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renormalize line endings. add .gitattributes to configure them explicitly

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Axel Kohlmeyer
2022-03-17 18:21:31 -04:00
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.github export-ignore .github export-ignore
.lgtm.yml export-ignore .lgtm.yml export-ignore
SECURITY.md export-ignore SECURITY.md export-ignore
* text=auto
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bench/POTENTIALS/ffield.comb
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# COMB parameters for various elements (Si, Cu, Hf, Ti, Zr, U, O) and mixtures (their oxides and alloys) # 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 # Edited by Tzu-Ray Shan from MSE, Univ. FL in Apr 2010
# #
# Elements currently available: Si, Cu, Hf, Ti, Zr, U, O # Elements currently available: Si, Cu, Hf, Ti, Zr, U, O
# Oxides currently available: Si-O, Cu-O, Hf-O, Ti-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) # 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) # ,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) # 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) # 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) # 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) # 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) # 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) # 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 # 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 # 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 # 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 # 27 entries for a system containing three elements A, B and C
# These entries are in LAMMPS "metal" units # 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

144
examples/PACKAGES/atc/drift_diffusion/in.convective_pulse
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@ -1,72 +1,72 @@
# DESCRIPTION: haynes-schockley # DESCRIPTION: haynes-schockley
echo both echo both
units metal units metal
variable V equal 5000.0 variable V equal 5000.0
variable n0 equal 0.085 variable n0 equal 0.085
variable dn equal 2.0*${n0} variable dn equal 2.0*${n0}
variable dt equal 0.0005 variable dt equal 0.0005
variable s equal 10 variable s equal 10
timestep ${dt} timestep ${dt}
atom_style atomic atom_style atomic
lattice fcc 1.0 lattice fcc 1.0
region simRegion block -50 50 0 1 0 1 region simRegion block -50 50 0 1 0 1
boundary f p p boundary f p p
create_box 1 simRegion create_box 1 simRegion
mass 1 1.0 # need to keep this mass 1 1.0 # need to keep this
atom_modify sort 0 1 atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile # ID group atc PhysicsType ParameterFile
fix AtC all atc convective_drift_diffusion Cu_cddm.mat fix AtC all atc convective_drift_diffusion Cu_cddm.mat
# ID part keywords nx ny nz region # ID part keywords nx ny nz region
fix_modify AtC mesh create 100 1 1 simRegion f p p fix_modify AtC mesh create 100 1 1 simRegion f p p
fix_modify AtC material all Cu 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 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_modify AtC mesh create_nodeset rbc 50.0 50.0 -INF INF -INF INF
# fix a temperature # fix a temperature
fix_modify AtC initial temperature all 300.0 fix_modify AtC initial temperature all 300.0
#fix_modify AtC initial electron_temperature all 300.0 #fix_modify AtC initial electron_temperature all 300.0
fix_modify AtC fix electron_temperature all 300. 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_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 initial electron_density all gaussian 0 0 0 1 0 0 5.0 ${dn} ${n0}
#fix_modify AtC fix electron_density all ${n0} #fix_modify AtC fix electron_density all ${n0}
# isolate system: # isolate system:
# diffusion: dn/dx = 0 # diffusion: dn/dx = 0
# drift : n = 0 # drift : n = 0
fix_modify AtC fix electron_density lbc ${n0} fix_modify AtC fix electron_density lbc ${n0}
fix_modify AtC fix electron_density rbc ${n0} fix_modify AtC fix electron_density rbc ${n0}
fix_modify AtC fix temperature lbc 300.0 fix_modify AtC fix temperature lbc 300.0
fix_modify AtC fix temperature rbc 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 lbc 300.0
fix_modify AtC fix electron_temperature rbc 300.0 fix_modify AtC fix electron_temperature rbc 300.0
fix_modify AtC fix electric_potential all 0. fix_modify AtC fix electric_potential all 0.
fix_modify AtC extrinsic electron_integration implicit fix_modify AtC extrinsic electron_integration implicit
# electron velocity # electron velocity
fix_modify AtC initial electron_velocity x all 0. fix_modify AtC initial electron_velocity x all 0.
#fix_modify AtC fix 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 initial electron_velocity y all 0.
fix_modify AtC fix 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 initial electron_velocity z all 0.
fix_modify AtC fix 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 # 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_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 thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output convective_pulseFE $s text binary fix_modify AtC output convective_pulseFE $s text binary
thermo $s thermo $s
#run 100 #run 100
# free electric field and allow shielding # free electric field and allow shielding
fix_modify AtC unfix electric_potential all fix_modify AtC unfix electric_potential all
fix_modify AtC fix electric_potential lbc -$V fix_modify AtC fix electric_potential lbc -$V
fix_modify AtC fix electric_potential rbc 0 fix_modify AtC fix electric_potential rbc 0
fix_modify AtC source electric_potential all ${n0} fix_modify AtC source electric_potential all ${n0}
fix_modify AtC extrinsic electron_integration implicit 10 fix_modify AtC extrinsic electron_integration implicit 10
run 100 run 100

132
examples/PACKAGES/atc/drift_diffusion/in.ddm_schrodinger
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@ -1,66 +1,66 @@
# needs description # needs description
# DESCRIPTION: haynes-schockley # DESCRIPTION: haynes-schockley
# poisson eqn for E-field: epsilon phi,xx = -e (n - p + N_D - N_A) # poisson eqn for E-field: epsilon phi,xx = -e (n - p + N_D - N_A)
# w/ E = phi,x # w/ E = phi,x
echo both echo both
units metal units metal
variable dt equal 0.0000001 variable dt equal 0.0000001
variable s equal 1 variable s equal 1
variable L equal 10.0 variable L equal 10.0
variable N equal 40 variable N equal 40
variable T equal 30000.0 variable T equal 30000.0
variable E equal 0.5 variable E equal 0.5
timestep ${dt} timestep ${dt}
atom_style atomic atom_style atomic
lattice fcc 1.0 lattice fcc 1.0
region simRegion block 0 $L 0 1 0 1 region simRegion block 0 $L 0 1 0 1
boundary f p p boundary f p p
create_box 1 simRegion create_box 1 simRegion
mass 1 1.0 # need to keep this mass 1 1.0 # need to keep this
atom_modify sort 0 1 atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile # ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion-schrodinger Si_ddm_schrodinger.mat fix AtC all atc drift_diffusion-schrodinger Si_ddm_schrodinger.mat
# ID part keywords nx ny nz region # ID part keywords nx ny nz region
fix_modify AtC mesh create $N 1 1 simRegion f p p fix_modify AtC mesh create $N 1 1 simRegion f p p
variable a equal $L-0.1 variable a equal $L-0.1
variable b 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 lbc -0.1 0.1 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF
# ics/bcs : density consistent with wave function # ics/bcs : density consistent with wave function
fix_modify AtC initial temperature all 300.0 fix_modify AtC initial temperature all 300.0
fix_modify AtC fix temperature all 300.0 fix_modify AtC fix temperature all 300.0
fix_modify AtC initial electron_temperature all $T fix_modify AtC initial electron_temperature all $T
fix_modify AtC fix electron_temperature all $T fix_modify AtC fix electron_temperature all $T
fix_modify AtC initial electron_density all 0.0 fix_modify AtC initial electron_density all 0.0
#fix_modify AtC fix electron_density lbc 0 #fix_modify AtC fix electron_density lbc 0
#fix_modify AtC fix electron_density rbc 0 #fix_modify AtC fix electron_density rbc 0
fix_modify AtC initial electric_potential all 0.0 fix_modify AtC initial electric_potential all 0.0
fix_modify AtC initial electron_wavefunction 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 lbc 0
fix_modify AtC fix electron_wavefunction rbc 0 fix_modify AtC fix electron_wavefunction rbc 0
thermo $s thermo $s
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n # 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_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 thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output ddm_schrodingerFE $s text fix_modify AtC output ddm_schrodingerFE $s text
fix_modify AtC extrinsic electron_integration implicit 1 fix_modify AtC extrinsic electron_integration implicit 1
fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 1 # 100 fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 1 # 100
fix_modify AtC unfix electric_potential all fix_modify AtC unfix electric_potential all
# ends zero # ends zero
fix_modify AtC fix electric_potential lbc 0 fix_modify AtC fix electric_potential lbc 0
fix_modify AtC fix electric_potential rbc 0 fix_modify AtC fix electric_potential rbc 0
run 1 run 1
# ends from gradient # ends from gradient
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 0 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 fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 0
run 1 run 1

150
examples/PACKAGES/atc/drift_diffusion/in.finite_well
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@ -1,75 +1,75 @@
#needs description #needs description
echo both echo both
units metal units metal
variable E equal 0.1 variable E equal 0.1
variable L equal 10.0 variable L equal 10.0
#variable N equal 100 #variable N equal 100
variable N equal 80 variable N equal 80
variable T equal 1000 variable T equal 1000
variable n0 equal 0.0001 variable n0 equal 0.0001
variable dn equal 2.0*${n0} variable dn equal 2.0*${n0}
variable dt equal 0.0000001 variable dt equal 0.0000001
variable s equal 1 variable s equal 1
timestep ${dt} timestep ${dt}
atom_style atomic atom_style atomic
lattice fcc 1.0 lattice fcc 1.0
variable a equal 0.5*$L variable a equal 0.5*$L
region simRegion block -$a $a 0 1 0 1 region simRegion block -$a $a 0 1 0 1
boundary f p p boundary f p p
create_box 1 simRegion create_box 1 simRegion
mass 1 1.0 # need to keep this mass 1 1.0 # need to keep this
atom_modify sort 0 1 atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile # ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion-schrodinger SiGe_ddm_schrodinger.mat fix AtC all atc drift_diffusion-schrodinger SiGe_ddm_schrodinger.mat
# ID part keywords nx ny nz region # ID part keywords nx ny nz region
fix_modify AtC mesh create $N 1 1 simRegion f p p fix_modify AtC mesh create $N 1 1 simRegion f p p
variable a equal 0.2*$L+0.001 variable a equal 0.2*$L+0.001
fix_modify AtC mesh create_elementset well -$a $a -INF INF -INF INF fix_modify AtC mesh create_elementset well -$a $a -INF INF -INF INF
fix_modify AtC mesh create_nodeset well -$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 fix_modify AtC material well Ge
variable b equal $a-0.002 variable b equal $a-0.002
fix_modify AtC mesh create_nodeset lbc -$a -$b -INF INF -INF INF fix_modify AtC mesh create_nodeset lbc -$a -$b -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc $b $a -INF INF -INF INF fix_modify AtC mesh create_nodeset rbc $b $a -INF INF -INF INF
# ics/bcs # ics/bcs
fix_modify AtC initial temperature all 300.0 fix_modify AtC initial temperature all 300.0
fix_modify AtC fix temperature all 300.0 fix_modify AtC fix temperature all 300.0
# #
fix_modify AtC initial electron_temperature all $T fix_modify AtC initial electron_temperature all $T
fix_modify AtC fix electron_temperature all $T fix_modify AtC fix electron_temperature all $T
# #
fix_modify AtC initial electron_density all 0.0 fix_modify AtC initial electron_density all 0.0
#fix_modify AtC fix electron_density all -0.001 #fix_modify AtC fix electron_density all -0.001
#fix_modify AtC fix electron_density well 0.002 #fix_modify AtC fix electron_density well 0.002
# #
fix_modify AtC initial electric_potential all 0.0 fix_modify AtC initial electric_potential all 0.0
#fix_modify AtC fix electric_potential lbc 0.5 #fix_modify AtC fix electric_potential lbc 0.5
#fix_modify AtC fix electric_potential rbc 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 lbc 0.0
fix_modify AtC fix electric_potential rbc 0.0 fix_modify AtC fix electric_potential rbc 0.0
# #
fix_modify AtC initial electron_wavefunction all 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 lbc 0.0
fix_modify AtC fix electron_wavefunction rbc 0.0 fix_modify AtC fix electron_wavefunction rbc 0.0
thermo $s thermo $s
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n # 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_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 thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output finite_wellFE $s text fix_modify AtC output finite_wellFE $s text
fix_modify AtC extrinsic electron_integration implicit 3 fix_modify AtC extrinsic electron_integration implicit 3
fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 3 # 30 fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 3 # 30
variable m equal 1*$s variable m equal 1*$s
# (A) no field # (A) no field
run $m run $m
# (B) fixed boundary field # (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 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 fix electric_potential rbc linear 0 0 0 $E 0 0 1
run $m run $m

