 5.131751
|
||||
17 2 1.00 0 0.000000 0.251667 5.202465 1.579125
|
||||
18 2 1.00 0 0.000000 2.074796 -4.663951 1.320307
|
||||
19 2 1.00 0 0.000000 3.542471 -2.144066 3.551451
|
||||
20 2 1.00 0 0.000000 5.087753 -1.511020 -1.201338
|
||||
21 2 1.00 0 0.000000 -1.077021 3.711707 -3.045901
|
||||
22 2 1.00 0 0.000000 -3.783389 3.148492 -0.629227
|
||||
23 2 1.00 0 0.000000 1.671766 -0.104421 -4.626344
|
||||
24 2 1.00 0 0.000000 0.999815 -3.491890 -3.379184
|
||||
25 2 1.00 0 0.000000 4.450647 2.434018 1.865941
|
||||
26 2 1.00 0 0.000000 3.654660 3.300997 -1.612081
|
||||
27 3 0.00 -1 0.328405 -0.634804 1.315020 3.391634
|
||||
28 3 0.00 -1 0.328107 -0.670512 -1.590826 2.676675
|
||||
29 3 0.00 -1 0.328405 -2.587889 -2.038591 0.422899
|
||||
30 3 0.00 -1 0.328107 -1.729909 -0.435889 -1.954405
|
||||
31 3 0.00 -1 0.328405 -1.693676 2.469262 -1.236661
|
||||
32 3 0.00 -1 0.328405 2.072091 -2.443067 1.835165
|
||||
33 3 0.00 -1 0.328405 2.966303 2.064861 0.175553
|
||||
34 3 0.00 -1 0.328405 1.013370 -1.288814 -2.793067
|
||||
35 3 0.00 -1 0.328108 2.932965 -0.840567 -0.541247
|
||||
36 3 0.00 -1 1.326096 -0.210743 2.123398 2.223462
|
||||
37 3 0.00 -1 1.326096 -0.657351 -0.127988 3.052304
|
||||
38 3 0.00 -1 1.326093 -1.646634 -1.826737 1.548546
|
||||
39 3 0.00 -1 1.326095 -2.175416 -1.250260 -0.762988
|
||||
40 3 0.00 -1 1.326093 -0.747076 2.708081 -0.120938
|
||||
41 3 0.00 -1 1.326095 -1.722464 1.033139 -1.603613
|
||||
42 3 0.00 -1 1.326092 0.713852 -2.031645 2.263933
|
||||
43 3 0.00 -1 1.326092 1.613424 2.503259 0.594420
|
||||
44 3 0.00 -1 1.326098 -0.351222 -0.870483 -2.392027
|
||||
45 3 0.00 -1 1.326100 2.512477 -1.657113 0.657756
|
||||
46 3 0.00 -1 1.326099 2.965428 0.626295 -0.182887
|
||||
47 3 0.00 -1 1.326101 1.976186 -1.072464 -1.686660
|
||||
48 3 0.00 -1 1.603792 -2.952851 -0.722000 -3.390526
|
||||
49 3 0.00 -1 1.558563 -4.265445 -1.534526 0.932369
|
||||
50 3 0.00 -1 1.558562 -2.625986 -3.810249 -0.010226
|
||||
51 3 0.00 -1 1.603792 -1.218394 -2.612849 4.191661
|
||||
52 3 0.00 -1 1.558507 -2.300135 1.839753 3.919625
|
||||
53 3 0.00 -1 1.558620 0.522041 1.594565 4.774310
|
||||
54 3 0.00 -1 1.603792 0.246496 4.772002 1.472951
|
||||
55 3 0.00 -1 1.558582 2.062319 -4.217199 1.410516
|
||||
56 3 0.00 -1 1.558537 3.245048 -2.186529 3.208486
|
||||
57 3 0.00 -1 1.603791 4.681408 -1.384588 -1.076860
|
||||
58 3 0.00 -1 1.558565 -1.184793 3.454906 -2.684898
|
||||
59 3 0.00 -1 1.558559 -3.365733 3.001032 -0.737405
|
||||
60 3 0.00 -1 1.558551 1.538708 -0.326106 -4.250794
|
||||
61 3 0.00 -1 1.558563 0.997214 -3.055912 -3.245768
|
||||
62 3 0.00 -1 1.558524 4.144833 2.349324 1.538532
|
||||
63 3 0.00 -1 1.558594 3.503398 3.047996 -1.264247
|
||||
64 3 0.00 1 0.328107 0.224244 2.919790 1.016104
|
||||
65 3 0.00 1 0.328405 -0.634804 1.315020 3.391634
|
||||
66 3 0.00 1 0.328107 -0.670512 -1.590826 2.676675
|
||||
67 3 0.00 1 0.328405 -2.587889 -2.038591 0.422899
|
||||
68 3 0.00 1 0.328107 -1.729909 -0.435889 -1.954405
|
||||
69 3 0.00 1 0.328405 -1.693676 2.469262 -1.236661
|
||||
70 3 0.00 1 0.328405 2.072091 -2.443067 1.835165
|
||||
71 3 0.00 1 0.328405 2.966303 2.064861 0.175553
|
||||
72 3 0.00 1 0.328405 1.013370 -1.288814 -2.793067
|
||||
73 3 0.00 1 0.328108 2.932965 -0.840567 -0.541247
|
||||
74 3 0.00 1 1.326096 -0.210743 2.123398 2.223462
|
||||
75 3 0.00 1 1.326096 -0.657351 -0.127988 3.052304
|
||||
76 3 0.00 1 1.326093 -1.646634 -1.826737 1.548546
|
||||
77 3 0.00 1 1.326094 -2.175416 -1.250259 -0.762988
|
||||
78 3 0.00 1 1.326094 -0.747076 2.708081 -0.120938
|
||||
79 3 0.00 1 1.326096 -1.722464 1.033139 -1.603613
|
||||
80 3 0.00 1 1.326092 0.713852 -2.031645 2.263933
|
||||
81 3 0.00 1 1.326092 1.613424 2.503259 0.594420
|
||||
82 3 0.00 1 1.326098 -0.351222 -0.870483 -2.392027
|
||||
83 3 0.00 1 1.326100 2.512477 -1.657113 0.657756
|
||||
84 3 0.00 1 1.326099 2.965428 0.626295 -0.182887
|
||||
85 3 0.00 1 1.326101 1.976186 -1.072464 -1.686660
|
||||
86 3 0.00 1 1.603792 -2.952851 -0.722000 -3.390526
|
||||
87 3 0.00 1 1.558563 -4.265445 -1.534526 0.932369
|
||||
88 3 0.00 1 1.558562 -2.625986 -3.810249 -0.010226
|
||||
89 3 0.00 1 1.603792 -1.218394 -2.612849 4.191661
|
||||
90 3 0.00 1 1.558507 -2.300135 1.839753 3.919625
|
||||
91 3 0.00 1 1.558620 0.522041 1.594565 4.774310
|
||||
92 3 0.00 1 1.603792 0.246496 4.772002 1.472951
|
||||
93 3 0.00 1 1.558582 2.062319 -4.217199 1.410516
|
||||
94 3 0.00 1 1.558537 3.245048 -2.186529 3.208486
|
||||
95 3 0.00 1 1.603791 4.681408 -1.384588 -1.076860
|
||||
96 3 0.00 1 1.558565 -1.184793 3.454906 -2.684898
|
||||
97 3 0.00 1 1.558559 -3.365733 3.001032 -0.737405
|
||||
98 3 0.00 1 1.558551 1.538708 -0.326106 -4.250794
|
||||
99 3 0.00 1 1.558563 0.997214 -3.055912 -3.245768
|
||||
100 3 0.00 1 1.558524 4.144833 2.349324 1.538532
|
||||
101 3 0.00 1 1.558594 3.503398 3.047996 -1.264247
|
||||
Created by AJB
|
||||
|
||||
101 atoms
|
||||
3 atom types
|
||||
|
||||
-50.0 50.0 xlo xhi
|
||||
-50.0 50.0 ylo yhi
|
||||
-50.0 50.0 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 12.01070 # C nuclei
|
||||
2 1.000794 # H nuclei
|
||||
3 1.000000 # electron
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 6.00 0 0.000000 0.224230 2.918607 1.015812
|
||||
2 1 6.00 0 0.000000 -0.634450 1.314460 3.390303
|
||||
3 1 6.00 0 0.000000 -0.670162 -1.590173 2.675707
|
||||
4 1 6.00 0 0.000000 -2.586695 -2.037708 0.422846
|
||||
5 1 6.00 0 0.000000 -1.729127 -0.435706 -1.953488
|
||||
6 1 6.00 0 0.000000 -1.692867 2.468206 -1.236000
|
||||
7 1 6.00 0 0.000000 2.071281 -2.442011 1.834504
|
||||
8 1 6.00 0 0.000000 2.965108 2.063979 0.175607
|
||||
9 1 6.00 0 0.000000 1.013015 -1.288254 -2.791737
|
||||
10 1 6.00 0 0.000000 2.931847 -0.840220 -0.540904
|
||||
11 2 1.00 0 0.000000 -3.237070 -0.788493 -3.724286
|
||||
12 2 1.00 0 0.000000 -4.691469 -1.429253 1.056080
|
||||
13 2 1.00 0 0.000000 -2.657034 -4.253233 -0.113602
|
||||
14 2 1.00 0 0.000000 -1.345725 -2.850372 4.543752
|
||||
15 2 1.00 0 0.000000 -2.707861 1.976434 4.071194
|
||||
16 2 1.00 0 0.000000 0.794230 1.672161 5.131751
|
||||
17 2 1.00 0 0.000000 0.251667 5.202465 1.579125
|
||||
18 2 1.00 0 0.000000 2.074796 -4.663951 1.320307
|
||||
19 2 1.00 0 0.000000 3.542471 -2.144066 3.551451
|
||||
20 2 1.00 0 0.000000 5.087753 -1.511020 -1.201338
|
||||
21 2 1.00 0 0.000000 -1.077021 3.711707 -3.045901
|
||||
22 2 1.00 0 0.000000 -3.783389 3.148492 -0.629227
|
||||
23 2 1.00 0 0.000000 1.671766 -0.104421 -4.626344
|
||||
24 2 1.00 0 0.000000 0.999815 -3.491890 -3.379184
|
||||
25 2 1.00 0 0.000000 4.450647 2.434018 1.865941
|
||||
26 2 1.00 0 0.000000 3.654660 3.300997 -1.612081
|
||||
27 3 0.00 -1 0.328405 -0.634804 1.315020 3.391634
|
||||
28 3 0.00 -1 0.328107 -0.670512 -1.590826 2.676675
|
||||
29 3 0.00 -1 0.328405 -2.587889 -2.038591 0.422899
|
||||
30 3 0.00 -1 0.328107 -1.729909 -0.435889 -1.954405
|
||||
31 3 0.00 -1 0.328405 -1.693676 2.469262 -1.236661
|
||||
32 3 0.00 -1 0.328405 2.072091 -2.443067 1.835165
|
||||
33 3 0.00 -1 0.328405 2.966303 2.064861 0.175553
|
||||
34 3 0.00 -1 0.328405 1.013370 -1.288814 -2.793067
|
||||
35 3 0.00 -1 0.328108 2.932965 -0.840567 -0.541247
|
||||
36 3 0.00 -1 1.326096 -0.210743 2.123398 2.223462
|
||||
37 3 0.00 -1 1.326096 -0.657351 -0.127988 3.052304
|
||||
38 3 0.00 -1 1.326093 -1.646634 -1.826737 1.548546
|
||||
39 3 0.00 -1 1.326095 -2.175416 -1.250260 -0.762988
|
||||
40 3 0.00 -1 1.326093 -0.747076 2.708081 -0.120938
|
||||
41 3 0.00 -1 1.326095 -1.722464 1.033139 -1.603613
|
||||
42 3 0.00 -1 1.326092 0.713852 -2.031645 2.263933
|
||||
43 3 0.00 -1 1.326092 1.613424 2.503259 0.594420
|
||||
44 3 0.00 -1 1.326098 -0.351222 -0.870483 -2.392027
|
||||
45 3 0.00 -1 1.326100 2.512477 -1.657113 0.657756
|
||||
46 3 0.00 -1 1.326099 2.965428 0.626295 -0.182887
|
||||
47 3 0.00 -1 1.326101 1.976186 -1.072464 -1.686660
|
||||
48 3 0.00 -1 1.603792 -2.952851 -0.722000 -3.390526
|
||||
49 3 0.00 -1 1.558563 -4.265445 -1.534526 0.932369
|
||||
50 3 0.00 -1 1.558562 -2.625986 -3.810249 -0.010226
|
||||
51 3 0.00 -1 1.603792 -1.218394 -2.612849 4.191661
|
||||
52 3 0.00 -1 1.558507 -2.300135 1.839753 3.919625
|
||||
53 3 0.00 -1 1.558620 0.522041 1.594565 4.774310
|
||||
54 3 0.00 -1 1.603792 0.246496 4.772002 1.472951
|
||||
55 3 0.00 -1 1.558582 2.062319 -4.217199 1.410516
|
||||
56 3 0.00 -1 1.558537 3.245048 -2.186529 3.208486
|
||||
57 3 0.00 -1 1.603791 4.681408 -1.384588 -1.076860
|
||||
58 3 0.00 -1 1.558565 -1.184793 3.454906 -2.684898
|
||||
59 3 0.00 -1 1.558559 -3.365733 3.001032 -0.737405
|
||||
60 3 0.00 -1 1.558551 1.538708 -0.326106 -4.250794
|
||||
61 3 0.00 -1 1.558563 0.997214 -3.055912 -3.245768
|
||||
62 3 0.00 -1 1.558524 4.144833 2.349324 1.538532
|
||||
63 3 0.00 -1 1.558594 3.503398 3.047996 -1.264247
|
||||
64 3 0.00 1 0.328107 0.224244 2.919790 1.016104
|
||||
65 3 0.00 1 0.328405 -0.634804 1.315020 3.391634
|
||||
66 3 0.00 1 0.328107 -0.670512 -1.590826 2.676675
|
||||
67 3 0.00 1 0.328405 -2.587889 -2.038591 0.422899
|
||||
68 3 0.00 1 0.328107 -1.729909 -0.435889 -1.954405
|
||||
69 3 0.00 1 0.328405 -1.693676 2.469262 -1.236661
|
||||
70 3 0.00 1 0.328405 2.072091 -2.443067 1.835165
|
||||
71 3 0.00 1 0.328405 2.966303 2.064861 0.175553
|
||||
72 3 0.00 1 0.328405 1.013370 -1.288814 -2.793067
|
||||
73 3 0.00 1 0.328108 2.932965 -0.840567 -0.541247
|
||||
74 3 0.00 1 1.326096 -0.210743 2.123398 2.223462
|
||||
75 3 0.00 1 1.326096 -0.657351 -0.127988 3.052304
|
||||
76 3 0.00 1 1.326093 -1.646634 -1.826737 1.548546
|
||||
77 3 0.00 1 1.326094 -2.175416 -1.250259 -0.762988
|
||||
78 3 0.00 1 1.326094 -0.747076 2.708081 -0.120938
|
||||
79 3 0.00 1 1.326096 -1.722464 1.033139 -1.603613
|
||||
80 3 0.00 1 1.326092 0.713852 -2.031645 2.263933
|
||||
81 3 0.00 1 1.326092 1.613424 2.503259 0.594420
|
||||
82 3 0.00 1 1.326098 -0.351222 -0.870483 -2.392027
|
||||
83 3 0.00 1 1.326100 2.512477 -1.657113 0.657756
|
||||
84 3 0.00 1 1.326099 2.965428 0.626295 -0.182887
|
||||
85 3 0.00 1 1.326101 1.976186 -1.072464 -1.686660
|
||||
86 3 0.00 1 1.603792 -2.952851 -0.722000 -3.390526
|
||||
87 3 0.00 1 1.558563 -4.265445 -1.534526 0.932369
|
||||
88 3 0.00 1 1.558562 -2.625986 -3.810249 -0.010226
|
||||
89 3 0.00 1 1.603792 -1.218394 -2.612849 4.191661
|
||||
90 3 0.00 1 1.558507 -2.300135 1.839753 3.919625
|
||||
91 3 0.00 1 1.558620 0.522041 1.594565 4.774310
|
||||
92 3 0.00 1 1.603792 0.246496 4.772002 1.472951
|
||||
93 3 0.00 1 1.558582 2.062319 -4.217199 1.410516
|
||||
94 3 0.00 1 1.558537 3.245048 -2.186529 3.208486
|
||||
95 3 0.00 1 1.603791 4.681408 -1.384588 -1.076860
|
||||
96 3 0.00 1 1.558565 -1.184793 3.454906 -2.684898
|
||||
97 3 0.00 1 1.558559 -3.365733 3.001032 -0.737405
|
||||
98 3 0.00 1 1.558551 1.538708 -0.326106 -4.250794
|
||||
99 3 0.00 1 1.558563 0.997214 -3.055912 -3.245768
|
||||
100 3 0.00 1 1.558524 4.144833 2.349324 1.538532
|
||||
101 3 0.00 1 1.558594 3.503398 3.047996 -1.264247
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,63 +1,63 @@
|
||||
# After running LAMMPS with this input script a number of dump files is created.
|
||||
# To extract the data from there I used grep script:
|
||||
# grep '^2 ' *cfg > LammpsResult.dat
|
||||
# After that after removing some text from LammpsResult.dat,
|
||||
# the data can be viewed by lebedeva00.plot
|
||||
#
|
||||
# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland
|
||||
# Email: softquake@gmail.com
|
||||
|
||||
|
||||
# ---------- Start simulation ---------------------
|
||||
clear
|
||||
units metal
|
||||
dimension 3
|
||||
boundary f f f
|
||||
atom_style atomic
|
||||
|
||||
# ========================== Create Atomistic Structure ===========================
|
||||
|
||||
region whole block 0 20 0 20 0 10
|
||||
create_box 2 whole
|
||||
|
||||
read_data 2particles.dat add append
|
||||
|
||||
region graphite block INF INF INF INF 0 10 units box
|
||||
group graphite type 1 2
|
||||
group graphene1 type 1
|
||||
group graphene2 type 2
|
||||
|
||||
pair_style hybrid/overlay lebedeva/z 20
|
||||
pair_coeff * * none
|
||||
pair_coeff 1 2 lebedeva/z CC.Lebedeva C C
|
||||
|
||||
mass 1 12.01 # Carbon
|
||||
mass 2 12.01 # Carbon
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 1 check yes
|
||||
|
||||
compute peratom all pe/atom
|
||||
|
||||
dump 1 all custom 1 dump_lebedeva_*.cfg id x y z c_peratom fx fy fz
|
||||
dump_modify 1 pad 3
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step pe press temp
|
||||
thermo_modify lost ignore
|
||||
|
||||
label STEP_LOOP
|
||||
|
||||
variable MYSTEP loop 0 400 pad # in degrees
|
||||
variable DELTA_STEP equal 0.05
|
||||
|
||||
displace_atoms graphene2 move ${DELTA_STEP} ${DELTA_STEP} 0
|
||||
|
||||
run 1
|
||||
|
||||
next MYSTEP
|
||||
jump SELF STEP_LOOP
|
||||
|
||||
print "all done"
|
||||
|
||||
|
||||
# After running LAMMPS with this input script a number of dump files is created.
|
||||
# To extract the data from there I used grep script:
|
||||
# grep '^2 ' *cfg > LammpsResult.dat
|
||||
# After that after removing some text from LammpsResult.dat,
|
||||
# the data can be viewed by lebedeva00.plot
|
||||
#
|
||||
# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland
|
||||
# Email: softquake@gmail.com
|
||||
|
||||
|
||||
# ---------- Start simulation ---------------------
|
||||
clear
|
||||
units metal
|
||||
dimension 3
|
||||
boundary f f f
|
||||
atom_style atomic
|
||||
|
||||
# ========================== Create Atomistic Structure ===========================
|
||||
|
||||
region whole block 0 20 0 20 0 10
|
||||
create_box 2 whole
|
||||
|
||||
read_data 2particles.dat add append
|
||||
|
||||
region graphite block INF INF INF INF 0 10 units box
|
||||
group graphite type 1 2
|
||||
group graphene1 type 1
|
||||
group graphene2 type 2
|
||||
|
||||
pair_style hybrid/overlay lebedeva/z 20
|
||||
pair_coeff * * none
|
||||
pair_coeff 1 2 lebedeva/z CC.Lebedeva C C
|
||||
|
||||
mass 1 12.01 # Carbon
|
||||
mass 2 12.01 # Carbon
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 1 check yes
|
||||
|
||||
compute peratom all pe/atom
|
||||
|
||||
dump 1 all custom 1 dump_lebedeva_*.cfg id x y z c_peratom fx fy fz
|
||||
dump_modify 1 pad 3
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step pe press temp
|
||||
thermo_modify lost ignore
|
||||
|
||||
label STEP_LOOP
|
||||
|
||||
variable MYSTEP loop 0 400 pad # in degrees
|
||||
variable DELTA_STEP equal 0.05
|
||||
|
||||
displace_atoms graphene2 move ${DELTA_STEP} ${DELTA_STEP} 0
|
||||
|
||||
run 1
|
||||
|
||||
next MYSTEP
|
||||
jump SELF STEP_LOOP
|
||||
|
||||
print "all done"
|
||||
|
||||
|
||||
|
||||
@ -11,6 +11,7 @@ units cgs
|
||||
dimension 3
|
||||
boundary p p f
|
||||
atom_style atomic
|
||||
processors * 1 *
|
||||
|
||||
#-------------------------------------------------------------------------#
|
||||
# Set up the simulation box
|
||||
@ -464,11 +465,11 @@ pair_style lj/cut 1.2
|
||||
pair_coeff * * 0.0 0.0
|
||||
|
||||
timestep 0.025
|
||||
|
||||
unfix FL
|
||||
if "$(is_defined(dump,mydump))" then "undump mydump"
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
#dump mydump all atom 10000 run.lammpstrj
|
||||
#variable total_force equal 0.2
|
||||
#variable node_force equal "v_total_force / 178"
|
||||
#fix drag all addforce 0.0 0.0 0.0
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,130 +1,130 @@
|
||||
# Ti-O cubic spline potential where O is in the dilute limit. DATE: 2016-06-05 CONTRIBUTOR: Pinchao Zhang, Dallas R. Trinkle
|
||||
meam/spline 2 Ti O
|
||||
spline3eq
|
||||
13
|
||||
-20 0
|
||||
1.742692837 3.744277175966 99.4865081627958
|
||||
2.05580176725 0.910839730906 10.8702523265355
|
||||
2.3689106975 0.388045896634 -1.55322418749562
|
||||
2.68201962775 -0.018840906533 2.43630041329215
|
||||
2.995128558 -0.248098929639 2.67912713976835
|
||||
3.30823748825 -0.264489550297 -0.125056384603077
|
||||
3.6213464185 -0.227196189283 1.10662555360438
|
||||
3.93445534875 -0.129293090176 -0.592053676745914
|
||||
4.247564279 -0.059685366933 -0.470123414607672
|
||||
4.56067320925 -0.031100025561 -0.0380739973059663
|
||||
4.8737821395 -0.013847363202 -0.0711547960695406
|
||||
5.18689106975 -0.003203412728 -0.081768292420175
|
||||
5.5 0 -0.0571422964883619
|
||||
spline3eq
|
||||
5
|
||||
0.155001355787331 0
|
||||
1.9 0.533321679606674 0
|
||||
2.8 0.456402081843862 -1.60311717015859
|
||||
3.7 -0.324281383502201 1.19940299483249
|
||||
4.6 -0.474029826906675 1.47909794595154
|
||||
5.5 0 -2.49521499855605
|
||||
spline3eq
|
||||
13
|
||||
0 0
|
||||
1.742692837 0 0
|
||||
2.05580176725 0 0
|
||||
2.3689106975 0 0
|
||||
2.68201962775 0 0
|
||||
2.995128558 0 0
|
||||
3.30823748825 0 0
|
||||
3.6213464185 0 0
|
||||
3.93445534875 0 0
|
||||
4.247564279 0 0
|
||||
4.56067320925 0 0
|
||||
4.8737821395 0 0
|
||||
5.18689106975 0 0
|
||||
5.5 0 0
|
||||
spline3eq
|
||||
11
|
||||
-1 0
|
||||
2.055801767 1.7475279661 -525.869786904802
|
||||
2.2912215903 -5.8677963945 252.796316927755
|
||||
2.5266414136 -8.3376288737 71.7318388721015
|
||||
2.7620612369 -5.8398712842 -1.93587742753693
|
||||
2.9974810602 -3.1140648231 -39.2999192667503
|
||||
3.2329008835 -1.7257245065 14.3424136002004
|
||||
3.4683207068 -0.4428977017 -29.4925534559498
|
||||
3.7037405301 -0.1466643003 -3.18010534572236
|
||||
3.9391603534 -0.2095507945 3.33490838803603
|
||||
4.1745801767 -0.1442384563 3.71918691359508
|
||||
4.41 0 -9.66717019857564
|
||||
spline3eq
|
||||
5
|
||||
-61.9827585211652 0
|
||||
1.9 11.2293641315584 0
|
||||
2.8 -27.9976343076148 122.648031332411
|
||||
3.7 -8.32979773113248 -54.3340881766381
|
||||
4.6 -1.00863195297399 3.23150064581724
|
||||
5.5 0 -5.3514242228123
|
||||
spline3eq
|
||||
4
|
||||
0.00776934946045395 0.105197706160344
|
||||
-55.14233165 -0.29745568008 0.00152870603877451
|
||||
-44.7409899033333 -0.15449458722 0.00038933722543571
|
||||
-34.3396481566667 0.05098657168 0.00038124926922248
|
||||
-23.93830641 0.57342694704 0.0156639264890892
|
||||
spline3eq
|
||||
5
|
||||
-0.00676745157022662 -0.0159520381982146
|
||||
-23.9928 0.297607384684645 0
|
||||
-15.9241175 0.216691597077105 -0.0024248755353942
|
||||
-7.855435 0.0637598673719069 0.00306245895013358
|
||||
0.213247499999998 -0.00183450621970427 -0.00177588407633909
|
||||
8.28193 -0.111277018874367 0
|
||||
spline3eq
|
||||
10
|
||||
2.77327511656661 0
|
||||
2.055801767 -0.1485215264 72.2010867146919
|
||||
2.31737934844444 1.6845304918 -47.2744689053404
|
||||
2.57895692988889 2.0113365977 -15.1859578405326
|
||||
2.84053451133333 1.1444092747 3.33978204841873
|
||||
3.10211209277778 0.2861606803 2.587867603808
|
||||
3.36368967422222 -0.3459281126 6.14070694084556
|
||||
3.62526725566667 -0.6257480601 3.7397696717154
|
||||
3.88684483711111 -0.6119510826 4.64749084871402
|
||||
4.14842241855556 -0.3112059651 2.83275746415936
|
||||
4.41 0 -15.0612086827734
|
||||
spline3eq
|
||||
5
|
||||
12.3315547862781 0
|
||||
1.9 2.62105440156724 0
|
||||
2.8 10.2850803058354 -25.439802988016
|
||||
3.7 3.23933763743897 -7.20203673434025
|
||||
4.6 -5.79049355858613 39.5509978688682
|
||||
5.5 0 -41.221771373642
|
||||
spline3eq
|
||||
8
|
||||
8.33642274810572 -60.4024574736564
|
||||
-1 0.07651409193 -110.652321293778
|
||||
-0.724509054371429 0.14155824541 44.8853405500508
|
||||
-0.449018108742857 0.75788697341 -25.3065115342002
|
||||
-0.173527163114286 0.63011570378 -2.48510144915082
|
||||
0.101963782514286 0.09049597305 2.68769386908235
|
||||
0.377454728142857 -0.35741586657 -1.01558570129633
|
||||
0.652945673771428 -0.65293217647 13.4224786001212
|
||||
0.9284366194 -6.00912190653 -452.752542694929
|
||||
spline3eq
|
||||
5
|
||||
0.137191606537625 -1.55094230968985
|
||||
-1 0.0513843442016519 0
|
||||
-0.5 0.0179024412245673 -2.44986494990154
|
||||
0 -0.260650876879273 3.91774583656401
|
||||
0.5 -0.190163791764901 -4.84414871911743
|
||||
1 -0.763795416646599 0
|
||||
spline3eq
|
||||
8
|
||||
0 0
|
||||
-1 0 0
|
||||
-0.724509054371429 0 0
|
||||
-0.449018108742857 0 0
|
||||
-0.173527163114286 0 0
|
||||
0.101963782514286 0 0
|
||||
0.377454728142857 0 0
|
||||
0.652945673771428 0 0
|
||||
0.9284366194 0 0
|
||||
# Ti-O cubic spline potential where O is in the dilute limit. DATE: 2016-06-05 CONTRIBUTOR: Pinchao Zhang, Dallas R. Trinkle
|
||||
meam/spline 2 Ti O
|
||||
spline3eq
|
||||
13
|
||||
-20 0
|
||||
1.742692837 3.744277175966 99.4865081627958
|
||||
2.05580176725 0.910839730906 10.8702523265355
|
||||
2.3689106975 0.388045896634 -1.55322418749562
|
||||
2.68201962775 -0.018840906533 2.43630041329215
|
||||
2.995128558 -0.248098929639 2.67912713976835
|
||||
3.30823748825 -0.264489550297 -0.125056384603077
|
||||
3.6213464185 -0.227196189283 1.10662555360438
|
||||
3.93445534875 -0.129293090176 -0.592053676745914
|
||||
4.247564279 -0.059685366933 -0.470123414607672
|
||||
4.56067320925 -0.031100025561 -0.0380739973059663
|
||||
4.8737821395 -0.013847363202 -0.0711547960695406
|
||||
5.18689106975 -0.003203412728 -0.081768292420175
|
||||
5.5 0 -0.0571422964883619
|
||||
spline3eq
|
||||
5
|
||||
0.155001355787331 0
|
||||
1.9 0.533321679606674 0
|
||||
2.8 0.456402081843862 -1.60311717015859
|
||||
3.7 -0.324281383502201 1.19940299483249
|
||||
4.6 -0.474029826906675 1.47909794595154
|
||||
5.5 0 -2.49521499855605
|
||||
spline3eq
|
||||
13
|
||||
0 0
|
||||
1.742692837 0 0
|
||||
2.05580176725 0 0
|
||||
2.3689106975 0 0
|
||||
2.68201962775 0 0
|
||||
2.995128558 0 0
|
||||
3.30823748825 0 0
|
||||
3.6213464185 0 0
|
||||
3.93445534875 0 0
|
||||
4.247564279 0 0
|
||||
4.56067320925 0 0
|
||||
4.8737821395 0 0
|
||||
5.18689106975 0 0
|
||||
5.5 0 0
|
||||
spline3eq
|
||||
11
|
||||
-1 0
|
||||
2.055801767 1.7475279661 -525.869786904802
|
||||
2.2912215903 -5.8677963945 252.796316927755
|
||||
2.5266414136 -8.3376288737 71.7318388721015
|
||||
2.7620612369 -5.8398712842 -1.93587742753693
|
||||
2.9974810602 -3.1140648231 -39.2999192667503
|
||||
3.2329008835 -1.7257245065 14.3424136002004
|
||||
3.4683207068 -0.4428977017 -29.4925534559498
|
||||
3.7037405301 -0.1466643003 -3.18010534572236
|
||||
3.9391603534 -0.2095507945 3.33490838803603
|
||||
4.1745801767 -0.1442384563 3.71918691359508
|
||||
4.41 0 -9.66717019857564
|
||||
spline3eq
|
||||
5
|
||||
-61.9827585211652 0
|
||||
1.9 11.2293641315584 0
|
||||
2.8 -27.9976343076148 122.648031332411
|
||||
3.7 -8.32979773113248 -54.3340881766381
|
||||
4.6 -1.00863195297399 3.23150064581724
|
||||
5.5 0 -5.3514242228123
|
||||
spline3eq
|
||||
4
|
||||
0.00776934946045395 0.105197706160344
|
||||
-55.14233165 -0.29745568008 0.00152870603877451
|
||||
-44.7409899033333 -0.15449458722 0.00038933722543571
|
||||
-34.3396481566667 0.05098657168 0.00038124926922248
|
||||
-23.93830641 0.57342694704 0.0156639264890892
|
||||
spline3eq
|
||||
5
|
||||
-0.00676745157022662 -0.0159520381982146
|
||||
-23.9928 0.297607384684645 0
|
||||
-15.9241175 0.216691597077105 -0.0024248755353942
|
||||
-7.855435 0.0637598673719069 0.00306245895013358
|
||||
0.213247499999998 -0.00183450621970427 -0.00177588407633909
|
||||
8.28193 -0.111277018874367 0
|
||||
spline3eq
|
||||
10
|
||||
2.77327511656661 0
|
||||
2.055801767 -0.1485215264 72.2010867146919
|
||||
2.31737934844444 1.6845304918 -47.2744689053404
|
||||
2.57895692988889 2.0113365977 -15.1859578405326
|
||||
2.84053451133333 1.1444092747 3.33978204841873
|
||||
3.10211209277778 0.2861606803 2.587867603808
|
||||
3.36368967422222 -0.3459281126 6.14070694084556
|
||||
3.62526725566667 -0.6257480601 3.7397696717154
|
||||
3.88684483711111 -0.6119510826 4.64749084871402
|
||||
4.14842241855556 -0.3112059651 2.83275746415936
|
||||
4.41 0 -15.0612086827734
|
||||
spline3eq
|
||||
5
|
||||
12.3315547862781 0
|
||||
1.9 2.62105440156724 0
|
||||
2.8 10.2850803058354 -25.439802988016
|
||||
3.7 3.23933763743897 -7.20203673434025
|
||||
4.6 -5.79049355858613 39.5509978688682
|
||||
5.5 0 -41.221771373642
|
||||
spline3eq
|
||||
8
|
||||
8.33642274810572 -60.4024574736564
|
||||
-1 0.07651409193 -110.652321293778
|
||||
-0.724509054371429 0.14155824541 44.8853405500508
|
||||
-0.449018108742857 0.75788697341 -25.3065115342002
|
||||
-0.173527163114286 0.63011570378 -2.48510144915082
|
||||
0.101963782514286 0.09049597305 2.68769386908235
|
||||
0.377454728142857 -0.35741586657 -1.01558570129633
|
||||
0.652945673771428 -0.65293217647 13.4224786001212
|
||||
0.9284366194 -6.00912190653 -452.752542694929
|
||||
spline3eq
|
||||
5
|
||||
0.137191606537625 -1.55094230968985
|
||||
-1 0.0513843442016519 0
|
||||
-0.5 0.0179024412245673 -2.44986494990154
|
||||
0 -0.260650876879273 3.91774583656401
|
||||
0.5 -0.190163791764901 -4.84414871911743
|
||||
1 -0.763795416646599 0
|
||||
spline3eq
|
||||
8
|
||||
0 0
|
||||
-1 0 0
|
||||
-0.724509054371429 0 0
|
||||
-0.449018108742857 0 0
|
||||
-0.173527163114286 0 0
|
||||
0.101963782514286 0 0
|
||||
0.377454728142857 0 0
|
||||
0.652945673771428 0 0
|
||||
0.9284366194 0 0
|
||||
|
||||
@ -1,40 +1,40 @@
|
||||
variable T equal 0.8
|
||||
variable p_solid equal 0.05
|
||||
|
||||
read_data data.mop
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 1 2 0.5 1.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
neigh_modify delay 0
|
||||
|
||||
group liquid type 1
|
||||
group solid type 2
|
||||
region bottom block INF INF INF INF INF 7.0
|
||||
group bottom region bottom
|
||||
group solid_bottom intersect solid bottom
|
||||
group solid_up subtract solid solid_bottom
|
||||
|
||||
variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
|
||||
fix piston_up solid_up aveforce NULL NULL -${faSolid}
|
||||
fix freeze_up solid_up setforce 0.0 0.0 NULL
|
||||
fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
|
||||
fix nvesol solid nve
|
||||
compute Tliq liquid temp
|
||||
fix nvtliq liquid nvt temp $T $T 0.5
|
||||
fix_modify nvtliq temp Tliq
|
||||
|
||||
thermo 1000
|
||||
thermo_modify flush yes temp Tliq
|
||||
|
||||
fix fxbal all balance 1000 1.05 shift z 10 1.05
|
||||
|
||||
compute mopz0 all stress/mop z center kin conf
|
||||
fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
|
||||
|
||||
compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
|
||||
fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
|
||||
|
||||
run 0
|
||||
|
||||
variable T equal 0.8
|
||||
variable p_solid equal 0.05
|
||||
|
||||
read_data data.mop
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 1 2 0.5 1.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
neigh_modify delay 0
|
||||
|
||||
group liquid type 1
|
||||
group solid type 2
|
||||
region bottom block INF INF INF INF INF 7.0
|
||||
group bottom region bottom
|
||||
group solid_bottom intersect solid bottom
|
||||
group solid_up subtract solid solid_bottom
|
||||
|
||||
variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
|
||||
fix piston_up solid_up aveforce NULL NULL -${faSolid}
|
||||
fix freeze_up solid_up setforce 0.0 0.0 NULL
|
||||
fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
|
||||
fix nvesol solid nve
|
||||
compute Tliq liquid temp
|
||||
fix nvtliq liquid nvt temp $T $T 0.5
|
||||
fix_modify nvtliq temp Tliq
|
||||
|
||||
thermo 1000
|
||||
thermo_modify flush yes temp Tliq
|
||||
|
||||
fix fxbal all balance 1000 1.05 shift z 10 1.05
|
||||
|
||||
compute mopz0 all stress/mop z center kin conf
|
||||
fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
|
||||
|
||||
compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
|
||||
fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
|
||||
|
||||
run 0
|
||||
|
||||
|
||||
@ -1,66 +1,66 @@
|
||||
map file: styrene growth
|
||||
|
||||
1 edgeIDs
|
||||
30 equivalences
|
||||
16 createIDs
|
||||
|
||||
InitiatorIDs
|
||||
|
||||
4
|
||||
13
|
||||
|
||||
EdgeIDs
|
||||
|
||||
30
|
||||
|
||||
CreateIDs
|
||||
|
||||
1
|
||||
2
|
||||
3
|
||||
4
|
||||
5
|
||||
6
|
||||
7
|
||||
8
|
||||
9
|
||||
10
|
||||
11
|
||||
12
|
||||
13
|
||||
14
|
||||
15
|
||||
16
|
||||
|
||||
Equivalences
|
||||
|
||||
1 45
|
||||
2 46
|
||||
3 44
|
||||
4 43
|
||||
5 42
|
||||
6 41
|
||||
7 40
|
||||
8 39
|
||||
9 38
|
||||
10 37
|
||||
11 36
|
||||
12 35
|
||||
13 34
|
||||
14 33
|
||||
15 32
|
||||
16 31
|
||||
17 17
|
||||
18 18
|
||||
19 19
|
||||
20 20
|
||||
21 21
|
||||
22 22
|
||||
23 23
|
||||
24 24
|
||||
25 25
|
||||
26 26
|
||||
27 27
|
||||
28 28
|
||||
29 29
|
||||
30 30
|
||||
map file: styrene growth
|
||||
|
||||
1 edgeIDs
|
||||
30 equivalences
|
||||
16 createIDs
|
||||
|
||||
InitiatorIDs
|
||||
|
||||
4
|
||||
13
|
||||
|
||||
EdgeIDs
|
||||
|
||||
30
|
||||
|
||||
CreateIDs
|
||||
|
||||
1
|
||||
2
|
||||
3
|
||||
4
|
||||
5
|
||||
6
|
||||
7
|
||||
8
|
||||
9
|
||||
10
|
||||
11
|
||||
12
|
||||
13
|
||||
14
|
||||
15
|
||||
16
|
||||
|
||||
Equivalences
|
||||
|
||||
1 45
|
||||
2 46
|
||||
3 44
|
||||
4 43
|
||||
5 42
|
||||
6 41
|
||||
7 40
|
||||
8 39
|
||||
9 38
|
||||
10 37
|
||||
11 36
|
||||
12 35
|
||||
13 34
|
||||
14 33
|
||||
15 32
|
||||
16 31
|
||||
17 17
|
||||
18 18
|
||||
19 19
|
||||
20 20
|
||||
21 21
|
||||
22 22
|
||||
23 23
|
||||
24 24
|
||||
25 25
|
||||
26 26
|
||||
27 27
|
||||
28 28
|
||||
29 29
|
||||
30 30
|
||||
|
||||
@ -1,456 +1,456 @@
|
||||
molecule template: end of chain plus polymerized styrene
|
||||
|
||||
46 atoms
|
||||
48 bonds
|
||||
81 angles
|
||||
121 dihedrals
|
||||
35 impropers
|
||||
1 fragments
|
||||
|
||||
Fragments
|
||||
|
||||
create_fit 34 44
|
||||
|
||||
Types
|
||||
|
||||
1 1
|
||||
2 2
|
||||
3 1
|
||||
4 5
|
||||
5 1
|
||||
6 2
|
||||
7 1
|
||||
8 2
|
||||
9 1
|
||||
10 2
|
||||
11 1
|
||||
12 2
|
||||
13 2
|
||||
14 6
|
||||
15 2
|
||||
16 2
|
||||
17 1
|
||||
18 2
|
||||
19 1
|
||||
20 5
|
||||
21 1
|
||||
22 2
|
||||
23 1
|
||||
24 2
|
||||
25 1
|
||||
26 2
|
||||
27 1
|
||||
28 2
|
||||
29 2
|
||||
30 6
|
||||
31 1
|
||||
32 2
|
||||
33 1
|
||||
34 5
|
||||
35 1
|
||||
36 2
|
||||
37 1
|
||||
38 2
|
||||
39 1
|
||||
40 2
|
||||
41 1
|
||||
42 2
|
||||
43 2
|
||||
44 6
|
||||
45 2
|
||||
46 2
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.129000
|
||||
2 0.123700
|
||||
3 0.026600
|
||||
4 -0.018200
|
||||
5 -0.129000
|
||||
6 0.123700
|
||||
7 -0.173400
|
||||
8 0.140300
|
||||
9 -0.113400
|
||||
10 0.128800
|
||||
11 -0.173400
|
||||
12 0.140300
|
||||
13 0.051600
|
||||
14 -0.069600
|
||||
15 0.035400
|
||||
16 0.035400
|
||||
17 -0.129000
|
||||
18 0.123700
|
||||
19 0.026600
|
||||
20 -0.018200
|
||||
21 -0.129000
|
||||
22 0.123700
|
||||
23 -0.173400
|
||||
24 0.140300
|
||||
25 -0.113400
|
||||
26 0.128800
|
||||
27 -0.173400
|
||||
28 0.140300
|
||||
29 0.051600
|
||||
30 -0.069600
|
||||
31 -0.129000
|
||||
32 0.123700
|
||||
33 0.026600
|
||||
34 -0.018200
|
||||
35 -0.129000
|
||||
36 0.123700
|
||||
37 -0.173400
|
||||
38 0.140300
|
||||
39 -0.113400
|
||||
40 0.128800
|
||||
41 -0.173400
|
||||
42 0.140300
|
||||
43 0.051600
|
||||
44 -0.069600
|
||||
45 0.035400
|
||||
46 0.035400
|
||||
|
||||
Coords
|
||||
|
||||
1 24.130699 1.043900 -1.309300
|
||||
2 25.062700 1.582900 -1.309300
|
||||
3 22.900700 1.753900 -1.309300
|
||||
4 22.900700 3.253900 -1.309300
|
||||
5 21.670700 1.043900 -1.309300
|
||||
6 20.738701 1.582900 -1.309300
|
||||
7 21.670700 -0.376100 -1.309300
|
||||
8 20.738701 -0.915100 -1.309300
|
||||
9 22.900700 -1.086100 -1.309300
|
||||
10 22.900700 -2.163100 -1.309300
|
||||
11 24.130699 -0.376100 -1.309300
|
||||
12 25.062700 -0.915100 -1.309300
|
||||
13 23.766701 3.658900 -0.952300
|
||||
14 21.622700 3.802900 -1.871300
|
||||
15 21.672701 4.544900 -1.970300
|
||||
16 20.979700 2.979900 -2.165300
|
||||
17 13.465800 0.682500 -1.658900
|
||||
18 14.397800 1.221500 -1.658900
|
||||
19 12.235800 1.392500 -1.658900
|
||||
20 12.235800 2.892500 -1.658900
|
||||
21 11.005800 0.682500 -1.658900
|
||||
22 10.073800 1.221500 -1.658900
|
||||
23 11.005800 -0.737500 -1.658900
|
||||
24 10.073800 -1.276500 -1.658900
|
||||
25 12.235800 -1.447500 -1.658900
|
||||
26 12.235800 -2.524500 -1.658900
|
||||
27 13.465800 -0.737500 -1.658900
|
||||
28 14.397800 -1.276500 -1.658900
|
||||
29 13.101800 3.297500 -1.301900
|
||||
30 10.957800 3.441500 -2.220900
|
||||
31 18.663500 0.855500 -1.372100
|
||||
32 19.595501 1.394500 -1.372100
|
||||
33 17.433500 1.565500 -1.372100
|
||||
34 17.433500 3.065500 -1.372100
|
||||
35 16.203501 0.855500 -1.372100
|
||||
36 15.271500 1.394500 -1.372100
|
||||
37 16.203501 -0.564500 -1.372100
|
||||
38 15.271500 -1.103500 -1.372100
|
||||
39 17.433500 -1.274500 -1.372100
|
||||
40 17.433500 -2.351500 -1.372100
|
||||
41 18.663500 -0.564500 -1.372100
|
||||
42 19.595501 -1.103500 -1.372100
|
||||
43 18.299500 3.470500 -1.015100
|
||||
44 16.155500 3.614500 -1.934100
|
||||
45 16.205500 4.356500 -2.033100
|
||||
46 15.512500 2.791500 -2.228100
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 2 1 3
|
||||
3 2 1 11
|
||||
4 11 3 4
|
||||
5 2 3 5
|
||||
6 12 13 4
|
||||
7 13 4 14
|
||||
8 1 5 6
|
||||
9 2 5 7
|
||||
10 1 7 8
|
||||
11 2 7 9
|
||||
12 1 9 10
|
||||
13 2 9 11
|
||||
14 1 11 12
|
||||
15 10 15 14
|
||||
16 10 16 14
|
||||
17 9 14 34
|
||||
18 1 17 18
|
||||
19 2 17 19
|
||||
20 2 17 27
|
||||
21 7 19 20
|
||||
22 2 19 21
|
||||
23 8 29 20
|
||||
24 9 30 20
|
||||
25 9 44 20
|
||||
26 1 21 22
|
||||
27 2 21 23
|
||||
28 1 23 24
|
||||
29 2 23 25
|
||||
30 1 25 26
|
||||
31 2 25 27
|
||||
32 1 27 28
|
||||
33 1 31 32
|
||||
34 2 31 33
|
||||
35 2 31 41
|
||||
36 7 33 34
|
||||
37 2 33 35
|
||||
38 8 43 34
|
||||
39 9 44 34
|
||||
40 1 35 36
|
||||
41 2 35 37
|
||||
42 1 37 38
|
||||
43 2 37 39
|
||||
44 1 39 40
|
||||
45 2 39 41
|
||||
46 1 41 42
|
||||
47 10 45 44
|
||||
48 10 46 44
|
||||
|
||||
Angles
|
||||
|
||||
1 1 3 1 2
|
||||
2 1 11 1 2
|
||||
3 2 3 1 11
|
||||
4 17 1 3 4
|
||||
5 2 1 3 5
|
||||
6 17 5 3 4
|
||||
7 18 3 4 13
|
||||
8 19 3 4 14
|
||||
9 20 13 4 14
|
||||
10 1 3 5 6
|
||||
11 2 3 5 7
|
||||
12 1 7 5 6
|
||||
13 1 5 7 8
|
||||
14 2 5 7 9
|
||||
15 1 9 7 8
|
||||
16 1 7 9 10
|
||||
17 2 7 9 11
|
||||
18 1 11 9 10
|
||||
19 2 1 11 9
|
||||
20 1 1 11 12
|
||||
21 1 9 11 12
|
||||
22 21 15 14 4
|
||||
23 21 16 14 4
|
||||
24 22 4 14 34
|
||||
25 15 15 14 16