130
examples/PACKAGES/atc/drift_diffusion/in.no_atoms_ddm
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@ -1,65 +1,65 @@
# needs description # needs description
# DESCRIPTION: haynes-schockley # DESCRIPTION: haynes-schockley
# continuity eqn: n,t = J,x + (G-R) = D n,xx + mu (n E),x + G - 1/tau (n - n_0) # 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 # w/ J = D n,x + mu n phi,x
# poisson eqn for E-field: epsilon phi,xx = -e (n - p + N_D - N_A) # poisson eqn for E-field: epsilon phi,xx = -e (n - p + N_D - N_A)
# w/ E = phi,x # w/ E = phi,x
# NOTE: does not conserve electrons even with fixed E field and zero mobility # NOTE: does not conserve electrons even with fixed E field and zero mobility
# if J=0 --> n,x = mu/D n phi,x # if J=0 --> n,x = mu/D n phi,x
echo both echo both
units metal units metal
variable E equal 10.0 variable E equal 10.0
variable n0 equal 0.0001 variable n0 equal 0.0001
variable dn equal 2.0*${n0} variable dn equal 2.0*${n0}
variable dt equal 0.0000001 variable dt equal 0.0000001
timestep ${dt} timestep ${dt}
atom_style atomic atom_style atomic
lattice fcc 1.0 lattice fcc 1.0
region simRegion block -50 50 0 1 0 1 region simRegion block -50 50 0 1 0 1
boundary f p p boundary f p p
create_box 1 simRegion create_box 1 simRegion
mass 1 1.0 # need to keep this mass 1 1.0 # need to keep this
atom_modify sort 0 1 atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile # ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion Si_ddm.mat fix AtC all atc drift_diffusion Si_ddm.mat
# ID part keywords nx ny nz region # ID part keywords nx ny nz region
fix_modify AtC mesh create 100 1 1 simRegion f p p 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 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_modify AtC mesh create_nodeset rbc 49.9 50.1 -INF INF -INF INF
# fix a temperature # fix a temperature
fix_modify AtC initial temperature all 300.0 fix_modify AtC initial temperature all 300.0
fix_modify AtC initial electron_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} fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 ${dn} ${n0}
# isolate system: # isolate system:
# diffusion: dn/dx = 0 # diffusion: dn/dx = 0
# drift : n = 0 # drift : n = 0
fix_modify AtC fix electron_density lbc ${n0} fix_modify AtC fix electron_density lbc ${n0}
fix_modify AtC fix electron_density rbc ${n0} fix_modify AtC fix electron_density rbc ${n0}
fix_modify AtC fix electric_potential all linear 0 0 0 $E 0 0 1 fix_modify AtC fix electric_potential all linear 0 0 0 $E 0 0 1
variable perm equal 0.06 variable perm equal 0.06
variable nD equal 1.0e-4 variable nD equal 1.0e-4
fix_modify AtC source electric_potential all ${nD} fix_modify AtC source electric_potential all ${nD}
variable s equal 10 variable s equal 10
thermo $s thermo $s
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n # 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_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 thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output no_atoms_ddmFE $s text fix_modify AtC output no_atoms_ddmFE $s text
fix_modify AtC extrinsic electron_integration implicit fix_modify AtC extrinsic electron_integration implicit
run 40 run 40
# free electric field and allow shielding # free electric field and allow shielding
fix_modify AtC unfix electric_potential all 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 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 fix electric_potential rbc linear 0 0 0 $E 0 0 1
fix_modify AtC extrinsic electron_integration implicit 10 fix_modify AtC extrinsic electron_integration implicit 10
run 40 run 40

158
examples/PACKAGES/atc/drift_diffusion/in.null_material_ddm
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@ -1,79 +1,79 @@
# needs description # needs description
#AtC drift diffusion Coupling #AtC drift diffusion Coupling
# DESCRIPTION: # DESCRIPTION:
# electric potential solved over whole domain # electric potential solved over whole domain
# all others only over the lower half # all others only over the lower half
# temperature is fixed over whole domain # temperature is fixed over whole domain
# NOTE the vacuum can fully masked out by making the material # NOTE the vacuum can fully masked out by making the material
# have null electron_density in Ar_ddm.mat # have null electron_density in Ar_ddm.mat
echo both echo both
units metal units metal
variable s equal 100 variable s equal 100
variable T equal 20 variable T equal 20
variable n equal 0.000004 variable n equal 0.000004
variable tol equal 0.1 variable tol equal 0.1
variable W equal 1000 variable W equal 1000
atom_style atomic atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25 lattice fcc 5.405 origin 0.25 0.25 0.25
region FE block -8 8 -6 6 0 3 region FE block -8 8 -6 6 0 3
region MD block -7 7 -6 0 0 3 region MD block -7 7 -6 0 0 3
region FREE block -4 4 -6 0 0 3 region FREE block -4 4 -6 0 0 3
boundary f f p boundary f f p
# create atoms # create atoms
create_box 1 FE create_box 1 FE
mass 1 39.95 mass 1 39.95
atom_modify sort 0 1 atom_modify sort 0 1
timestep 0.002 timestep 0.002
thermo $s thermo $s
# ID group atc PhysicsType ParameterFile # ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion Ar_ddm.mat fix AtC all atc drift_diffusion Ar_ddm.mat
# ID part keywords nx ny nz region # ID part keywords nx ny nz region
fix_modify AtC mesh create 4 4 1 FE f f p fix_modify AtC mesh create 4 4 1 FE f f p
variable a equal $W+${tol} variable a equal $W+${tol}
fix_modify AtC mesh create_elementset wire -$a $a -INF ${tol} -INF INF fix_modify AtC mesh create_elementset wire -$a $a -INF ${tol} -INF INF
fix_modify AtC mesh create_elementset gap -$a $a -${tol} INF -INF INF fix_modify AtC mesh create_elementset gap -$a $a -${tol} INF -INF INF
# void is the complement of the wire nodeset # void is the complement of the wire nodeset
variable a equal $W-${tol} variable a equal $W-${tol}
fix_modify AtC mesh create_nodeset void -$a $a ${tol} INF -INF INF fix_modify AtC mesh create_nodeset void -$a $a ${tol} INF -INF INF
fix_modify AtC mesh output null_material_ddmMESH binary fix_modify AtC mesh output null_material_ddmMESH binary
fix_modify AtC control thermal none fix_modify AtC control thermal none
# fix a temperature # fix a temperature
fix_modify AtC initial temperature all $T fix_modify AtC initial temperature all $T
fix_modify AtC initial electron_temperature all $T fix_modify AtC initial electron_temperature all $T
fix_modify AtC initial electron_density all $n fix_modify AtC initial electron_density all $n
fix_modify AtC initial electric_potential all 0.0 fix_modify AtC initial electric_potential all 0.0
fix_modify AtC initial temperature void 0.0 fix_modify AtC initial temperature void 0.0
fix_modify AtC initial electron_density void 0.0 fix_modify AtC initial electron_density void 0.0
fix_modify AtC initial electric_potential void 0.0 fix_modify AtC initial electric_potential void 0.0
# create vacuum # create vacuum
fix_modify AtC material gap Vacuum fix_modify AtC material gap Vacuum
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] 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 output null_material_ddmFE $s full_text binary
fix_modify AtC extrinsic electron_integration implicit 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 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 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 lbc $T
fix_modify AtC fix electron_temperature rbc $T fix_modify AtC fix electron_temperature rbc $T
fix_modify AtC fix electron_density lbc $n fix_modify AtC fix electron_density lbc $n
fix_modify AtC fix electric_potential lbc 0.0 fix_modify AtC fix electric_potential lbc 0.0
variable m equal $s*10 variable m equal $s*10
run $m run $m

182
examples/PACKAGES/atc/elastic/in.bar1d
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@ -1,91 +1,91 @@
# needs description # needs description
#AtC Thermal Coupling #AtC Thermal Coupling
echo both echo both
units real units real
atom_style atomic atom_style atomic
# create domain # 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 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 lattice fcc 5.405 origin 0.25 0.25 0.25
# create atoms # create atoms
region simRegion block -12 12 -3 3 -3 3 region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3 region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3 region mdRegion block -8 8 -3 3 -3 3
boundary f p p boundary f p p
create_box 1 simRegion create_box 1 simRegion
create_atoms 1 region mdRegion create_atoms 1 region mdRegion
mass 1 39.95 mass 1 39.95
# specify interal/ghost atoms # specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3 region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3 region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3 region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal group internal region mdInternal
group Lghost region leftghost group Lghost region leftghost
group Rghost region rightghost group Rghost region rightghost
group ghosts union Lghost Rghost group ghosts union Lghost Rghost
# velocities have Vcm = 0 # velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom #velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.5 pair_style lj/cut 13.5
#pair_coeff 1 1 0.010323166 3.405 13.5 #pair_coeff 1 1 0.010323166 3.405 13.5
pair_coeff 1 1 .238 3.405 13.5 pair_coeff 1 1 .238 3.405 13.5
neighbor 5. bin neighbor 5. bin
neigh_modify every 10 delay 0 check no neigh_modify every 10 delay 0 check no
# define layer # define layer
# ID group atc PhysicsType ParameterFile # ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat fix AtC internal atc elastic Ar_elastic.mat
# ID part keywords nx ny nz region # ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions # initial conditions
fix_modify AtC initial displacement x all 0.0 fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y 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 displacement z all 0.0
fix_modify AtC initial velocity x 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 y all 0.0
fix_modify AtC initial velocity z all 0.0 fix_modify AtC initial velocity z all 0.0
# set node sets and bcs # set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax # 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 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 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 0.00000004
fix_modify AtC fix displacement x lbc 0. fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0. fix_modify AtC fix velocity x lbc 0.
# specify atom types # specify atom types
#fix_modify AtC boundary Lghost #fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost #fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts fix_modify AtC boundary ghosts
#fix_modify AtC output follow_ex.fe 50 #fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on fix_modify AtC control localized_lambda on
fix_modify AtC control momentum glc_velocity fix_modify AtC control momentum glc_velocity
fix_modify AtC filter type exponential fix_modify AtC filter type exponential
fix_modify AtC filter scale 1000.0 fix_modify AtC filter scale 1000.0
fix_modify AtC filter on fix_modify AtC filter on
# run to extension # run to extension
#fix_modify AtC output bar1dFE 50 text #fix_modify AtC output bar1dFE 50 text
timestep 5 timestep 5
thermo 100 thermo 100
run 1000 run 1000
# change nodes to fixed # change nodes to fixed
fix_modify AtC fix velocity x rbc 0. fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002 fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1dFE 500 text fix_modify AtC output bar1dFE 500 text
# run to equilibrium # run to equilibrium
timestep 5 timestep 5
thermo 100 thermo 100
run 10000 run 10000