|
||||
26 14 15 14 34
|
||||
27 14 16 14 34
|
||||
28 1 19 17 18
|
||||
29 1 27 17 18
|
||||
30 2 19 17 27
|
||||
31 9 17 19 20
|
||||
32 2 17 19 21
|
||||
33 9 21 19 20
|
||||
34 10 19 20 29
|
||||
35 11 19 20 30
|
||||
36 11 19 20 44
|
||||
37 12 29 20 30
|
||||
38 12 29 20 44
|
||||
39 13 30 20 44
|
||||
40 1 19 21 22
|
||||
41 2 19 21 23
|
||||
42 1 23 21 22
|
||||
43 1 21 23 24
|
||||
44 2 21 23 25
|
||||
45 1 25 23 24
|
||||
46 1 23 25 26
|
||||
47 2 23 25 27
|
||||
48 1 27 25 26
|
||||
49 2 17 27 25
|
||||
50 1 17 27 28
|
||||
51 1 25 27 28
|
||||
52 1 33 31 32
|
||||
53 1 41 31 32
|
||||
54 2 33 31 41
|
||||
55 9 31 33 34
|
||||
56 2 31 33 35
|
||||
57 9 35 33 34
|
||||
58 11 33 34 14
|
||||
59 12 43 34 14
|
||||
60 13 14 34 44
|
||||
61 10 33 34 43
|
||||
62 11 33 34 44
|
||||
63 12 43 34 44
|
||||
64 1 33 35 36
|
||||
65 2 33 35 37
|
||||
66 1 37 35 36
|
||||
67 1 35 37 38
|
||||
68 2 35 37 39
|
||||
69 1 39 37 38
|
||||
70 1 37 39 40
|
||||
71 2 37 39 41
|
||||
72 1 41 39 40
|
||||
73 2 31 41 39
|
||||
74 1 31 41 42
|
||||
75 1 39 41 42
|
||||
76 16 20 44 34
|
||||
77 14 45 44 20
|
||||
78 14 46 44 20
|
||||
79 14 45 44 34
|
||||
80 14 46 44 34
|
||||
81 15 45 44 46
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 20 2 1 3 4
|
||||
2 2 5 3 1 2
|
||||
3 21 11 1 3 4
|
||||
4 4 11 1 3 5
|
||||
5 2 9 11 1 2
|
||||
6 5 2 1 11 12
|
||||
7 4 3 1 11 9
|
||||
8 2 3 1 11 12
|
||||
9 22 1 3 4 13
|
||||
10 23 1 3 4 14
|
||||
11 22 5 3 4 13
|
||||
12 23 5 3 4 14
|
||||
13 2 1 3 5 6
|
||||
14 4 1 3 5 7
|
||||
15 20 6 5 3 4
|
||||
16 21 7 5 3 4
|
||||
17 24 3 4 14 15
|
||||
18 24 3 4 14 16
|
||||
19 25 3 4 14 34
|
||||
20 26 13 4 14 15
|
||||
21 26 13 4 14 16
|
||||
22 27 13 4 14 34
|
||||
23 2 3 5 7 8
|
||||
24 4 3 5 7 9
|
||||
25 5 6 5 7 8
|
||||
26 2 9 7 5 6
|
||||
27 2 5 7 9 10
|
||||
28 4 5 7 9 11
|
||||
29 5 8 7 9 10
|
||||
30 2 11 9 7 8
|
||||
31 4 7 9 11 1
|
||||
32 2 7 9 11 12
|
||||
33 2 1 11 9 10
|
||||
34 5 10 9 11 12
|
||||
35 28 4 14 34 33
|
||||
36 29 4 14 34 43
|
||||
37 30 4 14 34 44
|
||||
38 31 15 14 34 33
|
||||
39 32 15 14 34 43
|
||||
40 33 15 14 34 44
|
||||
41 31 16 14 34 33
|
||||
42 32 16 14 34 43
|
||||
43 33 16 14 34 44
|
||||
44 10 18 17 19 20
|
||||
45 2 21 19 17 18
|
||||
46 11 27 17 19 20
|
||||
47 4 27 17 19 21
|
||||
48 2 25 27 17 18
|
||||
49 5 18 17 27 28
|
||||
50 4 19 17 27 25
|
||||
51 2 19 17 27 28
|
||||
52 12 17 19 20 29
|
||||
53 13 17 19 20 30
|
||||
54 13 17 19 20 44
|
||||
55 12 21 19 20 29
|
||||
56 13 21 19 20 30
|
||||
57 13 21 19 20 44
|
||||
58 2 17 19 21 22
|
||||
59 4 17 19 21 23
|
||||
60 10 22 21 19 20
|
||||
61 11 23 21 19 20
|
||||
62 34 34 44 20 19
|
||||
63 31 45 44 20 19
|
||||
64 31 46 44 20 19
|
||||
65 35 34 44 20 29
|
||||
66 32 45 44 20 29
|
||||
67 32 46 44 20 29
|
||||
68 36 34 44 20 30
|
||||
69 33 45 44 20 30
|
||||
70 33 46 44 20 30
|
||||
71 2 19 21 23 24
|
||||
72 4 19 21 23 25
|
||||
73 5 22 21 23 24
|
||||
74 2 25 23 21 22
|
||||
75 2 21 23 25 26
|
||||
76 4 21 23 25 27
|
||||
77 5 24 23 25 26
|
||||
78 2 27 25 23 24
|
||||
79 4 23 25 27 17
|
||||
80 2 23 25 27 28
|
||||
81 2 17 27 25 26
|
||||
82 5 26 25 27 28
|
||||
83 10 32 31 33 34
|
||||
84 2 35 33 31 32
|
||||
85 11 41 31 33 34
|
||||
86 4 41 31 33 35
|
||||
87 2 39 41 31 32
|
||||
88 5 32 31 41 42
|
||||
89 4 33 31 41 39
|
||||
90 2 33 31 41 42
|
||||
91 13 31 33 34 14
|
||||
92 12 31 33 34 43
|
||||
93 13 31 33 34 44
|
||||
94 13 35 33 34 14
|
||||
95 12 35 33 34 43
|
||||
96 13 35 33 34 44
|
||||
97 2 31 33 35 36
|
||||
98 4 31 33 35 37
|
||||
99 10 36 35 33 34
|
||||
100 11 37 35 33 34
|
||||
101 36 20 44 34 14
|
||||
102 33 45 44 34 14
|
||||
103 33 46 44 34 14
|
||||
104 34 20 44 34 33
|
||||
105 31 45 44 34 33
|
||||
106 31 46 44 34 33
|
||||
107 35 20 44 34 43
|
||||
108 32 45 44 34 43
|
||||
109 32 46 44 34 43
|
||||
110 2 33 35 37 38
|
||||
111 4 33 35 37 39
|
||||
112 5 36 35 37 38
|
||||
113 2 39 37 35 36
|
||||
114 2 35 37 39 40
|
||||
115 4 35 37 39 41
|
||||
116 5 38 37 39 40
|
||||
117 2 41 39 37 38
|
||||
118 4 37 39 41 31
|
||||
119 2 37 39 41 42
|
||||
120 2 31 41 39 40
|
||||
121 5 40 39 41 42
|
||||
|
||||
Impropers
|
||||
|
||||
1 1 3 1 11 2
|
||||
2 8 1 3 5 4
|
||||
3 9 3 4 13 14
|
||||
4 1 3 5 7 6
|
||||
5 1 5 7 9 8
|
||||
6 1 7 9 11 10
|
||||
7 1 1 11 9 12
|
||||
8 1 19 17 27 18
|
||||
9 5 17 19 21 20
|
||||
10 1 19 21 23 22
|
||||
11 1 21 23 25 24
|
||||
12 1 23 25 27 26
|
||||
13 1 17 27 25 28
|
||||
14 1 33 31 41 32
|
||||
15 5 31 33 35 34
|
||||
16 1 33 35 37 36
|
||||
17 1 35 37 39 38
|
||||
18 1 37 39 41 40
|
||||
19 1 31 41 39 42
|
||||
20 1 15 14 16 4
|
||||
21 1 15 14 4 34
|
||||
22 1 16 14 4 34
|
||||
23 1 15 14 16 34
|
||||
24 1 19 20 29 30
|
||||
25 1 19 20 29 44
|
||||
26 1 19 20 30 44
|
||||
27 1 29 20 30 44
|
||||
28 1 33 34 43 14
|
||||
29 1 33 34 14 44
|
||||
30 1 43 34 14 44
|
||||
31 1 33 34 43 44
|
||||
32 1 45 44 34 20
|
||||
33 1 46 44 34 20
|
||||
34 1 45 44 46 20
|
||||
35 1 45 44 46 34
|
||||
molecule template: end of chain plus polymerized styrene
|
||||
|
||||
46 atoms
|
||||
48 bonds
|
||||
81 angles
|
||||
121 dihedrals
|
||||
35 impropers
|
||||
1 fragments
|
||||
|
||||
Fragments
|
||||
|
||||
create_fit 34 44
|
||||
|
||||
Types
|
||||
|
||||
1 1
|
||||
2 2
|
||||
3 1
|
||||
4 5
|
||||
5 1
|
||||
6 2
|
||||
7 1
|
||||
8 2
|
||||
9 1
|
||||
10 2
|
||||
11 1
|
||||
12 2
|
||||
13 2
|
||||
14 6
|
||||
15 2
|
||||
16 2
|
||||
17 1
|
||||
18 2
|
||||
19 1
|
||||
20 5
|
||||
21 1
|
||||
22 2
|
||||
23 1
|
||||
24 2
|
||||
25 1
|
||||
26 2
|
||||
27 1
|
||||
28 2
|
||||
29 2
|
||||
30 6
|
||||
31 1
|
||||
32 2
|
||||
33 1
|
||||
34 5
|
||||
35 1
|
||||
36 2
|
||||
37 1
|
||||
38 2
|
||||
39 1
|
||||
40 2
|
||||
41 1
|
||||
42 2
|
||||
43 2
|
||||
44 6
|
||||
45 2
|
||||
46 2
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.129000
|
||||
2 0.123700
|
||||
3 0.026600
|
||||
4 -0.018200
|
||||
5 -0.129000
|
||||
6 0.123700
|
||||
7 -0.173400
|
||||
8 0.140300
|
||||
9 -0.113400
|
||||
10 0.128800
|
||||
11 -0.173400
|
||||
12 0.140300
|
||||
13 0.051600
|
||||
14 -0.069600
|
||||
15 0.035400
|
||||
16 0.035400
|
||||
17 -0.129000
|
||||
18 0.123700
|
||||
19 0.026600
|
||||
20 -0.018200
|
||||
21 -0.129000
|
||||
22 0.123700
|
||||
23 -0.173400
|
||||
24 0.140300
|
||||
25 -0.113400
|
||||
26 0.128800
|
||||
27 -0.173400
|
||||
28 0.140300
|
||||
29 0.051600
|
||||
30 -0.069600
|
||||
31 -0.129000
|
||||
32 0.123700
|
||||
33 0.026600
|
||||
34 -0.018200
|
||||
35 -0.129000
|
||||
36 0.123700
|
||||
37 -0.173400
|
||||
38 0.140300
|
||||
39 -0.113400
|
||||
40 0.128800
|
||||
41 -0.173400
|
||||
42 0.140300
|
||||
43 0.051600
|
||||
44 -0.069600
|
||||
45 0.035400
|
||||
46 0.035400
|
||||
|
||||
Coords
|
||||
|
||||
1 24.130699 1.043900 -1.309300
|
||||
2 25.062700 1.582900 -1.309300
|
||||
3 22.900700 1.753900 -1.309300
|
||||
4 22.900700 3.253900 -1.309300
|
||||
5 21.670700 1.043900 -1.309300
|
||||
6 20.738701 1.582900 -1.309300
|
||||
7 21.670700 -0.376100 -1.309300
|
||||
8 20.738701 -0.915100 -1.309300
|
||||
9 22.900700 -1.086100 -1.309300
|
||||
10 22.900700 -2.163100 -1.309300
|
||||
11 24.130699 -0.376100 -1.309300
|
||||
12 25.062700 -0.915100 -1.309300
|
||||
13 23.766701 3.658900 -0.952300
|
||||
14 21.622700 3.802900 -1.871300
|
||||
15 21.672701 4.544900 -1.970300
|
||||
16 20.979700 2.979900 -2.165300
|
||||
17 13.465800 0.682500 -1.658900
|
||||
18 14.397800 1.221500 -1.658900
|
||||
19 12.235800 1.392500 -1.658900
|
||||
20 12.235800 2.892500 -1.658900
|
||||
21 11.005800 0.682500 -1.658900
|
||||
22 10.073800 1.221500 -1.658900
|
||||
23 11.005800 -0.737500 -1.658900
|
||||
24 10.073800 -1.276500 -1.658900
|
||||
25 12.235800 -1.447500 -1.658900
|
||||
26 12.235800 -2.524500 -1.658900
|
||||
27 13.465800 -0.737500 -1.658900
|
||||
28 14.397800 -1.276500 -1.658900
|
||||
29 13.101800 3.297500 -1.301900
|
||||
30 10.957800 3.441500 -2.220900
|
||||
31 18.663500 0.855500 -1.372100
|
||||
32 19.595501 1.394500 -1.372100
|
||||
33 17.433500 1.565500 -1.372100
|
||||
34 17.433500 3.065500 -1.372100
|
||||
35 16.203501 0.855500 -1.372100
|
||||
36 15.271500 1.394500 -1.372100
|
||||
37 16.203501 -0.564500 -1.372100
|
||||
38 15.271500 -1.103500 -1.372100
|
||||
39 17.433500 -1.274500 -1.372100
|
||||
40 17.433500 -2.351500 -1.372100
|
||||
41 18.663500 -0.564500 -1.372100
|
||||
42 19.595501 -1.103500 -1.372100
|
||||
43 18.299500 3.470500 -1.015100
|
||||
44 16.155500 3.614500 -1.934100
|
||||
45 16.205500 4.356500 -2.033100
|
||||
46 15.512500 2.791500 -2.228100
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 2 1 3
|
||||
3 2 1 11
|
||||
4 11 3 4
|
||||
5 2 3 5
|
||||
6 12 13 4
|
||||
7 13 4 14
|
||||
8 1 5 6
|
||||
9 2 5 7
|
||||
10 1 7 8
|
||||
11 2 7 9
|
||||
12 1 9 10
|
||||
13 2 9 11
|
||||
14 1 11 12
|
||||
15 10 15 14
|
||||
16 10 16 14
|
||||
17 9 14 34
|
||||
18 1 17 18
|
||||
19 2 17 19
|
||||
20 2 17 27
|
||||
21 7 19 20
|
||||
22 2 19 21
|
||||
23 8 29 20
|
||||
24 9 30 20
|
||||
25 9 44 20
|
||||
26 1 21 22
|
||||
27 2 21 23
|
||||
28 1 23 24
|
||||
29 2 23 25
|
||||
30 1 25 26
|
||||
31 2 25 27
|
||||
32 1 27 28
|
||||
33 1 31 32
|
||||
34 2 31 33
|
||||
35 2 31 41
|
||||
36 7 33 34
|
||||
37 2 33 35
|
||||
38 8 43 34
|
||||
39 9 44 34
|
||||
40 1 35 36
|
||||
41 2 35 37
|
||||
42 1 37 38
|
||||
43 2 37 39
|
||||
44 1 39 40
|
||||
45 2 39 41
|
||||
46 1 41 42
|
||||
47 10 45 44
|
||||
48 10 46 44
|
||||
|
||||
Angles
|
||||
|
||||
1 1 3 1 2
|
||||
2 1 11 1 2
|
||||
3 2 3 1 11
|
||||
4 17 1 3 4
|
||||
5 2 1 3 5
|
||||
6 17 5 3 4
|
||||
7 18 3 4 13
|
||||
8 19 3 4 14
|
||||
9 20 13 4 14
|
||||
10 1 3 5 6
|
||||
11 2 3 5 7
|
||||
12 1 7 5 6
|
||||
13 1 5 7 8
|
||||
14 2 5 7 9
|
||||
15 1 9 7 8
|
||||
16 1 7 9 10
|
||||
17 2 7 9 11
|
||||
18 1 11 9 10
|
||||
19 2 1 11 9
|
||||
20 1 1 11 12
|
||||
21 1 9 11 12
|
||||
22 21 15 14 4
|
||||
23 21 16 14 4
|
||||
24 22 4 14 34
|
||||
25 15 15 14 16
|
||||
26 14 15 14 34
|
||||
27 14 16 14 34
|
||||
28 1 19 17 18
|
||||
29 1 27 17 18
|
||||
30 2 19 17 27
|
||||
31 9 17 19 20
|
||||
32 2 17 19 21
|
||||
33 9 21 19 20
|
||||
34 10 19 20 29
|
||||
35 11 19 20 30
|
||||
36 11 19 20 44
|
||||
37 12 29 20 30
|
||||
38 12 29 20 44
|
||||
39 13 30 20 44
|
||||
40 1 19 21 22
|
||||
41 2 19 21 23
|
||||
42 1 23 21 22
|
||||
43 1 21 23 24
|
||||
44 2 21 23 25
|
||||
45 1 25 23 24
|
||||
46 1 23 25 26
|
||||
47 2 23 25 27
|
||||
48 1 27 25 26
|
||||
49 2 17 27 25
|
||||
50 1 17 27 28
|
||||
51 1 25 27 28
|
||||
52 1 33 31 32
|
||||
53 1 41 31 32
|
||||
54 2 33 31 41
|
||||
55 9 31 33 34
|
||||
56 2 31 33 35
|
||||
57 9 35 33 34
|
||||
58 11 33 34 14
|
||||
59 12 43 34 14
|
||||
60 13 14 34 44
|
||||
61 10 33 34 43
|
||||
62 11 33 34 44
|
||||
63 12 43 34 44
|
||||
64 1 33 35 36
|
||||
65 2 33 35 37
|
||||
66 1 37 35 36
|
||||
67 1 35 37 38
|
||||
68 2 35 37 39
|
||||
69 1 39 37 38
|
||||
70 1 37 39 40
|
||||
71 2 37 39 41
|
||||
72 1 41 39 40
|
||||
73 2 31 41 39
|
||||
74 1 31 41 42
|
||||
75 1 39 41 42
|
||||
76 16 20 44 34
|
||||
77 14 45 44 20
|
||||
78 14 46 44 20
|
||||
79 14 45 44 34
|
||||
80 14 46 44 34
|
||||
81 15 45 44 46
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 20 2 1 3 4
|
||||
2 2 5 3 1 2
|
||||
3 21 11 1 3 4
|
||||
4 4 11 1 3 5
|
||||
5 2 9 11 1 2
|
||||
6 5 2 1 11 12
|
||||
7 4 3 1 11 9
|
||||
8 2 3 1 11 12
|
||||
9 22 1 3 4 13
|
||||
10 23 1 3 4 14
|
||||
11 22 5 3 4 13
|
||||
12 23 5 3 4 14
|
||||
13 2 1 3 5 6
|
||||
14 4 1 3 5 7
|
||||
15 20 6 5 3 4
|
||||
16 21 7 5 3 4
|
||||
17 24 3 4 14 15
|
||||
18 24 3 4 14 16
|
||||
19 25 3 4 14 34
|
||||
20 26 13 4 14 15
|
||||
21 26 13 4 14 16
|
||||
22 27 13 4 14 34
|
||||
23 2 3 5 7 8
|
||||
24 4 3 5 7 9
|
||||
25 5 6 5 7 8
|
||||
26 2 9 7 5 6
|
||||
27 2 5 7 9 10
|
||||
28 4 5 7 9 11
|
||||
29 5 8 7 9 10
|
||||
30 2 11 9 7 8
|
||||
31 4 7 9 11 1
|
||||
32 2 7 9 11 12
|
||||
33 2 1 11 9 10
|
||||
34 5 10 9 11 12
|
||||
35 28 4 14 34 33
|
||||
36 29 4 14 34 43
|
||||
37 30 4 14 34 44
|
||||
38 31 15 14 34 33
|
||||
39 32 15 14 34 43
|
||||
40 33 15 14 34 44
|
||||
41 31 16 14 34 33
|
||||
42 32 16 14 34 43
|
||||
43 33 16 14 34 44
|
||||
44 10 18 17 19 20
|
||||
45 2 21 19 17 18
|
||||
46 11 27 17 19 20
|
||||
47 4 27 17 19 21
|
||||
48 2 25 27 17 18
|
||||
49 5 18 17 27 28
|
||||
50 4 19 17 27 25
|
||||
51 2 19 17 27 28
|
||||
52 12 17 19 20 29
|
||||
53 13 17 19 20 30
|
||||
54 13 17 19 20 44
|
||||
55 12 21 19 20 29
|
||||
56 13 21 19 20 30
|
||||
57 13 21 19 20 44
|
||||
58 2 17 19 21 22
|
||||
59 4 17 19 21 23
|
||||
60 10 22 21 19 20
|
||||
61 11 23 21 19 20
|
||||
62 34 34 44 20 19
|
||||
63 31 45 44 20 19
|
||||
64 31 46 44 20 19
|
||||
65 35 34 44 20 29
|
||||
66 32 45 44 20 29
|
||||
67 32 46 44 20 29
|
||||
68 36 34 44 20 30
|
||||
69 33 45 44 20 30
|
||||
70 33 46 44 20 30
|
||||
71 2 19 21 23 24
|
||||
72 4 19 21 23 25
|
||||
73 5 22 21 23 24
|
||||
74 2 25 23 21 22
|
||||
75 2 21 23 25 26
|
||||
76 4 21 23 25 27
|
||||
77 5 24 23 25 26
|
||||
78 2 27 25 23 24
|
||||
79 4 23 25 27 17
|
||||
80 2 23 25 27 28
|
||||
81 2 17 27 25 26
|
||||
82 5 26 25 27 28
|
||||
83 10 32 31 33 34
|
||||
84 2 35 33 31 32
|
||||
85 11 41 31 33 34
|
||||
86 4 41 31 33 35
|
||||
87 2 39 41 31 32
|
||||
88 5 32 31 41 42
|
||||
89 4 33 31 41 39
|
||||
90 2 33 31 41 42
|
||||
91 13 31 33 34 14
|
||||
92 12 31 33 34 43
|
||||
93 13 31 33 34 44
|
||||
94 13 35 33 34 14
|
||||
95 12 35 33 34 43
|
||||
96 13 35 33 34 44
|
||||
97 2 31 33 35 36
|
||||
98 4 31 33 35 37
|
||||
99 10 36 35 33 34
|
||||
100 11 37 35 33 34
|
||||
101 36 20 44 34 14
|
||||
102 33 45 44 34 14
|
||||
103 33 46 44 34 14
|
||||
104 34 20 44 34 33
|
||||
105 31 45 44 34 33
|
||||
106 31 46 44 34 33
|
||||
107 35 20 44 34 43
|
||||
108 32 45 44 34 43
|
||||
109 32 46 44 34 43
|
||||
110 2 33 35 37 38
|
||||
111 4 33 35 37 39
|
||||
112 5 36 35 37 38
|
||||
113 2 39 37 35 36
|
||||
114 2 35 37 39 40
|
||||
115 4 35 37 39 41
|
||||
116 5 38 37 39 40
|
||||
117 2 41 39 37 38
|
||||
118 4 37 39 41 31
|
||||
119 2 37 39 41 42
|
||||
120 2 31 41 39 40
|
||||
121 5 40 39 41 42
|
||||
|
||||
Impropers
|
||||
|
||||
1 1 3 1 11 2
|
||||
2 8 1 3 5 4
|
||||
3 9 3 4 13 14
|
||||
4 1 3 5 7 6
|
||||
5 1 5 7 9 8
|
||||
6 1 7 9 11 10
|
||||
7 1 1 11 9 12
|
||||
8 1 19 17 27 18
|
||||
9 5 17 19 21 20
|
||||
10 1 19 21 23 22
|
||||
11 1 21 23 25 24
|
||||
12 1 23 25 27 26
|
||||
13 1 17 27 25 28
|
||||
14 1 33 31 41 32
|
||||
15 5 31 33 35 34
|
||||
16 1 33 35 37 36
|
||||
17 1 35 37 39 38
|
||||
18 1 37 39 41 40
|
||||
19 1 31 41 39 42
|
||||
20 1 15 14 16 4
|
||||
21 1 15 14 4 34
|
||||
22 1 16 14 4 34
|
||||
23 1 15 14 16 34
|
||||
24 1 19 20 29 30
|
||||
25 1 19 20 29 44
|
||||
26 1 19 20 30 44
|
||||
27 1 29 20 30 44
|
||||
28 1 33 34 43 14
|
||||
29 1 33 34 14 44
|
||||
30 1 43 34 14 44
|
||||
31 1 33 34 43 44
|
||||
32 1 45 44 34 20
|
||||
33 1 46 44 34 20
|
||||
34 1 45 44 46 20
|
||||
35 1 45 44 46 34
|
||||
|
||||
@ -1,48 +1,48 @@
|
||||
# use bond/react 'create atoms' feature to add 30 new styrene monomers to chain
|
||||
|
||||
units real
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_style lj/class2/coul/long 8.5
|
||||
|
||||
angle_style class2
|
||||
|
||||
bond_style class2
|
||||
|
||||
dihedral_style class2
|
||||
|
||||
improper_style class2
|
||||
|
||||
variable T equal 530
|
||||
|
||||
read_data trimer.data &
|
||||
extra/bond/per/atom 5 &
|
||||
extra/angle/per/atom 15 &
|
||||
extra/dihedral/per/atom 15 &
|
||||
extra/improper/per/atom 25 &
|
||||
extra/special/per/atom 25
|
||||
|
||||
molecule mol1 grow_styrene_pre.data_template
|
||||
molecule mol2 grow_styrene_post.data_template
|
||||
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 &
|
||||
react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map &
|
||||
modify_create fit create_fit overlap 2.0 &
|
||||
stabilize_steps 100 max_rxn 30
|
||||
|
||||
fix 1 statted_grp_REACT nvt temp $T $T 100
|
||||
|
||||
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
|
||||
|
||||
thermo_style custom step temp press density f_myrxns[1]
|
||||
|
||||
thermo 100
|
||||
|
||||
run 8000
|
||||
|
||||
# write_data final.data nofix
|
||||
# use bond/react 'create atoms' feature to add 30 new styrene monomers to chain
|
||||
|
||||
units real
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_style lj/class2/coul/long 8.5
|
||||
|
||||
angle_style class2
|
||||
|
||||
bond_style class2
|
||||
|
||||
dihedral_style class2
|
||||
|
||||
improper_style class2
|
||||
|
||||
variable T equal 530
|
||||
|
||||
read_data trimer.data &
|
||||
extra/bond/per/atom 5 &
|
||||
extra/angle/per/atom 15 &
|
||||
extra/dihedral/per/atom 15 &
|
||||
extra/improper/per/atom 25 &
|
||||
extra/special/per/atom 25
|
||||
|
||||
molecule mol1 grow_styrene_pre.data_template
|
||||
molecule mol2 grow_styrene_post.data_template
|
||||
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 &
|
||||
react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map &
|
||||
modify_create fit create_fit overlap 2.0 &
|
||||
stabilize_steps 100 max_rxn 30
|
||||
|
||||
fix 1 statted_grp_REACT nvt temp $T $T 100
|
||||
|
||||
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
|
||||
|
||||
thermo_style custom step temp press density f_myrxns[1]
|
||||
|
||||
thermo 100
|
||||
|
||||
run 8000
|
||||
|
||||
# write_data final.data nofix
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,79 +1,79 @@
|
||||
proc vmd_draw_arrow {mol start end} {
|
||||
set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]]
|
||||
graphics $mol cylinder $start $middle radius 0.05
|
||||
graphics $mol cone $middle $end radius 0.01 color 3
|
||||
}
|
||||
|
||||
proc vmd_draw_vector {args} {
|
||||
set usage {"draw vector {x1 y1 z1} {x2 y2 z2} [scale <s>] [resolution <res>] [radius <r>] [filled <yes/no>]"}
|
||||
# defaults
|
||||
set scale 2.0
|
||||
set res 50
|
||||
set radius 0.1
|
||||
set filled yes
|
||||
|
||||
if {[llength $args] < 3} {
|
||||
error "wrong # args: should be $usage"
|
||||
}
|
||||
set mol [lindex $args 0]
|
||||
set center [lindex $args 1]
|
||||
set vector [lindex $args 2]
|
||||
if {[llength $center] != 3 || [llength $vector] != 3} {
|
||||
error "wrong type of args: should be $usage"
|
||||
}
|
||||
|
||||
foreach {flag value} [lrange $args 3 end] {
|
||||
switch -glob $flag {
|
||||
scale {set scale $value}
|
||||
res* {set res $value}
|
||||
rad* {set radius $value}
|
||||
fill* {set filled $value}
|
||||
default {error "unknown option '$flag': should be $usage" }
|
||||
}
|
||||
}
|
||||
|
||||
set vechalf [vecscale [expr $scale * 0.5] $vector]
|
||||
return [list \
|
||||
[graphics $mol color yellow]\
|
||||
[graphics $mol cylinder [vecsub $center $vechalf]\
|
||||
[vecadd $center [vecscale 0.7 $vechalf]] \
|
||||
radius $radius resolution $res filled $filled] \
|
||||
[graphics $mol color orange]\
|
||||
[graphics $mol cone [vecadd $center [vecscale 0.6 $vechalf]] \
|
||||
[vecadd $center $vechalf] radius [expr $radius * 2.5] \
|
||||
resolution $res]]
|
||||
}
|
||||
|
||||
proc vmd_draw_spin {args} {
|
||||
global molid
|
||||
graphics $molid delete all
|
||||
set frame [molinfo $molid get frame]
|
||||
set natoms [molinfo $molid get numatoms]
|
||||
for {set i 0} {$i < $natoms} {incr i} {
|
||||
set sel [atomselect top "index $i"]
|
||||
# set sel [atomselect top "index 1200"]
|
||||
set coords [lindex [$sel get {x y z}] $molid]
|
||||
set velocities [lindex [$sel get {vx vy vz}] $molid]
|
||||
draw vector $coords $velocities
|
||||
set uvx [lindex [$sel get {vx}] $molid]
|
||||
set uvy [lindex [$sel get {vy}] $molid]
|
||||
set uvz [lindex [$sel get {vz}] $molid]
|
||||
$sel set user [vecadd [vecadd [vecscale $uvy $uvy] [vecscale $uvz $uvz] ] [vecscale $uvx $uvx]]
|
||||
$sel set user $uvy
|
||||
#draw vector $coords {0.0 uvy 0.0}
|
||||
}
|
||||
#pbc box -color 3
|
||||
}
|
||||
|
||||
proc enable_trace {} {
|
||||
global vmd_frame
|
||||
trace variable vmd_frame([molinfo top]) w vmd_draw_spin
|
||||
}
|
||||
|
||||
set molid [mol addfile {/home/jtranch/Documents/lammps/src/dump.lammpstrj} type {lammpstrj} autobonds off first 0 last -1 step 1 waitfor all]
|
||||
scale by 0.5
|
||||
animate style Loop
|
||||
enable_trace
|
||||
|
||||
|
||||
|
||||
proc vmd_draw_arrow {mol start end} {
|
||||
set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]]
|
||||
graphics $mol cylinder $start $middle radius 0.05
|
||||
graphics $mol cone $middle $end radius 0.01 color 3
|
||||
}
|
||||
|
||||
proc vmd_draw_vector {args} {
|
||||
set usage {"draw vector {x1 y1 z1} {x2 y2 z2} [scale <s>] [resolution <res>] [radius <r>] [filled <yes/no>]"}
|
||||
# defaults
|
||||
set scale 2.0
|
||||
set res 50
|
||||
set radius 0.1
|
||||
set filled yes
|
||||
|
||||
if {[llength $args] < 3} {
|
||||
error "wrong # args: should be $usage"
|
||||
}
|
||||
set mol [lindex $args 0]
|
||||
set center [lindex $args 1]
|
||||
set vector [lindex $args 2]
|
||||
if {[llength $center] != 3 || [llength $vector] != 3} {
|
||||
error "wrong type of args: should be $usage"
|
||||
}
|
||||
|
||||
foreach {flag value} [lrange $args 3 end] {
|
||||
switch -glob $flag {
|
||||
scale {set scale $value}
|
||||
res* {set res $value}
|
||||
rad* {set radius $value}
|
||||
fill* {set filled $value}
|
||||
default {error "unknown option '$flag': should be $usage" }
|
||||
}
|
||||
}
|
||||
|
||||
set vechalf [vecscale [expr $scale * 0.5] $vector]
|
||||
return [list \
|
||||
[graphics $mol color yellow]\
|
||||
[graphics $mol cylinder [vecsub $center $vechalf]\
|
||||
[vecadd $center [vecscale 0.7 $vechalf]] \
|
||||
radius $radius resolution $res filled $filled] \
|
||||
[graphics $mol color orange]\
|
||||
[graphics $mol cone [vecadd $center [vecscale 0.6 $vechalf]] \
|
||||
[vecadd $center $vechalf] radius [expr $radius * 2.5] \
|
||||
resolution $res]]
|
||||
}
|
||||
|
||||
proc vmd_draw_spin {args} {
|
||||
global molid
|
||||
graphics $molid delete all
|
||||
set frame [molinfo $molid get frame]
|
||||
set natoms [molinfo $molid get numatoms]
|
||||
for {set i 0} {$i < $natoms} {incr i} {
|
||||
set sel [atomselect top "index $i"]
|
||||
# set sel [atomselect top "index 1200"]
|
||||
set coords [lindex [$sel get {x y z}] $molid]
|
||||
set velocities [lindex [$sel get {vx vy vz}] $molid]
|
||||
draw vector $coords $velocities
|
||||
set uvx [lindex [$sel get {vx}] $molid]
|
||||
set uvy [lindex [$sel get {vy}] $molid]
|
||||
set uvz [lindex [$sel get {vz}] $molid]
|
||||
$sel set user [vecadd [vecadd [vecscale $uvy $uvy] [vecscale $uvz $uvz] ] [vecscale $uvx $uvx]]
|
||||
$sel set user $uvy
|
||||
#draw vector $coords {0.0 uvy 0.0}
|
||||
}
|
||||
#pbc box -color 3
|
||||
}
|
||||
|
||||
proc enable_trace {} {
|
||||
global vmd_frame
|
||||
trace variable vmd_frame([molinfo top]) w vmd_draw_spin
|
||||
}
|
||||
|
||||
set molid [mol addfile {/home/jtranch/Documents/lammps/src/dump.lammpstrj} type {lammpstrj} autobonds off first 0 last -1 step 1 waitfor all]
|
||||
scale by 0.5
|
||||
animate style Loop
|
||||
enable_trace
|
||||
|
||||
|
||||
|
||||
|
||||
@ -1,12 +1,12 @@
|
||||
block_size 1
|
||||
start_frame 1
|
||||
n_frames 19
|
||||
nonbonded_cutoff 10.0
|
||||
basis_type 0
|
||||
primary_output_style 0
|
||||
output_solution_flag 1
|
||||
output_spline_coeffs_flag 1
|
||||
pair_nonbonded_bspline_basis_order 6
|
||||
pair_nonbonded_basis_set_resolution 0.7
|
||||
pair_nonbonded_output_binwidth 0.1
|
||||
matrix_type 0
|
||||
block_size 1
|
||||
start_frame 1
|
||||
n_frames 19
|
||||
nonbonded_cutoff 10.0
|
||||
basis_type 0
|
||||
primary_output_style 0
|
||||
output_solution_flag 1
|
||||
output_spline_coeffs_flag 1
|
||||
pair_nonbonded_bspline_basis_order 6
|
||||
pair_nonbonded_basis_set_resolution 0.7
|
||||
pair_nonbonded_output_binwidth 0.1
|
||||
matrix_type 0
|
||||
|
||||
@ -1,21 +1,21 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
python end_of_step_callback here """
|
||||
from __future__ import print_function
|
||||
@ -32,19 +32,19 @@ def post_force_callback(lmp, v):
|
||||
print("### POST_FORCE ###", t)
|
||||
"""
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
fix 2 all python/invoke 50 end_of_step end_of_step_callback
|
||||
fix 3 all python/invoke 50 post_force post_force_callback
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
#dump id all atom 50 dump.melt
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
#dump 2 all image 25 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
#dump 3 all movie 25 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
thermo 50
|
||||
run 250
|
||||
|
||||
@ -1,22 +1,22 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 2 0 2 0 2
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
lattice fcc 0.8442
|
||||
region box block 0 2 0 2 0 2
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.1 bin
|
||||
neighbor 0.1 bin
|
||||
|
||||
neigh_modify every 20 delay 0 check no
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
python post_force_callback here """
|
||||
from __future__ import print_function
|
||||
@ -55,18 +55,18 @@ def post_force_callback(lmp, v):
|
||||
print(e)
|
||||
"""
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
fix 3 all python/invoke 50 post_force post_force_callback
|
||||
|
||||
#dump id all atom 1 dump.melt
|
||||
#dump id all atom 1 dump.melt
|
||||
|
||||
#dump 2 all image 1 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
#dump 2 all image 1 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 1 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
#dump 3 all movie 1 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 1
|
||||
run 100
|
||||
thermo 1
|
||||
run 100
|
||||
|
||||
@ -1,23 +1,23 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all python/move py_nve.NVE
|
||||
fix 1 all python/move py_nve.NVE
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
thermo 50
|
||||
run 250
|
||||
|
||||
@ -1,23 +1,23 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all python/move py_nve.NVE_Opt
|
||||
fix 1 all python/move py_nve.NVE_Opt
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
thermo 50
|
||||
run 250
|
||||
|
||||
@ -1,27 +1,27 @@
|
||||
units real
|
||||
atom_style full
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
read_data data.spce
|
||||
|
||||
pair_style hybrid/overlay coul/cut 12.0 python 12.0
|
||||
pair_style hybrid/overlay coul/cut 12.0 python 12.0
|
||||
|
||||
pair_coeff * * coul/cut
|
||||
pair_coeff * * python py_pot.LJCutSPCE OW NULL
|
||||
pair_coeff * * coul/cut
|
||||
pair_coeff * * python py_pot.LJCutSPCE OW NULL
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
|
||||
# create combined lj/coul table for all atom types
|
||||
# generate tabulated potential from python variant
|
||||
|
||||
84
examples/python/in.pair_python_harmonic
Normal file
84
examples/python/in.pair_python_harmonic
Normal file
@ -0,0 +1,84 @@
|
||||
# 3d soft repulsive particles
|
||||
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 5.0 origin 0.1 0.1 0.1
|
||||
region box block -5 5 -5 5 -5 5
|
||||
create_box 2 box
|
||||
create_atoms 1 box
|
||||
set type 1 type/ratio 2 0.5 424662346
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style python 9.0
|
||||
pair_coeff * * py_pot.Harmonic A B
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
|
||||
write_restart repulsive.restart
|
||||
|
||||
clear
|
||||
|
||||
read_restart repulsive.restart
|
||||
|
||||
pair_style python 10.0
|
||||
pair_coeff * * py_pot.Harmonic A B
|
||||
|
||||
shell rm -f python.dat
|
||||
pair_write 1 1 1000 rsq 0.1 10.0 python.dat PYTH_A_A
|
||||
pair_write 2 2 1000 rsq 0.1 10.0 python.dat PYTH_B_B
|
||||
pair_write 1 2 1000 rsq 0.1 10.0 python.dat PYTH_A_B
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
|
||||
clear
|
||||
|
||||
read_restart repulsive.restart
|
||||
|
||||
pair_style harmonic/cut
|
||||
pair_coeff 1 1 0.2 9.0
|
||||
pair_coeff 2 2 0.4 9.0
|
||||
|
||||
shell rm -f harmonic.dat
|
||||
pair_write 1 1 1000 rsq 0.1 10.0 harmonic.dat HARM_1_1
|
||||
pair_write 2 2 1000 rsq 0.1 10.0 harmonic.dat HARM_2_2
|
||||
pair_write 1 2 1000 rsq 0.1 10.0 harmonic.dat HARM_1_2
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
|
||||
clear
|
||||
|
||||
read_restart repulsive.restart
|
||||
|
||||
pair_style table spline 1000
|
||||
pair_coeff 1 1 python.dat PYTH_A_A
|
||||
pair_coeff 1 2 python.dat PYTH_A_B
|
||||
pair_coeff 2 2 python.dat PYTH_B_B
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
|
||||
# remove temporary files
|
||||
shell rm repulsive.restart harmonic.dat python.dat
|
||||
@ -1,29 +1,29 @@
|
||||
# 3d Lennard-Jones hybrid
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 2 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 2 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
region half block -0.1 4.9 0 10 0 10
|
||||
set region half type 2
|
||||
|
||||
velocity all create 3.0 87287
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style hybrid lj/cut 2.5 python 2.5
|
||||
pair_coeff * * python py_pot.LJCutMelt lj NULL
|
||||
pair_style hybrid lj/cut 2.5 python 2.5
|
||||
pair_coeff * * python py_pot.LJCutMelt lj NULL
|
||||
pair_coeff * 2 lj/cut 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
thermo 50
|
||||
run 250
|
||||
|
||||
write_data hybrid.data
|
||||
write_restart hybrid.restart
|
||||
@ -32,32 +32,32 @@ clear
|
||||
|
||||
read_restart hybrid.restart
|
||||
|
||||
pair_style hybrid lj/cut 2.5 python 2.5
|
||||
pair_coeff * * python py_pot.LJCutMelt lj NULL
|
||||
pair_style hybrid lj/cut 2.5 python 2.5
|
||||
pair_coeff * * python py_pot.LJCutMelt lj NULL
|
||||
pair_coeff * 2 lj/cut 1.0 1.0
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
thermo 50
|
||||
run 250
|
||||
|
||||
clear
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data hybrid.data
|
||||
|
||||
pair_style hybrid lj/cut 2.5 python 2.5
|
||||
pair_coeff * * python py_pot.LJCutMelt lj NULL
|
||||
pair_style hybrid lj/cut 2.5 python 2.5
|
||||
pair_coeff * * python py_pot.LJCutMelt lj NULL
|
||||
pair_coeff * 2 lj/cut 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
thermo 50
|
||||
run 250
|
||||
|
||||
shell rm hybrid.data hybrid.restart
|
||||
|
||||
@ -1,25 +1,25 @@
|
||||
units real
|
||||
atom_style full
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
read_data data.spce
|
||||
|
||||
pair_style python 12.0
|
||||
pair_coeff * * py_pot.LJCutSPCE OW HW
|
||||
pair_style python 12.0
|
||||
pair_coeff * * py_pot.LJCutSPCE OW HW
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
|
||||
# create only lj/cut table for the oxygen atoms from python
|
||||
shell rm -f spce.table
|
||||
@ -27,7 +27,7 @@ pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW
|
||||
|
||||
# switch to tabulated potential with long-range coulomb as overlay
|
||||
pair_style hybrid/overlay coul/long 12.0 table linear 2000
|
||||
kspace_style pppm 1.0e-6
|
||||
kspace_style pppm 1.0e-6
|
||||
pair_coeff * * coul/long
|
||||
pair_coeff 1 1 table spce.table OW-OW
|
||||
|
||||
|
||||
@ -1,26 +1,26 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
thermo 50
|
||||
run 250
|
||||
|
||||
write_data melt.data
|
||||
write_restart melt.restart
|
||||
@ -29,30 +29,30 @@ clear
|
||||
|
||||
read_restart melt.restart
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
thermo 50
|
||||
run 250
|
||||
|
||||
clear
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data melt.data
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
thermo 50
|
||||
run 250
|
||||
|
||||
shell rm melt.data melt.restart
|
||||
|
||||
@ -1,28 +1,28 @@
|
||||
units real
|
||||
atom_style full
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
read_data data.spce
|
||||
|
||||
pair_style hybrid/overlay coul/long 12.0 python 12.0
|
||||
kspace_style pppm 1.0e-6
|
||||
pair_style hybrid/overlay coul/long 12.0 python 12.0
|
||||
kspace_style pppm 1.0e-6
|
||||
|
||||
pair_coeff * * coul/long
|
||||
pair_coeff * * python py_pot.LJCutSPCE OW NULL
|
||||
pair_coeff * * coul/long
|
||||
pair_coeff * * python py_pot.LJCutSPCE OW NULL
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
|
||||
@ -1,18 +1,18 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
|
||||
# generate tabulated potential from python variant
|
||||
pair_write 1 1 2000 rsq 0.01 2.5 lj_1_1.table LJ
|
||||
@ -20,13 +20,13 @@ pair_write 1 1 2000 rsq 0.01 2.5 lj_1_1.table LJ
|
||||
pair_style table linear 2000
|
||||
pair_coeff 1 1 lj_1_1.table LJ
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
thermo 50
|
||||
run 250
|
||||
|
||||
shell rm lj_1_1.table
|
||||
|
||||
|
||||
@ -1,25 +1,25 @@
|
||||
# 3d Lennard-Jones melt with Python functions added
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
|
||||
run 10
|
||||
run 10
|
||||
|
||||
# 1st Python function
|
||||
# example of catching a syntax error
|
||||
|
||||
235
examples/python/log.18Mar22.pair_python_harmonic.g++.1
Normal file
235
examples/python/log.18Mar22.pair_python_harmonic.g++.1
Normal file
@ -0,0 +1,235 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d soft repulsive particles
|
||||
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 5.0 origin 0.1 0.1 0.1
|
||||
Lattice spacing in x,y,z = 5 5 5
|
||||
region box block -5 5 -5 5 -5 5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
using lattice units in orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
set type 1 type/ratio 2 0.5 424662346
|
||||
Setting atom values ...
|
||||
2000 settings made for type/ratio
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style python 9.0
|
||||
pair_coeff * * py_pot.Harmonic A B
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.139 | 4.139 | 4.139 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3 423789.56 0 423825.32 249259.3
|
||||
50 75.889551 422919.46 0 423824.08 248893.24
|
||||
100 105.20972 422570.47 0 423824.6 250756.6
|
||||
150 132.08764 422249.71 0 423824.23 251894.29
|
||||
200 118.14116 422416.43 0 423824.7 252088.96
|
||||
250 128.40086 422293.71 0 423824.28 252057.16
|
||||
Loop time of 17.4414 on 1 procs for 250 steps with 4000 atoms
|
||||
|
||||
|
||||
write_restart repulsive.restart
|
||||
System init for write_restart ...