232
examples/PACKAGES/atc/elastic/in.bar1d_damped
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@ -1,116 +1,116 @@
# needs description # needs description
echo both echo both
units metal units metal
atom_style atomic atom_style atomic
# create domain # 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 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 lattice fcc 5.405 origin 0.25 0.25 0.25
# create atoms # create atoms
region simRegion block -12 12 -3 3 -3 3 region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3 region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3 region mdRegion block -8 8 -3 3 -3 3
boundary f p p boundary f p p
create_box 2 simRegion create_box 2 simRegion
create_atoms 1 region mdRegion create_atoms 1 region mdRegion
mass * 39.95 mass * 39.95
# specify interal/ghost atoms # specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3 region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3 region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3 region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal group internal region mdInternal
group Lghost region leftghost group Lghost region leftghost
group Rghost region rightghost group Rghost region rightghost
group ghosts union Lghost Rghost group ghosts union Lghost Rghost
# velocities have Vcm = 0 # velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom #velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.5 pair_style lj/cut 13.5
#pair_coeff * * .238 3.405 13.5 #pair_coeff * * .238 3.405 13.5
pair_coeff * * 0.010323166 3.405 13.5 pair_coeff * * 0.010323166 3.405 13.5
neighbor 5. bin neighbor 5. bin
neigh_modify every 10 delay 0 check no neigh_modify every 10 delay 0 check no
# define layer # define layer
# ID group atc PhysicsType ParameterFile # ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_damped.mat fix AtC internal atc elastic Ar_damped.mat
# ID part keywords nx ny nz region # ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions # initial conditions
fix_modify AtC initial displacement x all 0.0 fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y 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 displacement z all 0.0
fix_modify AtC initial velocity x 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 y all 0.0
fix_modify AtC initial velocity z all 0.0 fix_modify AtC initial velocity z all 0.0
variable v equal 0.00000004e3 variable v equal 0.00000004e3
variable n equal 1000 variable n equal 1000
variable dt equal 0.005 variable dt equal 0.005
variable u equal $v*$n*${dt} variable u equal $v*$n*${dt}
# set node sets and bcs # set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax # 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 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 mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc $v fix_modify AtC fix velocity x rbc $v
fix_modify AtC fix displacement x lbc 0. fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0. fix_modify AtC fix velocity x lbc 0.
# specify atom types # specify atom types
fix_modify AtC boundary ghosts fix_modify AtC boundary ghosts
#fix_modify AtC output follow_ex.fe 50 #fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on fix_modify AtC control localized_lambda on
fix_modify AtC control momentum glc_velocity fix_modify AtC control momentum glc_velocity
#fix_modify AtC filter type exponential #fix_modify AtC filter type exponential
#fix_modify AtC filter scale 1.0 #fix_modify AtC filter scale 1.0
#fix_modify AtC filter on #fix_modify AtC filter on
# run to extension # run to extension
timestep 0.005 timestep 0.005
thermo 100 thermo 100
thermo_style custom step cpu ke pe thermo_style custom step cpu ke pe
run 0 run 0
variable pe0 equal pe variable pe0 equal pe
variable pe equal pe-${pe0} 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] thermo_style custom step cpu ke pe v_pe f_AtC[1] f_AtC[2] f_AtC[4] f_AtC[5]
run $n run $n
fix_modify AtC output bar1d_dampedFE 500 text fix_modify AtC output bar1d_dampedFE 500 text
dump CONFIG all custom 500 bar1d_damped.dmp id type x y z vx vy vz dump CONFIG all custom 500 bar1d_damped.dmp id type x y z vx vy vz
# change nodes to fixed # change nodes to fixed
fix_modify AtC fix velocity x rbc 0. fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc $u fix_modify AtC fix displacement x rbc $u
# run to equilibrium # run to equilibrium
thermo 100 thermo 100
log bar1d_damped.log log bar1d_damped.log
run 2000 run 2000
fix_modify AtC material all cubic # M damping fix_modify AtC material all cubic # M damping
run 2000 run 2000
fix_modify AtC material all damped # K damping fix_modify AtC material all damped # K damping
run 2000 run 2000
# ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 from Ar_CauchyBorn.mat # ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 from Ar_CauchyBorn.mat
# real to metal 1 kcal/mol = 0.04336 eV # real to metal 1 kcal/mol = 0.04336 eV
variable kCal2eV equal 0.04336 variable kCal2eV equal 0.04336
variable fconv equal 1./0.000103643 # NOTE old routine was doing calculations in lammps units, not atc units, so this conversion is necessary for bmark to pass variable fconv equal 1./0.000103643 # NOTE old routine was doing calculations in lammps units, not atc units, so this conversion is necessary for bmark to pass
#variable k equal 1.e-3 # 7.56717*${kCal2eV} NOTE <<< #variable k equal 1.e-3 # 7.56717*${kCal2eV} NOTE <<<
#variable k equal 0.75*0.355649e3*${kCal2eV} #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 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 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 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 variable m equal 2. #0.5*39.95
fix_modify AtC boundary_dynamics damped_harmonic $k $g $m fix_modify AtC boundary_dynamics damped_harmonic $k $g $m
run 2000 run 2000

196
examples/PACKAGES/atc/elastic/in.bar1d_flux
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@ -1,98 +1,98 @@
# needs description # needs description
#AtC Thermal Coupling #AtC Thermal Coupling
echo both echo both
units real units real
atom_style atomic atom_style atomic
# create domain # 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 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 lattice fcc 5.2582305 origin 0.25 0.25 0.25
# create atoms # create atoms
region simRegion block -12 12 -3 3 -3 3 region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3 region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3 region mdRegion block -8 8 -3 3 -3 3
boundary f p p boundary f p p
create_box 1 simRegion create_box 1 simRegion
create_atoms 1 region mdRegion create_atoms 1 region mdRegion
mass 1 39.95 mass 1 39.95
# specify interal/ghost atoms # specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3 region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3 region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3 region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal group internal region mdInternal
group Lghost region leftghost group Lghost region leftghost
group Rghost region rightghost group Rghost region rightghost
group ghosts union Lghost Rghost group ghosts union Lghost Rghost
# velocities have Vcm = 0 # velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom #velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13. pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13. #pair_coeff 1 1 0.010323166 3.405 13.
pair_coeff 1 1 .2381 3.405 13. pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin neighbor 5. bin
neigh_modify every 10 delay 0 check no neigh_modify every 10 delay 0 check no
# define layer # define layer
# ID group atc PhysicsType ParameterFile # ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat fix AtC internal atc elastic Ar_elastic.mat
#fix_modify AtC boundary Lghost #fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost #fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region # ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p 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 mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
# initial conditions # initial conditions
fix_modify AtC initial displacement x all 0.0 fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y 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 displacement z all 0.0
fix_modify AtC initial velocity x 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 y all 0.0
fix_modify AtC initial velocity z all 0.0 fix_modify AtC initial velocity z all 0.0
# set node sets and bcs # set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax # 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 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 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 0.00000004
#fix_modify AtC fix velocity x rbc 0. #fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0. #fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0. fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0. fix_modify AtC fix velocity x lbc 0.
#fix_modify AtC output follow_ex.fe 50 #fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off fix_modify AtC internal_quadrature off
#fix_modify AtC control lumped_lambda_solve on #fix_modify AtC control lumped_lambda_solve on
#fix_modify AtC momentum control glc_velocity #fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy #fix_modify AtC momentum control flux faceset obndy
fix_modify AtC control momentum flux interpolate fix_modify AtC control momentum flux interpolate
#fix_modify AtC filter scale 1000.0 #fix_modify AtC filter scale 1000.0
# run to extension # run to extension
compute myTemp internal temp compute myTemp internal temp
compute atomStress internal stress/atom NULL compute atomStress internal stress/atom NULL
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3] 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) variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_fluxFE 10 text fix_modify AtC output bar1d_fluxFE 10 text
timestep 5 timestep 5
thermo 100 thermo 100
run 1000 run 1000
# change nodes to fixed # change nodes to fixed
fix_modify AtC fix velocity x rbc 0. fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002 fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1d_fluxFE 500 text fix_modify AtC output bar1d_fluxFE 500 text
# run to equilibrium # run to equilibrium
timestep 5 timestep 5
thermo 100 thermo 100
run 10000 run 10000