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
read_restart repulsive.restart
|
||||
Reading restart file ...
|
||||
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style python stores no restart info
|
||||
4000 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
pair_style python 10.0
|
||||
pair_coeff * * py_pot.Harmonic A B
|
||||
|
||||
shell rm -f python.dat
|
||||
pair_write 1 1 1000 rsq 0.1 10.0 python.dat PYTH_A_A
|
||||
Creating table file python.dat with DATE: 2022-03-18
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
pair_write 2 2 1000 rsq 0.1 10.0 python.dat PYTH_B_B
|
||||
Appending to table file python.dat with DATE: 2022-03-18
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
pair_write 1 2 1000 rsq 0.1 10.0 python.dat PYTH_A_B
|
||||
Appending to table file python.dat with DATE: 2022-03-18
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.977 | 4.977 | 4.977 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 128.40086 422293.71 0 423824.28 252057.16
|
||||
300 119.72871 422397.4 0 423824.6 251985.11
|
||||
350 124.88375 422335.77 0 423824.42 252051.28
|
||||
400 121.76143 422373.11 0 423824.53 252006.39
|
||||
450 125.29847 422330.9 0 423824.49 251997.23
|
||||
500 126.87408 422312.08 0 423824.45 252053.51
|
||||
Loop time of 23.4715 on 1 procs for 250 steps with 4000 atoms
|
||||
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
read_restart repulsive.restart
|
||||
Reading restart file ...
|
||||
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style python stores no restart info
|
||||
4000 atoms
|
||||
read_restart CPU = 0.000 seconds
|
||||
|
||||
pair_style harmonic/cut
|
||||
pair_coeff 1 1 0.2 9.0
|
||||
pair_coeff 2 2 0.4 9.0
|
||||
|
||||
shell rm -f harmonic.dat
|
||||
pair_write 1 1 1000 rsq 0.1 10.0 harmonic.dat HARM_1_1
|
||||
Creating table file harmonic.dat with DATE: 2022-03-18
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11
|
||||
ghost atom cutoff = 11
|
||||
binsize = 5.5, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair harmonic/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
pair_write 2 2 1000 rsq 0.1 10.0 harmonic.dat HARM_2_2
|
||||
Appending to table file harmonic.dat with DATE: 2022-03-18
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
pair_write 1 2 1000 rsq 0.1 10.0 harmonic.dat HARM_1_2
|
||||
Appending to table file harmonic.dat with DATE: 2022-03-18
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.138 | 4.138 | 4.138 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 128.40086 422293.71 0 423824.28 252057.16
|
||||
300 119.72871 422397.4 0 423824.6 251985.11
|
||||
350 124.88375 422335.77 0 423824.42 252051.28
|
||||
400 121.76143 422373.11 0 423824.53 252006.39
|
||||
450 125.29847 422330.9 0 423824.49 251997.23
|
||||
500 126.87408 422312.08 0 423824.45 252053.51
|
||||
Loop time of 0.843376 on 1 procs for 250 steps with 4000 atoms
|
||||
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
read_restart repulsive.restart
|
||||
Reading restart file ...
|
||||
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style python stores no restart info
|
||||
4000 atoms
|
||||
read_restart CPU = 0.000 seconds
|
||||
|
||||
pair_style table spline 1000
|
||||
pair_coeff 1 1 python.dat PYTH_A_A
|
||||
Reading pair table potential file python.dat with DATE: 2022-03-18
|
||||
pair_coeff 1 2 python.dat PYTH_A_B
|
||||
Reading pair table potential file python.dat with DATE: 2022-03-18
|
||||
pair_coeff 2 2 python.dat PYTH_B_B
|
||||
Reading pair table potential file python.dat with DATE: 2022-03-18
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11
|
||||
ghost atom cutoff = 11
|
||||
binsize = 5.5, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.552 | 4.552 | 4.552 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 128.40086 422293.71 0 423824.28 252057.14
|
||||
300 119.72876 422397.4 0 423824.6 251985.1
|
||||
350 124.88381 422335.77 0 423824.42 252051.26
|
||||
400 121.76148 422373.11 0 423824.53 252006.37
|
||||
450 125.29842 422330.9 0 423824.49 251997.21
|
||||
500 126.87418 422312.08 0 423824.46 252053.48
|
||||
Loop time of 1.57415 on 1 procs for 250 steps with 4000 atoms
|
||||
|
||||
|
||||
# remove temporary files
|
||||
shell rm repulsive.restart harmonic.dat python.dat
|
||||
Total wall time: 0:00:43
|
||||
235
examples/python/log.18Mar22.pair_python_harmonic.g++.4
Normal file
235
examples/python/log.18Mar22.pair_python_harmonic.g++.4
Normal file
@ -0,0 +1,235 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d soft repulsive particles
|
||||
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 5.0 origin 0.1 0.1 0.1
|
||||
Lattice spacing in x,y,z = 5 5 5
|
||||
region box block -5 5 -5 5 -5 5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
using lattice units in orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
set type 1 type/ratio 2 0.5 424662346
|
||||
Setting atom values ...
|
||||
2000 settings made for type/ratio
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style python 9.0
|
||||
pair_coeff * * py_pot.Harmonic A B
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.225 | 3.225 | 3.225 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3 423843.22 0 423878.98 249277.9
|
||||
50 79.665061 422928.03 0 423877.66 248995.64
|
||||
100 108.5878 422583.81 0 423878.21 250822.76
|
||||
150 130.90607 422317.45 0 423877.89 251949.08
|
||||
200 120.05458 422447.24 0 423878.33 252105.09
|
||||
250 135.76605 422259.47 0 423877.84 252077.41
|
||||
Loop time of 4.70112 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
|
||||
write_restart repulsive.restart
|
||||
System init for write_restart ...
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
read_restart repulsive.restart
|
||||
Reading restart file ...
|
||||
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style python stores no restart info
|
||||
4000 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
pair_style python 10.0
|
||||
pair_coeff * * py_pot.Harmonic A B
|
||||
|
||||
shell rm -f python.dat
|
||||
pair_write 1 1 1000 rsq 0.1 10.0 python.dat PYTH_A_A
|
||||
Creating table file python.dat with DATE: 2022-03-18
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
pair_write 2 2 1000 rsq 0.1 10.0 python.dat PYTH_B_B
|
||||
Appending to table file python.dat with DATE: 2022-03-18
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
pair_write 1 2 1000 rsq 0.1 10.0 python.dat PYTH_A_B
|
||||
Appending to table file python.dat with DATE: 2022-03-18
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.667 | 3.667 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 135.76605 422259.47 0 423877.84 252077.41
|
||||
300 119.63404 422452.21 0 423878.28 251958.74
|
||||
350 129.35013 422336.12 0 423878 252069.99
|
||||
400 123.04377 422411.48 0 423878.19 252024.23
|
||||
450 126.01375 422375.98 0 423878.1 252019.19
|
||||
500 126.91094 422365.34 0 423878.15 252012.59
|
||||
Loop time of 6.20423 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
read_restart repulsive.restart
|
||||
Reading restart file ...
|
||||
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style python stores no restart info
|
||||
4000 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
pair_style harmonic/cut
|
||||
pair_coeff 1 1 0.2 9.0
|
||||
pair_coeff 2 2 0.4 9.0
|
||||
|
||||
shell rm -f harmonic.dat
|
||||
pair_write 1 1 1000 rsq 0.1 10.0 harmonic.dat HARM_1_1
|
||||
Creating table file harmonic.dat with DATE: 2022-03-18
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11
|
||||
ghost atom cutoff = 11
|
||||
binsize = 5.5, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair harmonic/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
pair_write 2 2 1000 rsq 0.1 10.0 harmonic.dat HARM_2_2
|
||||
Appending to table file harmonic.dat with DATE: 2022-03-18
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
pair_write 1 2 1000 rsq 0.1 10.0 harmonic.dat HARM_1_2
|
||||
Appending to table file harmonic.dat with DATE: 2022-03-18
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.227 | 3.227 | 3.229 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 135.76605 422259.47 0 423877.84 252077.41
|
||||
300 119.63404 422452.21 0 423878.28 251958.74
|
||||
350 129.35013 422336.12 0 423878 252069.99
|
||||
400 123.04377 422411.48 0 423878.19 252024.23
|
||||
450 126.01375 422375.98 0 423878.1 252019.19
|
||||
500 126.91094 422365.34 0 423878.15 252012.59
|
||||
Loop time of 0.257048 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
read_restart repulsive.restart
|
||||
Reading restart file ...
|
||||
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style python stores no restart info
|
||||
4000 atoms
|
||||
read_restart CPU = 0.000 seconds
|
||||
|
||||
pair_style table spline 1000
|
||||
pair_coeff 1 1 python.dat PYTH_A_A
|
||||
Reading pair table potential file python.dat with DATE: 2022-03-18
|
||||
pair_coeff 1 2 python.dat PYTH_A_B
|
||||
Reading pair table potential file python.dat with DATE: 2022-03-18
|
||||
pair_coeff 2 2 python.dat PYTH_B_B
|
||||
Reading pair table potential file python.dat with DATE: 2022-03-18
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11
|
||||
ghost atom cutoff = 11
|
||||
binsize = 5.5, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.257 | 3.257 | 3.257 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 135.76605 422259.47 0 423877.84 252077.38
|
||||
300 119.63401 422452.21 0 423878.28 251958.73
|
||||
350 129.35009 422336.11 0 423878 252069.98
|
||||
400 123.04383 422411.48 0 423878.19 252024.21
|
||||
450 126.01378 422375.98 0 423878.1 252019.16
|
||||
500 126.91078 422365.34 0 423878.15 252012.57
|
||||
Loop time of 0.497624 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
|
||||
# remove temporary files
|
||||
shell rm repulsive.restart harmonic.dat python.dat
|
||||
Total wall time: 0:00:11
|
||||
288
examples/python/log.18Mar22.pair_python_harmonic.opencl.1
Normal file
288
examples/python/log.18Mar22.pair_python_harmonic.opencl.1
Normal file
@ -0,0 +1,288 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
package gpu 0
|
||||
# 3d soft repulsive particles
|
||||
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 5.0 origin 0.1 0.1 0.1
|
||||
Lattice spacing in x,y,z = 5 5 5
|
||||
region box block -5 5 -5 5 -5 5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
using lattice units in orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
set type 1 type/ratio 2 0.5 424662346
|
||||
Setting atom values ...
|
||||
2000 settings made for type/ratio
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style python 9.0
|
||||
pair_coeff * * py_pot.Harmonic A B
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- GPU package (short-range, long-range and three-body potentials):
|
||||
|
||||
@Article{Brown11,
|
||||
author = {W. M. Brown, P. Wang, S. J. Plimpton, A. N. Tharrington},
|
||||
title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Short Range Forces},
|
||||
journal = {Comp.~Phys.~Comm.},
|
||||
year = 2011,
|
||||
volume = 182,
|
||||
pages = {898--911}
|
||||
}
|
||||
|
||||
@Article{Brown12,
|
||||
author = {W. M. Brown, A. Kohlmeyer, S. J. Plimpton, A. N. Tharrington},
|
||||
title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh},
|
||||
journal = {Comp.~Phys.~Comm.},
|
||||
year = 2012,
|
||||
volume = 183,
|
||||
pages = {449--459}
|
||||
}
|
||||
|
||||
@Article{Brown13,
|
||||
author = {W. M. Brown, Y. Masako},
|
||||
title = {Implementing Molecular Dynamics on Hybrid High Performance Computers – Three-Body Potentials},
|
||||
journal = {Comp.~Phys.~Comm.},
|
||||
year = 2013,
|
||||
volume = 184,
|
||||
pages = {2785--2793}
|
||||
}
|
||||
|
||||
@Article{Trung15,
|
||||
author = {T. D. Nguyen, S. J. Plimpton},
|
||||
title = {Accelerating dissipative particle dynamics simulations for soft matter systems},
|
||||
journal = {Comput.~Mater.~Sci.},
|
||||
year = 2015,
|
||||
volume = 100,
|
||||
pages = {173--180}
|
||||
}
|
||||
|
||||
@Article{Trung17,
|
||||
author = {T. D. Nguyen},
|
||||
title = {GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations},
|
||||
journal = {Comp.~Phys.~Comm.},
|
||||
year = 2017,
|
||||
volume = 212,
|
||||
pages = {113--122}
|
||||
}
|
||||
|
||||
@Article{Nikolskiy19,
|
||||
author = {V. Nikolskiy, V. Stegailov},
|
||||
title = {GPU acceleration of four-site water models in LAMMPS},
|
||||
journal = {Proceeding of the International Conference on Parallel Computing (ParCo 2019), Prague, Czech Republic},
|
||||
year = 2019
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.612 | 4.612 | 4.612 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3 423789.56 0 423825.32 249259.3
|
||||
50 75.889551 422919.46 0 423824.08 248893.24
|
||||
100 105.20972 422570.47 0 423824.6 250756.6
|
||||
150 132.08764 422249.71 0 423824.23 251894.29
|
||||
200 118.14116 422416.43 0 423824.7 252088.96
|
||||
250 128.40086 422293.71 0 423824.28 252057.16
|
||||
Loop time of 21.1837 on 1 procs for 250 steps with 4000 atoms
|
||||
|
||||
|
||||
write_restart repulsive.restart
|
||||
System init for write_restart ...
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
package gpu 0
|
||||
|
||||
read_restart repulsive.restart
|
||||
Reading restart file ...
|
||||
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style python stores no restart info
|
||||
4000 atoms
|
||||
read_restart CPU = 0.000 seconds
|
||||
|
||||
pair_style python 10.0
|
||||
pair_coeff * * py_pot.Harmonic A B
|
||||
|
||||
shell rm -f python.dat
|
||||
pair_write 1 1 1000 rsq 0.1 10.0 python.dat PYTH_A_A
|
||||
Creating table file python.dat with DATE: 2022-03-18
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
pair_write 2 2 1000 rsq 0.1 10.0 python.dat PYTH_B_B
|
||||
Appending to table file python.dat with DATE: 2022-03-18
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
pair_write 1 2 1000 rsq 0.1 10.0 python.dat PYTH_A_B
|
||||
Appending to table file python.dat with DATE: 2022-03-18
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.451 | 5.451 | 5.451 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 128.40086 422293.71 0 423824.28 252057.16
|
||||
300 119.72871 422397.4 0 423824.6 251985.11
|
||||
350 124.88375 422335.77 0 423824.42 252051.28
|
||||
400 121.76143 422373.11 0 423824.53 252006.39
|
||||
450 125.29847 422330.9 0 423824.49 251997.23
|
||||
500 126.87408 422312.08 0 423824.45 252053.51
|
||||
Loop time of 28.5184 on 1 procs for 250 steps with 4000 atoms
|
||||
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
package gpu 0
|
||||
|
||||
read_restart repulsive.restart
|
||||
Reading restart file ...
|
||||
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style python stores no restart info
|
||||
4000 atoms
|
||||
read_restart CPU = 0.000 seconds
|
||||
|
||||
pair_style harmonic/cut
|
||||
pair_coeff 1 1 0.2 9.0
|
||||
pair_coeff 2 2 0.4 9.0
|
||||
|
||||
shell rm -f harmonic.dat
|
||||
pair_write 1 1 1000 rsq 0.1 10.0 harmonic.dat HARM_1_1
|
||||
Creating table file harmonic.dat with DATE: 2022-03-18
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11
|
||||
ghost atom cutoff = 11
|
||||
binsize = 5.5, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair harmonic/cut, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
pair_write 2 2 1000 rsq 0.1 10.0 harmonic.dat HARM_2_2
|
||||
Appending to table file harmonic.dat with DATE: 2022-03-18
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
pair_write 1 2 1000 rsq 0.1 10.0 harmonic.dat HARM_1_2
|
||||
Appending to table file harmonic.dat with DATE: 2022-03-18
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.611 | 4.611 | 4.611 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 128.40086 422293.71 0 423824.28 252057.16
|
||||
300 119.72871 422397.4 0 423824.6 251985.11
|
||||
350 124.88375 422335.77 0 423824.42 252051.28
|
||||
400 121.76143 422373.11 0 423824.53 252006.39
|
||||
450 125.29847 422330.9 0 423824.49 251997.23
|
||||
500 126.87408 422312.08 0 423824.45 252053.51
|
||||
Loop time of 1.1146 on 1 procs for 250 steps with 4000 atoms
|
||||
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
package gpu 0
|
||||
|
||||
read_restart repulsive.restart
|
||||
Reading restart file ...
|
||||
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style python stores no restart info
|
||||
4000 atoms
|
||||
read_restart CPU = 0.000 seconds
|
||||
|
||||
pair_style table spline 1000
|
||||
pair_coeff 1 1 python.dat PYTH_A_A
|
||||
Reading pair table potential file python.dat with DATE: 2022-03-18
|
||||
pair_coeff 1 2 python.dat PYTH_A_B
|
||||
Reading pair table potential file python.dat with DATE: 2022-03-18
|
||||
pair_coeff 2 2 python.dat PYTH_B_B
|
||||
Reading pair table potential file python.dat with DATE: 2022-03-18
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 128.40086 422293.71 0 423824.28 252057.14
|
||||
300 119.72876 422397.4 0 423824.6 251985.09
|
||||
350 124.88381 422335.77 0 423824.42 252051.26
|
||||
400 121.76148 422373.11 0 423824.53 252006.37
|
||||
450 125.29841 422330.9 0 423824.49 251997.2
|
||||
500 126.87418 422312.08 0 423824.45 252053.48
|
||||
Loop time of 0.389958 on 1 procs for 250 steps with 4000 atoms
|
||||
|
||||
|
||||
# remove temporary files
|
||||
shell rm repulsive.restart harmonic.dat python.dat
|
||||
Total wall time: 0:00:54
|
||||
268
examples/python/log.18Mar22.pair_python_harmonic.openmp.1
Normal file
268
examples/python/log.18Mar22.pair_python_harmonic.openmp.1
Normal file
@ -0,0 +1,268 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
using 4 OpenMP thread(s) per MPI task
|
||||
package omp 0
|
||||
using multi-threaded neighbor list subroutines
|
||||
# 3d soft repulsive particles
|
||||
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 5.0 origin 0.1 0.1 0.1
|
||||
Lattice spacing in x,y,z = 5 5 5
|
||||
region box block -5 5 -5 5 -5 5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
using lattice units in orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
set type 1 type/ratio 2 0.5 424662346
|
||||
Setting atom values ...
|
||||
2000 settings made for type/ratio
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style python 9.0
|
||||
pair_coeff * * py_pot.Harmonic A B
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
No /omp style for force computation currently active
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on, omp
|
||||
pair build: half/bin/atomonly/newton/omp
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.024 | 6.024 | 6.024 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3 423789.56 0 423825.32 249259.3
|
||||
50 75.889551 422919.46 0 423824.08 248893.24
|
||||
100 105.20972 422570.47 0 423824.6 250756.6
|
||||
150 132.08764 422249.71 0 423824.23 251894.29
|
||||
200 118.14116 422416.43 0 423824.7 252088.96
|
||||
250 128.40086 422293.71 0 423824.28 252057.16
|
||||
Loop time of 18.9294 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
|
||||
write_restart repulsive.restart
|
||||
System init for write_restart ...
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
No /omp style for force computation currently active
|
||||
|
||||
clear
|
||||
using 4 OpenMP thread(s) per MPI task
|
||||
package omp 0
|
||||
using multi-threaded neighbor list subroutines
|
||||
|
||||
read_restart repulsive.restart
|
||||
Reading restart file ...
|
||||
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style python stores no restart info
|
||||
4000 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
pair_style python 10.0
|
||||
pair_coeff * * py_pot.Harmonic A B
|
||||
|
||||
shell rm -f python.dat
|
||||
pair_write 1 1 1000 rsq 0.1 10.0 python.dat PYTH_A_A
|
||||
Creating table file python.dat with DATE: 2022-03-18
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
pair_write 2 2 1000 rsq 0.1 10.0 python.dat PYTH_B_B
|
||||
Appending to table file python.dat with DATE: 2022-03-18
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
pair_write 1 2 1000 rsq 0.1 10.0 python.dat PYTH_A_B
|
||||
Appending to table file python.dat with DATE: 2022-03-18
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
No /omp style for force computation currently active
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on, omp
|
||||
pair build: half/bin/atomonly/newton/omp
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.626 | 7.626 | 7.626 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 128.40086 422293.71 0 423824.28 252057.16
|
||||
300 119.72871 422397.4 0 423824.6 251985.11
|
||||
350 124.88375 422335.77 0 423824.42 252051.28
|
||||
400 121.76143 422373.11 0 423824.53 252006.39
|
||||
450 125.29847 422330.9 0 423824.49 251997.23
|
||||
500 126.87408 422312.08 0 423824.45 252053.51
|
||||
Loop time of 24.3294 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
|
||||
clear
|
||||
using 4 OpenMP thread(s) per MPI task
|
||||
package omp 0
|
||||
using multi-threaded neighbor list subroutines
|
||||
|
||||
read_restart repulsive.restart
|
||||
Reading restart file ...
|
||||
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style python stores no restart info
|
||||
4000 atoms
|
||||
read_restart CPU = 0.000 seconds
|
||||
|
||||
pair_style harmonic/cut
|
||||
pair_coeff 1 1 0.2 9.0
|
||||
pair_coeff 2 2 0.4 9.0
|
||||
|
||||
shell rm -f harmonic.dat
|
||||
pair_write 1 1 1000 rsq 0.1 10.0 harmonic.dat HARM_1_1
|
||||
Creating table file harmonic.dat with DATE: 2022-03-18
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11
|
||||
ghost atom cutoff = 11
|
||||
binsize = 5.5, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair harmonic/cut/omp, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
pair_write 2 2 1000 rsq 0.1 10.0 harmonic.dat HARM_2_2
|
||||
Appending to table file harmonic.dat with DATE: 2022-03-18
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
pair_write 1 2 1000 rsq 0.1 10.0 harmonic.dat HARM_1_2
|
||||
Appending to table file harmonic.dat with DATE: 2022-03-18
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Last active /omp style is pair_style harmonic/cut/omp
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair harmonic/cut/omp, perpetual
|
||||
attributes: half, newton on, omp
|
||||
pair build: half/bin/atomonly/newton/omp
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.023 | 6.023 | 6.023 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 128.40086 422293.71 0 423824.28 252057.16
|
||||
300 119.72871 422397.4 0 423824.6 251985.11
|
||||
350 124.88375 422335.77 0 423824.42 252051.28
|
||||
400 121.76143 422373.11 0 423824.53 252006.39
|
||||
450 125.29847 422330.9 0 423824.49 251997.23
|
||||
500 126.87408 422312.08 0 423824.45 252053.51
|
||||
Loop time of 0.219199 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
|
||||
clear
|
||||
using 4 OpenMP thread(s) per MPI task
|
||||
package omp 0
|
||||
using multi-threaded neighbor list subroutines
|
||||
|
||||
read_restart repulsive.restart
|
||||
Reading restart file ...
|
||||
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (-25 -25 -25) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style python stores no restart info
|
||||
4000 atoms
|
||||
read_restart CPU = 0.000 seconds
|
||||
|
||||
pair_style table spline 1000
|
||||
pair_coeff 1 1 python.dat PYTH_A_A
|
||||
Reading pair table potential file python.dat with DATE: 2022-03-18
|
||||
pair_coeff 1 2 python.dat PYTH_A_B
|
||||
Reading pair table potential file python.dat with DATE: 2022-03-18
|
||||
pair_coeff 2 2 python.dat PYTH_B_B
|
||||
Reading pair table potential file python.dat with DATE: 2022-03-18
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Last active /omp style is pair_style table/omp
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11
|
||||
ghost atom cutoff = 11
|
||||
binsize = 5.5, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair table/omp, perpetual
|
||||
attributes: half, newton on, omp
|
||||
pair build: half/bin/atomonly/newton/omp
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.056 | 6.056 | 6.056 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 128.40086 422293.71 0 423824.28 252057.14
|
||||
300 119.72876 422397.4 0 423824.6 251985.1
|
||||
350 124.88381 422335.77 0 423824.42 252051.26
|
||||
400 121.76148 422373.11 0 423824.53 252006.37
|
||||
450 125.29842 422330.9 0 423824.49 251997.21
|
||||
500 126.87418 422312.08 0 423824.46 252053.48
|
||||
Loop time of 0.374806 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
|
||||
# remove temporary files
|
||||
shell rm repulsive.restart harmonic.dat python.dat
|
||||
Total wall time: 0:00:44
|
||||
@ -1,4 +1,5 @@
|
||||
from __future__ import print_function
|
||||
import math
|
||||
|
||||
class LAMMPSPairPotential(object):
|
||||
def __init__(self):
|
||||
@ -10,6 +11,34 @@ class LAMMPSPairPotential(object):
|
||||
if (units != self.units):
|
||||
raise Exception("Conflicting units: %s vs. %s" % (self.units,units))
|
||||
|
||||
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
|
||||
|
||||
class LJCutMelt(LAMMPSPairPotential):
|
||||
def __init__(self):
|
||||
super(LJCutMelt,self).__init__()
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -206,7 +206,7 @@ void ComputeStressCartesian::init_list(int /* id */, NeighList *ptr)
|
||||
void ComputeStressCartesian::compute_array()
|
||||
{
|
||||
int i, j, ii, jj, inum, jnum, itype, jtype;
|
||||
int bin, bin1, bin2, bin3;
|
||||
int bin, bin1, bin2;
|
||||
tagint itag, jtag;
|
||||
double xtmp, ytmp, ztmp, delx, dely, delz;
|
||||
double rsq, fpair, factor_coul, factor_lj;
|
||||
@ -266,7 +266,6 @@ void ComputeStressCartesian::compute_array()
|
||||
Pair *pair = force->pair;
|
||||
double **cutsq = force->pair->cutsq;
|
||||
|
||||
double risq, rjsq;
|
||||
double xi1, xi2, xj1, xj2;
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
@ -362,7 +361,7 @@ void ComputeStressCartesian::compute_pressure_1d(double fpair, double xi, double
|
||||
double dely, double delz)
|
||||
{
|
||||
int bin_s, bin_e, bin_step, bin, bin_limit;
|
||||
double xa, xb, l_sum;
|
||||
double xa, xb;
|
||||
|
||||
if (xi < domain->boxlo[dir1])
|
||||
xi += (domain->boxhi[dir1] - domain->boxlo[dir1]);
|
||||
@ -456,8 +455,8 @@ void ComputeStressCartesian::compute_pressure_1d(double fpair, double xi, double
|
||||
}
|
||||
}
|
||||
|
||||
void ComputeStressCartesian::compute_pressure_2d(double fpair, double xi, double yi, double xj,
|
||||
double yj, double delx, double dely, double delz)
|
||||
void ComputeStressCartesian::compute_pressure_2d(double fpair, double xi, double yi, double /*xj*/,
|
||||
double /*yj*/, double delx, double dely, double delz)
|
||||
{
|
||||
int bin1, bin2, next_bin1, next_bin2;
|
||||
double la = 0.0, lb = 0.0, l_sum = 0.0;
|
||||
|
||||
@ -189,7 +189,6 @@ void ComputeStressSpherical::compute_array()
|
||||
double r, vr, vt, vp, theta;
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double *mass = atom->mass;
|
||||
tagint *tag = atom->tag;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
@ -247,10 +246,6 @@ void ComputeStressSpherical::compute_array()
|
||||
Pair *pair = force->pair;
|
||||
double **cutsq = force->pair->cutsq;
|
||||
|
||||
double risq, rjsq;
|
||||
double dir1i, dir2i, dir3i, dir1j, dir2j, dir3j;
|
||||
double xi, yi, zi, xj, yj, zj;
|
||||
|
||||
double qi[3], l1, l2, l3, l4, R1, R2, Fa, Fb, l_sum;
|
||||
double rij, f, ririj, sqr, la, lb, sql0, lambda0;
|
||||
double rsqxy, ririjxy, sqrixy, sqlxy0, A, B, C;
|
||||
|
||||
@ -99,8 +99,8 @@ void PairHarmonicCut::compute(int eflag, int vflag)
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
const double r = sqrt(rsq);
|
||||
const double delta = cut[itype][jtype] - r;
|
||||
const double philj = factor_lj * delta * k[itype][jtype];
|
||||
const double fpair = delta * philj / r;
|
||||
const double prefactor = factor_lj * delta * k[itype][jtype];
|
||||
const double fpair = 2.0 * prefactor / r;
|
||||
|
||||
fxtmp += delx * fpair;
|
||||
fytmp += dely * fpair;
|
||||
@ -111,7 +111,10 @@ void PairHarmonicCut::compute(int eflag, int vflag)
|
||||
f[j][2] -= delz * fpair;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i, j, nlocal, newton_pair, philj, 0.0, fpair, delx, dely, delz);
|
||||
if (evflag) {
|
||||
const double philj = prefactor * delta;
|
||||
ev_tally(i, j, nlocal, newton_pair, philj, 0.0, fpair, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
f[i][0] += fxtmp;
|
||||
@ -186,10 +189,10 @@ double PairHarmonicCut::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) {
|
||||
cut[i][j] = mix_distance(cut[i][i], cut[j][j]);
|
||||
cut[j][i] = cut[i][j];
|
||||
k[i][j] = mix_energy(k[i][i], k[j][j], cut[i][i], cut[j][j]);
|
||||
k[j][i] = k[i][j];
|
||||
}
|
||||
k[j][i] = k[i][j];
|
||||
cut[j][i] = cut[i][j];
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
@ -296,8 +299,8 @@ double PairHarmonicCut::single(int /*i*/, int /*j*/, int itype, int jtype, doubl
|
||||
}
|
||||
const double r = sqrt(rsq);
|
||||
const double delta = cut[itype][jtype] - r;
|
||||
const double philj = factor_lj * delta * k[itype][jtype];
|
||||
fforce = delta * philj / r;
|
||||
const double philj = factor_lj * delta * delta * k[itype][jtype];
|
||||
fforce = 2.0 * philj / (r * delta);
|
||||
return philj;
|
||||
}
|
||||
|
||||
|
||||
@ -233,55 +233,62 @@ FixLbFluid::FixLbFluid(LAMMPS *lmp, int narg, char **arg) :
|
||||
else
|
||||
itype = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
|
||||
double scalefactor = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
|
||||
if (itype < 0 || itype > ntypes)
|
||||
error->all(FLERR, "Illegal fix lb/fluid command: scaleGamma");
|
||||
if ((itype < 0) || (itype > ntypes))
|
||||
error->all(FLERR, "Illegal fix lb/fluid command: {}", arg[iarg]);
|
||||
if (itype)
|
||||
Gamma[itype] = scalefactor;
|
||||
else
|
||||
for (int it = 1; it <= atom->ntypes; it++) Gamma[it] = scalefactor;
|
||||
iarg += 3;
|
||||
} else if (strcmp(arg[iarg], "dx") == 0) {
|
||||
if ((iarg + 2) > narg) error->all(FLERR, "Illegal fix lb/fluid command: {}", arg[iarg]);
|
||||
dx_lb = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
||||
iarg += 2;
|
||||
setdx = 0;
|
||||
} else if (strcmp(arg[iarg], "dm") == 0) {
|
||||
if ((iarg + 2) > narg) error->all(FLERR, "Illegal fix lb/fluid command: {}", arg[iarg]);
|
||||
dm_lb = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg], "a0") == 0) {
|
||||
if ((iarg + 2) > narg) error->all(FLERR, "Illegal fix lb/fluid command: {}", arg[iarg]);
|
||||
a_0_real = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
||||
iarg += 2;
|
||||
seta0 = 0;
|
||||
} else if (strcmp(arg[iarg], "noise") == 0) {
|
||||
if ((iarg + 3) > narg) error->all(FLERR, "Illegal fix lb/fluid command: {}", arg[iarg]);
|
||||
noisestress = 1;
|
||||
T = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
||||
seed = atoi(arg[iarg + 2]);
|
||||
seed = utils::inumeric(FLERR, arg[iarg + 2], false, lmp);
|
||||
iarg += 3;
|
||||
} else if (strcmp(arg[iarg], "stencil") == 0) {
|
||||
if ((iarg + 2) > narg) error->all(FLERR, "Illegal fix lb/fluid command: {}", arg[iarg]);
|
||||
n_stencil = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg], "read_restart") == 0) {
|
||||
if ((iarg + 2) > narg) error->all(FLERR, "Illegal fix lb/fluid command: {}", arg[iarg]);
|
||||
readrestart = 1;
|
||||
int nlength = strlen(arg[iarg + 1]) + 16;
|
||||
char *filename = new char[nlength];
|
||||
strcpy(filename, arg[iarg + 1]);
|
||||
char *filename = utils::strdup(arg[iarg + 1]);
|
||||
MPI_File_open(world, filename, MPI_MODE_RDONLY, MPI_INFO_NULL, &pFileRead);
|
||||
delete[] filename;
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg], "write_restart") == 0) {
|
||||
if ((iarg + 2) > narg) error->all(FLERR, "Illegal fix lb/fluid command: {}", arg[iarg]);
|
||||
printrestart = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg], "zwall_velocity") == 0) {
|
||||
if ((iarg + 3) > narg) error->all(FLERR, "Illegal fix lb/fluid command: {}", arg[iarg]);
|
||||
if (domain->periodicity[2] != 0)
|
||||
error->all(FLERR, "fix lb/fluid error: setting \
|
||||
a z wall velocity without implementing fixed BCs in z");
|
||||
error->all(FLERR, "setting a z wall velocity without implementing fixed BCs in z");
|
||||
vwbt = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
||||
vwtp = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
|
||||
iarg += 3;
|
||||
} else if (strcmp(arg[iarg], "pressurebcx") == 0) {
|
||||
if ((iarg + 2) > narg) error->all(FLERR, "Illegal fix lb/fluid command: {}", arg[iarg]);
|
||||
pressure = 1;
|
||||
rhofactor = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg], "bodyforce") == 0) {
|
||||
if ((iarg + 4) > narg) error->all(FLERR, "Illegal fix lb/fluid command: {}", arg[iarg]);
|
||||
bodyforcex = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
||||
bodyforcey = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
|
||||
bodyforcez = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
|
||||
@ -290,6 +297,7 @@ a z wall velocity without implementing fixed BCs in z");
|
||||
numvel = 19;
|
||||
iarg += 1;
|
||||
} else if (strcmp(arg[iarg], "dumpxdmf") == 0) {
|
||||
if ((iarg + 4) > narg) error->all(FLERR, "Illegal fix lb/fluid command: {}", arg[iarg]);
|
||||
dump_interval = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
|
||||
dump_file_name_xdmf = std::string(arg[iarg + 2]) + std::string(".xdmf");
|
||||
dump_file_name_raw = std::string(arg[iarg + 2]) + std::string(".raw");
|
||||
@ -299,9 +307,11 @@ a z wall velocity without implementing fixed BCs in z");
|
||||
lin_init = 1;
|
||||
iarg += 1;
|
||||
} else if (strcmp(arg[iarg], "dof") == 0) {
|
||||
if ((iarg + 2) > narg) error->all(FLERR, "Illegal fix lb/fluid command: {}", arg[iarg]);
|
||||
setdof = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg], "npits") == 0) {
|
||||
if ((iarg + 6) > narg) error->all(FLERR, "Illegal fix lb/fluid command: {}", arg[iarg]);
|
||||
npits = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
|
||||
h_p = utils::inumeric(FLERR, arg[iarg + 2], false, lmp);
|
||||
l_p = utils::inumeric(FLERR, arg[iarg + 3], false, lmp);
|
||||
@ -312,10 +322,11 @@ a z wall velocity without implementing fixed BCs in z");
|
||||
sw = 1;
|
||||
iarg += 1;
|
||||
} else if (strcmp(arg[iarg], "wp") == 0) {
|
||||
if ((iarg + 2) > narg) error->all(FLERR, "Illegal fix lb/fluid command: {}", arg[iarg]);
|
||||
w_p = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
|
||||
iarg += 2;
|
||||
} else
|
||||
error->all(FLERR, "Illegal fix lb/fluid command");
|
||||
error->all(FLERR, "Illegal fix lb/fluid command: {}", arg[iarg]);
|
||||
}
|
||||
|
||||
//-------------------------------------------------------------------------
|
||||
@ -2339,59 +2350,59 @@ void FixLbFluid::SetupBuffers(void)
|
||||
//==========================================================================
|
||||
// Output fluid density and velocity to file in XDMF format
|
||||
//==========================================================================
|
||||
void FixLbFluid::dump(const int step)
|
||||
void FixLbFluid::dump(const bigint step)
|
||||
{
|
||||
static int frameindex = 0;
|
||||
static bigint frameindex = 0;
|
||||
|
||||
if (dump_interval && step % dump_interval == 0) {
|
||||
// Write XDMF grid entry for time step
|
||||
if (me == 0) {
|
||||
long int block = (long int) fluid_global_n0[0] * fluid_global_n0[1] * fluid_global_n0[2] *
|
||||
sizeof(MPI_DOUBLE);
|
||||
long int offset = frameindex * block * (1 + 3);
|
||||
bigint block =
|
||||
(bigint) fluid_global_n0[0] * fluid_global_n0[1] * fluid_global_n0[2] * sizeof(double);
|
||||
bigint offset = frameindex * block * (1 + 3);
|
||||
double time = dump_time_index ? update->ntimestep * dt_lb : frameindex;
|
||||
|
||||
fprintf(dump_file_handle_xdmf,
|
||||
" <Grid Name=\"%d\">\n"
|
||||
" <Time Value=\"%f\"/>\n\n"
|
||||
" <Topology TopologyType=\"3DCoRectMesh\" Dimensions=\"%d %d %d\"/>\n"
|
||||
" <Geometry GeometryType=\"ORIGIN_DXDYDZ\">\n"
|
||||
" <DataItem Dimensions=\"3\">\n"
|
||||
" %f %f %f\n"
|
||||
" </DataItem>\n"
|
||||
" <DataItem Dimensions=\"3\">\n"
|
||||
" %f %f %f\n"
|
||||
" </DataItem>\n"
|
||||
" </Geometry>\n\n",
|
||||
step, time, fluid_global_n0[2], fluid_global_n0[1], fluid_global_n0[0],
|
||||
domain->boxlo[2], domain->boxlo[1], domain->boxlo[0], dx_lb, dx_lb, dx_lb);
|
||||
fprintf(dump_file_handle_xdmf,
|
||||
" <Attribute Name=\"density\">\n"
|
||||
" <DataItem ItemType=\"Function\" Function=\"$0 * %f\" Dimensions=\"%d %d "
|
||||
"%d\">\n"
|
||||
" <DataItem Precision=\"%zd\" Format=\"Binary\" Seek=\"%ld\" "
|
||||
"Dimensions=\"%d %d %d\">\n"
|
||||
" %s\n"
|
||||
" </DataItem>\n"
|
||||
" </DataItem>\n"
|
||||
" </Attribute>\n\n",
|
||||
dm_lb / (dx_lb * dx_lb * dx_lb), fluid_global_n0[2], fluid_global_n0[1],
|
||||
fluid_global_n0[0], sizeof(MPI_DOUBLE), offset, fluid_global_n0[2],
|
||||
fluid_global_n0[1], fluid_global_n0[0], dump_file_name_raw.c_str());
|
||||
fprintf(dump_file_handle_xdmf,
|
||||
" <Attribute Name=\"velocity\" AttributeType=\"Vector\">\n"
|
||||
" <DataItem ItemType=\"Function\" Function=\"$0 * %f\" Dimensions=\"%d %d "
|
||||
"%d 3\">\n"
|
||||
" <DataItem Precision=\"%zd\" Format=\"Binary\" Seek=\"%ld\" "
|
||||
"Dimensions=\"%d %d %d 3\">\n"
|
||||
" %s\n"
|
||||
" </DataItem>\n"
|
||||
" </DataItem>\n"
|
||||
" </Attribute>\n\n",
|
||||
dx_lb / dt_lb, fluid_global_n0[2], fluid_global_n0[1], fluid_global_n0[0],
|
||||
sizeof(MPI_DOUBLE), offset + block * 1, fluid_global_n0[2], fluid_global_n0[1],
|
||||
fluid_global_n0[0], dump_file_name_raw.c_str());
|
||||
fprintf(dump_file_handle_xdmf, " </Grid>\n\n");
|
||||
fmt::print(dump_file_handle_xdmf,
|
||||
" <Grid Name=\"{}\">\n"
|
||||
" <Time Value=\"{:f}\"/>\n\n"
|
||||
" <Topology TopologyType=\"3DCoRectMesh\" Dimensions=\"{} {} {}\"/>\n"
|
||||
" <Geometry GeometryType=\"ORIGIN_DXDYDZ\">\n"
|
||||
" <DataItem Dimensions=\"3\">\n"
|
||||
" {:f} {:f} {:f}\n"
|
||||
" </DataItem>\n"
|
||||
" <DataItem Dimensions=\"3\">\n"
|
||||
" {:f} {:f} {:f}\n"
|
||||
" </DataItem>\n"
|
||||
" </Geometry>\n\n",
|
||||
step, time, fluid_global_n0[2], fluid_global_n0[1], fluid_global_n0[0],
|
||||
domain->boxlo[2], domain->boxlo[1], domain->boxlo[0], dx_lb, dx_lb, dx_lb);
|
||||
fmt::print(dump_file_handle_xdmf,
|
||||
" <Attribute Name=\"density\">\n"
|
||||
" <DataItem ItemType=\"Function\" Function=\"$0 * {:f}\" "
|
||||
"Dimensions=\"{} {} {}\">\n"
|
||||
" <DataItem Precision=\"{}\" Format=\"Binary\" Seek=\"{}\" "
|
||||
"Dimensions=\"{} {} {}\">\n"
|
||||
" {}\n"
|
||||
" </DataItem>\n"
|
||||
" </DataItem>\n"
|
||||
" </Attribute>\n\n",
|
||||
dm_lb / (dx_lb * dx_lb * dx_lb), fluid_global_n0[2], fluid_global_n0[1],
|
||||
fluid_global_n0[0], sizeof(double), offset, fluid_global_n0[2],
|
||||
fluid_global_n0[1], fluid_global_n0[0], dump_file_name_raw.c_str());
|
||||
fmt::print(dump_file_handle_xdmf,
|
||||
" <Attribute Name=\"velocity\" AttributeType=\"Vector\">\n"
|
||||
" <DataItem ItemType=\"Function\" Function=\"$0 * {:f}\" "
|
||||
"Dimensions=\"{} {} {} 3\">\n"
|
||||
" <DataItem Precision=\"{}\" Format=\"Binary\" Seek=\"{}\" "
|
||||
"Dimensions=\"{} {} {} 3\">\n"
|
||||
" {}\n"
|
||||
" </DataItem>\n"
|
||||
" </DataItem>\n"
|
||||
" </Attribute>\n\n",
|
||||
dx_lb / dt_lb, fluid_global_n0[2], fluid_global_n0[1], fluid_global_n0[0],
|
||||
sizeof(double), offset + block * 1, fluid_global_n0[2], fluid_global_n0[1],
|
||||
fluid_global_n0[0], dump_file_name_raw.c_str());
|
||||
fmt::print(dump_file_handle_xdmf, " </Grid>\n\n");
|
||||
|
||||
frameindex++;
|
||||
}
|
||||
@ -3658,7 +3669,8 @@ void FixLbFluid::initializeGeometry()
|
||||
// initializeGeometry defines the local lattice
|
||||
// structure through the sublattice array
|
||||
// --------------------------------------------
|
||||
int geodump = 0;
|
||||
#define GEODUMP 0
|
||||
|
||||
int i, j, k;
|
||||
int boxlims[3][2]; // absolute subvolume coordinates
|
||||
|
||||
@ -3705,61 +3717,61 @@ void FixLbFluid::initializeGeometry()
|
||||
}
|
||||
}
|
||||
|
||||
// Output local geometry to data files labeled with processor number
|
||||
// Type dump
|
||||
if (geodump) {
|
||||
auto datfile = fmt::format("subgeom_{}_end_type.dmp", me);
|
||||
FILE *outfile = fopen(datfile.c_str(), "w");
|
||||
if (!outfile)
|
||||
error->one(FLERR, " file {} could not be opened: {}", datfile, utils::getsyserror());
|
||||
// Output local geometry to data files labeled with processor number
|
||||
// Type dump
|
||||
#if GEODUMP
|
||||
auto datfile = fmt::format("subgeom_{}_end_type.dmp", me);
|
||||
FILE *outfile = fopen(datfile.c_str(), "w");
|
||||
if (!outfile)
|
||||
error->one(FLERR, " file {} could not be opened: {}", datfile, utils::getsyserror());
|
||||
|
||||
fmt::print(outfile, "\n me: {} px: {} py: {} pz: {}\n", me, comm->myloc[0], comm->myloc[1],
|
||||
comm->myloc[2]);
|
||||
fmt::print(outfile, "\n me: {} px: {} py: {} pz: {}\n", me, comm->myloc[0], comm->myloc[1],