198
examples/PACKAGES/atc/elastic/in.bar1d_frac_step
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@ -1,99 +1,99 @@
# needs description # needs description
#AtC Elastic Coupling #AtC Elastic Coupling
echo both echo both
units real units real
atom_style atomic atom_style atomic
# create domain # 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 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 lattice fcc 5.2582305 origin 0.25 0.25 0.25
# create atoms # create atoms
region simRegion block -12 12 -3 3 -3 3 region simRegion block -12 12 -3 3 -3 3
region atomRegion block -8 8 -3 3 -3 3 region atomRegion block -8 8 -3 3 -3 3
region mdRegion block -6 6 -3 3 -3 3 region mdRegion block -6 6 -3 3 -3 3
boundary f p p boundary f p p
create_box 1 simRegion create_box 1 simRegion
create_atoms 1 region atomRegion create_atoms 1 region atomRegion
mass 1 39.95 mass 1 39.95
# specify interal/ghost atoms # specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3 region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3 region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3 region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal group internal region mdInternal
group Lghost region leftghost group Lghost region leftghost
group Rghost region rightghost group Rghost region rightghost
group ghosts union Lghost Rghost group ghosts union Lghost Rghost
pair_style lj/cut 13. pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.5 #pair_coeff 1 1 0.010323166 3.405 13.5
pair_coeff 1 1 .2381 3.405 13. pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin neighbor 5. bin
neigh_modify every 10 delay 0 check no neigh_modify every 10 delay 0 check no
# define layer # define layer
# ID group atc PhysicsType ParameterFile # ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat fix AtC internal atc elastic Ar_elastic.mat
# ID part keywords nx ny nz region # ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions # initial conditions
fix_modify AtC initial displacement x all 0.0 fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y 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 displacement z all 0.0
fix_modify AtC initial velocity x 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 y all 0.0
fix_modify AtC initial velocity z all 0.0 fix_modify AtC initial velocity z all 0.0
fix_modify AtC time_integration fractional_step fix_modify AtC time_integration fractional_step
fix_modify AtC internal_atom_integrate off fix_modify AtC internal_atom_integrate off
fix iNVE internal nve fix iNVE internal nve
# set node sets and bcs # set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax # 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 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 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 0.00000004
fix_modify AtC fix displacement x lbc 0. fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0. fix_modify AtC fix velocity x lbc 0.
# specify atom types # specify atom types
#fix_modify AtC boundary Lghost #fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost #fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts fix_modify AtC boundary ghosts
fix_modify AtC internal_quadrature off fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on fix_modify AtC control localized_lambda on
fix_modify AtC control momentum flux interpolate fix_modify AtC control momentum flux interpolate
#fix_modify AtC control momentum hoover # tested in this mode #fix_modify AtC control momentum hoover # tested in this mode
#fix_modify AtC filter type exponential #fix_modify AtC filter type exponential
#fix_modify AtC filter scale 1000.0 #fix_modify AtC filter scale 1000.0
#fix_modify AtC filter on #fix_modify AtC filter on
# run to extension # run to extension
#fix_modify AtC output bar1d_frac_step_initFE 50 text binary #fix_modify AtC output bar1d_frac_step_initFE 50 text binary
#dump D1 all atom 50 bar1d_frac_step_init.dmp #dump D1 all atom 50 bar1d_frac_step_init.dmp
timestep 5 timestep 5
thermo 100 thermo 100
run 1000 run 1000
# reset time # reset time
fix_modify AtC reset_time 0. fix_modify AtC reset_time 0.
reset_timestep 0 reset_timestep 0
# change nodes to fixed # change nodes to fixed
fix_modify AtC fix velocity x rbc 0. fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002 fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1d_frac_stepFE 500 text #binary fix_modify AtC output bar1d_frac_stepFE 500 text #binary
#fix_modify AtC output index step #fix_modify AtC output index step
#undump D1 #undump D1
#dump D1 all atom 500 bar1d_frac_step.dmp #dump D1 all atom 500 bar1d_frac_step.dmp
# run to equilibrium # run to equilibrium
timestep 5 timestep 5
thermo 100 thermo 100
run 5000 run 5000

202
examples/PACKAGES/atc/elastic/in.bar1d_ghost_flux
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@ -1,101 +1,101 @@
# Computes elastic waves propagating in and out of a finite temperature region # Computes elastic waves propagating in and out of a finite temperature region
#AtC ThermoElastic Coupling #AtC ThermoElastic Coupling
echo both echo both
units real units real
atom_style atomic atom_style atomic
# create domain # 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 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 lattice fcc 5.2582305 origin 0.25 0.25 0.25
region simRegion block -12 12 -3 3 -3 3 region simRegion block -12 12 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3 region mdRegion block -8 8 -3 3 -3 3
boundary f p p boundary f p p
create_box 1 simRegion create_box 1 simRegion
create_atoms 1 region mdRegion create_atoms 1 region mdRegion
mass 1 39.95 mass 1 39.95
# specify interal/ghost atoms # specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3 region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3 region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3 region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal group internal region mdInternal
group Lghost region leftghost group Lghost region leftghost
group Rghost region rightghost group Rghost region rightghost
group ghosts union Lghost Rghost group ghosts union Lghost Rghost
# velocities have Vcm = 0, NOTE next for lines commented out for restart # velocities have Vcm = 0, NOTE next for lines commented out for restart
pair_style lj/cut 13. pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13. #pair_coeff 1 1 0.010323166 3.405 13.
pair_coeff 1 1 .2381 3.405 13. pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin neighbor 5. bin
neigh_modify every 10 delay 0 check no neigh_modify every 10 delay 0 check no
# define layer # define layer
# ID group atc PhysicsType ParameterFile # ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat fix AtC internal atc elastic Ar_elastic.mat
fix_modify AtC boundary ghosts fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region # ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p 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 mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off fix_modify AtC internal_quadrature off
fix_modify AtC internal_atom_integrate off fix_modify AtC internal_atom_integrate off
fix iNVE internal nve fix iNVE internal nve
# initial conditions # initial conditions
fix_modify AtC initial displacement x all 0.0 fix_modify AtC initial displacement x all 0.0
fix_modify AtC fix displacement y 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 displacement z all 0.0
fix_modify AtC initial velocity x 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 y all 0.0
fix_modify AtC fix velocity z all 0.0 fix_modify AtC fix velocity z all 0.0
# set node sets and bcs # set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax # 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 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 mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
#fix_modify AtC fix velocity x rbc 0. #fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0. #fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0. fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0. fix_modify AtC fix velocity x lbc 0.
# turn on multiscale # turn on multiscale
fix_modify AtC control momentum ghost_flux fix_modify AtC control momentum ghost_flux
# new boundary conditions # new boundary conditions
fix_modify AtC fix velocity x rbc 0.00000004 fix_modify AtC fix velocity x rbc 0.00000004
#fix_modify AtC output follow_ex.fe 50 #fix_modify AtC output follow_ex.fe 50
#fix_modify AtC localized_lambda on #fix_modify AtC localized_lambda on
#fix_modify AtC momentum control glc_velocity #fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy #fix_modify AtC momentum control flux faceset obndy
#fix_modify AtC control momentum flux #fix_modify AtC control momentum flux
#fix_modify AtC control momentum ghost_flux #fix_modify AtC control momentum ghost_flux
#fix_modify AtC filter scale 1000.0 #fix_modify AtC filter scale 1000.0
# run to extension # run to extension
compute myTemp internal temp compute myTemp internal temp
compute atomStress internal stress/atom NULL compute atomStress internal stress/atom NULL
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3] 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) variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_ghost_fluxFE 500 text fix_modify AtC output bar1d_ghost_fluxFE 500 text
#dump D1 all atom 100 bar1d_ghost_flux.dmp #dump D1 all atom 100 bar1d_ghost_flux.dmp
timestep 5 timestep 5
thermo 100 thermo 100
run 1000 run 1000
# change nodes to fixed # change nodes to fixed
fix_modify AtC unfix velocity x rbc fix_modify AtC unfix velocity x rbc
#fix_modify AtC fix displacement x rbc 0.0002 #fix_modify AtC fix displacement x rbc 0.0002
#fix_modify AtC output bar1d_fluxFE 500 text binary #fix_modify AtC output bar1d_fluxFE 500 text binary
# run to equilibrium # run to equilibrium
timestep 5 timestep 5
thermo 100 thermo 100
run 3000 run 3000

278
examples/PACKAGES/atc/elastic/in.bar1d_thermo_elastic
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@ -1,139 +1,139 @@
# Computes elastic waves propagating in and out of a finite temperature region # Computes elastic waves propagating in and out of a finite temperature region
#AtC ThermoElastic Coupling #AtC ThermoElastic Coupling
echo both echo both
units real units real
atom_style atomic atom_style atomic
# create domain # 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 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 lattice fcc 5.2582305 origin 0.25 0.25 0.25
# NOTE following 3 lines added for restart # NOTE following 3 lines added for restart
boundary f p p boundary f p p
pair_style lj/cut 13. pair_style lj/cut 13.
read_data temp.init read_data temp.init
region simRegion block -12 12 -3 3 -3 3 region simRegion block -12 12 -3 3 -3 3
# create atoms, NOTE commented out for restart # create atoms, NOTE commented out for restart
#region mdRegion block -8 8 -3 3 -3 3 #region mdRegion block -8 8 -3 3 -3 3
#boundary f p p #boundary f p p
#region mdBox block -9 9 -3 3 -3 3 #region mdBox block -9 9 -3 3 -3 3
#create_box 1 mdBox #create_box 1 mdBox
#create_atoms 1 region mdRegion #create_atoms 1 region mdRegion
#mass 1 39.95 #mass 1 39.95
# specify interal/ghost atoms # specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3 region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3 region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3 region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal group internal region mdInternal
group Lghost region leftghost group Lghost region leftghost
group Rghost region rightghost group Rghost region rightghost
group ghosts union Lghost Rghost group ghosts union Lghost Rghost
# velocities have Vcm = 0, NOTE next for lines commented out for restart # velocities have Vcm = 0, NOTE next for lines commented out for restart
#velocity internal create 40. 87287 mom yes loop geom #velocity internal create 40. 87287 mom yes loop geom
#pair_style lj/cut 13. #pair_style lj/cut 13.
##pair_coeff 1 1 0.010323166 3.405 13. ##pair_coeff 1 1 0.010323166 3.405 13.
#pair_coeff 1 1 .2381 3.405 13. #pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin neighbor 5. bin
neigh_modify every 10 delay 0 check no neigh_modify every 10 delay 0 check no
#write_restart tinit.dat #write_restart tinit.dat
# zero initial momentum # zero initial momentum
fix AtC internal atc elastic Ar_thermo_elastic.mat fix AtC internal atc elastic Ar_thermo_elastic.mat
# ID part keywords nx ny nz region # ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p 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 mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off fix_modify AtC internal_quadrature off
fix_modify AtC fix displacement x all 0. fix_modify AtC fix displacement x all 0.
fix_modify AtC fix displacement y all 0. fix_modify AtC fix displacement y all 0.
fix_modify AtC fix displacement z all 0. fix_modify AtC fix displacement z all 0.
fix_modify AtC fix velocity x all 0. fix_modify AtC fix velocity x all 0.
fix_modify AtC fix velocity y all 0. fix_modify AtC fix velocity y all 0.
fix_modify AtC fix velocity z all 0. fix_modify AtC fix velocity z all 0.
fix_modify AtC control momentum glc_velocity fix_modify AtC control momentum glc_velocity
#fix_modify AtC output bar1d_thermo_elastic_initializeFE 1 text #binary #fix_modify AtC output bar1d_thermo_elastic_initializeFE 1 text #binary
timestep 0 timestep 0
thermo 1 thermo 1
run 1 run 1
unfix AtC unfix AtC
# define layer # define layer
# ID group atc PhysicsType ParameterFile # ID group atc PhysicsType ParameterFile
fix AtC internal atc thermo_elastic Ar_thermo_elastic.mat fix AtC internal atc thermo_elastic Ar_thermo_elastic.mat
fix_modify AtC boundary ghosts fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region # ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p 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 mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off fix_modify AtC internal_quadrature off
# initial conditions # initial conditions
fix_modify AtC initial displacement x all 0.0 fix_modify AtC initial displacement x all 0.0
fix_modify AtC fix displacement y 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 displacement z all 0.0
fix_modify AtC initial velocity x 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 y all 0.0
fix_modify AtC fix velocity z all 0.0 fix_modify AtC fix velocity z all 0.0
fix_modify AtC fix temperature all 20. fix_modify AtC fix temperature all 20.
# set node sets and bcs # set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax # 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 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 mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
#fix_modify AtC fix velocity x rbc 0. #fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0. #fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0. fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0. fix_modify AtC fix velocity x lbc 0.
# rescale thermostat for initial atomic temperatures # rescale thermostat for initial atomic temperatures
fix_modify AtC control thermal rescale 10 fix_modify AtC control thermal rescale 10
fix_modify AtC control momentum ghost_flux fix_modify AtC control momentum ghost_flux
fix_modify AtC output bar1d_thermo_elasticFE 100 text #binary fix_modify AtC output bar1d_thermo_elasticFE 100 text #binary
timestep 5 timestep 5
thermo 100 thermo 100
run 1000 run 1000
# free all nodes # free all nodes
#fix_modify AtC unfix displacement x all #fix_modify AtC unfix displacement x all
#fix_modify AtC unfix velocity x all #fix_modify AtC unfix velocity x all
fix_modify AtC unfix temperature all fix_modify AtC unfix temperature all
# new boundary conditions # new boundary conditions
fix_modify AtC fix velocity x rbc 0.00000004 fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix temperature lbc 20. fix_modify AtC fix temperature lbc 20.
#fix_modify AtC output follow_ex.fe 50 #fix_modify AtC output follow_ex.fe 50
#fix_modify AtC localized_lambda on #fix_modify AtC localized_lambda on
#fix_modify AtC momentum control glc_velocity #fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy #fix_modify AtC momentum control flux faceset obndy
#fix_modify AtC control momentum flux #fix_modify AtC control momentum flux
#fix_modify AtC control momentum ghost_flux #fix_modify AtC control momentum ghost_flux
fix_modify AtC control thermal flux fix_modify AtC control thermal flux
#fix_modify AtC filter scale 1000.0 #fix_modify AtC filter scale 1000.0
# run to extension # run to extension
compute myTemp internal temp compute myTemp internal temp
compute atomStress internal stress/atom NULL compute atomStress internal stress/atom NULL
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3] 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) variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_thermo_elasticFE 500 text 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 #dump D1 all custom 100 bar1d_thermo_elastic.dmp id type x y z vx vy vz
timestep 5 timestep 5
thermo 100 thermo 100
run 1000 run 1000
# change nodes to fixed # change nodes to fixed
fix_modify AtC unfix velocity x rbc 0. fix_modify AtC unfix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.0002 #fix_modify AtC fix displacement x rbc 0.0002
#fix_modify AtC output bar1d_fluxFE 500 text binary #fix_modify AtC output bar1d_fluxFE 500 text binary
# run to equilibrium # run to equilibrium
timestep 5 timestep 5
thermo 100 thermo 100
run 3000 run 3000