|
||||
comm->myloc[2]);
|
||||
|
||||
for (i = 0; i < subNbx; i++) {
|
||||
fmt::print(outfile, "i={}\n", i);
|
||||
for (k = subNbz - 1; k > -1; k--) {
|
||||
if (k == subNbz - 2 || k == 0) {
|
||||
for (j = 0; j < subNby + 2; j++) fputs("---", outfile);
|
||||
fputs("\n", outfile);
|
||||
}
|
||||
for (j = 0; j < subNby; j++) {
|
||||
fmt::print(outfile, " {} ", sublattice[i][j][k].type);
|
||||
if (j == 0 || j == subNby - 2) fputs(" | ", outfile);
|
||||
if (j == subNby - 1) fputs("\n", outfile);
|
||||
}
|
||||
for (i = 0; i < subNbx; i++) {
|
||||
fmt::print(outfile, "i={}\n", i);
|
||||
for (k = subNbz - 1; k > -1; k--) {
|
||||
if (k == subNbz - 2 || k == 0) {
|
||||
for (j = 0; j < subNby + 2; j++) fputs("---", outfile);
|
||||
fputs("\n", outfile);
|
||||
}
|
||||
fputs(" \n \n", outfile);
|
||||
}
|
||||
fputs("\n", outfile);
|
||||
fclose(outfile);
|
||||
|
||||
// Orientation dump
|
||||
datfile = fmt::format("subgeom_{}_end_ori.dmp", me);
|
||||
outfile = fopen(datfile.c_str(), "w");
|
||||
|
||||
if (!outfile)
|
||||
error->one(FLERR, " file {} could not be opened: {}", datfile, utils::getsyserror());
|
||||
|
||||
fmt::print("\nme: {}\n", me);
|
||||
for (i = 0; i < subNbx; i++) {
|
||||
fmt::print("i={}\n", i);
|
||||
for (k = subNbz - 1; k > -1; k--) {
|
||||
if (k == subNbz - 2 || k == 0) {
|
||||
for (j = 0; j < subNby + 2; j++) fputs("---", outfile);
|
||||
fputs("\bn", outfile);
|
||||
}
|
||||
for (j = 0; j < subNby; j++) {
|
||||
fmt::print(outfile, " {} ", sublattice[i][j][k].orientation);
|
||||
if (j == 0 || j == subNby - 2) fputs(" | ", outfile);
|
||||
if (j == subNby - 1) fputs("\n", outfile);
|
||||
}
|
||||
for (j = 0; j < subNby; j++) {
|
||||
fmt::print(outfile, " {} ", sublattice[i][j][k].type);
|
||||
if (j == 0 || j == subNby - 2) fputs(" | ", outfile);
|
||||
if (j == subNby - 1) fputs("\n", outfile);
|
||||
}
|
||||
fputs(" \n \n", outfile);
|
||||
}
|
||||
fputs("\n", outfile);
|
||||
fclose(outfile);
|
||||
fputs(" \n \n", outfile);
|
||||
}
|
||||
fputs("\n", outfile);
|
||||
fclose(outfile);
|
||||
|
||||
// Orientation dump
|
||||
datfile = fmt::format("subgeom_{}_end_ori.dmp", me);
|
||||
outfile = fopen(datfile.c_str(), "w");
|
||||
|
||||
if (!outfile)
|
||||
error->one(FLERR, " file {} could not be opened: {}", datfile, utils::getsyserror());
|
||||
|
||||
fmt::print("\nme: {}\n", me);
|
||||
for (i = 0; i < subNbx; i++) {
|
||||
fmt::print("i={}\n", i);
|
||||
for (k = subNbz - 1; k > -1; k--) {
|
||||
if (k == subNbz - 2 || k == 0) {
|
||||
for (j = 0; j < subNby + 2; j++) fputs("---", outfile);
|
||||
fputs("\bn", outfile);
|
||||
}
|
||||
for (j = 0; j < subNby; j++) {
|
||||
fmt::print(outfile, " {} ", sublattice[i][j][k].orientation);
|
||||
if (j == 0 || j == subNby - 2) fputs(" | ", outfile);
|
||||
if (j == subNby - 1) fputs("\n", outfile);
|
||||
}
|
||||
}
|
||||
fputs(" \n \n", outfile);
|
||||
}
|
||||
fputs("\n", outfile);
|
||||
fclose(outfile);
|
||||
#endif
|
||||
}
|
||||
|
||||
void FixLbFluid::addslit(int &x0, const int HS, const int HP, const int LE, const int SW)
|
||||
|
||||
@ -51,7 +51,7 @@ class FixLbFluid : public Fix {
|
||||
double compute_scalar() override;
|
||||
double compute_vector(int) override;
|
||||
|
||||
void dump(int);
|
||||
void dump(const bigint);
|
||||
|
||||
private:
|
||||
double viscosity, densityinit_real, a_0_real, T;
|
||||
|
||||
@ -524,7 +524,6 @@ double PairMesoCNT::init_one(int /* i */, int /* j */)
|
||||
void PairMesoCNT::bond_neigh()
|
||||
{
|
||||
int nlocal = atom->nlocal;
|
||||
int nghost = atom->nghost;
|
||||
int **bondlist = neighbor->bondlist;
|
||||
int nbondlist = neighbor->nbondlist;
|
||||
|
||||
|
||||
@ -75,11 +75,8 @@ void MLIAPModelNN::read_coeffs(char *coefffilename)
|
||||
utils::getsyserror());
|
||||
}
|
||||
|
||||
char line[MAXLINE], *ptr, *tstr;
|
||||
int eof = 0;
|
||||
|
||||
int n;
|
||||
int nwords = 0;
|
||||
char line[MAXLINE], *ptr;
|
||||
int n, eof = 0, nwords = 0;
|
||||
while (nwords == 0) {
|
||||
if (comm->me == 0) {
|
||||
ptr = fgets(line, MAXLINE, fpcoeff);
|
||||
|
||||
@ -197,7 +197,6 @@ void PairPACE::compute(int eflag, int vflag)
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
const int jtype = type[j];
|
||||
j &= NEIGHMASK;
|
||||
delx = x[j][0] - xtmp;
|
||||
dely = x[j][1] - ytmp;
|
||||
|
||||
@ -17,12 +17,14 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "sna.h"
|
||||
#include <cmath>
|
||||
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "math_const.h"
|
||||
#include "math_special.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "comm.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
using namespace std;
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -18,25 +17,26 @@
|
||||
|
||||
#include "angle_charmm.h"
|
||||
|
||||
#include <cmath>
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "domain.h"
|
||||
#include "comm.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "neighbor.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
using MathConst::DEG2RAD;
|
||||
using MathConst::RAD2DEG;
|
||||
|
||||
#define SMALL 0.001
|
||||
static constexpr double SMALL = 0.001;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
AngleCharmm::AngleCharmm(LAMMPS *lmp) : Angle(lmp) {}
|
||||
AngleCharmm::AngleCharmm(LAMMPS *_lmp) : Angle(_lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -55,15 +55,15 @@ AngleCharmm::~AngleCharmm()
|
||||
|
||||
void AngleCharmm::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,i3,n,type;
|
||||
double delx1,dely1,delz1,delx2,dely2,delz2;
|
||||
double eangle,f1[3],f3[3];
|
||||
double dtheta,tk;
|
||||
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
|
||||
double delxUB,delyUB,delzUB,rsqUB,rUB,dr,rk,forceUB;
|
||||
int i1, i2, i3, n, type;
|
||||
double delx1, dely1, delz1, delx2, dely2, delz2;
|
||||
double eangle, f1[3], f3[3];
|
||||
double dtheta, tk;
|
||||
double rsq1, rsq2, r1, r2, c, s, a, a11, a12, a22;
|
||||
double delxUB, delyUB, delzUB, rsqUB, rUB, dr, rk, forceUB;
|
||||
|
||||
eangle = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
@ -84,7 +84,7 @@ void AngleCharmm::compute(int eflag, int vflag)
|
||||
dely1 = x[i1][1] - x[i2][1];
|
||||
delz1 = x[i1][2] - x[i2][2];
|
||||
|
||||
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
|
||||
rsq1 = delx1 * delx1 + dely1 * dely1 + delz1 * delz1;
|
||||
r1 = sqrt(rsq1);
|
||||
|
||||
// 2nd bond
|
||||
@ -93,7 +93,7 @@ void AngleCharmm::compute(int eflag, int vflag)
|
||||
dely2 = x[i3][1] - x[i2][1];
|
||||
delz2 = x[i3][2] - x[i2][2];
|
||||
|
||||
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
|
||||
rsq2 = delx2 * delx2 + dely2 * dely2 + delz2 * delz2;
|
||||
r2 = sqrt(rsq2);
|
||||
|
||||
// Urey-Bradley bond
|
||||
@ -102,7 +102,7 @@ void AngleCharmm::compute(int eflag, int vflag)
|
||||
delyUB = x[i3][1] - x[i1][1];
|
||||
delzUB = x[i3][2] - x[i1][2];
|
||||
|
||||
rsqUB = delxUB*delxUB + delyUB*delyUB + delzUB*delzUB;
|
||||
rsqUB = delxUB * delxUB + delyUB * delyUB + delzUB * delzUB;
|
||||
rUB = sqrt(rsqUB);
|
||||
|
||||
// Urey-Bradley force & energy
|
||||
@ -110,42 +110,44 @@ void AngleCharmm::compute(int eflag, int vflag)
|
||||
dr = rUB - r_ub[type];
|
||||
rk = k_ub[type] * dr;
|
||||
|
||||
if (rUB > 0.0) forceUB = -2.0*rk/rUB;
|
||||
else forceUB = 0.0;
|
||||
if (rUB > 0.0)
|
||||
forceUB = -2.0 * rk / rUB;
|
||||
else
|
||||
forceUB = 0.0;
|
||||
|
||||
if (eflag) eangle = rk*dr;
|
||||
if (eflag) eangle = rk * dr;
|
||||
|
||||
// angle (cos and sin)
|
||||
|
||||
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
|
||||
c /= r1*r2;
|
||||
c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
|
||||
c /= r1 * r2;
|
||||
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
|
||||
s = sqrt(1.0 - c*c);
|
||||
s = sqrt(1.0 - c * c);
|
||||
if (s < SMALL) s = SMALL;
|
||||
s = 1.0/s;
|
||||
s = 1.0 / s;
|
||||
|
||||
// harmonic force & energy
|
||||
|
||||
dtheta = acos(c) - theta0[type];
|
||||
tk = k[type] * dtheta;
|
||||
|
||||
if (eflag) eangle += tk*dtheta;
|
||||
if (eflag) eangle += tk * dtheta;
|
||||
|
||||
a = -2.0 * tk * s;
|
||||
a11 = a*c / rsq1;
|
||||
a12 = -a / (r1*r2);
|
||||
a22 = a*c / rsq2;
|
||||
a11 = a * c / rsq1;
|
||||
a12 = -a / (r1 * r2);
|
||||
a22 = a * c / rsq2;
|
||||
|
||||
f1[0] = a11*delx1 + a12*delx2 - delxUB*forceUB;
|
||||
f1[1] = a11*dely1 + a12*dely2 - delyUB*forceUB;
|
||||
f1[2] = a11*delz1 + a12*delz2 - delzUB*forceUB;
|
||||
f1[0] = a11 * delx1 + a12 * delx2 - delxUB * forceUB;
|
||||
f1[1] = a11 * dely1 + a12 * dely2 - delyUB * forceUB;
|
||||
f1[2] = a11 * delz1 + a12 * delz2 - delzUB * forceUB;
|
||||
|
||||
f3[0] = a22*delx2 + a12*delx1 + delxUB*forceUB;
|
||||
f3[1] = a22*dely2 + a12*dely1 + delyUB*forceUB;
|
||||
f3[2] = a22*delz2 + a12*delz1 + delzUB*forceUB;
|
||||
f3[0] = a22 * delx2 + a12 * delx1 + delxUB * forceUB;
|
||||
f3[1] = a22 * dely2 + a12 * dely1 + delyUB * forceUB;
|
||||
f3[2] = a22 * delz2 + a12 * delz1 + delzUB * forceUB;
|
||||
|
||||
// apply force to each of 3 atoms
|
||||
|
||||
@ -167,8 +169,9 @@ void AngleCharmm::compute(int eflag, int vflag)
|
||||
f[i3][2] += f3[2];
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
|
||||
delx1,dely1,delz1,delx2,dely2,delz2);
|
||||
if (evflag)
|
||||
ev_tally(i1, i2, i3, nlocal, newton_bond, eangle, f1, f3, delx1, dely1, delz1, delx2, dely2,
|
||||
delz2);
|
||||
}
|
||||
}
|
||||
|
||||
@ -177,14 +180,14 @@ void AngleCharmm::compute(int eflag, int vflag)
|
||||
void AngleCharmm::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nangletypes;
|
||||
const int np1 = atom->nangletypes + 1;
|
||||
|
||||
memory->create(k,n+1,"angle:k");
|
||||
memory->create(theta0,n+1,"angle:theta0");
|
||||
memory->create(k_ub,n+1,"angle:k_ub");
|
||||
memory->create(r_ub,n+1,"angle:r_ub");
|
||||
memory->create(setflag,n+1,"angle:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
memory->create(k, np1, "angle:k");
|
||||
memory->create(theta0, np1, "angle:theta0");
|
||||
memory->create(k_ub, np1, "angle:k_ub");
|
||||
memory->create(r_ub, np1, "angle:r_ub");
|
||||
memory->create(setflag, np1, "angle:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -193,30 +196,30 @@ void AngleCharmm::allocate()
|
||||
|
||||
void AngleCharmm::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 5) error->all(FLERR,"Incorrect args for angle coefficients");
|
||||
if (narg != 5) error->all(FLERR, "Incorrect args for angle coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
utils::bounds(FLERR,arg[0],1,atom->nangletypes,ilo,ihi,error);
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->nangletypes, ilo, ihi, error);
|
||||
|
||||
double k_one = utils::numeric(FLERR,arg[1],false,lmp);
|
||||
double theta0_one = utils::numeric(FLERR,arg[2],false,lmp);
|
||||
double k_ub_one = utils::numeric(FLERR,arg[3],false,lmp);
|
||||
double r_ub_one = utils::numeric(FLERR,arg[4],false,lmp);
|
||||
double k_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
double theta0_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
double k_ub_one = utils::numeric(FLERR, arg[3], false, lmp);
|
||||
double r_ub_one = utils::numeric(FLERR, arg[4], false, lmp);
|
||||
|
||||
// convert theta0 from degrees to radians
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
k[i] = k_one;
|
||||
theta0[i] = theta0_one/180.0 * MY_PI;
|
||||
theta0[i] = DEG2RAD * theta0_one;
|
||||
k_ub[i] = k_ub_one;
|
||||
r_ub[i] = r_ub_one;
|
||||
setflag[i] = 1;
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -232,10 +235,10 @@ double AngleCharmm::equilibrium_angle(int i)
|
||||
|
||||
void AngleCharmm::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&k[1],sizeof(double),atom->nangletypes,fp);
|
||||
fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp);
|
||||
fwrite(&k_ub[1],sizeof(double),atom->nangletypes,fp);
|
||||
fwrite(&r_ub[1],sizeof(double),atom->nangletypes,fp);
|
||||
fwrite(&k[1], sizeof(double), atom->nangletypes, fp);
|
||||
fwrite(&theta0[1], sizeof(double), atom->nangletypes, fp);
|
||||
fwrite(&k_ub[1], sizeof(double), atom->nangletypes, fp);
|
||||
fwrite(&r_ub[1], sizeof(double), atom->nangletypes, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -247,15 +250,15 @@ void AngleCharmm::read_restart(FILE *fp)
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&k_ub[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&r_ub[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR, &k[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &theta0[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &k_ub[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &r_ub[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&k_ub[1],atom->nangletypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&r_ub[1],atom->nangletypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&k[1], atom->nangletypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&theta0[1], atom->nangletypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&k_ub[1], atom->nangletypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&r_ub[1], atom->nangletypes, MPI_DOUBLE, 0, world);
|
||||
|
||||
for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
|
||||
}
|
||||
@ -267,8 +270,7 @@ void AngleCharmm::read_restart(FILE *fp)
|
||||
void AngleCharmm::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->nangletypes; i++)
|
||||
fprintf(fp,"%d %g %g %g %g\n",
|
||||
i,k[i],theta0[i]/MY_PI*180.0,k_ub[i],r_ub[i]);
|
||||
fprintf(fp, "%d %g %g %g %g\n", i, k[i], RAD2DEG * theta0[i], k_ub[i], r_ub[i]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -280,23 +282,23 @@ double AngleCharmm::single(int type, int i1, int i2, int i3)
|
||||
double delx1 = x[i1][0] - x[i2][0];
|
||||
double dely1 = x[i1][1] - x[i2][1];
|
||||
double delz1 = x[i1][2] - x[i2][2];
|
||||
domain->minimum_image(delx1,dely1,delz1);
|
||||
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
|
||||
domain->minimum_image(delx1, dely1, delz1);
|
||||
double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1);
|
||||
|
||||
double delx2 = x[i3][0] - x[i2][0];
|
||||
double dely2 = x[i3][1] - x[i2][1];
|
||||
double delz2 = x[i3][2] - x[i2][2];
|
||||
domain->minimum_image(delx2,dely2,delz2);
|
||||
double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
|
||||
domain->minimum_image(delx2, dely2, delz2);
|
||||
double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
|
||||
|
||||
double delxUB = x[i3][0] - x[i1][0];
|
||||
double delyUB = x[i3][1] - x[i1][1];
|
||||
double delzUB = x[i3][2] - x[i1][2];
|
||||
domain->minimum_image(delxUB,delyUB,delzUB);
|
||||
double rUB = sqrt(delxUB*delxUB + delyUB*delyUB + delzUB*delzUB);
|
||||
domain->minimum_image(delxUB, delyUB, delzUB);
|
||||
double rUB = sqrt(delxUB * delxUB + delyUB * delyUB + delzUB * delzUB);
|
||||
|
||||
double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
|
||||
c /= r1*r2;
|
||||
double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
|
||||
c /= r1 * r2;
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
|
||||
@ -305,5 +307,5 @@ double AngleCharmm::single(int type, int i1, int i2, int i3)
|
||||
double dr = rUB - r_ub[type];
|
||||
double rk = k_ub[type] * dr;
|
||||
|
||||
return (tk*dtheta + rk*dr);
|
||||
return (tk * dtheta + rk * dr);
|
||||
}
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -14,25 +13,23 @@
|
||||
|
||||
#include "angle_cosine.h"
|
||||
|
||||
#include <cmath>
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "domain.h"
|
||||
#include "comm.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "neighbor.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
#define SMALL 0.001
|
||||
using MathConst::MY_PI;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
AngleCosine::AngleCosine(LAMMPS *lmp) : Angle(lmp) {}
|
||||
AngleCosine::AngleCosine(LAMMPS *_lmp) : Angle(_lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -48,13 +45,13 @@ AngleCosine::~AngleCosine()
|
||||
|
||||
void AngleCosine::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,i3,n,type;
|
||||
double delx1,dely1,delz1,delx2,dely2,delz2;
|
||||
double eangle,f1[3],f3[3];
|
||||
double rsq1,rsq2,r1,r2,c,a,a11,a12,a22;
|
||||
int i1, i2, i3, n, type;
|
||||
double delx1, dely1, delz1, delx2, dely2, delz2;
|
||||
double eangle, f1[3], f3[3];
|
||||
double rsq1, rsq2, r1, r2, c, a, a11, a12, a22;
|
||||
|
||||
eangle = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
@ -75,7 +72,7 @@ void AngleCosine::compute(int eflag, int vflag)
|
||||
dely1 = x[i1][1] - x[i2][1];
|
||||
delz1 = x[i1][2] - x[i2][2];
|
||||
|
||||
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
|
||||
rsq1 = delx1 * delx1 + dely1 * dely1 + delz1 * delz1;
|
||||
r1 = sqrt(rsq1);
|
||||
|
||||
// 2nd bond
|
||||
@ -84,31 +81,31 @@ void AngleCosine::compute(int eflag, int vflag)
|
||||
dely2 = x[i3][1] - x[i2][1];
|
||||
delz2 = x[i3][2] - x[i2][2];
|
||||
|
||||
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
|
||||
rsq2 = delx2 * delx2 + dely2 * dely2 + delz2 * delz2;
|
||||
r2 = sqrt(rsq2);
|
||||
|
||||
// c = cosine of angle
|
||||
|
||||
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
|
||||
c /= r1*r2;
|
||||
c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
|
||||
c /= r1 * r2;
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
|
||||
// force & energy
|
||||
|
||||
if (eflag) eangle = k[type]*(1.0+c);
|
||||
if (eflag) eangle = k[type] * (1.0 + c);
|
||||
|
||||
a = k[type];
|
||||
a11 = a*c / rsq1;
|
||||
a12 = -a / (r1*r2);
|
||||
a22 = a*c / rsq2;
|
||||
a11 = a * c / rsq1;
|
||||
a12 = -a / (r1 * r2);
|
||||
a22 = a * c / rsq2;
|
||||
|
||||
f1[0] = a11*delx1 + a12*delx2;
|
||||
f1[1] = a11*dely1 + a12*dely2;
|
||||
f1[2] = a11*delz1 + a12*delz2;
|
||||
f3[0] = a22*delx2 + a12*delx1;
|
||||
f3[1] = a22*dely2 + a12*dely1;
|
||||
f3[2] = a22*delz2 + a12*delz1;
|
||||
f1[0] = a11 * delx1 + a12 * delx2;
|
||||
f1[1] = a11 * dely1 + a12 * dely2;
|
||||
f1[2] = a11 * delz1 + a12 * delz2;
|
||||
f3[0] = a22 * delx2 + a12 * delx1;
|
||||
f3[1] = a22 * dely2 + a12 * dely1;
|
||||
f3[2] = a22 * delz2 + a12 * delz1;
|
||||
|
||||
// apply force to each of 3 atoms
|
||||
|
||||
@ -130,8 +127,9 @@ void AngleCosine::compute(int eflag, int vflag)
|
||||
f[i3][2] += f3[2];
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
|
||||
delx1,dely1,delz1,delx2,dely2,delz2);
|
||||
if (evflag)
|
||||
ev_tally(i1, i2, i3, nlocal, newton_bond, eangle, f1, f3, delx1, dely1, delz1, delx2, dely2,
|
||||
delz2);
|
||||
}
|
||||
}
|
||||
|
||||
@ -140,11 +138,11 @@ void AngleCosine::compute(int eflag, int vflag)
|
||||
void AngleCosine::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nangletypes;
|
||||
const int np1 = atom->nangletypes + 1;
|
||||
|
||||
memory->create(k,n+1,"angle:k");
|
||||
memory->create(setflag,n+1,"angle:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
memory->create(k, np1, "angle:k");
|
||||
memory->create(setflag, np1, "angle:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -153,13 +151,13 @@ void AngleCosine::allocate()
|
||||
|
||||
void AngleCosine::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 2) error->all(FLERR,"Incorrect args for angle coefficients");
|
||||
if (narg != 2) error->all(FLERR, "Incorrect args for angle coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
utils::bounds(FLERR,arg[0],1,atom->nangletypes,ilo,ihi,error);
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->nangletypes, ilo, ihi, error);
|
||||
|
||||
double k_one = utils::numeric(FLERR,arg[1],false,lmp);
|
||||
double k_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
@ -168,7 +166,7 @@ void AngleCosine::coeff(int narg, char **arg)
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -184,7 +182,7 @@ double AngleCosine::equilibrium_angle(int /*i*/)
|
||||
|
||||
void AngleCosine::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&k[1],sizeof(double),atom->nangletypes,fp);
|
||||
fwrite(&k[1], sizeof(double), atom->nangletypes, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -195,8 +193,9 @@ void AngleCosine::read_restart(FILE *fp)
|
||||
{
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
|
||||
MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
|
||||
if (comm->me == 0)
|
||||
utils::sfread(FLERR, &k[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
|
||||
MPI_Bcast(&k[1], atom->nangletypes, MPI_DOUBLE, 0, world);
|
||||
|
||||
for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
|
||||
}
|
||||
@ -207,8 +206,7 @@ void AngleCosine::read_restart(FILE *fp)
|
||||
|
||||
void AngleCosine::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->nangletypes; i++)
|
||||
fprintf(fp,"%d %g\n",i,k[i]);
|
||||
for (int i = 1; i <= atom->nangletypes; i++) fprintf(fp, "%d %g\n", i, k[i]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -220,19 +218,19 @@ double AngleCosine::single(int type, int i1, int i2, int i3)
|
||||
double delx1 = x[i1][0] - x[i2][0];
|
||||
double dely1 = x[i1][1] - x[i2][1];
|
||||
double delz1 = x[i1][2] - x[i2][2];
|
||||
domain->minimum_image(delx1,dely1,delz1);
|
||||
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
|
||||
domain->minimum_image(delx1, dely1, delz1);
|
||||
double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1);
|
||||
|
||||
double delx2 = x[i3][0] - x[i2][0];
|
||||
double dely2 = x[i3][1] - x[i2][1];
|
||||
double delz2 = x[i3][2] - x[i2][2];
|
||||
domain->minimum_image(delx2,dely2,delz2);
|
||||
double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
|
||||
domain->minimum_image(delx2, dely2, delz2);
|
||||
double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
|
||||
|
||||
double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
|
||||
c /= r1*r2;
|
||||
double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
|
||||
c /= r1 * r2;
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
|
||||
return k[type]*(1.0+c);
|
||||
return k[type] * (1.0 + c);
|
||||
}
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -18,25 +17,24 @@
|
||||
|
||||
#include "angle_cosine_squared.h"
|
||||
|
||||
#include <cmath>
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "domain.h"
|
||||
#include "comm.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "neighbor.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
#define SMALL 0.001
|
||||
using MathConst::DEG2RAD;
|
||||
using MathConst::RAD2DEG;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
AngleCosineSquared::AngleCosineSquared(LAMMPS *lmp) : Angle(lmp)
|
||||
AngleCosineSquared::AngleCosineSquared(LAMMPS *_lmp) : Angle(_lmp)
|
||||
{
|
||||
k = nullptr;
|
||||
theta0 = nullptr;
|
||||
@ -57,14 +55,14 @@ AngleCosineSquared::~AngleCosineSquared()
|
||||
|
||||
void AngleCosineSquared::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,i3,n,type;
|
||||
double delx1,dely1,delz1,delx2,dely2,delz2;
|
||||
double eangle,f1[3],f3[3];
|
||||
double dcostheta,tk;
|
||||
double rsq1,rsq2,r1,r2,c,a,a11,a12,a22;
|
||||
int i1, i2, i3, n, type;
|
||||
double delx1, dely1, delz1, delx2, dely2, delz2;
|
||||
double eangle, f1[3], f3[3];
|
||||
double dcostheta, tk;
|
||||
double rsq1, rsq2, r1, r2, c, a, a11, a12, a22;
|
||||
|
||||
eangle = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
@ -85,7 +83,7 @@ void AngleCosineSquared::compute(int eflag, int vflag)
|
||||
dely1 = x[i1][1] - x[i2][1];
|
||||
delz1 = x[i1][2] - x[i2][2];
|
||||
|
||||
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
|
||||
rsq1 = delx1 * delx1 + dely1 * dely1 + delz1 * delz1;
|
||||
r1 = sqrt(rsq1);
|
||||
|
||||
// 2nd bond
|
||||
@ -94,13 +92,13 @@ void AngleCosineSquared::compute(int eflag, int vflag)
|
||||
dely2 = x[i3][1] - x[i2][1];
|
||||
delz2 = x[i3][2] - x[i2][2];
|
||||
|
||||
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
|
||||
rsq2 = delx2 * delx2 + dely2 * dely2 + delz2 * delz2;
|
||||
r2 = sqrt(rsq2);
|
||||
|
||||
// angle (cos and sin)
|
||||
|
||||
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
|
||||
c /= r1*r2;
|
||||
c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
|
||||
c /= r1 * r2;
|
||||
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
@ -110,19 +108,19 @@ void AngleCosineSquared::compute(int eflag, int vflag)
|
||||
dcostheta = c - cos(theta0[type]);
|
||||
tk = k[type] * dcostheta;
|
||||
|
||||
if (eflag) eangle = tk*dcostheta;
|
||||
if (eflag) eangle = tk * dcostheta;
|
||||
|
||||
a = 2.0 * tk;
|
||||
a11 = a*c / rsq1;
|
||||
a12 = -a / (r1*r2);
|
||||
a22 = a*c / rsq2;
|
||||
a11 = a * c / rsq1;
|
||||
a12 = -a / (r1 * r2);
|
||||
a22 = a * c / rsq2;
|
||||
|
||||
f1[0] = a11*delx1 + a12*delx2;
|
||||
f1[1] = a11*dely1 + a12*dely2;
|
||||
f1[2] = a11*delz1 + a12*delz2;
|
||||
f3[0] = a22*delx2 + a12*delx1;
|
||||
f3[1] = a22*dely2 + a12*dely1;
|
||||
f3[2] = a22*delz2 + a12*delz1;
|
||||
f1[0] = a11 * delx1 + a12 * delx2;
|
||||
f1[1] = a11 * dely1 + a12 * dely2;
|
||||
f1[2] = a11 * delz1 + a12 * delz2;
|
||||
f3[0] = a22 * delx2 + a12 * delx1;
|
||||
f3[1] = a22 * dely2 + a12 * dely1;
|
||||
f3[2] = a22 * delz2 + a12 * delz1;
|
||||
|
||||
// apply force to each of 3 atoms
|
||||
|
||||
@ -144,8 +142,9 @@ void AngleCosineSquared::compute(int eflag, int vflag)
|
||||
f[i3][2] += f3[2];
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
|
||||
delx1,dely1,delz1,delx2,dely2,delz2);
|
||||
if (evflag)
|
||||
ev_tally(i1, i2, i3, nlocal, newton_bond, eangle, f1, f3, delx1, dely1, delz1, delx2, dely2,
|
||||
delz2);
|
||||
}
|
||||
}
|
||||
|
||||
@ -154,13 +153,13 @@ void AngleCosineSquared::compute(int eflag, int vflag)
|
||||
void AngleCosineSquared::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nangletypes;
|
||||
const int np1 = atom->nangletypes + 1;
|
||||
|
||||
memory->create(k,n+1,"angle:k");
|
||||
memory->create(theta0,n+1,"angle:theta0");
|
||||
memory->create(k, np1, "angle:k");
|
||||
memory->create(theta0, np1, "angle:theta0");
|
||||
|
||||
memory->create(setflag,n+1,"angle:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
memory->create(setflag, np1, "angle:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -169,26 +168,26 @@ void AngleCosineSquared::allocate()
|
||||
|
||||
void AngleCosineSquared::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 3) error->all(FLERR,"Incorrect args for angle coefficients");
|
||||
if (narg != 3) error->all(FLERR, "Incorrect args for angle coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
utils::bounds(FLERR,arg[0],1,atom->nangletypes,ilo,ihi,error);
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->nangletypes, ilo, ihi, error);
|
||||
|
||||
double k_one = utils::numeric(FLERR,arg[1],false,lmp);
|
||||
double theta0_one = utils::numeric(FLERR,arg[2],false,lmp);
|
||||
double k_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
double theta0_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
|
||||
// convert theta0 from degrees to radians
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
k[i] = k_one;
|
||||
theta0[i] = theta0_one/180.0 * MY_PI;
|
||||
theta0[i] = DEG2RAD * theta0_one;
|
||||
setflag[i] = 1;
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -204,8 +203,8 @@ double AngleCosineSquared::equilibrium_angle(int i)
|
||||
|
||||
void AngleCosineSquared::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&k[1],sizeof(double),atom->nangletypes,fp);
|
||||
fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp);
|
||||
fwrite(&k[1], sizeof(double), atom->nangletypes, fp);
|
||||
fwrite(&theta0[1], sizeof(double), atom->nangletypes, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -217,11 +216,11 @@ void AngleCosineSquared::read_restart(FILE *fp)
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR, &k[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &theta0[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&k[1], atom->nangletypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&theta0[1], atom->nangletypes, MPI_DOUBLE, 0, world);
|
||||
|
||||
for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
|
||||
}
|
||||
@ -233,7 +232,7 @@ void AngleCosineSquared::read_restart(FILE *fp)
|
||||
void AngleCosineSquared::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->nangletypes; i++)
|
||||
fprintf(fp,"%d %g %g\n",i,k[i],theta0[i]/MY_PI*180.0);
|
||||
fprintf(fp, "%d %g %g\n", i, k[i], RAD2DEG * theta0[i]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -245,21 +244,21 @@ double AngleCosineSquared::single(int type, int i1, int i2, int i3)
|
||||
double delx1 = x[i1][0] - x[i2][0];
|
||||
double dely1 = x[i1][1] - x[i2][1];
|
||||
double delz1 = x[i1][2] - x[i2][2];
|
||||
domain->minimum_image(delx1,dely1,delz1);
|
||||
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
|
||||
domain->minimum_image(delx1, dely1, delz1);
|
||||
double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1);
|
||||
|
||||
double delx2 = x[i3][0] - x[i2][0];
|
||||
double dely2 = x[i3][1] - x[i2][1];
|
||||
double delz2 = x[i3][2] - x[i2][2];
|
||||
domain->minimum_image(delx2,dely2,delz2);
|
||||
double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
|
||||
domain->minimum_image(delx2, dely2, delz2);
|
||||
double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
|
||||
|
||||
double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
|
||||
c /= r1*r2;
|
||||
double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
|
||||
c /= r1 * r2;
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
|
||||
double dcostheta = c - cos(theta0[type]);
|
||||
double tk = k[type] * dcostheta;
|
||||
return tk*dcostheta;
|
||||
return tk * dcostheta;
|
||||
}
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -14,25 +13,26 @@
|
||||
|
||||
#include "angle_harmonic.h"
|
||||
|
||||
#include <cmath>
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "domain.h"
|
||||
#include "comm.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "neighbor.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
using MathConst::DEG2RAD;
|
||||
using MathConst::RAD2DEG;
|
||||
|
||||
#define SMALL 0.001
|
||||
static constexpr double SMALL = 0.001;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
AngleHarmonic::AngleHarmonic(LAMMPS *lmp) : Angle(lmp)
|
||||
AngleHarmonic::AngleHarmonic(LAMMPS *_lmp) : Angle(_lmp)
|
||||
{
|
||||
k = nullptr;
|
||||
theta0 = nullptr;
|
||||
@ -53,14 +53,14 @@ AngleHarmonic::~AngleHarmonic()
|
||||
|
||||
void AngleHarmonic::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,i3,n,type;
|
||||
double delx1,dely1,delz1,delx2,dely2,delz2;
|
||||
double eangle,f1[3],f3[3];
|
||||
double dtheta,tk;
|
||||
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
|
||||
int i1, i2, i3, n, type;
|
||||
double delx1, dely1, delz1, delx2, dely2, delz2;
|
||||
double eangle, f1[3], f3[3];
|
||||
double dtheta, tk;
|
||||
double rsq1, rsq2, r1, r2, c, s, a, a11, a12, a22;
|
||||
|
||||
eangle = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
@ -81,7 +81,7 @@ void AngleHarmonic::compute(int eflag, int vflag)
|
||||
dely1 = x[i1][1] - x[i2][1];
|
||||
delz1 = x[i1][2] - x[i2][2];
|
||||
|
||||
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
|
||||
rsq1 = delx1 * delx1 + dely1 * dely1 + delz1 * delz1;
|
||||
r1 = sqrt(rsq1);
|
||||
|
||||
// 2nd bond
|
||||
@ -90,39 +90,39 @@ void AngleHarmonic::compute(int eflag, int vflag)
|
||||
dely2 = x[i3][1] - x[i2][1];
|
||||
delz2 = x[i3][2] - x[i2][2];
|
||||
|
||||
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
|
||||
rsq2 = delx2 * delx2 + dely2 * dely2 + delz2 * delz2;
|
||||
r2 = sqrt(rsq2);
|
||||
|
||||
// angle (cos and sin)
|
||||
|
||||
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
|
||||
c /= r1*r2;
|
||||
c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
|
||||
c /= r1 * r2;
|
||||
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
|
||||
s = sqrt(1.0 - c*c);
|
||||
s = sqrt(1.0 - c * c);
|
||||
if (s < SMALL) s = SMALL;
|
||||
s = 1.0/s;
|
||||
s = 1.0 / s;
|
||||
|
||||
// force & energy
|
||||
|
||||
dtheta = acos(c) - theta0[type];
|
||||
tk = k[type] * dtheta;
|
||||
|
||||
if (eflag) eangle = tk*dtheta;
|
||||
if (eflag) eangle = tk * dtheta;
|
||||
|
||||
a = -2.0 * tk * s;
|
||||
a11 = a*c / rsq1;
|
||||
a12 = -a / (r1*r2);
|
||||
a22 = a*c / rsq2;
|
||||
a11 = a * c / rsq1;
|
||||
a12 = -a / (r1 * r2);
|
||||
a22 = a * c / rsq2;
|
||||
|
||||
f1[0] = a11*delx1 + a12*delx2;
|
||||
f1[1] = a11*dely1 + a12*dely2;
|
||||
f1[2] = a11*delz1 + a12*delz2;
|
||||
f3[0] = a22*delx2 + a12*delx1;
|
||||
f3[1] = a22*dely2 + a12*dely1;
|
||||
f3[2] = a22*delz2 + a12*delz1;
|
||||
f1[0] = a11 * delx1 + a12 * delx2;
|
||||
f1[1] = a11 * dely1 + a12 * dely2;
|
||||
f1[2] = a11 * delz1 + a12 * delz2;
|
||||
f3[0] = a22 * delx2 + a12 * delx1;
|
||||
f3[1] = a22 * dely2 + a12 * dely1;
|
||||
f3[2] = a22 * delz2 + a12 * delz1;
|
||||
|
||||
// apply force to each of 3 atoms
|
||||
|
||||
@ -144,8 +144,9 @@ void AngleHarmonic::compute(int eflag, int vflag)
|
||||
f[i3][2] += f3[2];
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
|
||||
delx1,dely1,delz1,delx2,dely2,delz2);
|
||||
if (evflag)
|
||||
ev_tally(i1, i2, i3, nlocal, newton_bond, eangle, f1, f3, delx1, dely1, delz1, delx2, dely2,
|
||||
delz2);
|
||||
}
|
||||
}
|
||||
|
||||
@ -154,13 +155,13 @@ void AngleHarmonic::compute(int eflag, int vflag)
|
||||
void AngleHarmonic::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nangletypes;
|
||||
const int np1 = atom->nangletypes + 1;
|
||||
|
||||
memory->create(k,n+1,"angle:k");
|
||||
memory->create(theta0,n+1,"angle:theta0");
|
||||
memory->create(k, np1, "angle:k");
|
||||
memory->create(theta0, np1, "angle:theta0");
|
||||
|
||||
memory->create(setflag,n+1,"angle:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
memory->create(setflag, np1, "angle:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -169,26 +170,26 @@ void AngleHarmonic::allocate()
|
||||
|
||||
void AngleHarmonic::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 3) error->all(FLERR,"Incorrect args for angle coefficients");
|
||||
if (narg != 3) error->all(FLERR, "Incorrect args for angle coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
utils::bounds(FLERR,arg[0],1,atom->nangletypes,ilo,ihi,error);
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->nangletypes, ilo, ihi, error);
|
||||
|
||||
double k_one = utils::numeric(FLERR,arg[1],false,lmp);
|
||||
double theta0_one = utils::numeric(FLERR,arg[2],false,lmp);
|
||||
double k_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
double theta0_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
|
||||
// convert theta0 from degrees to radians
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
k[i] = k_one;
|
||||
theta0[i] = theta0_one/180.0 * MY_PI;
|
||||
theta0[i] = DEG2RAD * theta0_one;
|
||||
setflag[i] = 1;
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -204,8 +205,8 @@ double AngleHarmonic::equilibrium_angle(int i)
|
||||
|
||||
void AngleHarmonic::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&k[1],sizeof(double),atom->nangletypes,fp);
|
||||
fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp);
|
||||
fwrite(&k[1], sizeof(double), atom->nangletypes, fp);
|
||||
fwrite(&theta0[1], sizeof(double), atom->nangletypes, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -217,11 +218,11 @@ void AngleHarmonic::read_restart(FILE *fp)
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR, &k[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &theta0[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&k[1], atom->nangletypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&theta0[1], atom->nangletypes, MPI_DOUBLE, 0, world);
|
||||
|
||||
for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
|
||||
}
|
||||
@ -233,7 +234,7 @@ void AngleHarmonic::read_restart(FILE *fp)
|
||||
void AngleHarmonic::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->nangletypes; i++)
|
||||
fprintf(fp,"%d %g %g\n",i,k[i],theta0[i]/MY_PI*180.0);
|
||||
fprintf(fp, "%d %g %g\n", i, k[i], RAD2DEG * theta0[i]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -245,21 +246,21 @@ double AngleHarmonic::single(int type, int i1, int i2, int i3)
|
||||
double delx1 = x[i1][0] - x[i2][0];
|
||||
double dely1 = x[i1][1] - x[i2][1];
|
||||
double delz1 = x[i1][2] - x[i2][2];
|
||||
domain->minimum_image(delx1,dely1,delz1);
|
||||
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
|
||||
domain->minimum_image(delx1, dely1, delz1);
|
||||
double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1);
|
||||
|
||||
double delx2 = x[i3][0] - x[i2][0];
|
||||
double dely2 = x[i3][1] - x[i2][1];
|
||||
double delz2 = x[i3][2] - x[i2][2];
|
||||
domain->minimum_image(delx2,dely2,delz2);
|
||||
double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
|
||||
domain->minimum_image(delx2, dely2, delz2);
|
||||
double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
|
||||
|
||||
double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
|
||||
c /= r1*r2;
|
||||
double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
|
||||
c /= r1 * r2;
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
|
||||
double dtheta = acos(c) - theta0[type];
|
||||
double tk = k[type] * dtheta;
|
||||
return tk*dtheta;
|
||||
return tk * dtheta;
|
||||
}
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -18,33 +17,33 @@
|
||||
|
||||
#include "angle_table.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
#include <cstring>
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "domain.h"
|
||||
#include "comm.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
#include "tokenizer.h"
|
||||
#include "neighbor.h"
|
||||
#include "table_file_reader.h"
|
||||
#include "tokenizer.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
using MathConst::DEG2RAD;
|
||||
using MathConst::MY_PI;
|
||||
using MathConst::RAD2DEG;
|
||||
|
||||
enum{LINEAR,SPLINE};
|
||||
enum { LINEAR, SPLINE };
|
||||
|
||||
#define SMALL 0.001
|
||||
#define TINY 1.E-10
|
||||
#define TINY 1.E-10
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
AngleTable::AngleTable(LAMMPS *lmp) : Angle(lmp)
|
||||
AngleTable::AngleTable(LAMMPS *_lmp) : Angle(_lmp)
|
||||
{
|
||||
writedata = 0;
|
||||
ntables = 0;
|
||||
@ -69,14 +68,14 @@ AngleTable::~AngleTable()
|
||||
|
||||
void AngleTable::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,i3,n,type;
|
||||
double eangle,f1[3],f3[3];
|
||||
double delx1,dely1,delz1,delx2,dely2,delz2;
|
||||
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
|
||||
double theta,u,mdu; //mdu: minus du, -du/dx=f
|
||||
int i1, i2, i3, n, type;
|
||||
double eangle, f1[3], f3[3];
|
||||
double delx1, dely1, delz1, delx2, dely2, delz2;
|
||||
double rsq1, rsq2, r1, r2, c, s, a, a11, a12, a22;
|
||||
double theta, u, mdu; //mdu: minus du, -du/dx=f
|
||||
|
||||
eangle = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
@ -97,7 +96,7 @@ void AngleTable::compute(int eflag, int vflag)
|
||||
dely1 = x[i1][1] - x[i2][1];
|
||||
delz1 = x[i1][2] - x[i2][2];
|
||||
|
||||
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
|
||||
rsq1 = delx1 * delx1 + dely1 * dely1 + delz1 * delz1;
|
||||
r1 = sqrt(rsq1);
|
||||
|
||||
// 2nd bond
|
||||
@ -106,39 +105,39 @@ void AngleTable::compute(int eflag, int vflag)
|
||||
dely2 = x[i3][1] - x[i2][1];
|
||||
delz2 = x[i3][2] - x[i2][2];
|
||||
|
||||
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
|
||||
rsq2 = delx2 * delx2 + dely2 * dely2 + delz2 * delz2;
|
||||
r2 = sqrt(rsq2);
|
||||
|
||||
// angle (cos and sin)
|
||||
|
||||
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
|
||||
c /= r1*r2;
|
||||
c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
|
||||
c /= r1 * r2;
|
||||
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
|
||||
s = sqrt(1.0 - c*c);
|
||||
s = sqrt(1.0 - c * c);
|
||||
if (s < SMALL) s = SMALL;
|
||||
s = 1.0/s;
|
||||
s = 1.0 / s;
|
||||
|
||||
// tabulated force & energy
|
||||
|
||||
theta = acos(c);
|
||||
uf_lookup(type,theta,u,mdu);
|
||||
uf_lookup(type, theta, u, mdu);
|
||||
|
||||
if (eflag) eangle = u;
|
||||
|
||||
a = mdu * s;
|
||||
a11 = a*c / rsq1;
|
||||
a12 = -a / (r1*r2);
|
||||
a22 = a*c / rsq2;
|
||||
a11 = a * c / rsq1;
|
||||
a12 = -a / (r1 * r2);
|
||||
a22 = a * c / rsq2;
|
||||
|
||||
f1[0] = a11*delx1 + a12*delx2;
|
||||
f1[1] = a11*dely1 + a12*dely2;
|
||||
f1[2] = a11*delz1 + a12*delz2;
|
||||
f3[0] = a22*delx2 + a12*delx1;
|
||||
f3[1] = a22*dely2 + a12*dely1;
|
||||
f3[2] = a22*delz2 + a12*delz1;
|
||||
f1[0] = a11 * delx1 + a12 * delx2;
|
||||
f1[1] = a11 * dely1 + a12 * dely2;
|
||||
f1[2] = a11 * delz1 + a12 * delz2;
|
||||
f3[0] = a22 * delx2 + a12 * delx1;
|
||||
f3[1] = a22 * dely2 + a12 * dely1;
|
||||
f3[2] = a22 * delz2 + a12 * delz1;
|
||||
|
||||
// apply force to each of 3 atoms
|
||||
|
||||
@ -160,8 +159,9 @@ void AngleTable::compute(int eflag, int vflag)
|
||||
f[i3][2] += f3[2];
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
|
||||
delx1,dely1,delz1,delx2,dely2,delz2);
|
||||
if (evflag)
|
||||
ev_tally(i1, i2, i3, nlocal, newton_bond, eangle, f1, f3, delx1, dely1, delz1, delx2, dely2,
|
||||
delz2);
|
||||
}
|
||||
}
|
||||
|
||||
@ -170,13 +170,13 @@ void AngleTable::compute(int eflag, int vflag)
|
||||
void AngleTable::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nangletypes;
|
||||
const int np1 = atom->nangletypes + 1;
|
||||
|
||||
memory->create(theta0,n+1,"angle:theta0");
|
||||
memory->create(tabindex,n+1,"angle:tabindex");
|
||||
memory->create(theta0, np1, "angle:theta0");
|
||||
memory->create(tabindex, np1, "angle:tabindex");
|
||||
|
||||
memory->create(setflag,n+1,"angle:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
memory->create(setflag, np1, "angle:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -185,14 +185,17 @@ void AngleTable::allocate()
|
||||
|
||||
void AngleTable::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 2) error->all(FLERR,"Illegal angle_style command");
|
||||
if (narg != 2) error->all(FLERR, "Illegal angle_style command");
|
||||
|
||||
if (strcmp(arg[0],"linear") == 0) tabstyle = LINEAR;
|
||||
else if (strcmp(arg[0],"spline") == 0) tabstyle = SPLINE;
|
||||
else error->all(FLERR,"Unknown table style in angle style table");
|
||||
if (strcmp(arg[0], "linear") == 0)
|
||||
tabstyle = LINEAR;
|
||||
else if (strcmp(arg[0], "spline") == 0)
|
||||
tabstyle = SPLINE;
|
||||
else
|
||||
error->all(FLERR, "Unknown table style in angle style table");
|
||||
|
||||
tablength = utils::inumeric(FLERR,arg[1],false,lmp);
|
||||
if (tablength < 2) error->all(FLERR,"Illegal number of angle table entries");
|
||||
tablength = utils::inumeric(FLERR, arg[1], false, lmp);
|
||||
if (tablength < 2) error->all(FLERR, "Illegal number of angle table entries");
|
||||
|
||||
// delete old tables, since cannot just change settings
|
||||
|
||||
@ -200,8 +203,8 @@ void AngleTable::settings(int narg, char **arg)
|
||||
memory->sfree(tables);
|
||||
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(tabindex);
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(tabindex);
|
||||
}
|
||||
allocated = 0;
|
||||
|
||||
@ -215,36 +218,35 @@ void AngleTable::settings(int narg, char **arg)
|
||||
|
||||
void AngleTable::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 3) error->all(FLERR,"Illegal angle_coeff command");
|
||||
if (narg != 3) error->all(FLERR, "Illegal angle_coeff command");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
utils::bounds(FLERR,arg[0],1,atom->nangletypes,ilo,ihi,error);
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->nangletypes, ilo, ihi, error);
|
||||
|
||||
int me;
|
||||
MPI_Comm_rank(world,&me);
|
||||
tables = (Table *)
|
||||
memory->srealloc(tables,(ntables+1)*sizeof(Table),"angle:tables");
|
||||
MPI_Comm_rank(world, &me);
|
||||
tables = (Table *) memory->srealloc(tables, (ntables + 1) * sizeof(Table), "angle:tables");
|
||||
Table *tb = &tables[ntables];
|
||||
null_table(tb);
|
||||
if (me == 0) read_table(tb,arg[1],arg[2]);
|
||||
if (me == 0) read_table(tb, arg[1], arg[2]);
|
||||
bcast_table(tb);
|
||||
|
||||
// error check on table parameters
|
||||
|
||||
if (tb->ninput <= 1) error->one(FLERR,"Invalid angle table length");
|
||||
if (tb->ninput <= 1) error->one(FLERR, "Invalid angle table length");
|
||||
|
||||
double alo,ahi;
|
||||
double alo, ahi;
|
||||
alo = tb->afile[0];
|
||||
ahi = tb->afile[tb->ninput-1];
|
||||
if (fabs(alo-0.0) > TINY || fabs(ahi-180.0) > TINY)
|
||||
error->all(FLERR,"Angle table must range from 0 to 180 degrees");
|
||||
ahi = tb->afile[tb->ninput - 1];
|
||||
if (fabs(alo - 0.0) > TINY || fabs(ahi - 180.0) > TINY)
|
||||
error->all(FLERR, "Angle table must range from 0 to 180 degrees");
|
||||
|
||||
// convert theta from degrees to radians
|
||||
|
||||
for (int i = 0; i < tb->ninput; i++) {
|
||||
tb->afile[i] *= MY_PI/180.0;
|
||||
tb->ffile[i] *= 180.0/MY_PI;
|
||||
tb->afile[i] *= DEG2RAD;
|
||||
tb->ffile[i] *= RAD2DEG;
|
||||
}
|
||||
|
||||
// spline read-in and compute a,e,f vectors within table
|
||||
@ -263,7 +265,7 @@ void AngleTable::coeff(int narg, char **arg)
|
||||
}
|
||||
ntables++;
|
||||
|
||||
if (count == 0) error->all(FLERR,"Illegal angle_coeff command");
|
||||
if (count == 0) error->all(FLERR, "Illegal angle_coeff command");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -301,8 +303,8 @@ void AngleTable::read_restart(FILE *fp)
|
||||
|
||||
void AngleTable::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&tabstyle,sizeof(int),1,fp);
|
||||
fwrite(&tablength,sizeof(int),1,fp);
|
||||
fwrite(&tabstyle, sizeof(int), 1, fp);
|
||||
fwrite(&tablength, sizeof(int), 1, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -312,11 +314,11 @@ void AngleTable::write_restart_settings(FILE *fp)
|
||||
void AngleTable::read_restart_settings(FILE *fp)
|
||||
{
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&tablength,sizeof(int),1,fp,nullptr,error);
|
||||
utils::sfread(FLERR, &tabstyle, sizeof(int), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &tablength, sizeof(int), 1, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&tabstyle,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&tablength,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&tabstyle, 1, MPI_INT, 0, world);
|
||||
MPI_Bcast(&tablength, 1, MPI_INT, 0, world);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -328,23 +330,23 @@ double AngleTable::single(int type, int i1, int i2, int i3)
|
||||
double delx1 = x[i1][0] - x[i2][0];
|
||||
double dely1 = x[i1][1] - x[i2][1];
|
||||
double delz1 = x[i1][2] - x[i2][2];
|
||||
domain->minimum_image(delx1,dely1,delz1);
|
||||
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
|
||||
domain->minimum_image(delx1, dely1, delz1);
|
||||
double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1);
|
||||
|
||||
double delx2 = x[i3][0] - x[i2][0];
|
||||
double dely2 = x[i3][1] - x[i2][1];
|
||||
double delz2 = x[i3][2] - x[i2][2];
|
||||
domain->minimum_image(delx2,dely2,delz2);
|
||||
double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
|
||||
domain->minimum_image(delx2, dely2, delz2);
|
||||
double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
|
||||
|
||||
double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
|
||||
c /= r1*r2;
|
||||
double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
|
||||
c /= r1 * r2;
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
|
||||
double theta = acos(c);
|
||||
double u=0.0;
|
||||
u_lookup(type,theta,u);
|
||||
double u = 0.0;
|
||||
u_lookup(type, theta, u);
|
||||
return u;
|
||||
}
|
||||
|
||||
@ -385,11 +387,9 @@ void AngleTable::read_table(Table *tb, char *file, char *keyword)
|
||||
{
|
||||
TableFileReader reader(lmp, file, "angle");
|
||||
|
||||
char * line = reader.find_section_start(keyword);
|
||||
char *line = reader.find_section_start(keyword);
|
||||
|
||||
if (!line) {
|
||||
error->one(FLERR,"Did not find keyword in table file");
|
||||
}
|
||||
if (!line) { error->one(FLERR, "Did not find keyword in table file"); }
|
||||
|
||||
// read args on 2nd line of section
|
||||
// allocate table arrays for file values
|
||||
@ -419,10 +419,9 @@ void AngleTable::read_table(Table *tb, char *file, char *keyword)
|
||||
|
||||
// warn if data was read incompletely, e.g. columns were missing
|
||||
|
||||
if (cerror) {
|
||||
std::string str = fmt::format("{} of {} lines in table were incomplete or could not be parsed completely", cerror, tb->ninput);
|
||||
error->warning(FLERR,str.c_str());
|
||||
}
|
||||
if (cerror)
|
||||
error->warning(FLERR, "{} of {} lines in table incomplete or could not be parsed", cerror,
|
||||
tb->ninput);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -432,22 +431,22 @@ void AngleTable::read_table(Table *tb, char *file, char *keyword)
|
||||
|
||||
void AngleTable::spline_table(Table *tb)
|
||||
{
|
||||
memory->create(tb->e2file,tb->ninput,"angle:e2file");
|
||||
memory->create(tb->f2file,tb->ninput,"angle:f2file");
|
||||
memory->create(tb->e2file, tb->ninput, "angle:e2file");
|
||||
memory->create(tb->f2file, tb->ninput, "angle:f2file");
|
||||
|
||||
double ep0 = - tb->ffile[0];
|
||||
double epn = - tb->ffile[tb->ninput-1];
|
||||
spline(tb->afile,tb->efile,tb->ninput,ep0,epn,tb->e2file);
|
||||
double ep0 = -tb->ffile[0];
|
||||
double epn = -tb->ffile[tb->ninput - 1];
|
||||
spline(tb->afile, tb->efile, tb->ninput, ep0, epn, tb->e2file);
|
||||
|
||||
if (tb->fpflag == 0) {
|
||||
tb->fplo = (tb->ffile[1] - tb->ffile[0]) / (tb->afile[1] - tb->afile[0]);
|
||||
tb->fphi = (tb->ffile[tb->ninput-1] - tb->ffile[tb->ninput-2]) /
|
||||
(tb->afile[tb->ninput-1] - tb->afile[tb->ninput-2]);
|
||||
tb->fphi = (tb->ffile[tb->ninput - 1] - tb->ffile[tb->ninput - 2]) /
|
||||
(tb->afile[tb->ninput - 1] - tb->afile[tb->ninput - 2]);
|
||||
}
|
||||
|
||||
double fp0 = tb->fplo;
|
||||
double fpn = tb->fphi;
|
||||
spline(tb->afile,tb->ffile,tb->ninput,fp0,fpn,tb->f2file);
|
||||
spline(tb->afile, tb->ffile, tb->ninput, fp0, fpn, tb->f2file);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -458,44 +457,44 @@ void AngleTable::compute_table(Table *tb)
|
||||
{
|
||||
// delta = table spacing in angle for N-1 bins
|
||||
|
||||
int tlm1 = tablength-1;
|
||||
int tlm1 = tablength - 1;
|
||||
tb->delta = MY_PI / tlm1;
|
||||
tb->invdelta = 1.0/tb->delta;
|
||||
tb->deltasq6 = tb->delta*tb->delta / 6.0;
|
||||
tb->invdelta = 1.0 / tb->delta;
|
||||
tb->deltasq6 = tb->delta * tb->delta / 6.0;
|
||||
|
||||
// N-1 evenly spaced bins in angle from 0 to PI
|
||||
// ang,e,f = value at lower edge of bin
|
||||
// de,df values = delta values of e,f
|
||||
// ang,e,f are N in length so de,df arrays can compute difference
|
||||
|
||||
memory->create(tb->ang,tablength,"angle:ang");
|
||||
memory->create(tb->e,tablength,"angle:e");
|
||||
memory->create(tb->de,tablength,"angle:de");
|
||||
memory->create(tb->f,tablength,"angle:f");
|
||||
memory->create(tb->df,tablength,"angle:df");
|
||||
memory->create(tb->e2,tablength,"angle:e2");
|
||||
memory->create(tb->f2,tablength,"angle:f2");
|
||||
memory->create(tb->ang, tablength, "angle:ang");
|
||||
memory->create(tb->e, tablength, "angle:e");
|
||||
memory->create(tb->de, tablength, "angle:de");
|
||||
memory->create(tb->f, tablength, "angle:f");
|
||||
memory->create(tb->df, tablength, "angle:df");
|
||||
memory->create(tb->e2, tablength, "angle:e2");
|
||||
memory->create(tb->f2, tablength, "angle:f2");
|
||||
|
||||
double a;
|
||||
for (int i = 0; i < tablength; i++) {
|
||||
a = i*tb->delta;
|
||||
a = i * tb->delta;
|
||||
tb->ang[i] = a;
|
||||
tb->e[i] = splint(tb->afile,tb->efile,tb->e2file,tb->ninput,a);
|
||||
tb->f[i] = splint(tb->afile,tb->ffile,tb->f2file,tb->ninput,a);
|
||||
tb->e[i] = splint(tb->afile, tb->efile, tb->e2file, tb->ninput, a);
|
||||
tb->f[i] = splint(tb->afile, tb->ffile, tb->f2file, tb->ninput, a);
|
||||
}
|
||||
|
||||
for (int i = 0; i < tlm1; i++) {
|
||||
tb->de[i] = tb->e[i+1] - tb->e[i];
|
||||
tb->df[i] = tb->f[i+1] - tb->f[i];
|
||||
tb->de[i] = tb->e[i + 1] - tb->e[i];
|
||||
tb->df[i] = tb->f[i + 1] - tb->f[i];
|
||||
}
|
||||
// get final elements from linear extrapolation
|
||||
tb->de[tlm1] = 2.0*tb->de[tlm1-1] - tb->de[tlm1-2];
|
||||
tb->df[tlm1] = 2.0*tb->df[tlm1-1] - tb->df[tlm1-2];
|
||||
tb->de[tlm1] = 2.0 * tb->de[tlm1 - 1] - tb->de[tlm1 - 2];
|
||||
tb->df[tlm1] = 2.0 * tb->df[tlm1 - 1] - tb->df[tlm1 - 2];
|
||||
|
||||
double ep0 = - tb->f[0];
|
||||
double epn = - tb->f[tlm1];
|
||||
spline(tb->ang,tb->e,tablength,ep0,epn,tb->e2);
|
||||
spline(tb->ang,tb->f,tablength,tb->fplo,tb->fphi,tb->f2);
|
||||
double ep0 = -tb->f[0];
|
||||
double epn = -tb->f[tlm1];
|
||||
spline(tb->ang, tb->e, tablength, ep0, epn, tb->e2);
|
||||
spline(tb->ang, tb->f, tablength, tb->fplo, tb->fphi, tb->f2);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -522,19 +521,19 @@ void AngleTable::param_extract(Table *tb, char *line)
|
||||
tb->fpflag = 1;
|
||||
tb->fplo = values.next_double();
|
||||
tb->fphi = values.next_double();
|
||||
tb->fplo *= (180.0/MY_PI)*(180.0/MY_PI);
|
||||
tb->fphi *= (180.0/MY_PI)*(180.0/MY_PI);
|
||||
tb->fplo *= RAD2DEG * RAD2DEG;
|
||||
tb->fphi *= RAD2DEG * RAD2DEG;
|
||||
} else if (word == "EQ") {
|
||||
tb->theta0 = values.next_double()/180.0*MY_PI;
|
||||
tb->theta0 = DEG2RAD * values.next_double();
|
||||
} else {
|
||||
error->one(FLERR,"Invalid keyword in angle table parameters");
|
||||
error->one(FLERR, "Invalid keyword in angle table parameters");
|
||||
}
|
||||
}
|
||||
} catch(TokenizerException &e) {
|
||||
} catch (TokenizerException &e) {
|
||||
error->one(FLERR, e.what());
|
||||
}
|
||||
|
||||
if (tb->ninput == 0) error->one(FLERR,"Angle table parameters did not set N");
|
||||
if (tb->ninput == 0) error->one(FLERR, "Angle table parameters did not set N");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -545,80 +544,84 @@ void AngleTable::param_extract(Table *tb, char *line)
|
||||
|
||||
void AngleTable::bcast_table(Table *tb)
|
||||
{
|
||||
MPI_Bcast(&tb->ninput,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&tb->ninput, 1, MPI_INT, 0, world);
|
||||
|
||||
int me;
|
||||
MPI_Comm_rank(world,&me);
|
||||
MPI_Comm_rank(world, &me);
|
||||
if (me > 0) {
|
||||
memory->create(tb->afile,tb->ninput,"angle:afile");
|
||||
memory->create(tb->efile,tb->ninput,"angle:efile");
|
||||
memory->create(tb->ffile,tb->ninput,"angle:ffile");
|
||||
memory->create(tb->afile, tb->ninput, "angle:afile");
|
||||
memory->create(tb->efile, tb->ninput, "angle:efile");
|
||||
memory->create(tb->ffile, tb->ninput, "angle:ffile");
|
||||
}
|
||||
|
||||
MPI_Bcast(tb->afile,tb->ninput,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(tb->efile,tb->ninput,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(tb->ffile,tb->ninput,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(tb->afile, tb->ninput, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(tb->efile, tb->ninput, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(tb->ffile, tb->ninput, MPI_DOUBLE, 0, world);
|
||||
|
||||
MPI_Bcast(&tb->fpflag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&tb->fpflag, 1, MPI_INT, 0, world);
|
||||
if (tb->fpflag) {
|
||||
MPI_Bcast(&tb->fplo,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&tb->fphi,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&tb->fplo, 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&tb->fphi, 1, MPI_DOUBLE, 0, world);
|
||||
}
|
||||
MPI_Bcast(&tb->theta0,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&tb->theta0, 1, MPI_DOUBLE, 0, world);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
spline and splint routines modified from Numerical Recipes
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AngleTable::spline(double *x, double *y, int n,
|
||||
double yp1, double ypn, double *y2)
|
||||
void AngleTable::spline(double *x, double *y, int n, double yp1, double ypn, double *y2)
|
||||
{
|
||||
int i,k;
|
||||
double p,qn,sig,un;
|
||||
int i, k;
|
||||
double p, qn, sig, un;
|
||||
double *u = new double[n];
|
||||
|
||||
if (yp1 > 0.99e300) y2[0] = u[0] = 0.0;
|
||||
if (yp1 > 0.99e300)
|
||||
y2[0] = u[0] = 0.0;
|
||||
else {
|
||||
y2[0] = -0.5;
|
||||
u[0] = (3.0/(x[1]-x[0])) * ((y[1]-y[0]) / (x[1]-x[0]) - yp1);
|
||||
u[0] = (3.0 / (x[1] - x[0])) * ((y[1] - y[0]) / (x[1] - x[0]) - yp1);
|
||||
}
|
||||
for (i = 1; i < n-1; i++) {
|
||||
sig = (x[i]-x[i-1]) / (x[i+1]-x[i-1]);
|
||||
p = sig*y2[i-1] + 2.0;
|
||||
y2[i] = (sig-1.0) / p;
|
||||
u[i] = (y[i+1]-y[i]) / (x[i+1]-x[i]) - (y[i]-y[i-1]) / (x[i]-x[i-1]);
|
||||
u[i] = (6.0*u[i] / (x[i+1]-x[i-1]) - sig*u[i-1]) / p;
|
||||
for (i = 1; i < n - 1; i++) {
|
||||
sig = (x[i] - x[i - 1]) / (x[i + 1] - x[i - 1]);
|
||||
p = sig * y2[i - 1] + 2.0;
|
||||
y2[i] = (sig - 1.0) / p;
|
||||
u[i] = (y[i + 1] - y[i]) / (x[i + 1] - x[i]) - (y[i] - y[i - 1]) / (x[i] - x[i - 1]);
|
||||
u[i] = (6.0 * u[i] / (x[i + 1] - x[i - 1]) - sig * u[i - 1]) / p;
|
||||
}
|
||||
if (ypn > 0.99e300) qn = un = 0.0;
|
||||
if (ypn > 0.99e300)
|
||||
qn = un = 0.0;
|
||||
else {
|
||||
qn = 0.5;
|
||||
un = (3.0/(x[n-1]-x[n-2])) * (ypn - (y[n-1]-y[n-2]) / (x[n-1]-x[n-2]));
|
||||
un = (3.0 / (x[n - 1] - x[n - 2])) * (ypn - (y[n - 1] - y[n - 2]) / (x[n - 1] - x[n - 2]));
|
||||
}
|
||||
y2[n-1] = (un-qn*u[n-2]) / (qn*y2[n-2] + 1.0);
|
||||
for (k = n-2; k >= 0; k--) y2[k] = y2[k]*y2[k+1] + u[k];
|
||||
y2[n - 1] = (un - qn * u[n - 2]) / (qn * y2[n - 2] + 1.0);
|
||||
for (k = n - 2; k >= 0; k--) y2[k] = y2[k] * y2[k + 1] + u[k];
|
||||
|
||||
delete [] u;
|
||||
delete[] u;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double AngleTable::splint(double *xa, double *ya, double *y2a, int n, double x)
|
||||
{
|
||||
int klo,khi,k;
|
||||
double h,b,a,y;
|
||||
int klo, khi, k;
|
||||
double h, b, a, y;
|
||||
|
||||
klo = 0;
|
||||
khi = n-1;
|
||||
while (khi-klo > 1) {
|
||||
k = (khi+klo) >> 1;
|
||||
if (xa[k] > x) khi = k;
|
||||
else klo = k;
|
||||
khi = n - 1;
|
||||
while (khi - klo > 1) {
|
||||
k = (khi + klo) >> 1;
|
||||
if (xa[k] > x)
|
||||
khi = k;
|
||||
else
|
||||
klo = k;
|
||||
}
|
||||
h = xa[khi]-xa[klo];
|
||||
a = (xa[khi]-x) / h;
|
||||
b = (x-xa[klo]) / h;
|
||||
y = a*ya[klo] + b*ya[khi] + ((a*a*a-a)*y2a[klo] + (b*b*b-b)*y2a[khi]) * (h*h)/6.0;
|
||||
h = xa[khi] - xa[klo];
|
||||
a = (xa[khi] - x) / h;
|
||||
b = (x - xa[klo]) / h;
|
||||
y = a * ya[klo] + b * ya[khi] +
|
||||
((a * a * a - a) * y2a[klo] + (b * b * b - b) * y2a[khi]) * (h * h) / 6.0;
|
||||
return y;
|
||||
}
|
||||
|
||||
@ -628,31 +631,29 @@ double AngleTable::splint(double *xa, double *ya, double *y2a, int n, double x)
|
||||
|
||||
void AngleTable::uf_lookup(int type, double x, double &u, double &f)
|
||||
{
|
||||
if (!std::isfinite(x)) {
|
||||
error->one(FLERR,"Illegal angle in angle style table");
|
||||
}
|
||||
if (!std::isfinite(x)) { error->one(FLERR, "Illegal angle in angle style table"); }
|
||||
|
||||
double fraction,a,b;
|
||||
double fraction, a, b;
|
||||
const Table *tb = &tables[tabindex[type]];
|
||||
|
||||
// invdelta is based on tablength-1
|
||||
int itable = static_cast<int> (x * tb->invdelta);
|
||||
int itable = static_cast<int>(x * tb->invdelta);
|
||||
if (itable < 0) itable = 0;
|
||||
if (itable >= tablength) itable = tablength-1;
|
||||
if (itable >= tablength) itable = tablength - 1;
|
||||
|
||||
if (tabstyle == LINEAR) {
|
||||
fraction = (x - tb->ang[itable]) * tb->invdelta;
|
||||
u = tb->e[itable] + fraction*tb->de[itable];
|
||||
f = tb->f[itable] + fraction*tb->df[itable];
|
||||
u = tb->e[itable] + fraction * tb->de[itable];
|
||||
f = tb->f[itable] + fraction * tb->df[itable];
|
||||
} else if (tabstyle == SPLINE) {
|
||||
fraction = (x - tb->ang[itable]) * tb->invdelta;
|
||||
|
||||
b = (x - tb->ang[itable]) * tb->invdelta;
|
||||
a = 1.0 - b;
|
||||
u = a * tb->e[itable] + b * tb->e[itable+1] +
|
||||
((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) * tb->deltasq6;
|
||||
f = a * tb->f[itable] + b * tb->f[itable+1] +
|
||||
((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) * tb->deltasq6;
|
||||
u = a * tb->e[itable] + b * tb->e[itable + 1] +
|
||||
((a * a * a - a) * tb->e2[itable] + (b * b * b - b) * tb->e2[itable + 1]) * tb->deltasq6;
|
||||
f = a * tb->f[itable] + b * tb->f[itable + 1] +
|
||||
((a * a * a - a) * tb->f2[itable] + (b * b * b - b) * tb->f2[itable + 1]) * tb->deltasq6;
|
||||
}
|
||||
}
|
||||
|
||||
@ -662,26 +663,24 @@ void AngleTable::uf_lookup(int type, double x, double &u, double &f)
|
||||
|
||||
void AngleTable::u_lookup(int type, double x, double &u)
|
||||
{
|
||||
if (!std::isfinite(x)) {
|
||||
error->one(FLERR,"Illegal angle in angle style table");
|
||||
}
|
||||
if (!std::isfinite(x)) { error->one(FLERR, "Illegal angle in angle style table"); }
|
||||
|
||||
double fraction,a,b;
|
||||
double fraction, a, b;
|
||||
const Table *tb = &tables[tabindex[type]];
|
||||
int itable = static_cast<int> ( x * tb->invdelta);
|
||||
int itable = static_cast<int>(x * tb->invdelta);
|
||||
|
||||
if (itable < 0) itable = 0;
|
||||
if (itable >= tablength) itable = tablength-1;
|
||||
if (itable >= tablength) itable = tablength - 1;
|
||||
|
||||
if (tabstyle == LINEAR) {
|
||||
fraction = (x - tb->ang[itable]) * tb->invdelta;
|
||||
u = tb->e[itable] + fraction*tb->de[itable];
|
||||
u = tb->e[itable] + fraction * tb->de[itable];
|
||||
} else if (tabstyle == SPLINE) {
|
||||
fraction = (x - tb->ang[itable]) * tb->invdelta;
|
||||
|
||||
b = (x - tb->ang[itable]) * tb->invdelta;
|
||||
a = 1.0 - b;
|
||||
u = a * tb->e[itable] + b * tb->e[itable+1] +
|
||||
((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) * tb->deltasq6;
|
||||
u = a * tb->e[itable] + b * tb->e[itable + 1] +
|
||||
((a * a * a - a) * tb->e2[itable] + (b * b * b - b) * tb->e2[itable + 1]) * tb->deltasq6;
|
||||
}
|
||||
}
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -46,12 +45,12 @@ BondFENE::~BondFENE()
|
||||
|
||||
void BondFENE::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,n,type;
|
||||
double delx,dely,delz,ebond,fbond;
|
||||
double rsq,r0sq,rlogarg,sr2,sr6;
|
||||
int i1, i2, n, type;
|
||||
double delx, dely, delz, ebond, fbond;
|
||||
double rsq, r0sq, rlogarg, sr2, sr6;
|
||||
|
||||
ebond = sr6 = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
@ -71,54 +70,54 @@ void BondFENE::compute(int eflag, int vflag)
|
||||
|
||||
// force from log term
|
||||
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
r0sq = r0[type] * r0[type];
|
||||
rlogarg = 1.0 - rsq/r0sq;
|
||||
rlogarg = 1.0 - rsq / r0sq;
|
||||
|
||||
// if r -> r0, then rlogarg < 0.0 which is an error
|
||||
// issue a warning and reset rlogarg = epsilon
|
||||
// if r > 2*r0 something serious is wrong, abort
|
||||
|
||||
if (rlogarg < 0.1) {
|
||||
error->warning(FLERR,"FENE bond too long: {} {} {} {}",
|
||||
update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
|
||||
if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
|
||||
error->warning(FLERR, "FENE bond too long: {} {} {} {}", update->ntimestep, atom->tag[i1],
|
||||
atom->tag[i2], sqrt(rsq));
|
||||
if (rlogarg <= -3.0) error->one(FLERR, "Bad FENE bond");
|
||||
rlogarg = 0.1;
|
||||
}
|
||||
|
||||
fbond = -k[type]/rlogarg;
|
||||
fbond = -k[type] / rlogarg;
|
||||
|
||||
// force from LJ term
|
||||
|
||||
if (rsq < MY_CUBEROOT2*sigma[type]*sigma[type]) {
|
||||
sr2 = sigma[type]*sigma[type]/rsq;
|
||||
sr6 = sr2*sr2*sr2;
|
||||
fbond += 48.0*epsilon[type]*sr6*(sr6-0.5)/rsq;
|
||||
if (rsq < MY_CUBEROOT2 * sigma[type] * sigma[type]) {
|
||||
sr2 = sigma[type] * sigma[type] / rsq;
|
||||
sr6 = sr2 * sr2 * sr2;
|
||||
fbond += 48.0 * epsilon[type] * sr6 * (sr6 - 0.5) / rsq;
|
||||
}
|
||||
|
||||
// energy
|
||||
|
||||
if (eflag) {
|
||||
ebond = -0.5 * k[type]*r0sq*log(rlogarg);
|
||||
if (rsq < MY_CUBEROOT2*sigma[type]*sigma[type])
|
||||
ebond += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
|
||||
ebond = -0.5 * k[type] * r0sq * log(rlogarg);
|
||||
if (rsq < MY_CUBEROOT2 * sigma[type] * sigma[type])
|
||||
ebond += 4.0 * epsilon[type] * sr6 * (sr6 - 1.0) + epsilon[type];
|
||||
}
|
||||
|
||||
// apply force to each of 2 atoms
|
||||
|
||||
if (newton_bond || i1 < nlocal) {
|
||||
f[i1][0] += delx*fbond;
|
||||
f[i1][1] += dely*fbond;
|
||||
f[i1][2] += delz*fbond;
|
||||
f[i1][0] += delx * fbond;
|
||||
f[i1][1] += dely * fbond;
|
||||
f[i1][2] += delz * fbond;
|
||||
}
|
||||
|
||||
if (newton_bond || i2 < nlocal) {
|
||||
f[i2][0] -= delx*fbond;
|
||||
f[i2][1] -= dely*fbond;
|
||||
f[i2][2] -= delz*fbond;
|
||||
f[i2][0] -= delx * fbond;
|
||||
f[i2][1] -= dely * fbond;
|
||||
f[i2][2] -= delz * fbond;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
|
||||
if (evflag) ev_tally(i1, i2, nlocal, newton_bond, ebond, fbond, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
|
||||
@ -127,14 +126,14 @@ void BondFENE::compute(int eflag, int vflag)
|
||||
void BondFENE::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nbondtypes;
|
||||
const int np1 = atom->nbondtypes + 1;
|
||||
|
||||
memory->create(k,n+1,"bond:k");
|
||||
memory->create(r0,n+1,"bond:r0");
|
||||
memory->create(epsilon,n+1,"bond:epsilon");
|
||||
memory->create(sigma,n+1,"bond:sigma");
|
||||
memory->create(setflag,n+1,"bond:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
memory->create(k, np1, "bond:k");
|
||||
memory->create(r0, np1, "bond:r0");
|
||||
memory->create(epsilon, np1, "bond:epsilon");
|
||||
memory->create(sigma, np1, "bond:sigma");
|
||||
memory->create(setflag, np1, "bond:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -143,16 +142,16 @@ void BondFENE::allocate()
|
||||
|
||||
void BondFENE::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 5) error->all(FLERR,"Incorrect args for bond coefficients");
|
||||
if (narg != 5) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error);
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
|
||||
|
||||
double k_one = utils::numeric(FLERR,arg[1],false,lmp);
|
||||
double r0_one = utils::numeric(FLERR,arg[2],false,lmp);
|
||||
double epsilon_one = utils::numeric(FLERR,arg[3],false,lmp);
|
||||
double sigma_one = utils::numeric(FLERR,arg[4],false,lmp);
|
||||
double k_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
double r0_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
double epsilon_one = utils::numeric(FLERR, arg[3], false, lmp);
|
||||
double sigma_one = utils::numeric(FLERR, arg[4], false, lmp);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
@ -164,7 +163,7 @@ void BondFENE::coeff(int narg, char **arg)
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients");
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -175,10 +174,8 @@ void BondFENE::init_style()
|
||||
{
|
||||
// special bonds should be 0 1 1
|
||||
|
||||
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 ||
|
||||
force->special_lj[3] != 1.0) {
|
||||
if (comm->me == 0)
|
||||
error->warning(FLERR,"Use special bonds = 0,1,1 with bond style fene");
|
||||
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0) {
|
||||
if (comm->me == 0) error->warning(FLERR, "Use special bonds = 0,1,1 with bond style fene");
|
||||
}
|
||||
}
|
||||
|
||||
@ -186,7 +183,7 @@ void BondFENE::init_style()
|
||||
|
||||
double BondFENE::equilibrium_distance(int i)
|
||||
{
|
||||
return 0.97*sigma[i];
|
||||
return 0.97 * sigma[i];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -195,10 +192,10 @@ double BondFENE::equilibrium_distance(int i)
|
||||
|
||||
void BondFENE::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&k[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&epsilon[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&sigma[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&k[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&r0[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&epsilon[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&sigma[1], sizeof(double), atom->nbondtypes, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -210,15 +207,15 @@ void BondFENE::read_restart(FILE *fp)
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&epsilon[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&sigma[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR, &k[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &r0[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &epsilon[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &sigma[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&epsilon[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&sigma[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&k[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&r0[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&epsilon[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&sigma[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
|
||||
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
|
||||
}
|
||||
@ -230,36 +227,34 @@ void BondFENE::read_restart(FILE *fp)
|
||||
void BondFENE::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->nbondtypes; i++)
|
||||
fprintf(fp,"%d %g %g %g %g\n",i,k[i],r0[i],epsilon[i],sigma[i]);
|
||||
fprintf(fp, "%d %g %g %g %g\n", i, k[i], r0[i], epsilon[i], sigma[i]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BondFENE::single(int type, double rsq, int /*i*/, int /*j*/,
|
||||
double &fforce)
|
||||
double BondFENE::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce)
|
||||
{
|
||||
double r0sq = r0[type] * r0[type];
|
||||
double rlogarg = 1.0 - rsq/r0sq;
|
||||
double rlogarg = 1.0 - rsq / r0sq;
|
||||
|
||||
// if r -> r0, then rlogarg < 0.0 which is an error
|
||||
// issue a warning and reset rlogarg = epsilon
|
||||
// if r > 2*r0 something serious is wrong, abort
|
||||
|
||||
if (rlogarg < 0.1) {
|
||||
error->warning(FLERR,"FENE bond too long: {} {:.8}",
|
||||
update->ntimestep,sqrt(rsq));
|
||||
if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
|
||||
error->warning(FLERR, "FENE bond too long: {} {:.8}", update->ntimestep, sqrt(rsq));
|
||||
if (rlogarg <= -3.0) error->one(FLERR, "Bad FENE bond");
|
||||
rlogarg = 0.1;
|
||||
}
|
||||
|
||||
double eng = -0.5 * k[type]*r0sq*log(rlogarg);
|
||||
fforce = -k[type]/rlogarg;
|
||||
if (rsq < MY_CUBEROOT2*sigma[type]*sigma[type]) {
|
||||
double sr2,sr6;
|
||||
sr2 = sigma[type]*sigma[type]/rsq;
|
||||
sr6 = sr2*sr2*sr2;
|
||||
eng += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
|
||||
fforce += 48.0*epsilon[type]*sr6*(sr6-0.5)/rsq;
|
||||
double eng = -0.5 * k[type] * r0sq * log(rlogarg);
|
||||
fforce = -k[type] / rlogarg;
|
||||
if (rsq < MY_CUBEROOT2 * sigma[type] * sigma[type]) {
|
||||
double sr2, sr6;
|
||||
sr2 = sigma[type] * sigma[type] / rsq;
|
||||
sr6 = sr2 * sr2 * sr2;
|
||||
eng += 4.0 * epsilon[type] * sr6 * (sr6 - 1.0) + epsilon[type];
|
||||
fforce += 48.0 * epsilon[type] * sr6 * (sr6 - 0.5) / rsq;
|
||||
}
|
||||
|
||||
return eng;
|
||||
@ -270,7 +265,7 @@ double BondFENE::single(int type, double rsq, int /*i*/, int /*j*/,
|
||||
void *BondFENE::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 1;
|
||||
if (strcmp(str,"kappa")==0) return (void*) k;
|
||||
if (strcmp(str,"r0")==0) return (void*) r0;
|
||||
if (strcmp(str, "kappa") == 0) return (void *) k;
|
||||
if (strcmp(str, "r0") == 0) return (void *) r0;
|
||||
return nullptr;
|
||||
}
|
||||
|
||||
@ -26,7 +26,7 @@ namespace LAMMPS_NS {
|
||||
|
||||
class BondFENE : public Bond {
|
||||
public:
|
||||
BondFENE(class LAMMPS *lmp) : Bond(lmp) {}
|
||||
BondFENE(class LAMMPS *_lmp) : Bond(_lmp) {}
|
||||
~BondFENE() override;
|
||||
void compute(int, int) override;
|
||||
void coeff(int, char **) override;
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -46,13 +45,13 @@ BondFENEExpand::~BondFENEExpand()
|
||||
|
||||
void BondFENEExpand::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,n,type;
|
||||
double delx,dely,delz,ebond,fbond;
|
||||
double rsq,r0sq,rlogarg,sr2,sr6;
|
||||
double r,rshift,rshiftsq;
|
||||
int i1, i2, n, type;
|
||||
double delx, dely, delz, ebond, fbond;
|
||||
double rsq, r0sq, rlogarg, sr2, sr6;
|
||||
double r, rshift, rshiftsq;
|
||||
|
||||
ebond = sr6 = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
@ -72,57 +71,57 @@ void BondFENEExpand::compute(int eflag, int vflag)
|
||||
|
||||
// force from log term
|
||||
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
r = sqrt(rsq);
|
||||
rshift = r - shift[type];
|
||||
rshiftsq = rshift*rshift;
|
||||
rshiftsq = rshift * rshift;
|
||||
r0sq = r0[type] * r0[type];
|
||||
rlogarg = 1.0 - rshiftsq/r0sq;
|
||||
rlogarg = 1.0 - rshiftsq / r0sq;
|
||||
|
||||
// if r -> r0, then rlogarg < 0.0 which is an error
|
||||
// issue a warning and reset rlogarg = epsilon
|
||||
// if r > 2*r0 something serious is wrong, abort
|
||||
|
||||
if (rlogarg < 0.1) {
|
||||
error->warning(FLERR,"FENE bond too long: {} {} {} {:.8}",
|
||||
update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
|
||||
if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
|
||||
error->warning(FLERR, "FENE bond too long: {} {} {} {:.8}", update->ntimestep, atom->tag[i1],
|
||||
atom->tag[i2], sqrt(rsq));
|
||||
if (rlogarg <= -3.0) error->one(FLERR, "Bad FENE bond");
|
||||
rlogarg = 0.1;
|
||||
}
|
||||
|
||||
fbond = -k[type]*rshift/rlogarg/r;
|
||||
fbond = -k[type] * rshift / rlogarg / r;
|
||||
|
||||
// force from LJ term
|
||||
|
||||
if (rshiftsq < MY_CUBEROOT2*sigma[type]*sigma[type]) {
|
||||
sr2 = sigma[type]*sigma[type]/rshiftsq;
|
||||
sr6 = sr2*sr2*sr2;
|
||||
fbond += 48.0*epsilon[type]*sr6*(sr6-0.5)/rshift/r;
|
||||
if (rshiftsq < MY_CUBEROOT2 * sigma[type] * sigma[type]) {
|
||||
sr2 = sigma[type] * sigma[type] / rshiftsq;
|
||||
sr6 = sr2 * sr2 * sr2;
|
||||
fbond += 48.0 * epsilon[type] * sr6 * (sr6 - 0.5) / rshift / r;
|
||||
}
|
||||
|
||||
// energy
|
||||
|
||||
if (eflag) {
|
||||
ebond = -0.5 * k[type]*r0sq*log(rlogarg);
|
||||
if (rshiftsq < MY_CUBEROOT2*sigma[type]*sigma[type])
|
||||
ebond += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
|
||||
ebond = -0.5 * k[type] * r0sq * log(rlogarg);
|
||||
if (rshiftsq < MY_CUBEROOT2 * sigma[type] * sigma[type])
|
||||
ebond += 4.0 * epsilon[type] * sr6 * (sr6 - 1.0) + epsilon[type];
|
||||
}
|
||||
|
||||
// apply force to each of 2 atoms
|
||||
|
||||
if (newton_bond || i1 < nlocal) {
|
||||
f[i1][0] += delx*fbond;
|
||||
f[i1][1] += dely*fbond;
|
||||
f[i1][2] += delz*fbond;
|
||||
f[i1][0] += delx * fbond;
|
||||
f[i1][1] += dely * fbond;
|
||||
f[i1][2] += delz * fbond;
|
||||
}
|
||||
|
||||
if (newton_bond || i2 < nlocal) {
|
||||
f[i2][0] -= delx*fbond;
|
||||
f[i2][1] -= dely*fbond;
|
||||
f[i2][2] -= delz*fbond;
|
||||
f[i2][0] -= delx * fbond;
|
||||
f[i2][1] -= dely * fbond;
|
||||
f[i2][2] -= delz * fbond;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
|
||||
if (evflag) ev_tally(i1, i2, nlocal, newton_bond, ebond, fbond, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
|
||||
@ -131,15 +130,15 @@ void BondFENEExpand::compute(int eflag, int vflag)
|
||||
void BondFENEExpand::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nbondtypes;
|
||||
const int np1 = atom->nbondtypes + 1;
|
||||
|
||||
memory->create(k,n+1,"bond:k");
|
||||
memory->create(r0,n+1,"bond:r0");
|
||||
memory->create(epsilon,n+1,"bond:epsilon");
|
||||
memory->create(sigma,n+1,"bond:sigma");
|
||||
memory->create(shift,n+1,"bond:shift");
|
||||
memory->create(setflag,n+1,"bond:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
memory->create(k, np1, "bond:k");
|
||||
memory->create(r0, np1, "bond:r0");
|
||||
memory->create(epsilon, np1, "bond:epsilon");
|
||||
memory->create(sigma, np1, "bond:sigma");
|
||||
memory->create(shift, np1, "bond:shift");
|
||||
memory->create(setflag, np1, "bond:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -148,17 +147,17 @@ void BondFENEExpand::allocate()
|
||||
|
||||
void BondFENEExpand::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 6) error->all(FLERR,"Incorrect args for bond coefficients");
|
||||
if (narg != 6) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error);
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
|
||||
|
||||
double k_one = utils::numeric(FLERR,arg[1],false,lmp);
|
||||
double r0_one = utils::numeric(FLERR,arg[2],false,lmp);
|
||||
double epsilon_one = utils::numeric(FLERR,arg[3],false,lmp);
|
||||
double sigma_one = utils::numeric(FLERR,arg[4],false,lmp);
|
||||
double shift_one = utils::numeric(FLERR,arg[5],false,lmp);
|
||||
double k_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
double r0_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
double epsilon_one = utils::numeric(FLERR, arg[3], false, lmp);
|
||||
double sigma_one = utils::numeric(FLERR, arg[4], false, lmp);
|
||||
double shift_one = utils::numeric(FLERR, arg[5], false, lmp);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
@ -171,7 +170,7 @@ void BondFENEExpand::coeff(int narg, char **arg)
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients");
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -182,10 +181,9 @@ void BondFENEExpand::init_style()
|
||||
{
|
||||
// special bonds should be 0 1 1
|
||||
|
||||
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 ||
|
||||
force->special_lj[3] != 1.0) {
|
||||
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0) {
|
||||
if (comm->me == 0)
|
||||
error->warning(FLERR,"Use special bonds = 0,1,1 with bond style fene/expand");
|
||||
error->warning(FLERR, "Use special bonds = 0,1,1 with bond style fene/expand");
|
||||
}
|
||||
}
|
||||
|
||||
@ -193,7 +191,7 @@ void BondFENEExpand::init_style()
|
||||
|
||||
double BondFENEExpand::equilibrium_distance(int i)
|
||||
{
|
||||
return 0.97*sigma[i] + shift[i];
|
||||
return 0.97 * sigma[i] + shift[i];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -202,11 +200,11 @@ double BondFENEExpand::equilibrium_distance(int i)
|
||||
|
||||
void BondFENEExpand::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&k[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&epsilon[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&sigma[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&shift[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&k[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&r0[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&epsilon[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&sigma[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&shift[1], sizeof(double), atom->nbondtypes, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -218,17 +216,17 @@ void BondFENEExpand::read_restart(FILE *fp)
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&epsilon[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&sigma[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&shift[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR, &k[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &r0[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &epsilon[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &sigma[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &shift[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&epsilon[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&sigma[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&shift[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&k[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&r0[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&epsilon[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&sigma[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&shift[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
|
||||
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
|
||||
}
|
||||
@ -240,39 +238,37 @@ void BondFENEExpand::read_restart(FILE *fp)
|
||||
void BondFENEExpand::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->nbondtypes; i++)
|
||||
fprintf(fp,"%d %g %g %g %g %g\n",i,k[i],r0[i],epsilon[i],sigma[i],shift[i]);
|
||||
fprintf(fp, "%d %g %g %g %g %g\n", i, k[i], r0[i], epsilon[i], sigma[i], shift[i]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BondFENEExpand::single(int type, double rsq, int /*i*/, int /*j*/,
|
||||
double &fforce)
|
||||
double BondFENEExpand::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce)
|
||||
{
|
||||
double r = sqrt(rsq);
|
||||
double rshift = r - shift[type];
|
||||
double rshiftsq = rshift*rshift;
|
||||
double rshiftsq = rshift * rshift;
|
||||
double r0sq = r0[type] * r0[type];
|
||||
double rlogarg = 1.0 - rshiftsq/r0sq;
|
||||
double rlogarg = 1.0 - rshiftsq / r0sq;
|
||||
|
||||
// if r -> r0, then rlogarg < 0.0 which is an error
|
||||
// issue a warning and reset rlogarg = epsilon
|
||||
// if r > 2*r0 something serious is wrong, abort
|
||||
|
||||
if (rlogarg < 0.1) {
|
||||
error->warning(FLERR,"FENE bond too long: {} {:.8}",
|
||||
update->ntimestep,sqrt(rsq));
|
||||
if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
|
||||
error->warning(FLERR, "FENE bond too long: {} {:.8}", update->ntimestep, sqrt(rsq));
|
||||
if (rlogarg <= -3.0) error->one(FLERR, "Bad FENE bond");
|
||||
rlogarg = 0.1;
|
||||
}
|
||||
|
||||
double eng = -0.5 * k[type]*r0sq*log(rlogarg);
|
||||
fforce = -k[type]*rshift/rlogarg/r;
|
||||
if (rshiftsq < MY_CUBEROOT2*sigma[type]*sigma[type]) {
|
||||
double sr2,sr6;
|
||||
sr2 = sigma[type]*sigma[type]/rshiftsq;
|
||||
sr6 = sr2*sr2*sr2;
|
||||
eng += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
|
||||
fforce += 48.0*epsilon[type]*sr6*(sr6-0.5)/rshift/r;
|
||||
double eng = -0.5 * k[type] * r0sq * log(rlogarg);
|
||||
fforce = -k[type] * rshift / rlogarg / r;
|
||||
if (rshiftsq < MY_CUBEROOT2 * sigma[type] * sigma[type]) {
|
||||
double sr2, sr6;
|
||||
sr2 = sigma[type] * sigma[type] / rshiftsq;
|
||||
sr6 = sr2 * sr2 * sr2;
|
||||
eng += 4.0 * epsilon[type] * sr6 * (sr6 - 1.0) + epsilon[type];
|
||||