160
examples/PACKAGES/atc/elastic/in.eam_energy
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@ -1,80 +1,80 @@
echo both echo both
units metal units metal
atom_style atomic atom_style atomic
atom_modify map hash atom_modify map hash
boundary p p p boundary p p p
variable l equal 3 variable l equal 3
variable l2 equal 0.5*$l variable l2 equal 0.5*$l
variable L equal 10 variable L equal 10
variable L2 equal 0.5*$L variable L2 equal 0.5*$L
variable h equal $L variable h equal $L
lattice fcc 4.08 origin 0.25 0.25 0.25 lattice fcc 4.08 origin 0.25 0.25 0.25
region BOX block -${l2} ${l2} -${L2} ${L2} -${l2} ${l2} region BOX block -${l2} ${l2} -${L2} ${L2} -${l2} ${l2}
create_box 1 BOX create_box 1 BOX
create_atoms 1 region BOX create_atoms 1 region BOX
pair_style eam pair_style eam
pair_coeff * * Au_u3.eam pair_coeff * * Au_u3.eam
mass * 196.97 mass * 196.97
### NOTE change to CB -linear ### NOTE change to CB -linear
fix PP all atc field Au_elastic.mat fix PP all atc field Au_elastic.mat
fix_modify PP mesh create 1 $h 1 BOX p f p 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 fields add displacement velocity potential_energy cauchy_born_energy # kinetic_energy
fix_modify PP gradients add displacement fix_modify PP gradients add displacement
fix_modify PP set reference_potential_energy fix_modify PP set reference_potential_energy
fix_modify PP output counter step fix_modify PP output counter step
fix_modify PP output eam_energyPP 1 text fix_modify PP output eam_energyPP 1 text
fix ATC all atc elastic Au_elastic.mat fix ATC all atc elastic Au_elastic.mat
fix_modify ATC mesh create 1 $h 1 BOX p f p fix_modify ATC mesh create 1 $h 1 BOX p f p
fix_modify ATC internal_quadrature off fix_modify ATC internal_quadrature off
fix_modify ATC control momentum none fix_modify ATC control momentum none
#fix_modify ATC consistent_fe_initialization on #fix_modify ATC consistent_fe_initialization on
fix_modify ATC output counter step fix_modify ATC output counter step
fix_modify ATC output eam_energyFE 1 text binary fix_modify ATC output eam_energyFE 1 text binary
fix_modify ATC material all Au_cubic fix_modify ATC material all Au_cubic
dump CONFIG all custom 1 eam_energy.dmp id type x y z dump CONFIG all custom 1 eam_energy.dmp id type x y z
thermo 1 thermo 1
timestep 0 # 1.e-20 # 0 timestep 0 # 1.e-20 # 0
variable e0 equal pe variable e0 equal pe
variable L0 equal ly variable L0 equal ly
run 0 run 0
variable pe equal pe-${e0} variable pe equal pe-${e0}
variable dL equal ly-${L0} variable dL equal ly-${L0}
variable strain equal v_dL/${L0} variable strain equal v_dL/${L0}
variable x equal y[1] variable x equal y[1]
variable x2 equal y[2] variable x2 equal y[2]
variable v equal vy[1] 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_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 thermo_modify format 2 %15.8g
############################################################################### ###############################################################################
log eam_energy.log log eam_energy.log
run 1 run 1
velocity all set 0 0.1 0 units box velocity all set 0 0.1 0 units box
fix_modify ATC fix velocity y all 0.1 fix_modify ATC fix velocity y all 0.1
run 1 run 1
velocity all set 0 0.2 0 units box velocity all set 0 0.2 0 units box
fix_modify ATC fix velocity y all 0.2 fix_modify ATC fix velocity y all 0.2
run 1 run 1
velocity all set 0 0.3 0 units box velocity all set 0 0.3 0 units box
fix_modify ATC fix velocity y all 0.3 fix_modify ATC fix velocity y all 0.3
run 1 run 1
change_box all y scale 1.01 remap change_box all y scale 1.01 remap
fix_modify ATC fix displacement y all linear 0 0 0 0 0.01 0 0 fix_modify ATC fix displacement y all linear 0 0 0 0 0.01 0 0
run 1 run 1
change_box all y scale 1.01 remap change_box all y scale 1.01 remap
fix_modify ATC fix displacement y all linear 0 0 0 0 0.0201 0 0 fix_modify ATC fix displacement y all linear 0 0 0 0 0.0201 0 0
run 1 run 1
change_box all y scale 1.01 remap change_box all y scale 1.01 remap
fix_modify ATC fix displacement y all linear 0 0 0 0 0.030301 0 0 fix_modify ATC fix displacement y all linear 0 0 0 0 0.030301 0 0
run 1 run 1

148
examples/PACKAGES/atc/elastic/in.electron_density
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@ -1,74 +1,74 @@
# needs description # needs description
echo both echo both
units metal units metal
# PARAMETERS----------------------------- # PARAMETERS-----------------------------
variable s equal 1 variable s equal 1
variable L equal 10 variable L equal 10
variable e equal 4 variable e equal 4
variable E equal 0.0001 variable E equal 0.0001
variable V equal $E*$L variable V equal $E*$L
# END ----------------------------------- # END -----------------------------------
atom_style atomic atom_style atomic
lattice diamond 1.0 lattice diamond 1.0
boundary f p p boundary f p p
region box block -$L $L 0 1 0 1 region box block -$L $L 0 1 0 1
create_box 1 box create_box 1 box
group box region box group box region box
atom_modify sort 0 1 atom_modify sort 0 1
timestep 0.0 timestep 0.0
mass * 12.01 mass * 12.01
# coupling # coupling
### NOTE ATC: material cnt does not provide all interfaces for charge_density physics and will be treated as null ### 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 AtC box atc electrostatic-equilibrium CNT.mat
fix_modify AtC internal_quadrature off 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 internal 1.0 NOTE penultimate is a group
fix_modify AtC atom_weight constant box 1.0 fix_modify AtC atom_weight constant box 1.0
fix_modify AtC omit atomic_charge fix_modify AtC omit atomic_charge
fix_modify AtC mesh create $e 1 1 box f p p fix_modify AtC mesh create $e 1 1 box f p p
#fix_modify AtC control momentum flux #fix_modify AtC control momentum flux
fix_modify AtC mesh create_elementset all -INF INF -INF INF -INF INF fix_modify AtC mesh create_elementset all -INF INF -INF INF -INF INF
# bcs/ics conditions # bcs/ics conditions
fix_modify AtC fix displacement x all 0.0 fix_modify AtC fix displacement x all 0.0
fix_modify AtC fix displacement y 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 displacement z all 0.0
fix_modify AtC fix velocity x 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 y all 0.0
fix_modify AtC fix velocity z 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 lbc -10 -10 INF INF INF INF
fix_modify AtC mesh create_nodeset rbc 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 lbc linear 0 0 0 $E 0 0 $V
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V
# run # run
thermo_style custom step cpu etotal ke thermo_style custom step cpu etotal ke
thermo $s thermo $s
fix_modify AtC output electron_densityFE $s text fix_modify AtC output electron_densityFE $s text
fix_modify AtC output index step fix_modify AtC output index step
log electron_density.log log electron_density.log
# run default material # run default material
print "default material - table linear" print "default material - table linear"
run $s run $s
# run CNT1 material # run CNT1 material
print "CNT1 material - analytical linear" print "CNT1 material - analytical linear"
fix_modify AtC material all CNT1 fix_modify AtC material all CNT1
run $s run $s
# run CNT2 material # run CNT2 material
print "CNT2 material - analytical exponetial" print "CNT2 material - analytical exponetial"
fix_modify AtC material all CNT2 fix_modify AtC material all CNT2
run $s run $s
# run CNT material # run CNT material
print "CNT material - table DOS" print "CNT material - table DOS"
fix_modify AtC material all CNT fix_modify AtC material all CNT
#variable E equal 10*$E #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 lbc linear 0 0 0 $E 0 0 $V
#fix_modify AtC fix electric_potential rbc 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 run $s

112
examples/PACKAGES/atc/mesh/in.gaussianIC1d_hex
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@ -1,56 +1,56 @@
echo both echo both
units real units real
atom_style atomic atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25 lattice fcc 5.405 origin 0.25 0.25 0.25
region mdRegion block -12 12 -3 3 -3 3 region mdRegion block -12 12 -3 3 -3 3
region mdInternal block -10 10 -3 3 -3 3 region mdInternal block -10 10 -3 3 -3 3
# create atoms # create atoms
boundary f p p boundary f p p
create_box 1 mdRegion create_box 1 mdRegion
create_atoms 1 region mdRegion create_atoms 1 region mdRegion
mass 1 39.95 mass 1 39.95
pair_style lj/cut 13.5 pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5 pair_coeff 1 1 .238 3.405 13.5
# specify interal/ghost atoms # specify interal/ghost atoms
group internal region mdInternal group internal region mdInternal
velocity internal create 40 87287 mom yes loop geom # <<< NOTE velocity internal create 40 87287 mom yes loop geom # <<< NOTE
neighbor 5. bin neighbor 5. bin
neigh_modify every 10 delay 0 check no neigh_modify every 10 delay 0 check no
# ID group atc PhysicsType ParameterFile # ID group atc PhysicsType ParameterFile
fix AtC internal atc two_temperature Ar_ttm.mat fix AtC internal atc two_temperature Ar_ttm.mat
fix_modify AtC mesh read gaussianIC1d_hex.mesh fix_modify AtC mesh read gaussianIC1d_hex.mesh
# fix a temperature # fix a temperature
fix_modify AtC fix temperature all 20.0 fix_modify AtC fix temperature all 20.0
fix_modify AtC initial 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 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 fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
# turn on thermostat # turn on thermostat
fix_modify AtC extrinsic exchange off fix_modify AtC extrinsic exchange off
fix_modify AtC control thermal rescale 10 fix_modify AtC control thermal rescale 10
# equilibrate MD field # equilibrate MD field
timestep 5.0 timestep 5.0
thermo 10 thermo 10
#output #output
fix_modify AtC output gaussianIC1d_hexFE 10 text fix_modify AtC output gaussianIC1d_hexFE 10 text
# change thermostat # change thermostat
fix_modify AtC unfix temperature all fix_modify AtC unfix temperature all
fix_modify AtC unfix electron_temperature all fix_modify AtC unfix electron_temperature all
fix_modify AtC control thermal flux fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10 fix_modify AtC extrinsic electron_integration explicit 10
# run with FE # run with FE
thermo_style custom step temp pe f_AtC[2] f_AtC[4] thermo_style custom step temp pe f_AtC[2] f_AtC[4]
reset_timestep 0 reset_timestep 0
run 100 # 400 run 100 # 400

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

74
examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex20_uniform
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@ -1,37 +1,37 @@
echo both echo both
units real units real
atom_style atomic atom_style atomic
variable L equal 12 variable L equal 12
variable l2 equal 6 variable l2 equal 6
variable l equal 4 variable l equal 4
variable w equal 2 variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25 lattice fcc 5.405 origin 0.25 0.25 0.25
region mdInternal block -$l $l -$l $l -$w $w region mdInternal block -$l $l -$l $l -$w $w
boundary f f f # p boundary f f f # p
pair_style lj/cut 13.5 pair_style lj/cut 13.5
read_data temp.init read_data temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95 mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5 pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal group internal region mdInternal
fix AtC internal atc two_temperature Ar_ttm.mat fix AtC internal atc two_temperature Ar_ttm.mat
fix_modify AtC mesh read gaussianIC2d_hex20_uniform.mesh fix_modify AtC mesh read gaussianIC2d_hex20_uniform.mesh
fix_modify AtC output gaussianIC2d_hex20_uniformFE 10 full_text fix_modify AtC output gaussianIC2d_hex20_uniformFE 10 full_text
fix_modify AtC initial temperature all 20.0 fix_modify AtC initial temperature all 20.0
# NOTE this is only gaussian in x # 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 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 11 20.0
fix_modify AtC fix temperature 12 20.0 fix_modify AtC fix temperature 12 20.0
fix_modify AtC control thermal flux fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10 fix_modify AtC extrinsic electron_integration explicit 10
thermo_style custom step temp pe f_AtC[2] f_AtC[4] thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0 timestep 1.0
thermo 10 thermo 10
run 100 run 100

74
examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex27_uniform
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@ -1,37 +1,37 @@
echo both echo both
units real units real
atom_style atomic atom_style atomic
variable L equal 12 variable L equal 12
variable l2 equal 6 variable l2 equal 6
variable l equal 4 variable l equal 4
variable w equal 2 variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25 lattice fcc 5.405 origin 0.25 0.25 0.25
region mdInternal block -$l $l -$l $l -$w $w region mdInternal block -$l $l -$l $l -$w $w
boundary f f f # p boundary f f f # p
pair_style lj/cut 13.5 pair_style lj/cut 13.5
read_data temp.init read_data temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95 mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5 pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal group internal region mdInternal
fix AtC internal atc two_temperature Ar_ttm.mat fix AtC internal atc two_temperature Ar_ttm.mat
fix_modify AtC mesh read gaussianIC2d_hex27_uniform.mesh fix_modify AtC mesh read gaussianIC2d_hex27_uniform.mesh
fix_modify AtC output gaussianIC2d_hex27_uniformFE 10 full_text fix_modify AtC output gaussianIC2d_hex27_uniformFE 10 full_text
fix_modify AtC initial temperature all 20.0 fix_modify AtC initial temperature all 20.0
# NOTE this is only gaussian in x # 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 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 11 20.0
fix_modify AtC fix temperature 12 20.0 fix_modify AtC fix temperature 12 20.0
fix_modify AtC control thermal flux fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10 fix_modify AtC extrinsic electron_integration explicit 10
thermo_style custom step temp pe f_AtC[2] f_AtC[4] thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0 timestep 1.0
thermo 10 thermo 10
run 100 run 100

80
examples/PACKAGES/atc/mesh/in.gaussianIC2d_tet
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@ -1,40 +1,40 @@
echo both echo both
units real units real
atom_style atomic atom_style atomic
variable L equal 12 variable L equal 12
variable l2 equal 6 variable l2 equal 6
variable l equal 4 variable l equal 4
variable w equal 2 variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25 lattice fcc 5.405 origin 0.25 0.25 0.25
region mdInternal block -$l $l -$l $l -$w $w region mdInternal block -$l $l -$l $l -$w $w
boundary f f f # p boundary f f f # p
pair_style lj/cut 13.5 pair_style lj/cut 13.5
read_data temp.init read_data temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95 mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5 pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal group internal region mdInternal
fix AtC internal atc two_temperature Ar_ttm.mat fix AtC internal atc two_temperature Ar_ttm.mat
fix_modify AtC mesh read gaussianIC2d_tet.mesh fix_modify AtC mesh read gaussianIC2d_tet.mesh
#fix_modify AtC mesh read gaussianIC2d_tet.exo #fix_modify AtC mesh read gaussianIC2d_tet.exo
fix_modify AtC mesh write parsed_gaussianIC2d_tet.mesh fix_modify AtC mesh write parsed_gaussianIC2d_tet.mesh
fix_modify AtC mesh output parsed_gaussianIC2d_tetMESH fix_modify AtC mesh output parsed_gaussianIC2d_tetMESH
fix_modify AtC output gaussianIC2d_tetFE 10 full_text fix_modify AtC output gaussianIC2d_tetFE 10 full_text
fix_modify AtC initial temperature all 20.0 fix_modify AtC initial temperature all 20.0
# NOTE this is only gaussian in x # 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 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 11 20.0
fix_modify AtC fix temperature 12 20.0 fix_modify AtC fix temperature 12 20.0
fix_modify AtC control thermal flux fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10 fix_modify AtC extrinsic electron_integration explicit 10
thermo_style custom step temp pe f_AtC[2] f_AtC[4] thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0 timestep 1.0
thermo 10 thermo 10
run 100 run 100

64
examples/PACKAGES/atc/mesh/in.kernel2d_hex
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@ -1,32 +1,32 @@
echo both echo both
units real units real
atom_style atomic atom_style atomic
# correct mass density = 1.0120 # correct mass density = 1.0120
# NOTE the mesh is not currently periodic, so the density estimate is off by a factor of 2 # NOTE the mesh is not currently periodic, so the density estimate is off by a factor of 2
variable L equal 6 variable L equal 6
variable w equal 2 variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25 lattice fcc 5.405 origin 0.25 0.25 0.25
region BOX block -$L $L -$L $L -$w $w region BOX block -$L $L -$L $L -$w $w
boundary f f p boundary f f p
create_box 1 BOX create_box 1 BOX
create_atoms 1 region BOX create_atoms 1 region BOX
mass 1 39.95 mass 1 39.95
pair_style lj/cut 13.5 pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5 pair_coeff 1 1 .238 3.405 13.5
group internal region BOX group internal region BOX
fix AtC internal atc hardy fix AtC internal atc hardy
fix_modify AtC kernel quartic_cylinder 5.0 fix_modify AtC kernel quartic_cylinder 5.0
fix_modify AtC mesh read gaussianIC2d_hex.mesh fix_modify AtC mesh read gaussianIC2d_hex.mesh
fix_modify AtC fields add mass_density fix_modify AtC fields add mass_density
fix_modify AtC output kernel2d_hexFE 1 full_text binary fix_modify AtC output kernel2d_hexFE 1 full_text binary
#dump CONFIG all custom 1 kernel2d_hexMD.dmp id type x y z #dump CONFIG all custom 1 kernel2d_hexMD.dmp id type x y z
thermo_style custom step cpu temp thermo_style custom step cpu temp
timestep 0.0 timestep 0.0
thermo 1 thermo 1
run 2 run 2

56
examples/PACKAGES/atc/mesh/in.kernel2d_tet
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@ -1,28 +1,28 @@
echo both echo both
units real units real
atom_style atomic atom_style atomic
variable L equal 6 variable L equal 6
variable w equal 2 variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25 lattice fcc 5.405 origin 0.25 0.25 0.25
region BOX block -$L $L -$L $L -$w $w region BOX block -$L $L -$L $L -$w $w
boundary f f p boundary f f p
create_box 1 BOX create_box 1 BOX
create_atoms 1 region BOX create_atoms 1 region BOX
mass 1 39.95 mass 1 39.95
pair_style lj/cut 13.5 pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5 pair_coeff 1 1 .238 3.405 13.5
group internal region BOX group internal region BOX
fix AtC internal atc hardy fix AtC internal atc hardy
fix_modify AtC kernel quartic_sphere 5.0 fix_modify AtC kernel quartic_sphere 5.0
fix_modify AtC mesh read gaussianIC2d_tet.mesh fix_modify AtC mesh read gaussianIC2d_tet.mesh
fix_modify AtC fields add mass_density fix_modify AtC fields add mass_density
fix_modify AtC output kernel2d_tetFE 1 full_text binary fix_modify AtC output kernel2d_tetFE 1 full_text binary
thermo_style custom step cpu temp thermo_style custom step cpu temp
timestep 0.0 timestep 0.0
thermo 1 thermo 1
run 2 run 2