fforce += 48.0 * epsilon[type] * sr6 * (sr6 - 0.5) / rshift / r;
|
||||
}
|
||||
|
||||
return eng;
|
||||
|
||||
@ -26,7 +26,7 @@ namespace LAMMPS_NS {
|
||||
|
||||
class BondFENEExpand : public Bond {
|
||||
public:
|
||||
BondFENEExpand(class LAMMPS *lmp) : Bond(lmp) {}
|
||||
BondFENEExpand(class LAMMPS *_lmp) : Bond(_lmp) {}
|
||||
~BondFENEExpand() override;
|
||||
void compute(int, int) override;
|
||||
void coeff(int, char **) override;
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -18,20 +17,20 @@
|
||||
|
||||
#include "bond_gromos.h"
|
||||
|
||||
#include <cstring>
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "neighbor.h"
|
||||
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondGromos::BondGromos(LAMMPS *lmp) : Bond(lmp)
|
||||
BondGromos::BondGromos(LAMMPS *_lmp) : Bond(_lmp)
|
||||
{
|
||||
reinitflag = 1;
|
||||
}
|
||||
@ -51,11 +50,11 @@ BondGromos::~BondGromos()
|
||||
|
||||
void BondGromos::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,n,type;
|
||||
double delx,dely,delz,ebond,fbond;
|
||||
int i1, i2, n, type;
|
||||
double delx, dely, delz, ebond, fbond;
|
||||
|
||||
ebond = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
@ -73,30 +72,30 @@ void BondGromos::compute(int eflag, int vflag)
|
||||
dely = x[i1][1] - x[i2][1];
|
||||
delz = x[i1][2] - x[i2][2];
|
||||
|
||||
const double rsq = delx*delx + dely*dely + delz*delz;
|
||||
const double dr = rsq - r0[type]*r0[type];
|
||||
const double kdr = k[type]*dr;
|
||||
const double rsq = delx * delx + dely * dely + delz * delz;
|
||||
const double dr = rsq - r0[type] * r0[type];
|
||||
const double kdr = k[type] * dr;
|
||||
|
||||
// force & energy
|
||||
|
||||
fbond = -4.0 * kdr;
|
||||
if (eflag) ebond = kdr*dr;
|
||||
if (eflag) ebond = kdr * dr;
|
||||
|
||||
// apply force to each of 2 atoms
|
||||
|
||||
if (newton_bond || i1 < nlocal) {
|
||||
f[i1][0] += delx*fbond;
|
||||
f[i1][1] += dely*fbond;
|
||||
f[i1][2] += delz*fbond;
|
||||
f[i1][0] += delx * fbond;
|
||||
f[i1][1] += dely * fbond;
|
||||
f[i1][2] += delz * fbond;
|
||||
}
|
||||
|
||||
if (newton_bond || i2 < nlocal) {
|
||||
f[i2][0] -= delx*fbond;
|
||||
f[i2][1] -= dely*fbond;
|
||||
f[i2][2] -= delz*fbond;
|
||||
f[i2][0] -= delx * fbond;
|
||||
f[i2][1] -= dely * fbond;
|
||||
f[i2][2] -= delz * fbond;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
|
||||
if (evflag) ev_tally(i1, i2, nlocal, newton_bond, ebond, fbond, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
|
||||
@ -105,13 +104,13 @@ void BondGromos::compute(int eflag, int vflag)
|
||||
void BondGromos::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nbondtypes;
|
||||
const int np1 = atom->nbondtypes + 1;
|
||||
|
||||
memory->create(k,n+1,"bond:k");
|
||||
memory->create(r0,n+1,"bond:r0");
|
||||
memory->create(k, np1, "bond:k");
|
||||
memory->create(r0, np1, "bond:r0");
|
||||
|
||||
memory->create(setflag,n+1,"bond:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
memory->create(setflag, np1, "bond:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -120,14 +119,14 @@ void BondGromos::allocate()
|
||||
|
||||
void BondGromos::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 3) error->all(FLERR,"Incorrect args for bond coefficients");
|
||||
if (narg != 3) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error);
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
|
||||
|
||||
double k_one = utils::numeric(FLERR,arg[1],false,lmp);
|
||||
double r0_one = utils::numeric(FLERR,arg[2],false,lmp);
|
||||
double k_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
double r0_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
@ -137,7 +136,7 @@ void BondGromos::coeff(int narg, char **arg)
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients");
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -155,8 +154,8 @@ double BondGromos::equilibrium_distance(int i)
|
||||
|
||||
void BondGromos::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&k[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&k[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&r0[1], sizeof(double), atom->nbondtypes, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -168,11 +167,11 @@ void BondGromos::read_restart(FILE *fp)
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR, &k[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &r0[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&k[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&r0[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
|
||||
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
|
||||
}
|
||||
@ -183,18 +182,16 @@ void BondGromos::read_restart(FILE *fp)
|
||||
|
||||
void BondGromos::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->nbondtypes; i++)
|
||||
fprintf(fp,"%d %g %g\n",i,k[i],r0[i]);
|
||||
for (int i = 1; i <= atom->nbondtypes; i++) fprintf(fp, "%d %g %g\n", i, k[i], r0[i]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BondGromos::single(int type, double rsq, int /*i*/, int /*j*/,
|
||||
double &fforce)
|
||||
double BondGromos::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce)
|
||||
{
|
||||
double dr = rsq - r0[type]*r0[type];
|
||||
fforce = -4.0*k[type] * dr;
|
||||
return k[type]*dr*dr;
|
||||
double dr = rsq - r0[type] * r0[type];
|
||||
fforce = -4.0 * k[type] * dr;
|
||||
return k[type] * dr * dr;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -203,7 +200,7 @@ double BondGromos::single(int type, double rsq, int /*i*/, int /*j*/,
|
||||
void *BondGromos::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 1;
|
||||
if (strcmp(str,"kappa")==0) return (void*) k;
|
||||
if (strcmp(str,"r0")==0) return (void*) r0;
|
||||
if (strcmp(str, "kappa") == 0) return (void *) k;
|
||||
if (strcmp(str, "r0") == 0) return (void *) r0;
|
||||
return nullptr;
|
||||
}
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -14,21 +13,21 @@
|
||||
|
||||
#include "bond_harmonic.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "neighbor.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondHarmonic::BondHarmonic(LAMMPS *lmp) : Bond(lmp)
|
||||
BondHarmonic::BondHarmonic(LAMMPS *_lmp) : Bond(_lmp)
|
||||
{
|
||||
reinitflag = 1;
|
||||
}
|
||||
@ -48,12 +47,12 @@ BondHarmonic::~BondHarmonic()
|
||||
|
||||
void BondHarmonic::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,n,type;
|
||||
double delx,dely,delz,ebond,fbond;
|
||||
double rsq,r,dr,rk;
|
||||
int i1, i2, n, type;
|
||||
double delx, dely, delz, ebond, fbond;
|
||||
double rsq, r, dr, rk;
|
||||
|
||||
ebond = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
@ -71,33 +70,35 @@ void BondHarmonic::compute(int eflag, int vflag)
|
||||
dely = x[i1][1] - x[i2][1];
|
||||
delz = x[i1][2] - x[i2][2];
|
||||
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
r = sqrt(rsq);
|
||||
dr = r - r0[type];
|
||||
rk = k[type] * dr;
|
||||
|
||||
// force & energy
|
||||
|
||||
if (r > 0.0) fbond = -2.0*rk/r;
|
||||
else fbond = 0.0;
|
||||
if (r > 0.0)
|
||||
fbond = -2.0 * rk / r;
|
||||
else
|
||||
fbond = 0.0;
|
||||
|
||||
if (eflag) ebond = rk*dr;
|
||||
if (eflag) ebond = rk * dr;
|
||||
|
||||
// apply force to each of 2 atoms
|
||||
|
||||
if (newton_bond || i1 < nlocal) {
|
||||
f[i1][0] += delx*fbond;
|
||||
f[i1][1] += dely*fbond;
|
||||
f[i1][2] += delz*fbond;
|
||||
f[i1][0] += delx * fbond;
|
||||
f[i1][1] += dely * fbond;
|
||||
f[i1][2] += delz * fbond;
|
||||
}
|
||||
|
||||
if (newton_bond || i2 < nlocal) {
|
||||
f[i2][0] -= delx*fbond;
|
||||
f[i2][1] -= dely*fbond;
|
||||
f[i2][2] -= delz*fbond;
|
||||
f[i2][0] -= delx * fbond;
|
||||
f[i2][1] -= dely * fbond;
|
||||
f[i2][2] -= delz * fbond;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
|
||||
if (evflag) ev_tally(i1, i2, nlocal, newton_bond, ebond, fbond, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
|
||||
@ -106,13 +107,13 @@ void BondHarmonic::compute(int eflag, int vflag)
|
||||
void BondHarmonic::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nbondtypes;
|
||||
const int np1 = atom->nbondtypes + 1;
|
||||
|
||||
memory->create(k,n+1,"bond:k");
|
||||
memory->create(r0,n+1,"bond:r0");
|
||||
memory->create(k, np1, "bond:k");
|
||||
memory->create(r0, np1, "bond:r0");
|
||||
|
||||
memory->create(setflag,n+1,"bond:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
memory->create(setflag, np1, "bond:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -121,14 +122,14 @@ void BondHarmonic::allocate()
|
||||
|
||||
void BondHarmonic::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 3) error->all(FLERR,"Incorrect args for bond coefficients");
|
||||
if (narg != 3) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error);
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
|
||||
|
||||
double k_one = utils::numeric(FLERR,arg[1],false,lmp);
|
||||
double r0_one = utils::numeric(FLERR,arg[2],false,lmp);
|
||||
double k_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
double r0_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
@ -138,7 +139,7 @@ void BondHarmonic::coeff(int narg, char **arg)
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients");
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -156,8 +157,8 @@ double BondHarmonic::equilibrium_distance(int i)
|
||||
|
||||
void BondHarmonic::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&k[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&k[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&r0[1], sizeof(double), atom->nbondtypes, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -169,11 +170,11 @@ void BondHarmonic::read_restart(FILE *fp)
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR, &k[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &r0[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&k[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&r0[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
|
||||
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
|
||||
}
|
||||
@ -184,21 +185,19 @@ void BondHarmonic::read_restart(FILE *fp)
|
||||
|
||||
void BondHarmonic::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->nbondtypes; i++)
|
||||
fprintf(fp,"%d %g %g\n",i,k[i],r0[i]);
|
||||
for (int i = 1; i <= atom->nbondtypes; i++) fprintf(fp, "%d %g %g\n", i, k[i], r0[i]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BondHarmonic::single(int type, double rsq, int /*i*/, int /*j*/,
|
||||
double &fforce)
|
||||
double BondHarmonic::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce)
|
||||
{
|
||||
double r = sqrt(rsq);
|
||||
double dr = r - r0[type];
|
||||
double rk = k[type] * dr;
|
||||
fforce = 0;
|
||||
if (r > 0.0) fforce = -2.0*rk/r;
|
||||
return rk*dr;
|
||||
if (r > 0.0) fforce = -2.0 * rk / r;
|
||||
return rk * dr;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -207,9 +206,7 @@ double BondHarmonic::single(int type, double rsq, int /*i*/, int /*j*/,
|
||||
void *BondHarmonic::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 1;
|
||||
if (strcmp(str,"kappa")==0) return (void*) k;
|
||||
if (strcmp(str,"r0")==0) return (void*) r0;
|
||||
if (strcmp(str, "kappa") == 0) return (void *) k;
|
||||
if (strcmp(str, "r0") == 0) return (void *) r0;
|
||||
return nullptr;
|
||||
}
|
||||
|
||||
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -18,21 +17,20 @@
|
||||
|
||||
#include "bond_morse.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
#include "neighbor.h"
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondMorse::BondMorse(LAMMPS *lmp) : Bond(lmp) {}
|
||||
BondMorse::BondMorse(LAMMPS *_lmp) : Bond(_lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -50,12 +48,12 @@ BondMorse::~BondMorse()
|
||||
|
||||
void BondMorse::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,n,type;
|
||||
double delx,dely,delz,ebond,fbond;
|
||||
double rsq,r,dr,ralpha;
|
||||
int i1, i2, n, type;
|
||||
double delx, dely, delz, ebond, fbond;
|
||||
double rsq, r, dr, ralpha;
|
||||
|
||||
ebond = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
@ -73,33 +71,35 @@ void BondMorse::compute(int eflag, int vflag)
|
||||
dely = x[i1][1] - x[i2][1];
|
||||
delz = x[i1][2] - x[i2][2];
|
||||
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
r = sqrt(rsq);
|
||||
dr = r - r0[type];
|
||||
ralpha = exp(-alpha[type]*dr);
|
||||
ralpha = exp(-alpha[type] * dr);
|
||||
|
||||
// force & energy
|
||||
|
||||
if (r > 0.0) fbond = -2.0*d0[type]*alpha[type]*(1-ralpha)*ralpha/r;
|
||||
else fbond = 0.0;
|
||||
if (r > 0.0)
|
||||
fbond = -2.0 * d0[type] * alpha[type] * (1 - ralpha) * ralpha / r;
|
||||
else
|
||||
fbond = 0.0;
|
||||
|
||||
if (eflag) ebond = d0[type]*(1-ralpha)*(1-ralpha);
|
||||
if (eflag) ebond = d0[type] * (1 - ralpha) * (1 - ralpha);
|
||||
|
||||
// apply force to each of 2 atoms
|
||||
|
||||
if (newton_bond || i1 < nlocal) {
|
||||
f[i1][0] += delx*fbond;
|
||||
f[i1][1] += dely*fbond;
|
||||
f[i1][2] += delz*fbond;
|
||||
f[i1][0] += delx * fbond;
|
||||
f[i1][1] += dely * fbond;
|
||||
f[i1][2] += delz * fbond;
|
||||
}
|
||||
|
||||
if (newton_bond || i2 < nlocal) {
|
||||
f[i2][0] -= delx*fbond;
|
||||
f[i2][1] -= dely*fbond;
|
||||
f[i2][2] -= delz*fbond;
|
||||
f[i2][0] -= delx * fbond;
|
||||
f[i2][1] -= dely * fbond;
|
||||
f[i2][2] -= delz * fbond;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
|
||||
if (evflag) ev_tally(i1, i2, nlocal, newton_bond, ebond, fbond, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
|
||||
@ -108,13 +108,13 @@ void BondMorse::compute(int eflag, int vflag)
|
||||
void BondMorse::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nbondtypes;
|
||||
const int np1 = atom->nbondtypes + 1;
|
||||
|
||||
memory->create(d0,n+1,"bond:d0");
|
||||
memory->create(alpha,n+1,"bond:alpha");
|
||||
memory->create(r0,n+1,"bond:r0");
|
||||
memory->create(setflag,n+1,"bond:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
memory->create(d0, np1, "bond:d0");
|
||||
memory->create(alpha, np1, "bond:alpha");
|
||||
memory->create(r0, np1, "bond:r0");
|
||||
memory->create(setflag, np1, "bond:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -123,15 +123,15 @@ void BondMorse::allocate()
|
||||
|
||||
void BondMorse::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 4) error->all(FLERR,"Incorrect args for bond coefficients");
|
||||
if (narg != 4) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error);
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
|
||||
|
||||
double d0_one = utils::numeric(FLERR,arg[1],false,lmp);
|
||||
double alpha_one = utils::numeric(FLERR,arg[2],false,lmp);
|
||||
double r0_one = utils::numeric(FLERR,arg[3],false,lmp);
|
||||
double d0_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
double alpha_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
double r0_one = utils::numeric(FLERR, arg[3], false, lmp);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
@ -142,7 +142,7 @@ void BondMorse::coeff(int narg, char **arg)
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients");
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -160,9 +160,9 @@ double BondMorse::equilibrium_distance(int i)
|
||||
|
||||
void BondMorse::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&d0[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&alpha[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&d0[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&alpha[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&r0[1], sizeof(double), atom->nbondtypes, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -174,13 +174,13 @@ void BondMorse::read_restart(FILE *fp)
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR,&d0[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&alpha[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR, &d0[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &alpha[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &r0[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&d0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&alpha[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&d0[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&alpha[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&r0[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
|
||||
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
|
||||
}
|
||||
@ -192,20 +192,19 @@ void BondMorse::read_restart(FILE *fp)
|
||||
void BondMorse::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->nbondtypes; i++)
|
||||
fprintf(fp,"%d %g %g %g\n",i,d0[i],alpha[i],r0[i]);
|
||||
fprintf(fp, "%d %g %g %g\n", i, d0[i], alpha[i], r0[i]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BondMorse::single(int type, double rsq, int /*i*/, int /*j*/,
|
||||
double &fforce)
|
||||
double BondMorse::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce)
|
||||
{
|
||||
double r = sqrt(rsq);
|
||||
double dr = r - r0[type];
|
||||
double ralpha = exp(-alpha[type]*dr);
|
||||
double ralpha = exp(-alpha[type] * dr);
|
||||
fforce = 0;
|
||||
if (r > 0.0) fforce = -2.0*d0[type]*alpha[type]*(1-ralpha)*ralpha/r;
|
||||
return d0[type]*(1-ralpha)*(1-ralpha);
|
||||
if (r > 0.0) fforce = -2.0 * d0[type] * alpha[type] * (1 - ralpha) * ralpha / r;
|
||||
return d0[type] * (1 - ralpha) * (1 - ralpha);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -213,6 +212,6 @@ double BondMorse::single(int type, double rsq, int /*i*/, int /*j*/,
|
||||
void *BondMorse::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 1;
|
||||
if (strcmp(str,"r0")==0) return (void*) r0;
|
||||
if (strcmp(str, "r0") == 0) return (void *) r0;
|
||||
return nullptr;
|
||||
}
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -22,21 +21,22 @@
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "neighbor.h"
|
||||
#include "pair.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
#include "math_const.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
using MathConst::MY_CUBEROOT2;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondQuartic::BondQuartic(LAMMPS *lmp) : Bond(lmp), k(nullptr),
|
||||
b1(nullptr), b2(nullptr), rc(nullptr), u0(nullptr) {}
|
||||
BondQuartic::BondQuartic(LAMMPS *_lmp) :
|
||||
Bond(_lmp), k(nullptr), b1(nullptr), b2(nullptr), rc(nullptr), u0(nullptr)
|
||||
{
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -56,17 +56,16 @@ BondQuartic::~BondQuartic()
|
||||
|
||||
void BondQuartic::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,n,m,type,itype,jtype;
|
||||
double delx,dely,delz,ebond,fbond,evdwl,fpair;
|
||||
double r,rsq,dr,r2,ra,rb,sr2,sr6;
|
||||
int i1, i2, n, m, type, itype, jtype;
|
||||
double delx, dely, delz, ebond, fbond, evdwl, fpair;
|
||||
double r, rsq, dr, r2, ra, rb, sr2, sr6;
|
||||
|
||||
ebond = evdwl = sr6 = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
// insure pair->ev_tally() will use 1-4 virial contribution
|
||||
|
||||
if (vflag_global == VIRIAL_FDOTR)
|
||||
force->pair->vflag_either = force->pair->vflag_global = 1;
|
||||
if (vflag_global == VIRIAL_FDOTR) force->pair->vflag_either = force->pair->vflag_global = 1;
|
||||
|
||||
double **cutsq = force->pair->cutsq;
|
||||
double **x = atom->x;
|
||||
@ -90,7 +89,7 @@ void BondQuartic::compute(int eflag, int vflag)
|
||||
dely = x[i1][1] - x[i2][1];
|
||||
delz = x[i1][2] - x[i2][2];
|
||||
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
|
||||
// if bond breaks, set type to 0
|
||||
// both in temporary bondlist and permanent bond_type
|
||||
@ -98,15 +97,13 @@ void BondQuartic::compute(int eflag, int vflag)
|
||||
// negate bond_type twice if other atom stores it
|
||||
// if other proc owns 2nd atom, other proc will also break bond
|
||||
|
||||
if (rsq > rc[type]*rc[type]) {
|
||||
if (rsq > rc[type] * rc[type]) {
|
||||
bondlist[n][2] = 0;
|
||||
for (m = 0; m < atom->num_bond[i1]; m++)
|
||||
if (atom->bond_atom[i1][m] == atom->tag[i2])
|
||||
atom->bond_type[i1][m] = 0;
|
||||
if (atom->bond_atom[i1][m] == atom->tag[i2]) atom->bond_type[i1][m] = 0;
|
||||
if (i2 < atom->nlocal)
|
||||
for (m = 0; m < atom->num_bond[i2]; m++)
|
||||
if (atom->bond_atom[i2][m] == atom->tag[i1])
|
||||
atom->bond_type[i2][m] = 0;
|
||||
if (atom->bond_atom[i2][m] == atom->tag[i1]) atom->bond_type[i2][m] = 0;
|
||||
continue;
|
||||
}
|
||||
|
||||
@ -116,37 +113,37 @@ void BondQuartic::compute(int eflag, int vflag)
|
||||
|
||||
r = sqrt(rsq);
|
||||
dr = r - rc[type];
|
||||
r2 = dr*dr;
|
||||
r2 = dr * dr;
|
||||
ra = dr - b1[type];
|
||||
rb = dr - b2[type];
|
||||
fbond = -k[type]/r * (r2*(ra+rb) + 2.0*dr*ra*rb);
|
||||
fbond = -k[type] / r * (r2 * (ra + rb) + 2.0 * dr * ra * rb);
|
||||
|
||||
if (rsq < MY_CUBEROOT2) {
|
||||
sr2 = 1.0/rsq;
|
||||
sr6 = sr2*sr2*sr2;
|
||||
fbond += 48.0*sr6*(sr6-0.5)/rsq;
|
||||
sr2 = 1.0 / rsq;
|
||||
sr6 = sr2 * sr2 * sr2;
|
||||
fbond += 48.0 * sr6 * (sr6 - 0.5) / rsq;
|
||||
}
|
||||
|
||||
if (eflag) {
|
||||
ebond = k[type]*r2*ra*rb + u0[type];
|
||||
if (rsq < MY_CUBEROOT2) ebond += 4.0*sr6*(sr6-1.0) + 1.0;
|
||||
ebond = k[type] * r2 * ra * rb + u0[type];
|
||||
if (rsq < MY_CUBEROOT2) ebond += 4.0 * sr6 * (sr6 - 1.0) + 1.0;
|
||||
}
|
||||
|
||||
// apply force to each of 2 atoms
|
||||
|
||||
if (newton_bond || i1 < nlocal) {
|
||||
f[i1][0] += delx*fbond;
|
||||
f[i1][1] += dely*fbond;
|
||||
f[i1][2] += delz*fbond;
|
||||
f[i1][0] += delx * fbond;
|
||||
f[i1][1] += dely * fbond;
|
||||
f[i1][2] += delz * fbond;
|
||||
}
|
||||
|
||||
if (newton_bond || i2 < nlocal) {
|
||||
f[i2][0] -= delx*fbond;
|
||||
f[i2][1] -= dely*fbond;
|
||||
f[i2][2] -= delz*fbond;
|
||||
f[i2][0] -= delx * fbond;
|
||||
f[i2][1] -= dely * fbond;
|
||||
f[i2][2] -= delz * fbond;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
|
||||
if (evflag) ev_tally(i1, i2, nlocal, newton_bond, ebond, fbond, delx, dely, delz);
|
||||
|
||||
// subtract out pairwise contribution from 2 atoms via pair->single()
|
||||
// required since special_bond = 1,1,1
|
||||
@ -156,22 +153,22 @@ void BondQuartic::compute(int eflag, int vflag)
|
||||
jtype = atom->type[i2];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
evdwl = -force->pair->single(i1,i2,itype,jtype,rsq,1.0,1.0,fpair);
|
||||
evdwl = -force->pair->single(i1, i2, itype, jtype, rsq, 1.0, 1.0, fpair);
|
||||
fpair = -fpair;
|
||||
|
||||
if (newton_bond || i1 < nlocal) {
|
||||
f[i1][0] += delx*fpair;
|
||||
f[i1][1] += dely*fpair;
|
||||
f[i1][2] += delz*fpair;
|
||||
f[i1][0] += delx * fpair;
|
||||
f[i1][1] += dely * fpair;
|
||||
f[i1][2] += delz * fpair;
|
||||
}
|
||||
if (newton_bond || i2 < nlocal) {
|
||||
f[i2][0] -= delx*fpair;
|
||||
f[i2][1] -= dely*fpair;
|
||||
f[i2][2] -= delz*fpair;
|
||||
f[i2][0] -= delx * fpair;
|
||||
f[i2][1] -= dely * fpair;
|
||||
f[i2][2] -= delz * fpair;
|
||||
}
|
||||
|
||||
if (evflag) force->pair->ev_tally(i1,i2,nlocal,newton_bond,
|
||||
evdwl,0.0,fpair,delx,dely,delz);
|
||||
if (evflag)
|
||||
force->pair->ev_tally(i1, i2, nlocal, newton_bond, evdwl, 0.0, fpair, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -181,16 +178,16 @@ void BondQuartic::compute(int eflag, int vflag)
|
||||
void BondQuartic::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nbondtypes;
|
||||
const int np1 = atom->nbondtypes + 1;
|
||||
|
||||
memory->create(k,n+1,"bond:k");
|
||||
memory->create(b1,n+1,"bond:b1");
|
||||
memory->create(b2,n+1,"bond:b2");
|
||||
memory->create(rc,n+1,"bond:rc");
|
||||
memory->create(u0,n+1,"bond:u0");
|
||||
memory->create(k, np1, "bond:k");
|
||||
memory->create(b1, np1, "bond:b1");
|
||||
memory->create(b2, np1, "bond:b2");
|
||||
memory->create(rc, np1, "bond:rc");
|
||||
memory->create(u0, np1, "bond:u0");
|
||||
|
||||
memory->create(setflag,n+1,"bond:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
memory->create(setflag, np1, "bond:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -199,17 +196,17 @@ void BondQuartic::allocate()
|
||||
|
||||
void BondQuartic::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 6) error->all(FLERR,"Incorrect args for bond coefficients");
|
||||
if (narg != 6) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error);
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
|
||||
|
||||
double k_one = utils::numeric(FLERR,arg[1],false,lmp);
|
||||
double b1_one = utils::numeric(FLERR,arg[2],false,lmp);
|
||||
double b2_one = utils::numeric(FLERR,arg[3],false,lmp);
|
||||
double rc_one = utils::numeric(FLERR,arg[4],false,lmp);
|
||||
double u0_one = utils::numeric(FLERR,arg[5],false,lmp);
|
||||
double k_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
double b1_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
double b2_one = utils::numeric(FLERR, arg[3], false, lmp);
|
||||
double rc_one = utils::numeric(FLERR, arg[4], false, lmp);
|
||||
double u0_one = utils::numeric(FLERR, arg[5], false, lmp);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
@ -222,7 +219,7 @@ void BondQuartic::coeff(int narg, char **arg)
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients");
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -232,19 +229,16 @@ void BondQuartic::coeff(int narg, char **arg)
|
||||
void BondQuartic::init_style()
|
||||
{
|
||||
if (force->pair == nullptr || force->pair->single_enable == 0)
|
||||
error->all(FLERR,"Pair style does not support bond_style quartic");
|
||||
error->all(FLERR, "Pair style does not support bond_style quartic");
|
||||
if (force->angle || force->dihedral || force->improper)
|
||||
error->all(FLERR,
|
||||
"Bond style quartic cannot be used with 3,4-body interactions");
|
||||
error->all(FLERR, "Bond style quartic cannot be used with 3,4-body interactions");
|
||||
if (atom->molecular == Atom::TEMPLATE)
|
||||
error->all(FLERR,
|
||||
"Bond style quartic cannot be used with atom style template");
|
||||
error->all(FLERR, "Bond style quartic cannot be used with atom style template");
|
||||
|
||||
// special bonds must be 1 1 1
|
||||
|
||||
if (force->special_lj[1] != 1.0 || force->special_lj[2] != 1.0 ||
|
||||
force->special_lj[3] != 1.0)
|
||||
error->all(FLERR,"Bond style quartic requires special_bonds = 1,1,1");
|
||||
if (force->special_lj[1] != 1.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0)
|
||||
error->all(FLERR, "Bond style quartic requires special_bonds = 1,1,1");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -262,11 +256,11 @@ double BondQuartic::equilibrium_distance(int /*i*/)
|
||||
|
||||
void BondQuartic::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&k[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&b1[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&b2[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&rc[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&u0[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&k[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&b1[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&b2[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&rc[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&u0[1], sizeof(double), atom->nbondtypes, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -278,17 +272,17 @@ void BondQuartic::read_restart(FILE *fp)
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&b1[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&b2[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&rc[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&u0[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR, &k[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &b1[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &b2[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &rc[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &u0[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&b1[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&b2[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&rc[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&u0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&k[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&b1[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&b2[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&rc[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&u0[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
|
||||
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
|
||||
}
|
||||
@ -300,15 +294,14 @@ void BondQuartic::read_restart(FILE *fp)
|
||||
void BondQuartic::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->nbondtypes; i++)
|
||||
fprintf(fp,"%d %g %g %g %g %g\n",i,k[i],b1[i],b2[i],rc[i],u0[i]);
|
||||
fprintf(fp, "%d %g %g %g %g %g\n", i, k[i], b1[i], b2[i], rc[i], u0[i]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BondQuartic::single(int type, double rsq, int i, int j,
|
||||
double &fforce)
|
||||
double BondQuartic::single(int type, double rsq, int i, int j, double &fforce)
|
||||
{
|
||||
double r,dr,r2,ra,rb,sr2,sr6;
|
||||
double r, dr, r2, ra, rb, sr2, sr6;
|
||||
|
||||
if (type <= 0) return 0.0;
|
||||
double eng = 0.0;
|
||||
@ -321,7 +314,7 @@ double BondQuartic::single(int type, double rsq, int i, int j,
|
||||
|
||||
if (rsq < force->pair->cutsq[itype][jtype]) {
|
||||
double tmp;
|
||||
eng = -force->pair->single(i,j,itype,jtype,rsq,1.0,1.0,tmp);
|
||||
eng = -force->pair->single(i, j, itype, jtype, rsq, 1.0, 1.0, tmp);
|
||||
}
|
||||
|
||||
// quartic bond
|
||||
@ -330,18 +323,18 @@ double BondQuartic::single(int type, double rsq, int i, int j,
|
||||
|
||||
r = sqrt(rsq);
|
||||
dr = r - rc[type];
|
||||
r2 = dr*dr;
|
||||
r2 = dr * dr;
|
||||
ra = dr - b1[type];
|
||||
rb = dr - b2[type];
|
||||
|
||||
eng += k[type]*r2*ra*rb + u0[type];
|
||||
fforce = -k[type]/r * (r2*(ra+rb) + 2.0*dr*ra*rb);
|
||||
eng += k[type] * r2 * ra * rb + u0[type];
|
||||
fforce = -k[type] / r * (r2 * (ra + rb) + 2.0 * dr * ra * rb);
|
||||
|
||||
if (rsq < MY_CUBEROOT2) {
|
||||
sr2 = 1.0/rsq;
|
||||
sr6 = sr2*sr2*sr2;
|
||||
eng += 4.0*sr6*(sr6-1.0) + 1.0;
|
||||
fforce += 48.0*sr6*(sr6-0.5)/rsq;
|
||||
sr2 = 1.0 / rsq;
|
||||
sr6 = sr2 * sr2 * sr2;
|
||||
eng += 4.0 * sr6 * (sr6 - 1.0) + 1.0;
|
||||
fforce += 48.0 * sr6 * (sr6 - 0.5) / rsq;
|
||||
}
|
||||
|
||||
return eng;
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -32,13 +31,13 @@
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
enum{NONE,LINEAR,SPLINE};
|
||||
enum { NONE, LINEAR, SPLINE };
|
||||
|
||||
#define BIGNUM 1.0e300
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondTable::BondTable(LAMMPS *lmp) : Bond(lmp)
|
||||
BondTable::BondTable(LAMMPS *_lmp) : Bond(_lmp)
|
||||
{
|
||||
writedata = 0;
|
||||
ntables = 0;
|
||||
@ -63,13 +62,13 @@ BondTable::~BondTable()
|
||||
|
||||
void BondTable::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,n,type;
|
||||
double delx,dely,delz,ebond,fbond;
|
||||
double rsq,r;
|
||||
double u,mdu;
|
||||
int i1, i2, n, type;
|
||||
double delx, dely, delz, ebond, fbond;
|
||||
double rsq, r;
|
||||
double u, mdu;
|
||||
|
||||
ebond = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
@ -87,30 +86,30 @@ void BondTable::compute(int eflag, int vflag)
|
||||
dely = x[i1][1] - x[i2][1];
|
||||
delz = x[i1][2] - x[i2][2];
|
||||
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
r = sqrt(rsq);
|
||||
|
||||
// force & energy
|
||||
|
||||
uf_lookup(type,r,u,mdu);
|
||||
fbond = mdu/r;
|
||||
uf_lookup(type, r, u, mdu);
|
||||
fbond = mdu / r;
|
||||
ebond = u;
|
||||
|
||||
// apply force to each of 2 atoms
|
||||
|
||||
if (newton_bond || i1 < nlocal) {
|
||||
f[i1][0] += delx*fbond;
|
||||
f[i1][1] += dely*fbond;
|
||||
f[i1][2] += delz*fbond;
|
||||
f[i1][0] += delx * fbond;
|
||||
f[i1][1] += dely * fbond;
|
||||
f[i1][2] += delz * fbond;
|
||||
}
|
||||
|
||||
if (newton_bond || i2 < nlocal) {
|
||||
f[i2][0] -= delx*fbond;
|
||||
f[i2][1] -= dely*fbond;
|
||||
f[i2][2] -= delz*fbond;
|
||||
f[i2][0] -= delx * fbond;
|
||||
f[i2][1] -= dely * fbond;
|
||||
f[i2][2] -= delz * fbond;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
|
||||
if (evflag) ev_tally(i1, i2, nlocal, newton_bond, ebond, fbond, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
|
||||
@ -119,30 +118,32 @@ void BondTable::compute(int eflag, int vflag)
|
||||
void BondTable::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nbondtypes;
|
||||
const int np1 = atom->nbondtypes + 1;
|
||||
|
||||
memory->create(tabindex,n+1,"bond:tabindex");
|
||||
memory->create(r0,n+1,"bond:r0");
|
||||
memory->create(setflag,n+1,"bond:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
memory->create(tabindex, np1, "bond:tabindex");
|
||||
memory->create(r0, np1, "bond:r0");
|
||||
memory->create(setflag, np1, "bond:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondTable::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 2) error->all(FLERR,"Illegal bond_style command");
|
||||
if (narg != 2) error->all(FLERR, "Illegal bond_style command");
|
||||
|
||||
tabstyle = NONE;
|
||||
if (strcmp(arg[0],"linear") == 0) tabstyle = LINEAR;
|
||||
else if (strcmp(arg[0],"spline") == 0) tabstyle = SPLINE;
|
||||
else error->all(FLERR,"Unknown table style in bond style table");
|
||||
if (strcmp(arg[0], "linear") == 0)
|
||||
tabstyle = LINEAR;
|
||||
else if (strcmp(arg[0], "spline") == 0)
|
||||
tabstyle = SPLINE;
|
||||
else
|
||||
error->all(FLERR, "Unknown table style in bond style table");
|
||||
|
||||
tablength = utils::inumeric(FLERR,arg[1],false,lmp);
|
||||
if (tablength < 2) error->all(FLERR,"Illegal number of bond table entries");
|
||||
tablength = utils::inumeric(FLERR, arg[1], false, lmp);
|
||||
if (tablength < 2) error->all(FLERR, "Illegal number of bond table entries");
|
||||
|
||||
// delete old tables, since cannot just change settings
|
||||
|
||||
@ -150,8 +151,8 @@ void BondTable::settings(int narg, char **arg)
|
||||
memory->sfree(tables);
|
||||
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(tabindex);
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(tabindex);
|
||||
}
|
||||
allocated = 0;
|
||||
|
||||
@ -165,28 +166,27 @@ void BondTable::settings(int narg, char **arg)
|
||||
|
||||
void BondTable::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 3) error->all(FLERR,"Illegal bond_coeff command");
|
||||
if (narg != 3) error->all(FLERR, "Illegal bond_coeff command");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error);
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
|
||||
|
||||
int me;
|
||||
MPI_Comm_rank(world,&me);
|
||||
tables = (Table *)
|
||||
memory->srealloc(tables,(ntables+1)*sizeof(Table),"bond:tables");
|
||||
MPI_Comm_rank(world, &me);
|
||||
tables = (Table *) memory->srealloc(tables, (ntables + 1) * sizeof(Table), "bond:tables");
|
||||
Table *tb = &tables[ntables];
|
||||
null_table(tb);
|
||||
if (me == 0) read_table(tb,arg[1],arg[2]);
|
||||
if (me == 0) read_table(tb, arg[1], arg[2]);
|
||||
bcast_table(tb);
|
||||
|
||||
// error check on table parameters
|
||||
|
||||
if (tb->ninput <= 1) error->one(FLERR,"Invalid bond table length");
|
||||
if (tb->ninput <= 1) error->one(FLERR, "Invalid bond table length");
|
||||
|
||||
tb->lo = tb->rfile[0];
|
||||
tb->hi = tb->rfile[tb->ninput-1];
|
||||
if (tb->lo >= tb->hi) error->all(FLERR,"Bond table values are not increasing");
|
||||
tb->hi = tb->rfile[tb->ninput - 1];
|
||||
if (tb->lo >= tb->hi) error->all(FLERR, "Bond table values are not increasing");
|
||||
|
||||
// spline read-in and compute r,e,f vectors within table
|
||||
|
||||
@ -204,7 +204,7 @@ void BondTable::coeff(int narg, char **arg)
|
||||
}
|
||||
ntables++;
|
||||
|
||||
if (count == 0) error->all(FLERR,"Illegal bond_coeff command");
|
||||
if (count == 0) error->all(FLERR, "Illegal bond_coeff command");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -242,8 +242,8 @@ void BondTable::read_restart(FILE *fp)
|
||||
|
||||
void BondTable::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&tabstyle,sizeof(int),1,fp);
|
||||
fwrite(&tablength,sizeof(int),1,fp);
|
||||
fwrite(&tabstyle, sizeof(int), 1, fp);
|
||||
fwrite(&tablength, sizeof(int), 1, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -253,23 +253,22 @@ void BondTable::write_restart_settings(FILE *fp)
|
||||
void BondTable::read_restart_settings(FILE *fp)
|
||||
{
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&tablength,sizeof(int),1,fp,nullptr,error);
|
||||
utils::sfread(FLERR, &tabstyle, sizeof(int), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &tablength, sizeof(int), 1, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&tabstyle,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&tablength,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&tabstyle, 1, MPI_INT, 0, world);
|
||||
MPI_Bcast(&tablength, 1, MPI_INT, 0, world);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BondTable::single(int type, double rsq, int /*i*/, int /*j*/,
|
||||
double &fforce)
|
||||
double BondTable::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce)
|
||||
{
|
||||
double r = sqrt(rsq);
|
||||
double u;
|
||||
double mdu;
|
||||
uf_lookup(type,r,u,mdu);
|
||||
fforce = mdu/r;
|
||||
uf_lookup(type, r, u, mdu);
|
||||
fforce = mdu / r;
|
||||
return u;
|
||||
}
|
||||
|
||||
@ -311,20 +310,18 @@ void BondTable::read_table(Table *tb, char *file, char *keyword)
|
||||
TableFileReader reader(lmp, file, "bond");
|
||||
double emin = BIGNUM;
|
||||
|
||||
char * line = reader.find_section_start(keyword);
|
||||
char *line = reader.find_section_start(keyword);
|
||||
|
||||
if (!line) {
|
||||
error->one(FLERR,"Did not find keyword in table file");
|
||||
}
|
||||
if (!line) { error->one(FLERR, "Did not find keyword in table file"); }
|
||||
|
||||
// read args on 2nd line of section
|
||||
// allocate table arrays for file values
|
||||
|
||||
line = reader.next_line();
|
||||
param_extract(tb,line);
|
||||
memory->create(tb->rfile,tb->ninput,"bond:rfile");
|
||||
memory->create(tb->efile,tb->ninput,"bond:efile");
|
||||
memory->create(tb->ffile,tb->ninput,"bond:ffile");
|
||||
param_extract(tb, line);
|
||||
memory->create(tb->rfile, tb->ninput, "bond:rfile");
|
||||
memory->create(tb->efile, tb->ninput, "bond:efile");
|
||||
memory->create(tb->ffile, tb->ninput, "bond:ffile");
|
||||
|
||||
// read r,e,f table values from file
|
||||
|
||||
@ -359,33 +356,37 @@ void BondTable::read_table(Table *tb, char *file, char *keyword)
|
||||
// skip two end points since do not have surrounding secants
|
||||
// inflection point is where curvature changes sign
|
||||
|
||||
double r,e,f,rprev,rnext,eprev,enext,fleft,fright;
|
||||
double r, e, f, rprev, rnext, eprev, enext, fleft, fright;
|
||||
|
||||
int ferror = 0;
|
||||
for (int i = 1; i < tb->ninput-1; i++) {
|
||||
for (int i = 1; i < tb->ninput - 1; i++) {
|
||||
r = tb->rfile[i];
|
||||
rprev = tb->rfile[i-1];
|
||||
rnext = tb->rfile[i+1];
|
||||
rprev = tb->rfile[i - 1];
|
||||
rnext = tb->rfile[i + 1];
|
||||
e = tb->efile[i];
|
||||
eprev = tb->efile[i-1];
|
||||
enext = tb->efile[i+1];
|
||||
eprev = tb->efile[i - 1];
|
||||
enext = tb->efile[i + 1];
|
||||
f = tb->ffile[i];
|
||||
fleft = - (e-eprev) / (r-rprev);
|
||||
fright = - (enext-e) / (rnext-r);
|
||||
fleft = -(e - eprev) / (r - rprev);
|
||||
fright = -(enext - e) / (rnext - r);
|
||||
if (f < fleft && f < fright) ferror++;
|
||||
if (f > fleft && f > fright) ferror++;
|
||||
}
|
||||
|
||||
if (ferror) {
|
||||
error->warning(FLERR, "{} of {} force values in table are inconsistent with -dE/dr.\n"
|
||||
"WARNING: Should only be flagged at inflection points",ferror,tb->ninput);
|
||||
error->warning(FLERR,
|
||||
"{} of {} force values in table are inconsistent with -dE/dr.\n"
|
||||
"WARNING: Should only be flagged at inflection points",
|
||||
ferror, tb->ninput);
|
||||
}
|
||||
|
||||
// warn if data was read incompletely, e.g. columns were missing
|
||||
|
||||
if (cerror) {
|
||||
error->warning(FLERR, "{} of {} lines in table were incomplete or could not be"
|
||||
" parsed completely",cerror,tb->ninput);
|
||||
error->warning(FLERR,
|
||||
"{} of {} lines in table were incomplete or could not be"
|
||||
" parsed completely",
|
||||
cerror, tb->ninput);
|
||||
}
|
||||
}
|
||||
|
||||
@ -396,23 +397,22 @@ void BondTable::read_table(Table *tb, char *file, char *keyword)
|
||||
|
||||
void BondTable::spline_table(Table *tb)
|
||||
{
|
||||
memory->create(tb->e2file,tb->ninput,"bond:e2file");
|
||||
memory->create(tb->f2file,tb->ninput,"bond:f2file");
|
||||
memory->create(tb->e2file, tb->ninput, "bond:e2file");
|
||||
memory->create(tb->f2file, tb->ninput, "bond:f2file");
|
||||
|
||||
double ep0 = - tb->ffile[0];
|
||||
double epn = - tb->ffile[tb->ninput-1];
|
||||
spline(tb->rfile,tb->efile,tb->ninput,ep0,epn,tb->e2file);
|
||||
double ep0 = -tb->ffile[0];
|
||||
double epn = -tb->ffile[tb->ninput - 1];
|
||||
spline(tb->rfile, tb->efile, tb->ninput, ep0, epn, tb->e2file);
|
||||
|
||||
if (tb->fpflag == 0) {
|
||||
tb->fplo = (tb->ffile[1] - tb->ffile[0]) / (tb->rfile[1] - tb->rfile[0]);
|
||||
tb->fphi = (tb->ffile[tb->ninput-1] - tb->ffile[tb->ninput-2]) /
|
||||
(tb->rfile[tb->ninput-1] - tb->rfile[tb->ninput-2]);
|
||||
tb->fphi = (tb->ffile[tb->ninput - 1] - tb->ffile[tb->ninput - 2]) /
|
||||
(tb->rfile[tb->ninput - 1] - tb->rfile[tb->ninput - 2]);
|
||||
}
|
||||
|
||||
double fp0 = tb->fplo;
|
||||
double fpn = tb->fphi;
|
||||
spline(tb->rfile,tb->ffile,tb->ninput,fp0,fpn,tb->f2file);
|
||||
|
||||
spline(tb->rfile, tb->ffile, tb->ninput, fp0, fpn, tb->f2file);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -422,45 +422,45 @@ void BondTable::spline_table(Table *tb)
|
||||
void BondTable::compute_table(Table *tb)
|
||||
{
|
||||
// delta = table spacing for N-1 bins
|
||||
int tlm1 = tablength-1;
|
||||
int tlm1 = tablength - 1;
|
||||
|
||||
tb->delta = (tb->hi - tb->lo)/ tlm1;
|
||||
tb->invdelta = 1.0/tb->delta;
|
||||
tb->deltasq6 = tb->delta*tb->delta / 6.0;
|
||||
tb->delta = (tb->hi - tb->lo) / tlm1;
|
||||
tb->invdelta = 1.0 / tb->delta;
|
||||
tb->deltasq6 = tb->delta * tb->delta / 6.0;
|
||||
|
||||
// N-1 evenly spaced bins in r from min to max
|
||||
// r,e,f = value at lower edge of bin
|
||||
// de,df values = delta values of e,f
|
||||
// r,e,f are N in length so de,df arrays can compute difference
|
||||
|
||||
memory->create(tb->r,tablength,"bond:r");
|
||||
memory->create(tb->e,tablength,"bond:e");
|
||||
memory->create(tb->de,tablength,"bond:de");
|
||||
memory->create(tb->f,tablength,"bond:f");
|
||||
memory->create(tb->df,tablength,"bond:df");
|
||||
memory->create(tb->e2,tablength,"bond:e2");
|
||||
memory->create(tb->f2,tablength,"bond:f2");
|
||||
memory->create(tb->r, tablength, "bond:r");
|
||||
memory->create(tb->e, tablength, "bond:e");
|
||||
memory->create(tb->de, tablength, "bond:de");
|
||||
memory->create(tb->f, tablength, "bond:f");
|
||||
memory->create(tb->df, tablength, "bond:df");
|
||||
memory->create(tb->e2, tablength, "bond:e2");
|
||||
memory->create(tb->f2, tablength, "bond:f2");
|
||||
|
||||
double a;
|
||||
for (int i = 0; i < tablength; i++) {
|
||||
a = tb->lo + i*tb->delta;
|
||||
a = tb->lo + i * tb->delta;
|
||||
tb->r[i] = a;
|
||||
tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,a);
|
||||
tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,a);
|
||||
tb->e[i] = splint(tb->rfile, tb->efile, tb->e2file, tb->ninput, a);
|
||||
tb->f[i] = splint(tb->rfile, tb->ffile, tb->f2file, tb->ninput, a);
|
||||
}
|
||||
|
||||
for (int i = 0; i < tlm1; i++) {
|
||||
tb->de[i] = tb->e[i+1] - tb->e[i];
|
||||
tb->df[i] = tb->f[i+1] - tb->f[i];
|
||||
tb->de[i] = tb->e[i + 1] - tb->e[i];
|
||||
tb->df[i] = tb->f[i + 1] - tb->f[i];
|
||||
}
|
||||
// get final elements from linear extrapolation
|
||||
tb->de[tlm1] = 2.0*tb->de[tlm1-1] - tb->de[tlm1-2];
|
||||
tb->df[tlm1] = 2.0*tb->df[tlm1-1] - tb->df[tlm1-2];
|
||||
tb->de[tlm1] = 2.0 * tb->de[tlm1 - 1] - tb->de[tlm1 - 2];
|
||||
tb->df[tlm1] = 2.0 * tb->df[tlm1 - 1] - tb->df[tlm1 - 2];
|
||||
|
||||
double ep0 = - tb->f[0];
|
||||
double epn = - tb->f[tlm1];
|
||||
spline(tb->r,tb->e,tablength,ep0,epn,tb->e2);
|
||||
spline(tb->r,tb->f,tablength,tb->fplo,tb->fphi,tb->f2);
|
||||
double ep0 = -tb->f[0];
|
||||
double epn = -tb->f[tlm1];
|
||||
spline(tb->r, tb->e, tablength, ep0, epn, tb->e2);
|
||||
spline(tb->r, tb->f, tablength, tb->fplo, tb->fphi, tb->f2);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -490,14 +490,14 @@ void BondTable::param_extract(Table *tb, char *line)
|
||||
} else if (word == "EQ") {
|
||||
tb->r0 = values.next_double();
|
||||
} else {
|
||||
error->one(FLERR,"Invalid keyword in bond table parameters");
|
||||
error->one(FLERR, "Invalid keyword in bond table parameters");
|
||||
}
|
||||
}
|
||||
} catch(TokenizerException &e) {
|
||||
} catch (TokenizerException &e) {
|
||||
error->one(FLERR, e.what());
|
||||
}
|
||||
|
||||
if (tb->ninput == 0) error->one(FLERR,"Bond table parameters did not set N");
|
||||
if (tb->ninput == 0) error->one(FLERR, "Bond table parameters did not set N");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -508,25 +508,25 @@ void BondTable::param_extract(Table *tb, char *line)
|
||||
|
||||
void BondTable::bcast_table(Table *tb)
|
||||
{
|
||||
MPI_Bcast(&tb->ninput,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&tb->r0,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&tb->ninput, 1, MPI_INT, 0, world);
|
||||
MPI_Bcast(&tb->r0, 1, MPI_DOUBLE, 0, world);
|
||||
|
||||
int me;
|
||||
MPI_Comm_rank(world,&me);
|
||||
MPI_Comm_rank(world, &me);
|
||||
if (me > 0) {
|
||||
memory->create(tb->rfile,tb->ninput,"angle:rfile");
|
||||
memory->create(tb->efile,tb->ninput,"angle:efile");
|
||||
memory->create(tb->ffile,tb->ninput,"angle:ffile");
|
||||
memory->create(tb->rfile, tb->ninput, "angle:rfile");
|
||||
memory->create(tb->efile, tb->ninput, "angle:efile");
|
||||
memory->create(tb->ffile, tb->ninput, "angle:ffile");
|
||||
}
|
||||
|
||||
MPI_Bcast(tb->rfile,tb->ninput,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(tb->efile,tb->ninput,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(tb->ffile,tb->ninput,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(tb->rfile, tb->ninput, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(tb->efile, tb->ninput, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(tb->ffile, tb->ninput, MPI_DOUBLE, 0, world);
|
||||
|
||||
MPI_Bcast(&tb->fpflag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&tb->fpflag, 1, MPI_INT, 0, world);
|
||||
if (tb->fpflag) {
|
||||
MPI_Bcast(&tb->fplo,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&tb->fphi,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&tb->fplo, 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&tb->fphi, 1, MPI_DOUBLE, 0, world);
|
||||
}
|
||||
}
|
||||
|
||||
@ -534,54 +534,58 @@ void BondTable::bcast_table(Table *tb)
|
||||
spline and splint routines modified from Numerical Recipes
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondTable::spline(double *x, double *y, int n,
|
||||
double yp1, double ypn, double *y2)
|
||||
void BondTable::spline(double *x, double *y, int n, double yp1, double ypn, double *y2)
|
||||
{
|
||||
int i,k;
|
||||
double p,qn,sig,un;
|
||||
int i, k;
|
||||
double p, qn, sig, un;
|
||||
double *u = new double[n];
|
||||
|
||||
if (yp1 > 0.99e300) y2[0] = u[0] = 0.0;
|
||||
if (yp1 > 0.99e300)
|
||||
y2[0] = u[0] = 0.0;
|
||||
else {
|
||||
y2[0] = -0.5;
|
||||
u[0] = (3.0/(x[1]-x[0])) * ((y[1]-y[0]) / (x[1]-x[0]) - yp1);
|
||||
u[0] = (3.0 / (x[1] - x[0])) * ((y[1] - y[0]) / (x[1] - x[0]) - yp1);
|
||||
}
|
||||
for (i = 1; i < n-1; i++) {
|
||||
sig = (x[i]-x[i-1]) / (x[i+1]-x[i-1]);
|
||||
p = sig*y2[i-1] + 2.0;
|
||||
y2[i] = (sig-1.0) / p;
|
||||
u[i] = (y[i+1]-y[i]) / (x[i+1]-x[i]) - (y[i]-y[i-1]) / (x[i]-x[i-1]);
|
||||
u[i] = (6.0*u[i] / (x[i+1]-x[i-1]) - sig*u[i-1]) / p;
|
||||
for (i = 1; i < n - 1; i++) {
|
||||
sig = (x[i] - x[i - 1]) / (x[i + 1] - x[i - 1]);
|
||||
p = sig * y2[i - 1] + 2.0;
|
||||
y2[i] = (sig - 1.0) / p;
|
||||
u[i] = (y[i + 1] - y[i]) / (x[i + 1] - x[i]) - (y[i] - y[i - 1]) / (x[i] - x[i - 1]);
|
||||
u[i] = (6.0 * u[i] / (x[i + 1] - x[i - 1]) - sig * u[i - 1]) / p;
|
||||
}
|
||||
if (ypn > 0.99e300) qn = un = 0.0;
|
||||
if (ypn > 0.99e300)
|
||||
qn = un = 0.0;
|
||||
else {
|
||||
qn = 0.5;
|
||||
un = (3.0/(x[n-1]-x[n-2])) * (ypn - (y[n-1]-y[n-2]) / (x[n-1]-x[n-2]));
|
||||
un = (3.0 / (x[n - 1] - x[n - 2])) * (ypn - (y[n - 1] - y[n - 2]) / (x[n - 1] - x[n - 2]));
|
||||
}
|
||||
y2[n-1] = (un-qn*u[n-2]) / (qn*y2[n-2] + 1.0);
|
||||
for (k = n-2; k >= 0; k--) y2[k] = y2[k]*y2[k+1] + u[k];
|
||||
y2[n - 1] = (un - qn * u[n - 2]) / (qn * y2[n - 2] + 1.0);
|
||||
for (k = n - 2; k >= 0; k--) y2[k] = y2[k] * y2[k + 1] + u[k];
|
||||
|
||||
delete [] u;
|
||||
delete[] u;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BondTable::splint(double *xa, double *ya, double *y2a, int n, double x)
|
||||
{
|
||||
int klo,khi,k;
|
||||
double h,b,a,y;
|
||||
int klo, khi, k;
|
||||
double h, b, a, y;
|
||||
|
||||
klo = 0;
|
||||
khi = n-1;
|
||||
while (khi-klo > 1) {
|
||||
k = (khi+klo) >> 1;
|
||||
if (xa[k] > x) khi = k;
|
||||
else klo = k;
|
||||
khi = n - 1;
|
||||
while (khi - klo > 1) {
|
||||
k = (khi + klo) >> 1;
|
||||
if (xa[k] > x)
|
||||
khi = k;
|
||||
else
|
||||
klo = k;
|
||||
}
|
||||
h = xa[khi]-xa[klo];
|
||||
a = (xa[khi]-x) / h;
|
||||
b = (x-xa[klo]) / h;
|
||||
y = a*ya[klo] + b*ya[khi] + ((a*a*a-a)*y2a[klo] + (b*b*b-b)*y2a[khi]) * (h*h)/6.0;
|
||||
h = xa[khi] - xa[klo];
|
||||
a = (xa[khi] - x) / h;
|
||||
b = (x - xa[klo]) / h;
|
||||
y = a * ya[klo] + b * ya[khi] +
|
||||
((a * a * a - a) * y2a[klo] + (b * b * b - b) * y2a[khi]) * (h * h) / 6.0;
|
||||
return y;
|
||||
}
|
||||
|
||||
@ -592,30 +596,28 @@ double BondTable::splint(double *xa, double *ya, double *y2a, int n, double x)
|
||||
|
||||
void BondTable::uf_lookup(int type, double x, double &u, double &f)
|
||||
{
|
||||
if (!std::isfinite(x)) {
|
||||
error->one(FLERR,"Illegal bond in bond style table");
|
||||
}
|
||||
if (!std::isfinite(x)) { error->one(FLERR, "Illegal bond in bond style table"); }
|
||||
|
||||
double fraction,a,b;
|
||||
double fraction, a, b;
|
||||
const Table *tb = &tables[tabindex[type]];
|
||||
const int itable = static_cast<int> ((x - tb->lo) * tb->invdelta);
|
||||
const int itable = static_cast<int>((x - tb->lo) * tb->invdelta);
|
||||
if (itable < 0)
|
||||
error->one(FLERR,"Bond length < table inner cutoff: type {} length {:.8}",type,x);
|
||||
error->one(FLERR, "Bond length < table inner cutoff: type {} length {:.8}", type, x);
|
||||
else if (itable >= tablength)
|
||||
error->one(FLERR,"Bond length > table outer cutoff: type {} length {:.8}",type,x);
|
||||
error->one(FLERR, "Bond length > table outer cutoff: type {} length {:.8}", type, x);
|
||||
|
||||
if (tabstyle == LINEAR) {
|
||||
fraction = (x - tb->r[itable]) * tb->invdelta;
|
||||
u = tb->e[itable] + fraction*tb->de[itable];
|
||||
f = tb->f[itable] + fraction*tb->df[itable];
|
||||
u = tb->e[itable] + fraction * tb->de[itable];
|
||||
f = tb->f[itable] + fraction * tb->df[itable];
|
||||
} else if (tabstyle == SPLINE) {
|
||||
fraction = (x - tb->r[itable]) * tb->invdelta;
|
||||
|
||||
b = (x - tb->r[itable]) * tb->invdelta;
|
||||
a = 1.0 - b;
|
||||
u = a * tb->e[itable] + b * tb->e[itable+1] +
|
||||
((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) * tb->deltasq6;
|
||||
f = a * tb->f[itable] + b * tb->f[itable+1] +
|
||||
((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) * tb->deltasq6;
|
||||
u = a * tb->e[itable] + b * tb->e[itable + 1] +
|
||||
((a * a * a - a) * tb->e2[itable] + (b * b * b - b) * tb->e2[itable + 1]) * tb->deltasq6;
|
||||
f = a * tb->f[itable] + b * tb->f[itable + 1] +
|
||||
((a * a * a - a) * tb->f2[itable] + (b * b * b - b) * tb->f2[itable + 1]) * tb->deltasq6;
|
||||
}
|
||||
}
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -32,13 +31,13 @@
|
||||
#include <cmath>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
using MathConst::DEG2RAD;
|
||||
|
||||
#define TOLERANCE 0.05
|
||||
static constexpr double TOLERANCE = 0.05;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DihedralCharmm::DihedralCharmm(LAMMPS *lmp) : Dihedral(lmp)
|
||||
DihedralCharmm::DihedralCharmm(LAMMPS *_lmp) : Dihedral(_lmp)
|
||||
{
|
||||
weightflag = 0;
|
||||
writedata = 1;
|
||||
@ -63,19 +62,19 @@ DihedralCharmm::~DihedralCharmm()
|
||||
|
||||
void DihedralCharmm::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,i3,i4,i,m,n,type;
|
||||
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
|
||||
double edihedral,f1[3],f2[3],f3[3],f4[3];
|
||||
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
|
||||
double df,df1,ddf1,fg,hg,fga,hgb,gaa,gbb;
|
||||
double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
|
||||
double c,s,p,sx2,sy2,sz2;
|
||||
int itype,jtype;
|
||||
double delx,dely,delz,rsq,r2inv,r6inv;
|
||||
double forcecoul,forcelj,fpair,ecoul,evdwl;
|
||||
int i1, i2, i3, i4, i, m, n, type;
|
||||
double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z, vb2xm, vb2ym, vb2zm;
|
||||
double edihedral, f1[3], f2[3], f3[3], f4[3];
|
||||
double ax, ay, az, bx, by, bz, rasq, rbsq, rgsq, rg, rginv, ra2inv, rb2inv, rabinv;
|
||||
double df, df1, ddf1, fg, hg, fga, hgb, gaa, gbb;
|
||||
double dtfx, dtfy, dtfz, dtgx, dtgy, dtgz, dthx, dthy, dthz;
|
||||
double c, s, p, sx2, sy2, sz2;
|
||||
int itype, jtype;
|
||||
double delx, dely, delz, rsq, r2inv, r6inv;
|
||||
double forcecoul, forcelj, fpair, ecoul, evdwl;
|
||||
|
||||
edihedral = evdwl = ecoul = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
// insure pair->ev_tally() will use 1-4 virial contribution
|
||||
|
||||
@ -121,31 +120,30 @@ void DihedralCharmm::compute(int eflag, int vflag)
|
||||
vb3y = x[i4][1] - x[i3][1];
|
||||
vb3z = x[i4][2] - x[i3][2];
|
||||
|
||||
ax = vb1y*vb2zm - vb1z*vb2ym;
|
||||
ay = vb1z*vb2xm - vb1x*vb2zm;
|
||||
az = vb1x*vb2ym - vb1y*vb2xm;
|
||||
bx = vb3y*vb2zm - vb3z*vb2ym;
|
||||
by = vb3z*vb2xm - vb3x*vb2zm;
|
||||
bz = vb3x*vb2ym - vb3y*vb2xm;
|
||||
ax = vb1y * vb2zm - vb1z * vb2ym;
|
||||
ay = vb1z * vb2xm - vb1x * vb2zm;
|
||||
az = vb1x * vb2ym - vb1y * vb2xm;
|
||||
bx = vb3y * vb2zm - vb3z * vb2ym;
|
||||
by = vb3z * vb2xm - vb3x * vb2zm;
|
||||
bz = vb3x * vb2ym - vb3y * vb2xm;
|
||||
|
||||
rasq = ax*ax + ay*ay + az*az;
|
||||
rbsq = bx*bx + by*by + bz*bz;
|
||||
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
|
||||
rasq = ax * ax + ay * ay + az * az;
|
||||
rbsq = bx * bx + by * by + bz * bz;
|
||||
rgsq = vb2xm * vb2xm + vb2ym * vb2ym + vb2zm * vb2zm;
|
||||
rg = sqrt(rgsq);
|
||||
|
||||
rginv = ra2inv = rb2inv = 0.0;
|
||||
if (rg > 0) rginv = 1.0/rg;
|
||||
if (rasq > 0) ra2inv = 1.0/rasq;
|
||||
if (rbsq > 0) rb2inv = 1.0/rbsq;
|
||||
rabinv = sqrt(ra2inv*rb2inv);
|
||||
if (rg > 0) rginv = 1.0 / rg;
|
||||
if (rasq > 0) ra2inv = 1.0 / rasq;
|
||||
if (rbsq > 0) rb2inv = 1.0 / rbsq;
|
||||
rabinv = sqrt(ra2inv * rb2inv);
|
||||
|
||||
c = (ax*bx + ay*by + az*bz)*rabinv;
|
||||
s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
|
||||
c = (ax * bx + ay * by + az * bz) * rabinv;
|
||||
s = rg * rabinv * (ax * vb3x + ay * vb3y + az * vb3z);
|
||||
|
||||
// error check
|
||||
|
||||
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE))
|
||||
problem(FLERR, i1, i2, i3, i4);
|
||||
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) problem(FLERR, i1, i2, i3, i4);
|
||||
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
@ -155,13 +153,13 @@ void DihedralCharmm::compute(int eflag, int vflag)
|
||||
ddf1 = df1 = 0.0;
|
||||
|
||||
for (i = 0; i < m; i++) {
|
||||
ddf1 = p*c - df1*s;
|
||||
df1 = p*s + df1*c;
|
||||
ddf1 = p * c - df1 * s;
|
||||
df1 = p * s + df1 * c;
|
||||
p = ddf1;
|
||||
}
|
||||
|
||||
p = p*cos_shift[type] + df1*sin_shift[type];
|
||||
df1 = df1*cos_shift[type] - ddf1*sin_shift[type];
|
||||
p = p * cos_shift[type] + df1 * sin_shift[type];
|
||||
df1 = df1 * cos_shift[type] - ddf1 * sin_shift[type];
|
||||
df1 *= -m;
|
||||
p += 1.0;
|
||||
|
||||
@ -172,40 +170,40 @@ void DihedralCharmm::compute(int eflag, int vflag)
|
||||
|
||||
if (eflag) edihedral = k[type] * p;
|
||||
|
||||
fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
|
||||
hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
|
||||
fga = fg*ra2inv*rginv;
|
||||
hgb = hg*rb2inv*rginv;
|
||||
gaa = -ra2inv*rg;
|
||||
gbb = rb2inv*rg;
|
||||
fg = vb1x * vb2xm + vb1y * vb2ym + vb1z * vb2zm;
|
||||
hg = vb3x * vb2xm + vb3y * vb2ym + vb3z * vb2zm;
|
||||
fga = fg * ra2inv * rginv;
|
||||
hgb = hg * rb2inv * rginv;
|
||||
gaa = -ra2inv * rg;
|
||||
gbb = rb2inv * rg;
|
||||
|
||||
dtfx = gaa*ax;
|
||||
dtfy = gaa*ay;
|
||||
dtfz = gaa*az;
|
||||
dtgx = fga*ax - hgb*bx;
|
||||
dtgy = fga*ay - hgb*by;
|
||||
dtgz = fga*az - hgb*bz;
|
||||
dthx = gbb*bx;
|
||||
dthy = gbb*by;
|
||||
dthz = gbb*bz;
|
||||
dtfx = gaa * ax;
|
||||
dtfy = gaa * ay;
|
||||
dtfz = gaa * az;
|
||||
dtgx = fga * ax - hgb * bx;
|
||||
dtgy = fga * ay - hgb * by;
|
||||
dtgz = fga * az - hgb * bz;
|
||||
dthx = gbb * bx;
|
||||
dthy = gbb * by;
|
||||
dthz = gbb * bz;
|
||||
|
||||
df = -k[type] * df1;
|
||||
|
||||
sx2 = df*dtgx;
|
||||
sy2 = df*dtgy;
|
||||
sz2 = df*dtgz;
|
||||
sx2 = df * dtgx;
|
||||
sy2 = df * dtgy;
|
||||
sz2 = df * dtgz;
|
||||
|
||||
f1[0] = df*dtfx;
|
||||
f1[1] = df*dtfy;
|
||||
f1[2] = df*dtfz;
|
||||
f1[0] = df * dtfx;
|
||||
f1[1] = df * dtfy;
|
||||
f1[2] = df * dtfz;
|
||||
|
||||
f2[0] = sx2 - f1[0];
|
||||
f2[1] = sy2 - f1[1];
|
||||
f2[2] = sz2 - f1[2];
|
||||
|
||||
f4[0] = df*dthx;
|
||||
f4[1] = df*dthy;
|
||||
f4[2] = df*dthz;
|
||||
f4[0] = df * dthx;
|
||||
f4[1] = df * dthy;
|
||||
f4[2] = df * dthz;
|
||||
|
||||
f3[0] = -sx2 - f4[0];
|
||||
f3[1] = -sy2 - f4[1];
|
||||
@ -238,8 +236,8 @@ void DihedralCharmm::compute(int eflag, int vflag)
|
||||
}
|
||||
|
||||
if (evflag)
|
||||
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
|
||||
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
|
||||
ev_tally(i1, i2, i3, i4, nlocal, newton_bond, edihedral, f1, f3, f4, vb1x, vb1y, vb1z, vb2x,
|
||||
vb2y, vb2z, vb3x, vb3y, vb3z);
|
||||
|
||||
// 1-4 LJ and Coulomb interactions
|
||||
// tally energy/virial in pair, using newton_bond as newton flag
|
||||
@ -251,34 +249,36 @@ void DihedralCharmm::compute(int eflag, int vflag)
|
||||
delx = x[i1][0] - x[i4][0];
|
||||
dely = x[i1][1] - x[i4][1];
|
||||
delz = x[i1][2] - x[i4][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
r2inv = 1.0/rsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
r2inv = 1.0 / rsq;
|
||||
r6inv = r2inv * r2inv * r2inv;
|
||||
|
||||
if (implicit) forcecoul = qqrd2e * q[i1]*q[i4]*r2inv;
|
||||
else forcecoul = qqrd2e * q[i1]*q[i4]*sqrt(r2inv);
|
||||
forcelj = r6inv * (lj14_1[itype][jtype]*r6inv - lj14_2[itype][jtype]);
|
||||
fpair = weight[type] * (forcelj+forcecoul)*r2inv;
|
||||
if (implicit)
|
||||
forcecoul = qqrd2e * q[i1] * q[i4] * r2inv;
|
||||
else
|
||||
forcecoul = qqrd2e * q[i1] * q[i4] * sqrt(r2inv);
|
||||
forcelj = r6inv * (lj14_1[itype][jtype] * r6inv - lj14_2[itype][jtype]);
|
||||
fpair = weight[type] * (forcelj + forcecoul) * r2inv;
|
||||
|
||||
if (eflag) {
|
||||
ecoul = weight[type] * forcecoul;
|
||||
evdwl = r6inv * (lj14_3[itype][jtype]*r6inv - lj14_4[itype][jtype]);
|
||||
evdwl = r6inv * (lj14_3[itype][jtype] * r6inv - lj14_4[itype][jtype]);
|
||||
evdwl *= weight[type];
|
||||
}
|
||||
|
||||
if (newton_bond || i1 < nlocal) {
|
||||
f[i1][0] += delx*fpair;
|
||||
f[i1][1] += dely*fpair;
|
||||
f[i1][2] += delz*fpair;
|
||||
f[i1][0] += delx * fpair;
|
||||
f[i1][1] += dely * fpair;
|
||||
f[i1][2] += delz * fpair;
|
||||
}
|
||||
if (newton_bond || i4 < nlocal) {
|
||||
f[i4][0] -= delx*fpair;
|
||||
f[i4][1] -= dely*fpair;
|
||||
f[i4][2] -= delz*fpair;
|
||||
f[i4][0] -= delx * fpair;
|
||||
f[i4][1] -= dely * fpair;
|
||||
f[i4][2] -= delz * fpair;
|
||||
}
|
||||
|
||||
if (evflag) force->pair->ev_tally(i1,i4,nlocal,newton_bond,
|
||||
evdwl,ecoul,fpair,delx,dely,delz);
|
||||
if (evflag)
|
||||
force->pair->ev_tally(i1, i4, nlocal, newton_bond, evdwl, ecoul, fpair, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -288,17 +288,17 @@ void DihedralCharmm::compute(int eflag, int vflag)
|
||||
void DihedralCharmm::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ndihedraltypes;
|
||||
const int np1 = atom->ndihedraltypes + 1;
|
||||
|
||||
memory->create(k,n+1,"dihedral:k");
|
||||
memory->create(multiplicity,n+1,"dihedral:multiplicity");
|
||||
memory->create(shift,n+1,"dihedral:shift");
|
||||
memory->create(cos_shift,n+1,"dihedral:cos_shift");
|
||||
memory->create(sin_shift,n+1,"dihedral:sin_shift");
|
||||
memory->create(weight,n+1,"dihedral:weight");
|
||||
memory->create(k, np1, "dihedral:k");
|
||||
memory->create(multiplicity, np1, "dihedral:multiplicity");
|
||||
memory->create(shift, np1, "dihedral:shift");
|
||||
memory->create(cos_shift, np1, "dihedral:cos_shift");
|
||||
memory->create(sin_shift, np1, "dihedral:sin_shift");
|
||||
memory->create(weight, np1, "dihedral:weight");
|
||||
|
||||
memory->create(setflag,n+1,"dihedral:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
memory->create(setflag, np1, "dihedral:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -307,40 +307,40 @@ void DihedralCharmm::allocate()
|
||||
|
||||
void DihedralCharmm::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 5) error->all(FLERR,"Incorrect args for dihedral coefficients");
|
||||
if (narg != 5) error->all(FLERR, "Incorrect args for dihedral coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
utils::bounds(FLERR,arg[0],1,atom->ndihedraltypes,ilo,ihi,error);
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->ndihedraltypes, ilo, ihi, error);
|
||||
|
||||
// require integer values of shift for backwards compatibility
|
||||
// arbitrary phase angle shift could be allowed, but would break
|
||||
// backwards compatibility and is probably not needed
|
||||
|
||||
double k_one = utils::numeric(FLERR,arg[1],false,lmp);
|
||||
int multiplicity_one = utils::inumeric(FLERR,arg[2],false,lmp);
|
||||
int shift_one = utils::inumeric(FLERR,arg[3],false,lmp);
|
||||
double weight_one = utils::numeric(FLERR,arg[4],false,lmp);
|
||||
double k_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
int multiplicity_one = utils::inumeric(FLERR, arg[2], false, lmp);
|
||||
int shift_one = utils::inumeric(FLERR, arg[3], false, lmp);
|
||||
double weight_one = utils::numeric(FLERR, arg[4], false, lmp);
|
||||
|
||||
if (multiplicity_one < 0)
|
||||
error->all(FLERR,"Incorrect multiplicity arg for dihedral coefficients");
|
||||
error->all(FLERR, "Incorrect multiplicity arg for dihedral coefficients");
|
||||
if (weight_one < 0.0 || weight_one > 1.0)
|
||||
error->all(FLERR,"Incorrect weight arg for dihedral coefficients");
|
||||
if (weight_one > 0.0) weightflag=1;
|
||||
error->all(FLERR, "Incorrect weight arg for dihedral coefficients");
|
||||
if (weight_one > 0.0) weightflag = 1;
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
k[i] = k_one;
|
||||
shift[i] = shift_one;
|
||||
cos_shift[i] = cos(MY_PI*shift_one/180.0);
|
||||
sin_shift[i] = sin(MY_PI*shift_one/180.0);
|
||||
cos_shift[i] = cos(DEG2RAD * shift_one);
|
||||
sin_shift[i] = sin(DEG2RAD * shift_one);
|
||||
multiplicity[i] = multiplicity_one;
|
||||
weight[i] = weight_one;
|
||||
setflag[i] = 1;
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -349,14 +349,12 @@ void DihedralCharmm::coeff(int narg, char **arg)
|
||||
|
||||
void DihedralCharmm::init_style()
|
||||
{
|
||||
if (utils::strmatch(update->integrate_style,"^respa")) {
|
||||
if (utils::strmatch(update->integrate_style, "^respa")) {
|
||||
Respa *r = (Respa *) update->integrate;
|
||||
if (r->level_pair >= 0 && (r->level_pair != r->level_dihedral))
|
||||
error->all(FLERR,"Dihedral style charmm must be set to same"
|
||||
" r-RESPA level as 'pair'");
|
||||
error->all(FLERR, "Dihedral style charmm must be set to same r-RESPA level as 'pair'");
|
||||
if (r->level_outer >= 0 && (r->level_outer != r->level_dihedral))
|
||||
error->all(FLERR,"Dihedral style charmm must be set to same"
|
||||
" r-RESPA level as 'outer'");
|
||||
error->all(FLERR, "Dihedral style charmm must be set to same r-RESPA level as 'outer'");
|
||||
}
|
||||
|
||||
// insure use of CHARMM pair_style if any weight factors are non-zero
|
||||
@ -366,19 +364,20 @@ void DihedralCharmm::init_style()
|
||||
if (weightflag) {
|
||||
|
||||
if ((force->special_lj[3] != 0.0) || (force->special_coul[3] != 0.0))
|
||||
error->all(FLERR,"Must use 'special_bonds charmm' with"
|
||||
" dihedral style charmm for use with CHARMM pair styles");
|
||||
error->all(FLERR,
|
||||
"Must use 'special_bonds charmm' with dihedral "
|
||||
"style charmm for use with CHARMM pair styles");
|
||||
|
||||
int itmp;
|
||||
if (force->pair == nullptr)
|
||||
error->all(FLERR,"Dihedral charmm is incompatible with Pair style");
|
||||
lj14_1 = (double **) force->pair->extract("lj14_1",itmp);
|
||||
lj14_2 = (double **) force->pair->extract("lj14_2",itmp);
|
||||
lj14_3 = (double **) force->pair->extract("lj14_3",itmp);
|
||||
lj14_4 = (double **) force->pair->extract("lj14_4",itmp);
|
||||
int *ptr = (int *) force->pair->extract("implicit",itmp);
|
||||
error->all(FLERR, "Dihedral charmm is incompatible with Pair style");
|
||||
lj14_1 = (double **) force->pair->extract("lj14_1", itmp);
|
||||
lj14_2 = (double **) force->pair->extract("lj14_2", itmp);
|
||||
lj14_3 = (double **) force->pair->extract("lj14_3", itmp);
|
||||
lj14_4 = (double **) force->pair->extract("lj14_4", itmp);
|
||||
int *ptr = (int *) force->pair->extract("implicit", itmp);
|
||||
if (!lj14_1 || !lj14_2 || !lj14_3 || !lj14_4 || !ptr)
|
||||
error->all(FLERR,"Dihedral charmm is incompatible with Pair style");
|
||||
error->all(FLERR, "Dihedral charmm is incompatible with Pair style");
|
||||
implicit = *ptr;
|
||||
}
|
||||
}
|
||||
@ -389,11 +388,11 @@ void DihedralCharmm::init_style()
|
||||
|
||||
void DihedralCharmm::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&k[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fwrite(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
|
||||
fwrite(&shift[1],sizeof(int),atom->ndihedraltypes,fp);
|
||||
fwrite(&weight[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fwrite(&weightflag,sizeof(int),1,fp);
|
||||
fwrite(&k[1], sizeof(double), atom->ndihedraltypes, fp);
|
||||
fwrite(&multiplicity[1], sizeof(int), atom->ndihedraltypes, fp);
|
||||
fwrite(&shift[1], sizeof(int), atom->ndihedraltypes, fp);
|
||||
fwrite(&weight[1], sizeof(double), atom->ndihedraltypes, fp);
|
||||
fwrite(&weightflag, sizeof(int), 1, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -405,22 +404,22 @@ void DihedralCharmm::read_restart(FILE *fp)
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR,&k[1],sizeof(double),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&shift[1],sizeof(int),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&weight[1],sizeof(double),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&weightflag,sizeof(int),1,fp,nullptr,error);
|
||||
utils::sfread(FLERR, &k[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &multiplicity[1], sizeof(int), atom->ndihedraltypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &shift[1], sizeof(int), atom->ndihedraltypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &weight[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &weightflag, sizeof(int), 1, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&multiplicity[1],atom->ndihedraltypes,MPI_INT,0,world);
|
||||
MPI_Bcast(&shift[1],atom->ndihedraltypes,MPI_INT,0,world);
|
||||
MPI_Bcast(&weight[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&weightflag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&k[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&multiplicity[1], atom->ndihedraltypes, MPI_INT, 0, world);
|
||||
MPI_Bcast(&shift[1], atom->ndihedraltypes, MPI_INT, 0, world);
|
||||
MPI_Bcast(&weight[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&weightflag, 1, MPI_INT, 0, world);
|
||||
|
||||
for (int i = 1; i <= atom->ndihedraltypes; i++) {
|
||||
setflag[i] = 1;
|
||||
cos_shift[i] = cos(MY_PI*shift[i]/180.0);
|
||||
sin_shift[i] = sin(MY_PI*shift[i]/180.0);
|
||||
cos_shift[i] = cos(DEG2RAD * shift[i]);
|
||||
sin_shift[i] = sin(DEG2RAD * shift[i]);
|
||||
}
|
||||
}
|
||||
|
||||
@ -431,6 +430,5 @@ void DihedralCharmm::read_restart(FILE *fp)
|
||||
void DihedralCharmm::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ndihedraltypes; i++)
|
||||
fprintf(fp,"%d %g %d %d %g\n",i,k[i],multiplicity[i],shift[i],weight[i]);
|
||||
fprintf(fp, "%d %g %d %d %g\n", i, k[i], multiplicity[i], shift[i], weight[i]);
|
||||
}
|
||||
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -35,13 +34,13 @@
|
||||
#include <cmath>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
using MathConst::DEG2RAD;
|
||||
|
||||
#define TOLERANCE 0.05
|
||||
static constexpr double TOLERANCE = 0.05;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DihedralCharmmfsw::DihedralCharmmfsw(LAMMPS *lmp) : Dihedral(lmp)
|
||||
DihedralCharmmfsw::DihedralCharmmfsw(LAMMPS *_lmp) : Dihedral(_lmp)
|
||||
{
|
||||
weightflag = 0;
|
||||
writedata = 1;
|
||||
@ -66,19 +65,19 @@ DihedralCharmmfsw::~DihedralCharmmfsw()
|
||||
|
||||
void DihedralCharmmfsw::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,i3,i4,i,m,n,type;
|
||||
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
|
||||
double edihedral,f1[3],f2[3],f3[3],f4[3];
|
||||
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
|
||||
double df,df1,ddf1,fg,hg,fga,hgb,gaa,gbb;
|
||||
double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
|
||||
double c,s,p,sx2,sy2,sz2;
|
||||
int itype,jtype;
|
||||
double delx,dely,delz,rsq,r2inv,r6inv,r;
|
||||
double forcecoul,forcelj,fpair,ecoul,evdwl;
|
||||
int i1, i2, i3, i4, i, m, n, type;
|
||||
double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z, vb2xm, vb2ym, vb2zm;
|
||||
double edihedral, f1[3], f2[3], f3[3], f4[3];
|
||||
double ax, ay, az, bx, by, bz, rasq, rbsq, rgsq, rg, rginv, ra2inv, rb2inv, rabinv;
|
||||
double df, df1, ddf1, fg, hg, fga, hgb, gaa, gbb;
|
||||
double dtfx, dtfy, dtfz, dtgx, dtgy, dtgz, dthx, dthy, dthz;
|
||||
double c, s, p, sx2, sy2, sz2;
|
||||
int itype, jtype;
|
||||
double delx, dely, delz, rsq, r2inv, r6inv, r;
|
||||
double forcecoul, forcelj, fpair, ecoul, evdwl;
|
||||
|
||||
edihedral = evdwl = ecoul = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
// insure pair->ev_tally() will use 1-4 virial contribution
|
||||
|
||||
@ -124,31 +123,30 @@ void DihedralCharmmfsw::compute(int eflag, int vflag)
|
||||
vb3y = x[i4][1] - x[i3][1];
|
||||
vb3z = x[i4][2] - x[i3][2];
|
||||
|
||||
ax = vb1y*vb2zm - vb1z*vb2ym;
|
||||
ay = vb1z*vb2xm - vb1x*vb2zm;
|
||||
az = vb1x*vb2ym - vb1y*vb2xm;
|
||||
bx = vb3y*vb2zm - vb3z*vb2ym;
|
||||
by = vb3z*vb2xm - vb3x*vb2zm;
|
||||
bz = vb3x*vb2ym - vb3y*vb2xm;
|
||||
ax = vb1y * vb2zm - vb1z * vb2ym;
|
||||
ay = vb1z * vb2xm - vb1x * vb2zm;
|
||||
az = vb1x * vb2ym - vb1y * vb2xm;
|
||||
bx = vb3y * vb2zm - vb3z * vb2ym;
|
||||
by = vb3z * vb2xm - vb3x * vb2zm;
|
||||
bz = vb3x * vb2ym - vb3y * vb2xm;
|
||||
|
||||
rasq = ax*ax + ay*ay + az*az;
|
||||
rbsq = bx*bx + by*by + bz*bz;
|
||||
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
|
||||
rasq = ax * ax + ay * ay + az * az;
|
||||
rbsq = bx * bx + by * by + bz * bz;
|
||||
rgsq = vb2xm * vb2xm + vb2ym * vb2ym + vb2zm * vb2zm;
|
||||
rg = sqrt(rgsq);
|
||||
|
||||
rginv = ra2inv = rb2inv = 0.0;
|
||||
if (rg > 0) rginv = 1.0/rg;
|
||||
if (rasq > 0) ra2inv = 1.0/rasq;
|
||||
if (rbsq > 0) rb2inv = 1.0/rbsq;
|
||||
rabinv = sqrt(ra2inv*rb2inv);
|
||||
if (rg > 0) rginv = 1.0 / rg;
|
||||
if (rasq > 0) ra2inv = 1.0 / rasq;
|
||||
if (rbsq > 0) rb2inv = 1.0 / rbsq;
|
||||
rabinv = sqrt(ra2inv * rb2inv);
|
||||
|
||||
c = (ax*bx + ay*by + az*bz)*rabinv;
|
||||
s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
|
||||
c = (ax * bx + ay * by + az * bz) * rabinv;
|
||||
s = rg * rabinv * (ax * vb3x + ay * vb3y + az * vb3z);
|
||||
|
||||
// error check
|
||||
|
||||
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE))
|
||||
problem(FLERR, i1, i2, i3, i4);
|
||||
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) problem(FLERR, i1, i2, i3, i4);
|
||||
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
@ -158,13 +156,13 @@ void DihedralCharmmfsw::compute(int eflag, int vflag)
|
||||
ddf1 = df1 = 0.0;
|
||||
|
||||
for (i = 0; i < m; i++) {
|
||||
ddf1 = p*c - df1*s;
|
||||
df1 = p*s + df1*c;
|
||||
ddf1 = p * c - df1 * s;
|
||||
df1 = p * s + df1 * c;
|
||||
p = ddf1;
|
||||
}
|
||||
|
||||
p = p*cos_shift[type] + df1*sin_shift[type];
|
||||
df1 = df1*cos_shift[type] - ddf1*sin_shift[type];
|
||||
p = p * cos_shift[type] + df1 * sin_shift[type];
|
||||
df1 = df1 * cos_shift[type] - ddf1 * sin_shift[type];
|
||||
df1 *= -m;
|
||||
p += 1.0;
|
||||
|
||||
@ -175,40 +173,40 @@ void DihedralCharmmfsw::compute(int eflag, int vflag)
|
||||
|
||||
if (eflag) edihedral = k[type] * p;
|
||||
|
||||
fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
|
||||
hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
|
||||
fga = fg*ra2inv*rginv;
|
||||
hgb = hg*rb2inv*rginv;
|
||||
gaa = -ra2inv*rg;
|
||||
gbb = rb2inv*rg;
|
||||
fg = vb1x * vb2xm + vb1y * vb2ym + vb1z * vb2zm;
|
||||
hg = vb3x * vb2xm + vb3y * vb2ym + vb3z * vb2zm;
|
||||
fga = fg * ra2inv * rginv;
|
||||
hgb = hg * rb2inv * rginv;
|
||||
gaa = -ra2inv * rg;
|
||||
gbb = rb2inv * rg;
|
||||
|
||||
dtfx = gaa*ax;
|
||||
dtfy = gaa*ay;
|
||||
dtfz = gaa*az;
|
||||
dtgx = fga*ax - hgb*bx;
|
||||
dtgy = fga*ay - hgb*by;
|
||||
dtgz = fga*az - hgb*bz;
|
||||
dthx = gbb*bx;
|
||||
dthy = gbb*by;
|
||||
dthz = gbb*bz;
|
||||
dtfx = gaa * ax;
|
||||
dtfy = gaa * ay;
|
||||
dtfz = gaa * az;
|
||||
dtgx = fga * ax - hgb * bx;
|
||||
dtgy = fga * ay - hgb * by;
|
||||
dtgz = fga * az - hgb * bz;
|
||||
dthx = gbb * bx;
|
||||
dthy = gbb * by;
|
||||
dthz = gbb * bz;
|
||||
|
||||
df = -k[type] * df1;
|
||||
|
||||
sx2 = df*dtgx;
|
||||
sy2 = df*dtgy;
|
||||
sz2 = df*dtgz;
|
||||
sx2 = df * dtgx;
|
||||
sy2 = df * dtgy;
|
||||
sz2 = df * dtgz;
|
||||
|
||||
f1[0] = df*dtfx;
|
||||
f1[1] = df*dtfy;
|
||||
f1[2] = df*dtfz;
|
||||
f1[0] = df * dtfx;
|
||||
f1[1] = df * dtfy;
|
||||
f1[2] = df * dtfz;
|
||||
|
||||
f2[0] = sx2 - f1[0];
|
||||
f2[1] = sy2 - f1[1];
|
||||
f2[2] = sz2 - f1[2];
|
||||
|
||||
f4[0] = df*dthx;
|
||||
f4[1] = df*dthy;
|
||||
f4[2] = df*dthz;
|
||||
f4[0] = df * dthx;
|
||||
f4[1] = df * dthy;
|
||||
f4[2] = df * dthz;
|
||||
|
||||
f3[0] = -sx2 - f4[0];
|
||||
f3[1] = -sy2 - f4[1];
|
||||
@ -241,8 +239,8 @@ void DihedralCharmmfsw::compute(int eflag, int vflag)
|
||||
}
|
||||
|
||||
if (evflag)
|
||||
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
|
||||
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
|
||||
ev_tally(i1, i2, i3, i4, nlocal, newton_bond, edihedral, f1, f3, f4, vb1x, vb1y, vb1z, vb2x,
|
||||
vb2y, vb2z, vb3x, vb3y, vb3z);
|
||||
|
||||
// 1-4 LJ and Coulomb interactions
|
||||
// tally energy/virial in pair, using newton_bond as newton flag
|
||||
@ -254,9 +252,9 @@ void DihedralCharmmfsw::compute(int eflag, int vflag)
|
||||
delx = x[i1][0] - x[i4][0];
|
||||
dely = x[i1][1] - x[i4][1];
|
||||
delz = x[i1][2] - x[i4][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
r2inv = 1.0/rsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
r2inv = 1.0 / rsq;
|
||||
r6inv = r2inv * r2inv * r2inv;
|
||||
|
||||
// modifying coul and LJ force and energies to apply
|
||||
// force_shift and force_switch as in CHARMM pairwise
|
||||
@ -264,39 +262,42 @@ void DihedralCharmmfsw::compute(int eflag, int vflag)
|
||||
// for r < cut_inner, so switching not applied
|
||||
|
||||
r = sqrt(rsq);
|
||||
if (implicit) forcecoul = qqrd2e * q[i1]*q[i4]*r2inv;
|
||||
else if (dihedflag) forcecoul = qqrd2e * q[i1]*q[i4]*sqrt(r2inv);
|
||||
else forcecoul = qqrd2e * q[i1]*q[i4]*(sqrt(r2inv) -
|
||||
r*cut_coulinv14*cut_coulinv14);
|
||||
forcelj = r6inv * (lj14_1[itype][jtype]*r6inv - lj14_2[itype][jtype]);
|
||||
fpair = weight[type] * (forcelj+forcecoul)*r2inv;
|
||||
if (implicit)
|
||||
forcecoul = qqrd2e * q[i1] * q[i4] * r2inv;
|
||||
else if (dihedflag)
|
||||
forcecoul = qqrd2e * q[i1] * q[i4] * sqrt(r2inv);
|
||||
else
|
||||
forcecoul = qqrd2e * q[i1] * q[i4] * (sqrt(r2inv) - r * cut_coulinv14 * cut_coulinv14);
|
||||
forcelj = r6inv * (lj14_1[itype][jtype] * r6inv - lj14_2[itype][jtype]);
|
||||
fpair = weight[type] * (forcelj + forcecoul) * r2inv;
|
||||
|
||||
if (eflag) {
|
||||
if (dihedflag) ecoul = weight[type] * forcecoul;
|
||||
else ecoul = weight[type] * qqrd2e * q[i1]*q[i4] *
|
||||
(sqrt(r2inv) + r*cut_coulinv14*cut_coulinv14 -
|
||||
2.0*cut_coulinv14);
|
||||
evdwl14_12 = r6inv*lj14_3[itype][jtype]*r6inv -
|
||||
lj14_3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv;
|
||||
evdwl14_6 = -lj14_4[itype][jtype]*r6inv +
|
||||
lj14_4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv;
|
||||
if (dihedflag)
|
||||
ecoul = weight[type] * forcecoul;
|
||||
else
|
||||
ecoul = weight[type] * qqrd2e * q[i1] * q[i4] *
|
||||
(sqrt(r2inv) + r * cut_coulinv14 * cut_coulinv14 - 2.0 * cut_coulinv14);
|
||||
evdwl14_12 = r6inv * lj14_3[itype][jtype] * r6inv -
|
||||
lj14_3[itype][jtype] * cut_lj_inner6inv * cut_lj6inv;
|
||||
evdwl14_6 =
|
||||
-lj14_4[itype][jtype] * r6inv + lj14_4[itype][jtype] * cut_lj_inner3inv * cut_lj3inv;
|
||||
evdwl = evdwl14_12 + evdwl14_6;
|
||||
evdwl *= weight[type];
|
||||
}
|
||||
|
||||
if (newton_bond || i1 < nlocal) {
|
||||
f[i1][0] += delx*fpair;
|
||||
f[i1][1] += dely*fpair;
|
||||
f[i1][2] += delz*fpair;
|
||||
f[i1][0] += delx * fpair;
|
||||
f[i1][1] += dely * fpair;
|
||||
f[i1][2] += delz * fpair;
|
||||
}
|
||||
if (newton_bond || i4 < nlocal) {
|
||||
f[i4][0] -= delx*fpair;
|
||||
f[i4][1] -= dely*fpair;
|
||||
f[i4][2] -= delz*fpair;
|
||||
f[i4][0] -= delx * fpair;
|
||||
f[i4][1] -= dely * fpair;
|
||||
f[i4][2] -= delz * fpair;
|
||||
}
|
||||
|
||||
if (evflag) force->pair->ev_tally(i1,i4,nlocal,newton_bond,
|
||||
evdwl,ecoul,fpair,delx,dely,delz);
|
||||
if (evflag)
|
||||
force->pair->ev_tally(i1, i4, nlocal, newton_bond, evdwl, ecoul, fpair, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -306,17 +307,17 @@ void DihedralCharmmfsw::compute(int eflag, int vflag)
|
||||
void DihedralCharmmfsw::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ndihedraltypes;
|
||||
const int np1 = atom->ndihedraltypes + 1;
|
||||
|
||||
memory->create(k,n+1,"dihedral:k");
|
||||
memory->create(multiplicity,n+1,"dihedral:multiplicity");
|
||||
memory->create(shift,n+1,"dihedral:shift");
|
||||
memory->create(cos_shift,n+1,"dihedral:cos_shift");
|
||||
memory->create(sin_shift,n+1,"dihedral:sin_shift");
|
||||
memory->create(weight,n+1,"dihedral:weight");
|
||||
memory->create(k, np1, "dihedral:k");
|
||||
memory->create(multiplicity, np1, "dihedral:multiplicity");
|
||||
memory->create(shift, np1, "dihedral:shift");
|
||||
memory->create(cos_shift, np1, "dihedral:cos_shift");
|
||||
memory->create(sin_shift, np1, "dihedral:sin_shift");
|
||||
memory->create(weight, np1, "dihedral:weight");
|
||||
|
||||
memory->create(setflag,n+1,"dihedral:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
memory->create(setflag, np1, "dihedral:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -325,40 +326,40 @@ void DihedralCharmmfsw::allocate()
|
||||
|
||||
void DihedralCharmmfsw::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 5) error->all(FLERR,"Incorrect args for dihedral coefficients");
|
||||
if (narg != 5) error->all(FLERR, "Incorrect args for dihedral coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
utils::bounds(FLERR,arg[0],1,atom->ndihedraltypes,ilo,ihi,error);
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->ndihedraltypes, ilo, ihi, error);
|
||||
|
||||
// require integer values of shift for backwards compatibility
|
||||
// arbitrary phase angle shift could be allowed, but would break
|
||||
// backwards compatibility and is probably not needed
|
||||
|
||||
double k_one = utils::numeric(FLERR,arg[1],false,lmp);
|
||||
int multiplicity_one = utils::inumeric(FLERR,arg[2],false,lmp);
|
||||
int shift_one = utils::inumeric(FLERR,arg[3],false,lmp);
|
||||
double weight_one = utils::numeric(FLERR,arg[4],false,lmp);
|
||||
double k_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
int multiplicity_one = utils::inumeric(FLERR, arg[2], false, lmp);
|
||||
int shift_one = utils::inumeric(FLERR, arg[3], false, lmp);
|
||||
double weight_one = utils::numeric(FLERR, arg[4], false, lmp);
|
||||
|
||||
if (multiplicity_one < 0)
|
||||
error->all(FLERR,"Incorrect multiplicity arg for dihedral coefficients");
|
||||
error->all(FLERR, "Incorrect multiplicity arg for dihedral coefficients");
|
||||
if (weight_one < 0.0 || weight_one > 1.0)
|
||||
error->all(FLERR,"Incorrect weight arg for dihedral coefficients");
|
||||
if (weight_one > 0.0) weightflag=1;
|
||||
error->all(FLERR, "Incorrect weight arg for dihedral coefficients");
|
||||
if (weight_one > 0.0) weightflag = 1;
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
k[i] = k_one;
|
||||
shift[i] = shift_one;
|
||||
cos_shift[i] = cos(MY_PI*shift_one/180.0);
|
||||
sin_shift[i] = sin(MY_PI*shift_one/180.0);
|
||||
cos_shift[i] = cos(DEG2RAD * shift_one);
|
||||
sin_shift[i] = sin(DEG2RAD * shift_one);
|
||||
multiplicity[i] = multiplicity_one;
|
||||
weight[i] = weight_one;
|
||||
setflag[i] = 1;
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -367,14 +368,12 @@ void DihedralCharmmfsw::coeff(int narg, char **arg)
|
||||
|
||||
void DihedralCharmmfsw::init_style()
|
||||
{
|
||||
if (utils::strmatch(update->integrate_style,"^respa")) {
|
||||