58
examples/PACKAGES/atc/mesh/in.mesh2d_tet
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@ -1,29 +1,29 @@
echo both echo both
units real units real
atom_style atomic atom_style atomic
variable L equal 6 variable L equal 6
variable w equal 2 variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25 lattice fcc 5.405 origin 0.25 0.25 0.25
region BOX block -$L $L -$L $L -$w $w region BOX block -$L $L -$L $L -$w $w
boundary f f p boundary f f p
create_box 1 BOX create_box 1 BOX
create_atoms 1 region BOX create_atoms 1 region BOX
mass 1 39.95 mass 1 39.95
pair_style lj/cut 13.5 pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5 pair_coeff 1 1 .238 3.405 13.5
group internal region BOX group internal region BOX
fix AtC internal atc field fix AtC internal atc field
fix_modify AtC mesh read gaussianIC2d_tet.mesh fix_modify AtC mesh read gaussianIC2d_tet.mesh
fix_modify AtC fields add mass_density fix_modify AtC fields add mass_density
fix_modify AtC output mesh2d_tetFE 1 full_text binary fix_modify AtC output mesh2d_tetFE 1 full_text binary
dump CONFIG all custom 10 mesh2d_tet.dmp id type x y z dump CONFIG all custom 10 mesh2d_tet.dmp id type x y z
thermo_style custom step cpu temp thermo_style custom step cpu temp
timestep 0.0 timestep 0.0
thermo 1 thermo 1
run 2 run 2

202
examples/PACKAGES/atc/mesh/in.semicircle
View File

@ -1,101 +1,101 @@
# this input can be used to generate the benchmark for in.gaussianIC2d_hex_uniform # this input can be used to generate the benchmark for in.gaussianIC2d_hex_uniform
echo both echo both
units real units real
atom_style atomic atom_style atomic
variable l equal 8 variable l equal 8
variable g equal 2 variable g equal 2
variable lg equal $l+$g variable lg equal $l+$g
variable w equal 2 variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25 lattice fcc 5.405 origin 0.25 0.25 0.25
boundary f f f boundary f f f
# region to create atoms # region to create atoms
region bigCyl cylinder z 0. 0. ${lg} -$w $w region bigCyl cylinder z 0. 0. ${lg} -$w $w
region offsetPlane block -${lg} $g -${lg} ${lg} -$w $w region offsetPlane block -${lg} $g -${lg} ${lg} -$w $w
region mdRegion intersect 2 bigCyl offsetPlane region mdRegion intersect 2 bigCyl offsetPlane
#create_box 1 mdRegion #create_box 1 mdRegion
pair_style lj/cut 13.5 pair_style lj/cut 13.5
read_data semicircle.init read_data semicircle.init
# region for internal atoms # region for internal atoms
region mdInternalCyl cylinder z 0. 0. $l -$w $w region mdInternalCyl cylinder z 0. 0. $l -$w $w
region leftHalfPlane block INF 0. INF INF INF INF region leftHalfPlane block INF 0. INF INF INF INF
region mdInternal intersect 2 mdInternalCyl leftHalfPlane region mdInternal intersect 2 mdInternalCyl leftHalfPlane
# region for coupling ghosts # region for coupling ghosts
region rightHalfPlane block 0. INF INF INF INF INF region rightHalfPlane block 0. INF INF INF INF INF
region mdGhost union 2 rightHalfPlane mdInternal side out region mdGhost union 2 rightHalfPlane mdInternal side out
#create_atoms 1 region mdRegion #create_atoms 1 region mdRegion
#create_atoms 1 region mdInternal #create_atoms 1 region mdInternal
#create_atoms 2 region mdGhost #create_atoms 2 region mdGhost
#region outerGhost intersect 2 rightHalfPlane mdRegion #region outerGhost intersect 2 rightHalfPlane mdRegion
#create_atoms 3 region outerGhost #create_atoms 3 region outerGhost
#pair_style lj/cut 13.5 #pair_style lj/cut 13.5
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
#mass 1 39.95 #mass 1 39.95
#pair_coeff 1 1 .238 3.405 13.5 #pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal group internal region mdInternal
group ghost region mdGhost group ghost region mdGhost
#velocity internal create 40 102486 mom yes rot yes dist gaussian #velocity internal create 40 102486 mom yes rot yes dist gaussian
#write_restart semicircle_init.rst #write_restart semicircle_init.rst
# ATC commands # ATC commands
fix AtC internal atc thermal Ar_ttm.mat fix AtC internal atc thermal Ar_ttm.mat
fix_modify AtC boundary ghost fix_modify AtC boundary ghost
fix_modify AtC mesh read semicircle.mesh f f p fix_modify AtC mesh read semicircle.mesh f f p
fix_modify AtC mesh nodeset_to_elementset 2 hole min fix_modify AtC mesh nodeset_to_elementset 2 hole min
fix_modify AtC internal_quadrature off fix_modify AtC internal_quadrature off
fix_modify AtC time_integration fractional_step fix_modify AtC time_integration fractional_step
# initial conditions # initial conditions
fix_modify AtC fix temperature all 20. fix_modify AtC fix temperature all 20.
fix_modify AtC control thermal rescale 10 fix_modify AtC control thermal rescale 10
fix_modify AtC control tolerance 1.e-14 # tolerance needed to produce consistent parallel and serial results fix_modify AtC control tolerance 1.e-14 # tolerance needed to produce consistent parallel and serial results
# initial output # initial output
#fix_modify AtC mesh output semicircle_mesh #fix_modify AtC mesh output semicircle_mesh
#fix_modify AtC output semicircle_init 100 text binary #fix_modify AtC output semicircle_init 100 text binary
#dump D1 all atom 100 semicircle_init.dmp #dump D1 all atom 100 semicircle_init.dmp
# run # run
timestep 5.0 timestep 5.0
thermo 100 thermo 100
run 500 run 500
# boundary conditions # boundary conditions
fix_modify AtC unfix temperature all fix_modify AtC unfix temperature all
fix_modify AtC fix temperature 1 20. fix_modify AtC fix temperature 1 20.
fix_modify AtC control thermal flux fix_modify AtC control thermal flux
fix_modify AtC control localized_lambda on fix_modify AtC control localized_lambda on
# NOTE appears to be a problem with the temporal ramp function # NOTE appears to be a problem with the temporal ramp function
variable delta_t equal 1000*5. variable delta_t equal 1000*5.
fix_modify AtC source temperature hole temporal_ramp 0. 0.0000000001 ${delta_t} fix_modify AtC source temperature hole temporal_ramp 0. 0.0000000001 ${delta_t}
# equilibrate filter # equilibrate filter
fix_modify AtC filter type exponential fix_modify AtC filter type exponential
fix_modify AtC filter scale 1000. fix_modify AtC filter scale 1000.
fix_modify AtC filter on fix_modify AtC filter on
# equilibration output # equilibration output
fix_modify AtC output semicircleFE 100 full_text #binary fix_modify AtC output semicircleFE 100 full_text #binary
#undump D1 #undump D1
#dump D1 all atom 100 semicircle_equil.dmp #dump D1 all atom 100 semicircle_equil.dmp
# run # run
fix_modify AtC reset_time 0. fix_modify AtC reset_time 0.
reset_timestep 0 reset_timestep 0
thermo 100 thermo 100
run 1000 run 1000
# heat source # heat source
# NOTE second run omitted as it causes diffs in parallel execution after just one timestep, not sure why # 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 source temperature hole 0.0000000001
#fix_modify AtC output semicircleFE 1 full_text #binary #fix_modify AtC output semicircleFE 1 full_text #binary
#undump D1 #undump D1
#dump D1 all atom 100 semicircle.dmp #dump D1 all atom 100 semicircle.dmp
#run 1#000 #run 1#000

112
examples/PACKAGES/atc/thermal/in.no_atoms
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@ -1,56 +1,56 @@
# needs description # needs description
#AtC thermal Coupling #AtC thermal Coupling
# #
echo both echo both
units real units real
atom_style atomic atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25 lattice fcc 5.405 origin 0.25 0.25 0.25
region feRegion block -10 10 -1 1 -1 1 region feRegion block -10 10 -1 1 -1 1
boundary f p p boundary f p p
create_box 1 feRegion create_box 1 feRegion
mass 1 39.95 # need to keep this mass 1 39.95 # need to keep this
atom_modify sort 0 1 atom_modify sort 0 1
region dummyRegion block -100 -99 -1 1 -1 1 region dummyRegion block -100 -99 -1 1 -1 1
group dummy region dummyRegion group dummy region dummyRegion
# ID group atc PhysicsType ParameterFile # ID group atc PhysicsType ParameterFile
fix AtC dummy atc thermal Ar_thermal.mat fix AtC dummy atc thermal Ar_thermal.mat
timestep 5.0 timestep 5.0
# ID part keywords nx ny nz region # ID part keywords nx ny nz region
fix_modify AtC mesh create 10 1 1 feRegion f p p fix_modify AtC mesh create 10 1 1 feRegion f p p
# fix end temperatures and an internal source # fix end temperatures and an internal source
fix_modify AtC initial temperature all 20.0 fix_modify AtC initial temperature all 20.0
fix_modify AtC source temperature all 0.0000000000632 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 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 mesh create_nodeset rbc 9.9 10.1 -INF INF -INF INF
fix_modify AtC fix temperature lbc 20. fix_modify AtC fix temperature lbc 20.
fix_modify AtC fix temperature rbc 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 mesh create_elementset middle -4.1 4.1 -INF INF -INF INF
fix_modify AtC material middle Ar2 fix_modify AtC material middle Ar2
thermo_style custom step cpu f_AtC[1] f_AtC[2] thermo_style custom step cpu f_AtC[1] f_AtC[2]
fix_modify AtC output no_atomsFE 1000 text binary fix_modify AtC output no_atomsFE 1000 text binary
thermo 100 thermo 100
run 10000 run 10000
fix_modify AtC remove_source temperature all fix_modify AtC remove_source temperature all
fix_modify AtC unfix temperature rbc fix_modify AtC unfix temperature rbc
fix_modify AtC fix temperature all 20. fix_modify AtC fix temperature all 20.
run 1 run 1
fix_modify AtC unfix temperature all fix_modify AtC unfix temperature all
reset_timestep 0 reset_timestep 0
# fix one end temperature and the a source at the other # fix one end temperature and the a source at the other
fix_modify AtC fix temperature lbc 20. fix_modify AtC fix temperature lbc 20.
fix_modify AtC mesh create_faceset rbcFace plane x 10.0 fix_modify AtC mesh create_faceset rbcFace plane x 10.0
fix_modify AtC fix_flux temperature rbcFace 0.000000001 fix_modify AtC fix_flux temperature rbcFace 0.000000001
fix_modify AtC output no_atoms_flux_FE 1000 text binary # NOTE not used fix_modify AtC output no_atoms_flux_FE 1000 text binary # NOTE not used
thermo 100 thermo 100
run 10000 run 10000