if (utils::strmatch(update->integrate_style, "^respa")) {
|
||||
Respa *r = (Respa *) update->integrate;
|
||||
if (r->level_pair >= 0 && (r->level_pair != r->level_dihedral))
|
||||
error->all(FLERR,"Dihedral style charmmfsw must be set to same"
|
||||
" r-RESPA level as 'pair'");
|
||||
error->all(FLERR, "Dihedral style charmmfsw must be set to same r-RESPA level as 'pair'");
|
||||
if (r->level_outer >= 0 && (r->level_outer != r->level_dihedral))
|
||||
error->all(FLERR,"Dihedral style charmmfsw must be set to same"
|
||||
" r-RESPA level as 'outer'");
|
||||
error->all(FLERR, "Dihedral style charmmfsw must be set to same r-RESPA level as 'outer'");
|
||||
}
|
||||
|
||||
// insure use of CHARMM pair_style if any weight factors are non-zero
|
||||
@ -384,19 +383,20 @@ void DihedralCharmmfsw::init_style()
|
||||
if (weightflag) {
|
||||
|
||||
if ((force->special_lj[3] != 0.0) || (force->special_coul[3] != 0.0))
|
||||
error->all(FLERR,"Must use 'special_bonds charmm' with"
|
||||
" dihedral style charmm for use with CHARMM pair styles");
|
||||
error->all(FLERR,
|
||||
"Must use 'special_bonds charmm' with dihedral "
|
||||
"style charmm for use with CHARMM pair styles");
|
||||
|
||||
int itmp;
|
||||
if (force->pair == nullptr)
|
||||
error->all(FLERR,"Dihedral charmmfsw is incompatible with Pair style");
|
||||
lj14_1 = (double **) force->pair->extract("lj14_1",itmp);
|
||||
lj14_2 = (double **) force->pair->extract("lj14_2",itmp);
|
||||
lj14_3 = (double **) force->pair->extract("lj14_3",itmp);
|
||||
lj14_4 = (double **) force->pair->extract("lj14_4",itmp);
|
||||
int *ptr = (int *) force->pair->extract("implicit",itmp);
|
||||
error->all(FLERR, "Dihedral charmmfsw is incompatible with Pair style");
|
||||
lj14_1 = (double **) force->pair->extract("lj14_1", itmp);
|
||||
lj14_2 = (double **) force->pair->extract("lj14_2", itmp);
|
||||
lj14_3 = (double **) force->pair->extract("lj14_3", itmp);
|
||||
lj14_4 = (double **) force->pair->extract("lj14_4", itmp);
|
||||
int *ptr = (int *) force->pair->extract("implicit", itmp);
|
||||
if (!lj14_1 || !lj14_2 || !lj14_3 || !lj14_4 || !ptr)
|
||||
error->all(FLERR,"Dihedral charmmfsw is incompatible with Pair style");
|
||||
error->all(FLERR, "Dihedral charmmfsw is incompatible with Pair style");
|
||||
implicit = *ptr;
|
||||
}
|
||||
|
||||
@ -404,25 +404,24 @@ void DihedralCharmmfsw::init_style()
|
||||
// to 1/4 dihedral atoms to match CHARMM pairwise interactions
|
||||
|
||||
int itmp;
|
||||
int *p_dihedflag = (int *) force->pair->extract("dihedflag",itmp);
|
||||
double *p_cutljinner = (double *) force->pair->extract("cut_lj_inner",itmp);
|
||||
double *p_cutlj = (double *) force->pair->extract("cut_lj",itmp);
|
||||
double *p_cutcoul = (double *) force->pair->extract("cut_coul",itmp);
|
||||
int *p_dihedflag = (int *) force->pair->extract("dihedflag", itmp);
|
||||
double *p_cutljinner = (double *) force->pair->extract("cut_lj_inner", itmp);
|
||||
double *p_cutlj = (double *) force->pair->extract("cut_lj", itmp);
|
||||
double *p_cutcoul = (double *) force->pair->extract("cut_coul", itmp);
|
||||
|
||||
if (p_cutcoul == nullptr || p_cutljinner == nullptr ||
|
||||
p_cutlj == nullptr || p_dihedflag == nullptr)
|
||||
error->all(FLERR,"Dihedral charmmfsw is incompatible with Pair style");
|
||||
if (p_cutcoul == nullptr || p_cutljinner == nullptr || p_cutlj == nullptr ||
|
||||
p_dihedflag == nullptr)
|
||||
error->all(FLERR, "Dihedral charmmfsw is incompatible with Pair style");
|
||||
|
||||
dihedflag = *p_dihedflag;
|
||||
cut_coul14 = *p_cutcoul;
|
||||
cut_lj_inner14 = *p_cutljinner;
|
||||
cut_lj14 = *p_cutlj;
|
||||
|
||||
cut_coulinv14 = 1/cut_coul14;
|
||||
cut_lj_inner3inv = (1/cut_lj_inner14) * (1/cut_lj_inner14) *
|
||||
(1/cut_lj_inner14);
|
||||
cut_coulinv14 = 1 / cut_coul14;
|
||||
cut_lj_inner3inv = (1 / cut_lj_inner14) * (1 / cut_lj_inner14) * (1 / cut_lj_inner14);
|
||||
cut_lj_inner6inv = cut_lj_inner3inv * cut_lj_inner3inv;
|
||||
cut_lj3inv = (1/cut_lj14) * (1/cut_lj14) * (1/cut_lj14);
|
||||
cut_lj3inv = (1 / cut_lj14) * (1 / cut_lj14) * (1 / cut_lj14);
|
||||
cut_lj6inv = cut_lj3inv * cut_lj3inv;
|
||||
}
|
||||
|
||||
@ -432,11 +431,11 @@ void DihedralCharmmfsw::init_style()
|
||||
|
||||
void DihedralCharmmfsw::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&k[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fwrite(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
|
||||
fwrite(&shift[1],sizeof(int),atom->ndihedraltypes,fp);
|
||||
fwrite(&weight[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fwrite(&weightflag,sizeof(int),1,fp);
|
||||
fwrite(&k[1], sizeof(double), atom->ndihedraltypes, fp);
|
||||
fwrite(&multiplicity[1], sizeof(int), atom->ndihedraltypes, fp);
|
||||
fwrite(&shift[1], sizeof(int), atom->ndihedraltypes, fp);
|
||||
fwrite(&weight[1], sizeof(double), atom->ndihedraltypes, fp);
|
||||
fwrite(&weightflag, sizeof(int), 1, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -448,22 +447,22 @@ void DihedralCharmmfsw::read_restart(FILE *fp)
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR,&k[1],sizeof(double),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&shift[1],sizeof(int),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&weight[1],sizeof(double),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&weightflag,sizeof(int),1,fp,nullptr,error);
|
||||
utils::sfread(FLERR, &k[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &multiplicity[1], sizeof(int), atom->ndihedraltypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &shift[1], sizeof(int), atom->ndihedraltypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &weight[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &weightflag, sizeof(int), 1, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&multiplicity[1],atom->ndihedraltypes,MPI_INT,0,world);
|
||||
MPI_Bcast(&shift[1],atom->ndihedraltypes,MPI_INT,0,world);
|
||||
MPI_Bcast(&weight[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&weightflag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&k[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&multiplicity[1], atom->ndihedraltypes, MPI_INT, 0, world);
|
||||
MPI_Bcast(&shift[1], atom->ndihedraltypes, MPI_INT, 0, world);
|
||||
MPI_Bcast(&weight[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&weightflag, 1, MPI_INT, 0, world);
|
||||
|
||||
for (int i = 1; i <= atom->ndihedraltypes; i++) {
|
||||
setflag[i] = 1;
|
||||
cos_shift[i] = cos(MY_PI*shift[i]/180.0);
|
||||
sin_shift[i] = sin(MY_PI*shift[i]/180.0);
|
||||
cos_shift[i] = cos(DEG2RAD * shift[i]);
|
||||
sin_shift[i] = sin(DEG2RAD * shift[i]);
|
||||
}
|
||||
}
|
||||
|
||||
@ -474,6 +473,5 @@ void DihedralCharmmfsw::read_restart(FILE *fp)
|
||||
void DihedralCharmmfsw::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ndihedraltypes; i++)
|
||||
fprintf(fp,"%d %g %d %d %g\n",i,k[i],multiplicity[i],shift[i],weight[i]);
|
||||
fprintf(fp, "%d %g %d %d %g\n", i, k[i], multiplicity[i], shift[i], weight[i]);
|
||||
}
|
||||
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -29,12 +28,11 @@
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define TOLERANCE 0.05
|
||||
#define SMALL 0.001
|
||||
static constexpr double TOLERANCE = 0.05;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DihedralHarmonic::DihedralHarmonic(LAMMPS *lmp) : Dihedral(lmp)
|
||||
DihedralHarmonic::DihedralHarmonic(LAMMPS *_lmp) : Dihedral(_lmp)
|
||||
{
|
||||
writedata = 1;
|
||||
}
|
||||
@ -57,16 +55,16 @@ DihedralHarmonic::~DihedralHarmonic()
|
||||
|
||||
void DihedralHarmonic::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,i3,i4,i,m,n,type;
|
||||
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
|
||||
double edihedral,f1[3],f2[3],f3[3],f4[3];
|
||||
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
|
||||
double df,df1,ddf1,fg,hg,fga,hgb,gaa,gbb;
|
||||
double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
|
||||
double c,s,p,sx2,sy2,sz2;
|
||||
int i1, i2, i3, i4, i, m, n, type;
|
||||
double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z, vb2xm, vb2ym, vb2zm;
|
||||
double edihedral, f1[3], f2[3], f3[3], f4[3];
|
||||
double ax, ay, az, bx, by, bz, rasq, rbsq, rgsq, rg, rginv, ra2inv, rb2inv, rabinv;
|
||||
double df, df1, ddf1, fg, hg, fga, hgb, gaa, gbb;
|
||||
double dtfx, dtfy, dtfz, dtgx, dtgy, dtgz, dthx, dthy, dthz;
|
||||
double c, s, p, sx2, sy2, sz2;
|
||||
|
||||
edihedral = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
@ -106,31 +104,30 @@ void DihedralHarmonic::compute(int eflag, int vflag)
|
||||
|
||||
// c,s calculation
|
||||
|
||||
ax = vb1y*vb2zm - vb1z*vb2ym;
|
||||
ay = vb1z*vb2xm - vb1x*vb2zm;
|
||||
az = vb1x*vb2ym - vb1y*vb2xm;
|
||||
bx = vb3y*vb2zm - vb3z*vb2ym;
|
||||
by = vb3z*vb2xm - vb3x*vb2zm;
|
||||
bz = vb3x*vb2ym - vb3y*vb2xm;
|
||||
ax = vb1y * vb2zm - vb1z * vb2ym;
|
||||
ay = vb1z * vb2xm - vb1x * vb2zm;
|
||||
az = vb1x * vb2ym - vb1y * vb2xm;
|
||||
bx = vb3y * vb2zm - vb3z * vb2ym;
|
||||
by = vb3z * vb2xm - vb3x * vb2zm;
|
||||
bz = vb3x * vb2ym - vb3y * vb2xm;
|
||||
|
||||
rasq = ax*ax + ay*ay + az*az;
|
||||
rbsq = bx*bx + by*by + bz*bz;
|
||||
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
|
||||
rasq = ax * ax + ay * ay + az * az;
|
||||
rbsq = bx * bx + by * by + bz * bz;
|
||||
rgsq = vb2xm * vb2xm + vb2ym * vb2ym + vb2zm * vb2zm;
|
||||
rg = sqrt(rgsq);
|
||||
|
||||
rginv = ra2inv = rb2inv = 0.0;
|
||||
if (rg > 0) rginv = 1.0/rg;
|
||||
if (rasq > 0) ra2inv = 1.0/rasq;
|
||||
if (rbsq > 0) rb2inv = 1.0/rbsq;
|
||||
rabinv = sqrt(ra2inv*rb2inv);
|
||||
if (rg > 0) rginv = 1.0 / rg;
|
||||
if (rasq > 0) ra2inv = 1.0 / rasq;
|
||||
if (rbsq > 0) rb2inv = 1.0 / rbsq;
|
||||
rabinv = sqrt(ra2inv * rb2inv);
|
||||
|
||||
c = (ax*bx + ay*by + az*bz)*rabinv;
|
||||
s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
|
||||
c = (ax * bx + ay * by + az * bz) * rabinv;
|
||||
s = rg * rabinv * (ax * vb3x + ay * vb3y + az * vb3z);
|
||||
|
||||
// error check
|
||||
|
||||
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE))
|
||||
problem(FLERR, i1, i2, i3, i4);
|
||||
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) problem(FLERR, i1, i2, i3, i4);
|
||||
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
@ -140,13 +137,13 @@ void DihedralHarmonic::compute(int eflag, int vflag)
|
||||
ddf1 = df1 = 0.0;
|
||||
|
||||
for (i = 0; i < m; i++) {
|
||||
ddf1 = p*c - df1*s;
|
||||
df1 = p*s + df1*c;
|
||||
ddf1 = p * c - df1 * s;
|
||||
df1 = p * s + df1 * c;
|
||||
p = ddf1;
|
||||
}
|
||||
|
||||
p = p*cos_shift[type] + df1*sin_shift[type];
|
||||
df1 = df1*cos_shift[type] - ddf1*sin_shift[type];
|
||||
p = p * cos_shift[type] + df1 * sin_shift[type];
|
||||
df1 = df1 * cos_shift[type] - ddf1 * sin_shift[type];
|
||||
df1 *= -m;
|
||||
p += 1.0;
|
||||
|
||||
@ -157,40 +154,40 @@ void DihedralHarmonic::compute(int eflag, int vflag)
|
||||
|
||||
if (eflag) edihedral = k[type] * p;
|
||||
|
||||
fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
|
||||
hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
|
||||
fga = fg*ra2inv*rginv;
|
||||
hgb = hg*rb2inv*rginv;
|
||||
gaa = -ra2inv*rg;
|
||||
gbb = rb2inv*rg;
|
||||
fg = vb1x * vb2xm + vb1y * vb2ym + vb1z * vb2zm;
|
||||
hg = vb3x * vb2xm + vb3y * vb2ym + vb3z * vb2zm;
|
||||
fga = fg * ra2inv * rginv;
|
||||
hgb = hg * rb2inv * rginv;
|
||||
gaa = -ra2inv * rg;
|
||||
gbb = rb2inv * rg;
|
||||
|
||||
dtfx = gaa*ax;
|
||||
dtfy = gaa*ay;
|
||||
dtfz = gaa*az;
|
||||
dtgx = fga*ax - hgb*bx;
|
||||
dtgy = fga*ay - hgb*by;
|
||||
dtgz = fga*az - hgb*bz;
|
||||
dthx = gbb*bx;
|
||||
dthy = gbb*by;
|
||||
dthz = gbb*bz;
|
||||
dtfx = gaa * ax;
|
||||
dtfy = gaa * ay;
|
||||
dtfz = gaa * az;
|
||||
dtgx = fga * ax - hgb * bx;
|
||||
dtgy = fga * ay - hgb * by;
|
||||
dtgz = fga * az - hgb * bz;
|
||||
dthx = gbb * bx;
|
||||
dthy = gbb * by;
|
||||
dthz = gbb * bz;
|
||||
|
||||
df = -k[type] * df1;
|
||||
|
||||
sx2 = df*dtgx;
|
||||
sy2 = df*dtgy;
|
||||
sz2 = df*dtgz;
|
||||
sx2 = df * dtgx;
|
||||
sy2 = df * dtgy;
|
||||
sz2 = df * dtgz;
|
||||
|
||||
f1[0] = df*dtfx;
|
||||
f1[1] = df*dtfy;
|
||||
f1[2] = df*dtfz;
|
||||
f1[0] = df * dtfx;
|
||||
f1[1] = df * dtfy;
|
||||
f1[2] = df * dtfz;
|
||||
|
||||
f2[0] = sx2 - f1[0];
|
||||
f2[1] = sy2 - f1[1];
|
||||
f2[2] = sz2 - f1[2];
|
||||
|
||||
f4[0] = df*dthx;
|
||||
f4[1] = df*dthy;
|
||||
f4[2] = df*dthz;
|
||||
f4[0] = df * dthx;
|
||||
f4[1] = df * dthy;
|
||||
f4[2] = df * dthz;
|
||||
|
||||
f3[0] = -sx2 - f4[0];
|
||||
f3[1] = -sy2 - f4[1];
|
||||
@ -223,8 +220,8 @@ void DihedralHarmonic::compute(int eflag, int vflag)
|
||||
}
|
||||
|
||||
if (evflag)
|
||||
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
|
||||
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
|
||||
ev_tally(i1, i2, i3, i4, nlocal, newton_bond, edihedral, f1, f3, f4, vb1x, vb1y, vb1z, vb2x,
|
||||
vb2y, vb2z, vb3x, vb3y, vb3z);
|
||||
}
|
||||
}
|
||||
|
||||
@ -233,16 +230,16 @@ void DihedralHarmonic::compute(int eflag, int vflag)
|
||||
void DihedralHarmonic::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ndihedraltypes;
|
||||
const int np1 = atom->ndihedraltypes + 1;
|
||||
|
||||
memory->create(k,n+1,"dihedral:k");
|
||||
memory->create(sign,n+1,"dihedral:sign");
|
||||
memory->create(multiplicity,n+1,"dihedral:multiplicity");
|
||||
memory->create(cos_shift,n+1,"dihedral:cos_shift");
|
||||
memory->create(sin_shift,n+1,"dihedral:sin_shift");
|
||||
memory->create(k, np1, "dihedral:k");
|
||||
memory->create(sign, np1, "dihedral:sign");
|
||||
memory->create(multiplicity, np1, "dihedral:multiplicity");
|
||||
memory->create(cos_shift, np1, "dihedral:cos_shift");
|
||||
memory->create(sin_shift, np1, "dihedral:sin_shift");
|
||||
|
||||
memory->create(setflag,n+1,"dihedral:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
memory->create(setflag, np1, "dihedral:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -251,24 +248,24 @@ void DihedralHarmonic::allocate()
|
||||
|
||||
void DihedralHarmonic::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 4) error->all(FLERR,"Incorrect args for dihedral coefficients");
|
||||
if (narg != 4) error->all(FLERR, "Incorrect args for dihedral coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
utils::bounds(FLERR,arg[0],1,atom->ndihedraltypes,ilo,ihi,error);
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->ndihedraltypes, ilo, ihi, error);
|
||||
|
||||
double k_one = utils::numeric(FLERR,arg[1],false,lmp);
|
||||
int sign_one = utils::inumeric(FLERR,arg[2],false,lmp);
|
||||
int multiplicity_one = utils::inumeric(FLERR,arg[3],false,lmp);
|
||||
double k_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
int sign_one = utils::inumeric(FLERR, arg[2], false, lmp);
|
||||
int multiplicity_one = utils::inumeric(FLERR, arg[3], false, lmp);
|
||||
|
||||
// require sign = +/- 1 for backwards compatibility
|
||||
// arbitrary phase angle shift could be allowed, but would break
|
||||
// backwards compatibility and is probably not needed
|
||||
|
||||
if (sign_one != -1 && sign_one != 1)
|
||||
error->all(FLERR,"Incorrect sign arg for dihedral coefficients");
|
||||
error->all(FLERR, "Incorrect sign arg for dihedral coefficients");
|
||||
if (multiplicity_one < 0)
|
||||
error->all(FLERR,"Incorrect multiplicity arg for dihedral coefficients");
|
||||
error->all(FLERR, "Incorrect multiplicity arg for dihedral coefficients");
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
@ -286,7 +283,7 @@ void DihedralHarmonic::coeff(int narg, char **arg)
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -295,9 +292,9 @@ void DihedralHarmonic::coeff(int narg, char **arg)
|
||||
|
||||
void DihedralHarmonic::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&k[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fwrite(&sign[1],sizeof(int),atom->ndihedraltypes,fp);
|
||||
fwrite(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
|
||||
fwrite(&k[1], sizeof(double), atom->ndihedraltypes, fp);
|
||||
fwrite(&sign[1], sizeof(int), atom->ndihedraltypes, fp);
|
||||
fwrite(&multiplicity[1], sizeof(int), atom->ndihedraltypes, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -309,13 +306,13 @@ void DihedralHarmonic::read_restart(FILE *fp)
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR,&k[1],sizeof(double),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&sign[1],sizeof(int),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR, &k[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &sign[1], sizeof(int), atom->ndihedraltypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &multiplicity[1], sizeof(int), atom->ndihedraltypes, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&sign[1],atom->ndihedraltypes,MPI_INT,0,world);
|
||||
MPI_Bcast(&multiplicity[1],atom->ndihedraltypes,MPI_INT,0,world);
|
||||
MPI_Bcast(&k[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&sign[1], atom->ndihedraltypes, MPI_INT, 0, world);
|
||||
MPI_Bcast(&multiplicity[1], atom->ndihedraltypes, MPI_INT, 0, world);
|
||||
|
||||
for (int i = 1; i <= atom->ndihedraltypes; i++) {
|
||||
setflag[i] = 1;
|
||||
@ -336,6 +333,5 @@ void DihedralHarmonic::read_restart(FILE *fp)
|
||||
void DihedralHarmonic::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ndihedraltypes; i++)
|
||||
fprintf(fp,"%d %g %d %d\n",i,k[i],sign[i],multiplicity[i]);
|
||||
fprintf(fp, "%d %g %d %d\n", i, k[i], sign[i], multiplicity[i]);
|
||||
}
|
||||
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -29,12 +28,12 @@
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define TOLERANCE 0.05
|
||||
#define SMALL 0.001
|
||||
static constexpr double TOLERANCE = 0.05;
|
||||
static constexpr double SMALL = 0.001;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DihedralMultiHarmonic::DihedralMultiHarmonic(LAMMPS *lmp) : Dihedral(lmp)
|
||||
DihedralMultiHarmonic::DihedralMultiHarmonic(LAMMPS *_lmp) : Dihedral(_lmp)
|
||||
{
|
||||
writedata = 1;
|
||||
}
|
||||
@ -57,17 +56,17 @@ DihedralMultiHarmonic::~DihedralMultiHarmonic()
|
||||
|
||||
void DihedralMultiHarmonic::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,i3,i4,n,type;
|
||||
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
|
||||
double edihedral,f1[3],f2[3],f3[3],f4[3];
|
||||
double sb1,sb2,sb3,rb1,rb3,c0,b1mag2,b1mag,b2mag2;
|
||||
double b2mag,b3mag2,b3mag,ctmp,r12c1,c1mag,r12c2;
|
||||
double c2mag,sc1,sc2,s1,s12,c,p,pd,a,a11,a22;
|
||||
double a33,a12,a13,a23,sx2,sy2,sz2;
|
||||
double s2,sin2;
|
||||
int i1, i2, i3, i4, n, type;
|
||||
double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z, vb2xm, vb2ym, vb2zm;
|
||||
double edihedral, f1[3], f2[3], f3[3], f4[3];
|
||||
double sb1, sb2, sb3, rb1, rb3, c0, b1mag2, b1mag, b2mag2;
|
||||
double b2mag, b3mag2, b3mag, ctmp, r12c1, c1mag, r12c2;
|
||||
double c2mag, sc1, sc2, s1, s12, c, p, pd, a, a11, a22;
|
||||
double a33, a12, a13, a23, sx2, sy2, sz2;
|
||||
double s2, sin2;
|
||||
|
||||
edihedral = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
@ -107,53 +106,52 @@ void DihedralMultiHarmonic::compute(int eflag, int vflag)
|
||||
|
||||
// c0 calculation
|
||||
|
||||
sb1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
|
||||
sb2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
|
||||
sb3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
|
||||
sb1 = 1.0 / (vb1x * vb1x + vb1y * vb1y + vb1z * vb1z);
|
||||
sb2 = 1.0 / (vb2x * vb2x + vb2y * vb2y + vb2z * vb2z);
|
||||
sb3 = 1.0 / (vb3x * vb3x + vb3y * vb3y + vb3z * vb3z);
|
||||
|
||||
rb1 = sqrt(sb1);
|
||||
rb3 = sqrt(sb3);
|
||||
|
||||
c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
|
||||
c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * rb1 * rb3;
|
||||
|
||||
// 1st and 2nd angle
|
||||
|
||||
b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
|
||||
b1mag2 = vb1x * vb1x + vb1y * vb1y + vb1z * vb1z;
|
||||
b1mag = sqrt(b1mag2);
|
||||
b2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
|
||||
b2mag2 = vb2x * vb2x + vb2y * vb2y + vb2z * vb2z;
|
||||
b2mag = sqrt(b2mag2);
|
||||
b3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
|
||||
b3mag2 = vb3x * vb3x + vb3y * vb3y + vb3z * vb3z;
|
||||
b3mag = sqrt(b3mag2);
|
||||
|
||||
ctmp = vb1x*vb2x + vb1y*vb2y + vb1z*vb2z;
|
||||
r12c1 = 1.0 / (b1mag*b2mag);
|
||||
ctmp = vb1x * vb2x + vb1y * vb2y + vb1z * vb2z;
|
||||
r12c1 = 1.0 / (b1mag * b2mag);
|
||||
c1mag = ctmp * r12c1;
|
||||
|
||||
ctmp = vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z;
|
||||
r12c2 = 1.0 / (b2mag*b3mag);
|
||||
ctmp = vb2xm * vb3x + vb2ym * vb3y + vb2zm * vb3z;
|
||||
r12c2 = 1.0 / (b2mag * b3mag);
|
||||
c2mag = ctmp * r12c2;
|
||||
|
||||
// cos and sin of 2 angles and final c
|
||||
|
||||
sin2 = MAX(1.0 - c1mag*c1mag,0.0);
|
||||
sin2 = MAX(1.0 - c1mag * c1mag, 0.0);
|
||||
sc1 = sqrt(sin2);
|
||||
if (sc1 < SMALL) sc1 = SMALL;
|
||||
sc1 = 1.0/sc1;
|
||||
sc1 = 1.0 / sc1;
|
||||
|
||||
sin2 = MAX(1.0 - c2mag*c2mag,0.0);
|
||||
sin2 = MAX(1.0 - c2mag * c2mag, 0.0);
|
||||
sc2 = sqrt(sin2);
|
||||
if (sc2 < SMALL) sc2 = SMALL;
|
||||
sc2 = 1.0/sc2;
|
||||
sc2 = 1.0 / sc2;
|
||||
|
||||
s1 = sc1 * sc1;
|
||||
s2 = sc2 * sc2;
|
||||
s12 = sc1 * sc2;
|
||||
c = (c0 + c1mag*c2mag) * s12;
|
||||
c = (c0 + c1mag * c2mag) * s12;
|
||||
|
||||
// error check
|
||||
|
||||
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE))
|
||||
problem(FLERR, i1, i2, i3, i4);
|
||||
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) problem(FLERR, i1, i2, i3, i4);
|
||||
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
@ -162,36 +160,36 @@ void DihedralMultiHarmonic::compute(int eflag, int vflag)
|
||||
// p = sum (i=1,5) a_i * c**(i-1)
|
||||
// pd = dp/dc
|
||||
|
||||
p = a1[type] + c*(a2[type] + c*(a3[type] + c*(a4[type] + c*a5[type])));
|
||||
pd = a2[type] + c*(2.0*a3[type] + c*(3.0*a4[type] + c*4.0*a5[type]));
|
||||
p = a1[type] + c * (a2[type] + c * (a3[type] + c * (a4[type] + c * a5[type])));
|
||||
pd = a2[type] + c * (2.0 * a3[type] + c * (3.0 * a4[type] + c * 4.0 * a5[type]));
|
||||
|
||||
if (eflag) edihedral = p;
|
||||
|
||||
a = pd;
|
||||
c = c * a;
|
||||
s12 = s12 * a;
|
||||
a11 = c*sb1*s1;
|
||||
a22 = -sb2 * (2.0*c0*s12 - c*(s1+s2));
|
||||
a33 = c*sb3*s2;
|
||||
a12 = -r12c1*(c1mag*c*s1 + c2mag*s12);
|
||||
a13 = -rb1*rb3*s12;
|
||||
a23 = r12c2*(c2mag*c*s2 + c1mag*s12);
|
||||
a11 = c * sb1 * s1;
|
||||
a22 = -sb2 * (2.0 * c0 * s12 - c * (s1 + s2));
|
||||
a33 = c * sb3 * s2;
|
||||
a12 = -r12c1 * (c1mag * c * s1 + c2mag * s12);
|
||||
a13 = -rb1 * rb3 * s12;
|
||||
a23 = r12c2 * (c2mag * c * s2 + c1mag * s12);
|
||||
|
||||
sx2 = a12*vb1x + a22*vb2x + a23*vb3x;
|
||||
sy2 = a12*vb1y + a22*vb2y + a23*vb3y;
|
||||
sz2 = a12*vb1z + a22*vb2z + a23*vb3z;
|
||||
sx2 = a12 * vb1x + a22 * vb2x + a23 * vb3x;
|
||||
sy2 = a12 * vb1y + a22 * vb2y + a23 * vb3y;
|
||||
sz2 = a12 * vb1z + a22 * vb2z + a23 * vb3z;
|
||||
|
||||
f1[0] = a11*vb1x + a12*vb2x + a13*vb3x;
|
||||
f1[1] = a11*vb1y + a12*vb2y + a13*vb3y;
|
||||
f1[2] = a11*vb1z + a12*vb2z + a13*vb3z;
|
||||
f1[0] = a11 * vb1x + a12 * vb2x + a13 * vb3x;
|
||||
f1[1] = a11 * vb1y + a12 * vb2y + a13 * vb3y;
|
||||
f1[2] = a11 * vb1z + a12 * vb2z + a13 * vb3z;
|
||||
|
||||
f2[0] = -sx2 - f1[0];
|
||||
f2[1] = -sy2 - f1[1];
|
||||
f2[2] = -sz2 - f1[2];
|
||||
|
||||
f4[0] = a13*vb1x + a23*vb2x + a33*vb3x;
|
||||
f4[1] = a13*vb1y + a23*vb2y + a33*vb3y;
|
||||
f4[2] = a13*vb1z + a23*vb2z + a33*vb3z;
|
||||
f4[0] = a13 * vb1x + a23 * vb2x + a33 * vb3x;
|
||||
f4[1] = a13 * vb1y + a23 * vb2y + a33 * vb3y;
|
||||
f4[2] = a13 * vb1z + a23 * vb2z + a33 * vb3z;
|
||||
|
||||
f3[0] = sx2 - f4[0];
|
||||
f3[1] = sy2 - f4[1];
|
||||
@ -224,8 +222,8 @@ void DihedralMultiHarmonic::compute(int eflag, int vflag)
|
||||
}
|
||||
|
||||
if (evflag)
|
||||
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
|
||||
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
|
||||
ev_tally(i1, i2, i3, i4, nlocal, newton_bond, edihedral, f1, f3, f4, vb1x, vb1y, vb1z, vb2x,
|
||||
vb2y, vb2z, vb3x, vb3y, vb3z);
|
||||
}
|
||||
}
|
||||
|
||||
@ -234,16 +232,16 @@ void DihedralMultiHarmonic::compute(int eflag, int vflag)
|
||||
void DihedralMultiHarmonic::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ndihedraltypes;
|
||||
const int np1 = atom->ndihedraltypes + 1;
|
||||
|
||||
memory->create(a1,n+1,"dihedral:a1");
|
||||
memory->create(a2,n+1,"dihedral:a2");
|
||||
memory->create(a3,n+1,"dihedral:a3");
|
||||
memory->create(a4,n+1,"dihedral:a4");
|
||||
memory->create(a5,n+1,"dihedral:a5");
|
||||
memory->create(a1, np1, "dihedral:a1");
|
||||
memory->create(a2, np1, "dihedral:a2");
|
||||
memory->create(a3, np1, "dihedral:a3");
|
||||
memory->create(a4, np1, "dihedral:a4");
|
||||
memory->create(a5, np1, "dihedral:a5");
|
||||
|
||||
memory->create(setflag,n+1,"dihedral:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
memory->create(setflag, np1, "dihedral:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -252,17 +250,17 @@ void DihedralMultiHarmonic::allocate()
|
||||
|
||||
void DihedralMultiHarmonic::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 6) error->all(FLERR,"Incorrect args for dihedral coefficients");
|
||||
if (narg != 6) error->all(FLERR, "Incorrect args for dihedral coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
utils::bounds(FLERR,arg[0],1,atom->ndihedraltypes,ilo,ihi,error);
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->ndihedraltypes, ilo, ihi, error);
|
||||
|
||||
double a1_one = utils::numeric(FLERR,arg[1],false,lmp);
|
||||
double a2_one = utils::numeric(FLERR,arg[2],false,lmp);
|
||||
double a3_one = utils::numeric(FLERR,arg[3],false,lmp);
|
||||
double a4_one = utils::numeric(FLERR,arg[4],false,lmp);
|
||||
double a5_one = utils::numeric(FLERR,arg[5],false,lmp);
|
||||
double a1_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
double a2_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
double a3_one = utils::numeric(FLERR, arg[3], false, lmp);
|
||||
double a4_one = utils::numeric(FLERR, arg[4], false, lmp);
|
||||
double a5_one = utils::numeric(FLERR, arg[5], false, lmp);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
@ -275,7 +273,7 @@ void DihedralMultiHarmonic::coeff(int narg, char **arg)
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -284,11 +282,11 @@ void DihedralMultiHarmonic::coeff(int narg, char **arg)
|
||||
|
||||
void DihedralMultiHarmonic::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&a1[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fwrite(&a2[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fwrite(&a3[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fwrite(&a4[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fwrite(&a5[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fwrite(&a1[1], sizeof(double), atom->ndihedraltypes, fp);
|
||||
fwrite(&a2[1], sizeof(double), atom->ndihedraltypes, fp);
|
||||
fwrite(&a3[1], sizeof(double), atom->ndihedraltypes, fp);
|
||||
fwrite(&a4[1], sizeof(double), atom->ndihedraltypes, fp);
|
||||
fwrite(&a5[1], sizeof(double), atom->ndihedraltypes, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -300,17 +298,17 @@ void DihedralMultiHarmonic::read_restart(FILE *fp)
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR,&a1[1],sizeof(double),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&a2[1],sizeof(double),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&a3[1],sizeof(double),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&a4[1],sizeof(double),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&a5[1],sizeof(double),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR, &a1[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &a2[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &a3[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &a4[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &a5[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&a1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&a2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&a3[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&a4[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&a5[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&a1[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&a2[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&a3[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&a4[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&a5[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
|
||||
|
||||
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
|
||||
}
|
||||
@ -322,5 +320,5 @@ void DihedralMultiHarmonic::read_restart(FILE *fp)
|
||||
void DihedralMultiHarmonic::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ndihedraltypes; i++)
|
||||
fprintf(fp,"%d %g %g %g %g %g\n",i,a1[i],a2[i],a3[i],a4[i],a5[i]);
|
||||
fprintf(fp, "%d %g %g %g %g %g\n", i, a1[i], a2[i], a3[i], a4[i], a5[i]);
|
||||
}
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -29,13 +28,13 @@
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define TOLERANCE 0.05
|
||||
#define SMALL 0.001
|
||||
#define SMALLER 0.00001
|
||||
static constexpr double TOLERANCE = 0.05;
|
||||
static constexpr double SMALL = 0.001;
|
||||
static constexpr double SMALLER = 0.00001;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DihedralOPLS::DihedralOPLS(LAMMPS *lmp) : Dihedral(lmp)
|
||||
DihedralOPLS::DihedralOPLS(LAMMPS *_lmp) : Dihedral(_lmp)
|
||||
{
|
||||
writedata = 1;
|
||||
}
|
||||
@ -57,17 +56,17 @@ DihedralOPLS::~DihedralOPLS()
|
||||
|
||||
void DihedralOPLS::compute(int eflag, int vflag)
|
||||
{
|
||||
int i1,i2,i3,i4,n,type;
|
||||
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
|
||||
double edihedral,f1[3],f2[3],f3[3],f4[3];
|
||||
double sb1,sb2,sb3,rb1,rb3,c0,b1mag2,b1mag,b2mag2;
|
||||
double b2mag,b3mag2,b3mag,ctmp,r12c1,c1mag,r12c2;
|
||||
double c2mag,sc1,sc2,s1,s12,c,p,pd,a,a11,a22;
|
||||
double a33,a12,a13,a23,sx2,sy2,sz2;
|
||||
double s2,cx,cy,cz,cmag,dx,phi,si,siinv,sin2;
|
||||
int i1, i2, i3, i4, n, type;
|
||||
double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z, vb2xm, vb2ym, vb2zm;
|
||||
double edihedral, f1[3], f2[3], f3[3], f4[3];
|
||||
double sb1, sb2, sb3, rb1, rb3, c0, b1mag2, b1mag, b2mag2;
|
||||
double b2mag, b3mag2, b3mag, ctmp, r12c1, c1mag, r12c2;
|
||||
double c2mag, sc1, sc2, s1, s12, c, p, pd, a, a11, a22;
|
||||
double a33, a12, a13, a23, sx2, sy2, sz2;
|
||||
double s2, cx, cy, cz, cmag, dx, phi, si, siinv, sin2;
|
||||
|
||||
edihedral = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
@ -107,59 +106,58 @@ void DihedralOPLS::compute(int eflag, int vflag)
|
||||
|
||||
// c0 calculation
|
||||
|
||||
sb1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
|
||||
sb2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
|
||||
sb3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
|
||||
sb1 = 1.0 / (vb1x * vb1x + vb1y * vb1y + vb1z * vb1z);
|
||||
sb2 = 1.0 / (vb2x * vb2x + vb2y * vb2y + vb2z * vb2z);
|
||||
sb3 = 1.0 / (vb3x * vb3x + vb3y * vb3y + vb3z * vb3z);
|
||||
|
||||
rb1 = sqrt(sb1);
|
||||
rb3 = sqrt(sb3);
|
||||
|
||||
c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
|
||||
c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * rb1 * rb3;
|
||||
|
||||
// 1st and 2nd angle
|
||||
|
||||
b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
|
||||
b1mag2 = vb1x * vb1x + vb1y * vb1y + vb1z * vb1z;
|
||||
b1mag = sqrt(b1mag2);
|
||||
b2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
|
||||
b2mag2 = vb2x * vb2x + vb2y * vb2y + vb2z * vb2z;
|
||||
b2mag = sqrt(b2mag2);
|
||||
b3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
|
||||
b3mag2 = vb3x * vb3x + vb3y * vb3y + vb3z * vb3z;
|
||||
b3mag = sqrt(b3mag2);
|
||||
|
||||
ctmp = vb1x*vb2x + vb1y*vb2y + vb1z*vb2z;
|
||||
r12c1 = 1.0 / (b1mag*b2mag);
|
||||
ctmp = vb1x * vb2x + vb1y * vb2y + vb1z * vb2z;
|
||||
r12c1 = 1.0 / (b1mag * b2mag);
|
||||
c1mag = ctmp * r12c1;
|
||||
|
||||
ctmp = vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z;
|
||||
r12c2 = 1.0 / (b2mag*b3mag);
|
||||
ctmp = vb2xm * vb3x + vb2ym * vb3y + vb2zm * vb3z;
|
||||
r12c2 = 1.0 / (b2mag * b3mag);
|
||||
c2mag = ctmp * r12c2;
|
||||
|
||||
// cos and sin of 2 angles and final c
|
||||
|
||||
sin2 = MAX(1.0 - c1mag*c1mag,0.0);
|
||||
sin2 = MAX(1.0 - c1mag * c1mag, 0.0);
|
||||
sc1 = sqrt(sin2);
|
||||
if (sc1 < SMALL) sc1 = SMALL;
|
||||
sc1 = 1.0/sc1;
|
||||
sc1 = 1.0 / sc1;
|
||||
|
||||
sin2 = MAX(1.0 - c2mag*c2mag,0.0);
|
||||
sin2 = MAX(1.0 - c2mag * c2mag, 0.0);
|
||||
sc2 = sqrt(sin2);
|
||||
if (sc2 < SMALL) sc2 = SMALL;
|
||||
sc2 = 1.0/sc2;
|
||||
sc2 = 1.0 / sc2;
|
||||
|
||||
s1 = sc1 * sc1;
|
||||
s2 = sc2 * sc2;
|
||||
s12 = sc1 * sc2;
|
||||
c = (c0 + c1mag*c2mag) * s12;
|
||||
c = (c0 + c1mag * c2mag) * s12;
|
||||
|
||||
cx = vb1y*vb2z - vb1z*vb2y;
|
||||
cy = vb1z*vb2x - vb1x*vb2z;
|
||||
cz = vb1x*vb2y - vb1y*vb2x;
|
||||
cmag = sqrt(cx*cx + cy*cy + cz*cz);
|
||||
dx = (cx*vb3x + cy*vb3y + cz*vb3z)/cmag/b3mag;
|
||||
cx = vb1y * vb2z - vb1z * vb2y;
|
||||
cy = vb1z * vb2x - vb1x * vb2z;
|
||||
cz = vb1x * vb2y - vb1y * vb2x;
|
||||
cmag = sqrt(cx * cx + cy * cy + cz * cz);
|
||||
dx = (cx * vb3x + cy * vb3y + cz * vb3z) / cmag / b3mag;
|
||||
|
||||
// error check
|
||||
|
||||
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE))
|
||||
problem(FLERR, i1, i2, i3, i4);
|
||||
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) problem(FLERR, i1, i2, i3, i4);
|
||||
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
@ -172,40 +170,40 @@ void DihedralOPLS::compute(int eflag, int vflag)
|
||||
if (dx < 0.0) phi *= -1.0;
|
||||
si = sin(phi);
|
||||
if (fabs(si) < SMALLER) si = SMALLER;
|
||||
siinv = 1.0/si;
|
||||
siinv = 1.0 / si;
|
||||
|
||||
p = k1[type]*(1.0 + c) + k2[type]*(1.0 - cos(2.0*phi)) +
|
||||
k3[type]*(1.0 + cos(3.0*phi)) + k4[type]*(1.0 - cos(4.0*phi)) ;
|
||||
pd = k1[type] - 2.0*k2[type]*sin(2.0*phi)*siinv +
|
||||
3.0*k3[type]*sin(3.0*phi)*siinv - 4.0*k4[type]*sin(4.0*phi)*siinv;
|
||||
p = k1[type] * (1.0 + c) + k2[type] * (1.0 - cos(2.0 * phi)) +
|
||||
k3[type] * (1.0 + cos(3.0 * phi)) + k4[type] * (1.0 - cos(4.0 * phi));
|
||||
pd = k1[type] - 2.0 * k2[type] * sin(2.0 * phi) * siinv +
|
||||
3.0 * k3[type] * sin(3.0 * phi) * siinv - 4.0 * k4[type] * sin(4.0 * phi) * siinv;
|
||||
|
||||
if (eflag) edihedral = p;
|
||||
|
||||
a = pd;
|
||||
c = c * a;
|
||||
s12 = s12 * a;
|
||||
a11 = c*sb1*s1;
|
||||
a22 = -sb2 * (2.0*c0*s12 - c*(s1+s2));
|
||||
a33 = c*sb3*s2;
|
||||
a12 = -r12c1 * (c1mag*c*s1 + c2mag*s12);
|
||||
a13 = -rb1*rb3*s12;
|
||||
a23 = r12c2 * (c2mag*c*s2 + c1mag*s12);
|
||||
a11 = c * sb1 * s1;
|
||||
a22 = -sb2 * (2.0 * c0 * s12 - c * (s1 + s2));
|
||||
a33 = c * sb3 * s2;
|
||||
a12 = -r12c1 * (c1mag * c * s1 + c2mag * s12);
|
||||
a13 = -rb1 * rb3 * s12;
|
||||
a23 = r12c2 * (c2mag * c * s2 + c1mag * s12);
|
||||
|
||||
sx2 = a12*vb1x + a22*vb2x + a23*vb3x;
|
||||
sy2 = a12*vb1y + a22*vb2y + a23*vb3y;
|
||||
sz2 = a12*vb1z + a22*vb2z + a23*vb3z;
|
||||
sx2 = a12 * vb1x + a22 * vb2x + a23 * vb3x;
|
||||
sy2 = a12 * vb1y + a22 * vb2y + a23 * vb3y;
|
||||
sz2 = a12 * vb1z + a22 * vb2z + a23 * vb3z;
|
||||
|
||||
f1[0] = a11*vb1x + a12*vb2x + a13*vb3x;
|
||||
f1[1] = a11*vb1y + a12*vb2y + a13*vb3y;
|
||||
f1[2] = a11*vb1z + a12*vb2z + a13*vb3z;
|
||||
f1[0] = a11 * vb1x + a12 * vb2x + a13 * vb3x;
|
||||
f1[1] = a11 * vb1y + a12 * vb2y + a13 * vb3y;
|
||||
f1[2] = a11 * vb1z + a12 * vb2z + a13 * vb3z;
|
||||
|
||||
f2[0] = -sx2 - f1[0];
|
||||
f2[1] = -sy2 - f1[1];
|
||||
f2[2] = -sz2 - f1[2];
|
||||
|
||||
f4[0] = a13*vb1x + a23*vb2x + a33*vb3x;
|
||||
f4[1] = a13*vb1y + a23*vb2y + a33*vb3y;
|
||||
f4[2] = a13*vb1z + a23*vb2z + a33*vb3z;
|
||||
f4[0] = a13 * vb1x + a23 * vb2x + a33 * vb3x;
|
||||
f4[1] = a13 * vb1y + a23 * vb2y + a33 * vb3y;
|
||||
f4[2] = a13 * vb1z + a23 * vb2z + a33 * vb3z;
|
||||
|
||||
f3[0] = sx2 - f4[0];
|
||||
f3[1] = sy2 - f4[1];
|
||||
@ -238,8 +236,8 @@ void DihedralOPLS::compute(int eflag, int vflag)
|
||||
}
|
||||
|
||||
if (evflag)
|
||||
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
|
||||
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
|
||||
ev_tally(i1, i2, i3, i4, nlocal, newton_bond, edihedral, f1, f3, f4, vb1x, vb1y, vb1z, vb2x,
|
||||
vb2y, vb2z, vb3x, vb3y, vb3z);
|
||||
}
|
||||
}
|
||||
|
||||
@ -248,15 +246,15 @@ void DihedralOPLS::compute(int eflag, int vflag)
|
||||
void DihedralOPLS::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ndihedraltypes;
|
||||
const int np1 = atom->ndihedraltypes + 1;
|
||||
|
||||
memory->create(k1,n+1,"dihedral:k1");
|
||||
memory->create(k2,n+1,"dihedral:k2");
|
||||
memory->create(k3,n+1,"dihedral:k3");
|
||||
memory->create(k4,n+1,"dihedral:k4");
|
||||
memory->create(k1, np1, "dihedral:k1");
|
||||
memory->create(k2, np1, "dihedral:k2");
|
||||
memory->create(k3, np1, "dihedral:k3");
|
||||
memory->create(k4, np1, "dihedral:k4");
|
||||
|
||||
memory->create(setflag,n+1,"dihedral:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
memory->create(setflag, np1, "dihedral:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -265,30 +263,30 @@ void DihedralOPLS::allocate()
|
||||
|
||||
void DihedralOPLS::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 5) error->all(FLERR,"Incorrect args for dihedral coefficients");
|
||||
if (narg != 5) error->all(FLERR, "Incorrect args for dihedral coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
utils::bounds(FLERR,arg[0],1,atom->ndihedraltypes,ilo,ihi,error);
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->ndihedraltypes, ilo, ihi, error);
|
||||
|
||||
double k1_one = utils::numeric(FLERR,arg[1],false,lmp);
|
||||
double k2_one = utils::numeric(FLERR,arg[2],false,lmp);
|
||||
double k3_one = utils::numeric(FLERR,arg[3],false,lmp);
|
||||
double k4_one = utils::numeric(FLERR,arg[4],false,lmp);
|
||||
double k1_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
double k2_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
double k3_one = utils::numeric(FLERR, arg[3], false, lmp);
|
||||
double k4_one = utils::numeric(FLERR, arg[4], false, lmp);
|
||||
|
||||
// store 1/2 factor with prefactor
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
k1[i] = 0.5*k1_one;
|
||||
k2[i] = 0.5*k2_one;
|
||||
k3[i] = 0.5*k3_one;
|
||||
k4[i] = 0.5*k4_one;
|
||||
k1[i] = 0.5 * k1_one;
|
||||
k2[i] = 0.5 * k2_one;
|
||||
k3[i] = 0.5 * k3_one;
|
||||
k4[i] = 0.5 * k4_one;
|
||||
setflag[i] = 1;
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for dihedral coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -297,10 +295,10 @@ void DihedralOPLS::coeff(int narg, char **arg)
|
||||
|
||||
void DihedralOPLS::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&k1[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fwrite(&k2[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fwrite(&k3[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fwrite(&k4[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||
fwrite(&k1[1], sizeof(double), atom->ndihedraltypes, fp);
|
||||
fwrite(&k2[1], sizeof(double), atom->ndihedraltypes, fp);
|
||||
fwrite(&k3[1], sizeof(double), atom->ndihedraltypes, fp);
|
||||
fwrite(&k4[1], sizeof(double), atom->ndihedraltypes, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -312,15 +310,15 @@ void DihedralOPLS::read_restart(FILE *fp)
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR,&k1[1],sizeof(double),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&k2[1],sizeof(double),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&k3[1],sizeof(double),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&k4[1],sizeof(double),atom->ndihedraltypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR, &k1[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &k2[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &k3[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &k4[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&k1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&k2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&k3[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&k4[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&k1[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&k2[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&k3[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&k4[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
|
||||
|
||||
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
|
||||
}
|
||||
@ -332,6 +330,5 @@ void DihedralOPLS::read_restart(FILE *fp)
|
||||
void DihedralOPLS::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ndihedraltypes; i++)
|
||||
fprintf(fp,"%d %g %g %g %g\n",i,2.0*k1[i],2.0*k2[i],2.0*k3[i],2.0*k4[i]);
|
||||
fprintf(fp, "%d %g %g %g %g\n", i, 2.0 * k1[i], 2.0 * k2[i], 2.0 * k3[i], 2.0 * k4[i]);
|
||||
}
|
||||
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user