174
examples/PACKAGES/atc/two_temperature/in.cutout
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@ -1,87 +1,87 @@
# needs description # needs description
#AtC Two temperature Coupling #AtC Two temperature Coupling
# DESCRIPTION: # DESCRIPTION:
# delete elements from the mesh # delete elements from the mesh
# heating and then relaxation # heating and then relaxation
echo both echo both
units metal units metal
variable INF equal 1000 variable INF equal 1000
variable T equal 20 variable T equal 20
atom_style atomic atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25 lattice fcc 5.405 origin 0.25 0.25 0.25
region FE block -8 8 -6 6 0 3 region FE block -8 8 -6 6 0 3
region MD block -7 7 -6 0 0 3 region MD block -7 7 -6 0 0 3
region FREE block -4 4 -6 0 0 3 region FREE block -4 4 -6 0 0 3
boundary f f p boundary f f p
# create atoms # create atoms
#create_box 1 FE #create_box 1 FE
#create_atoms 1 region MD #create_atoms 1 region MD
#group internal region FREE #group internal region FREE
#mass 1 39.95 #mass 1 39.95
#read_data cutout.data #read_data cutout.data
#pair_coeff * * .238 3.405 13.5 #pair_coeff * * .238 3.405 13.5
#velocity internal create 40 87287 mom yes loop geom #velocity internal create 40 87287 mom yes loop geom
#fix NVE internal nve #fix NVE internal nve
#thermo 100 #thermo 100
#dump CONFIG all atom 100 cutout.dump #dump CONFIG all atom 100 cutout.dump
##run 1000 ##run 1000
#unfix NVE #unfix NVE
#write_restart cutout.rst #write_restart cutout.rst
pair_style lj/cut 13.5 pair_style lj/cut 13.5
read_data cutout.init read_data cutout.init
group internal region FREE group internal region FREE
group ghost subtract all internal group ghost subtract all internal
timestep 0.002 timestep 0.002
thermo 20 thermo 20
# allow initial state to relax # allow initial state to relax
fix NVT internal nvt temp $T $T 10 drag 0.2 fix NVT internal nvt temp $T $T 10 drag 0.2
fix RESCALE internal temp/rescale 25 $T $T 0.05 1.0 fix RESCALE internal temp/rescale 25 $T $T 0.05 1.0
run 200 run 200
unfix RESCALE unfix RESCALE
run 800 run 800
unfix NVT unfix NVT
# ID group atc PhysicsType ParameterFile # ID group atc PhysicsType ParameterFile
fix AtC internal atc two_temperature Ar_ttm.mat fix AtC internal atc two_temperature Ar_ttm.mat
# ID part keywords nx ny nz region # ID part keywords nx ny nz region
fix_modify AtC mesh create 8 6 1 FE f f p 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_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_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 create_elementset gap -4 4 -0 INF -INF INF
fix_modify AtC mesh delete_elements gap fix_modify AtC mesh delete_elements gap
fix_modify AtC mesh create_faceset bndy box -4 4 -INF 0 -INF INF fix_modify AtC mesh create_faceset bndy box -4 4 -INF 0 -INF INF
fix_modify AtC control thermal flux faceset bndy fix_modify AtC control thermal flux faceset bndy
# fix a temperature # fix a temperature
fix_modify AtC initial temperature all 20.0 fix_modify AtC initial temperature all 20.0
fix_modify AtC initial electron_temperature all 30.0 fix_modify AtC initial electron_temperature all 30.0
fix_modify AtC initial temperature gap 0.0 fix_modify AtC initial temperature gap 0.0
# relaxation # relaxation
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] 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 output cutoutFE 10 text
fix_modify AtC extrinsic electron_integration implicit fix_modify AtC extrinsic electron_integration implicit
# heating # heating
fix_modify AtC mesh create_nodeset lbc -8 -8 -INF INF -INF INF 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 mesh create_nodeset rbc 8 8 -INF INF -INF INF
fix_modify AtC fix electron_temperature lbc 20. fix_modify AtC fix electron_temperature lbc 20.
fix_modify AtC fix electron_temperature rbc 20. fix_modify AtC fix electron_temperature rbc 20.
fix_modify AtC source electron_temperature wire 0.001 fix_modify AtC source electron_temperature wire 0.001
run 200 run 200
# relaxation # relaxation
fix_modify AtC remove_source electron_temperature wire fix_modify AtC remove_source electron_temperature wire
run 200 run 200

188
examples/PACKAGES/atc/two_temperature/in.gaussianIC_ttm
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@ -1,94 +1,94 @@
#AtC Two temperature Coupling #AtC Two temperature Coupling
# DESCRIPTION: # DESCRIPTION:
# full overlap of MD and FE regions w/ free ends & lateral periodic bcs # full overlap of MD and FE regions w/ free ends & lateral periodic bcs
# initial gaussian electron temperature profile and uniform phonon temperature # initial gaussian electron temperature profile and uniform phonon temperature
# results in fast exchange followed by slower diffusion and finally relaxation # results in fast exchange followed by slower diffusion and finally relaxation
# to equilibrium # to equilibrium
# #
echo both echo both
units real units real
atom_style atomic atom_style atomic
# create domain # create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, #lattice type reduced density rho* = 4*(sigma/a)^3,
# where N = 4 for fcc, # where N = 4 for fcc,
# s = 3.405 A (Wagner) # s = 3.405 A (Wagner)
# a = 5.25 A (Ashcroft & Mermin, p. 70) # a = 5.25 A (Ashcroft & Mermin, p. 70)
# to create restart : # to create restart :
# write_restart temp.bin # write_restart temp.bin
# then : restart2data temp.bin temp.init # then : restart2data temp.bin temp.init
#if {restart} #if {restart}
boundary f p p boundary f p p
pair_style lj/cut 13.5 pair_style lj/cut 13.5
read_data temp.init read_data temp.init
#endif #endif
lattice fcc 5.405 origin 0.25 0.25 0.25 lattice fcc 5.405 origin 0.25 0.25 0.25
region feRegion block -10 10 -3 3 -3 3 region feRegion block -10 10 -3 3 -3 3
region mdRegion block -12 12 -3 3 -3 3 region mdRegion block -12 12 -3 3 -3 3
region mdInternal block -10 10 -3 3 -3 3 region mdInternal block -10 10 -3 3 -3 3
# create atoms, NOTE commented out for restart # create atoms, NOTE commented out for restart
#if !{restart} #if !{restart}
#boundary f p p #boundary f p p
#create_box 1 mdRegion #create_box 1 mdRegion
#create_atoms 1 region mdRegion #create_atoms 1 region mdRegion
#mass 1 39.95 #mass 1 39.95
#pair_style lj/cut 13.5 #pair_style lj/cut 13.5
#pair_coeff 1 1 .238 3.405 13.5 #pair_coeff 1 1 .238 3.405 13.5
#velocity internal create 40 87287 mom yes loop geom #velocity internal create 40 87287 mom yes loop geom
#endif #endif
# specify interal/ghost atoms # specify interal/ghost atoms
group internal region mdInternal group internal region mdInternal
# do not define ghosts if outside fe region # do not define ghosts if outside fe region
#group ghost subtract all internal #group ghost subtract all internal
neighbor 5. bin neighbor 5. bin
neigh_modify every 10 delay 0 check no neigh_modify every 10 delay 0 check no
# ID group atc PhysicsType ParameterFile # ID group atc PhysicsType ParameterFile
fix AtC internal atc two_temperature Ar_ttm.mat fix AtC internal atc two_temperature Ar_ttm.mat
# ID part keywords nx ny nz region # ID part keywords nx ny nz region
fix_modify AtC mesh create 10 1 1 feRegion f p p fix_modify AtC mesh create 10 1 1 feRegion f p p
# fix a temperature # fix a temperature
fix_modify AtC fix temperature all 20.0 fix_modify AtC fix temperature all 20.0
fix_modify AtC initial 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 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 fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
# turn on thermostat # turn on thermostat
fix_modify AtC extrinsic exchange off fix_modify AtC extrinsic exchange off
fix_modify AtC control thermal rescale 10 fix_modify AtC control thermal rescale 10
# equilibrate MD field # equilibrate MD field
timestep 5.0 timestep 5.0
#timestep 0.1 #timestep 0.1
thermo 10 thermo 10
#if !{restart} #if !{restart}
#run 1000 #run 1000
#endif #endif
# write restart file (for atoms) # write restart file (for atoms)
#if !{restart} #if !{restart}
#write_restart gaussianT0.dat #write_restart gaussianT0.dat
#endif #endif
#output #output
fix_modify AtC output gaussianIC_ttmFE 10 text fix_modify AtC output gaussianIC_ttmFE 10 text
# change thermostat # change thermostat
fix_modify AtC unfix temperature all fix_modify AtC unfix temperature all
fix_modify AtC unfix electron_temperature all fix_modify AtC unfix electron_temperature all
fix_modify AtC control thermal flux fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10 fix_modify AtC extrinsic electron_integration explicit 10
# run with FE # run with FE
thermo_style custom step temp pe f_AtC[2] f_AtC[4] thermo_style custom step temp pe f_AtC[2] f_AtC[4]
reset_timestep 0 reset_timestep 0
run 400 run 400

122
examples/PACKAGES/atc/two_temperature/in.no_atoms
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@ -1,61 +1,61 @@
# needs description # needs description
#AtC Two temperature Coupling #AtC Two temperature Coupling
# DESCRIPTION: # DESCRIPTION:
# no atoms and FE regions with periodic boundary conditions. # no atoms and FE regions with periodic boundary conditions.
# heating and then relaxation # heating and then relaxation
echo both echo both
#units real #units real
units metal units metal
atom_style atomic atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25 lattice fcc 5.405 origin 0.25 0.25 0.25
region simRegion block -14 14 -3 3 -3 3 region simRegion block -14 14 -3 3 -3 3
region feRegion block -12 12 -3 3 -3 3 region feRegion block -12 12 -3 3 -3 3
# need to create atoms or lammps throws an error # need to create atoms or lammps throws an error
region mdRegion block -12 12 -3 3 -3 3 region mdRegion block -12 12 -3 3 -3 3
boundary f p p boundary f p p
create_box 1 mdRegion create_box 1 mdRegion
mass 1 39.95 # need to keep this mass 1 39.95 # need to keep this
atom_modify sort 0 1 atom_modify sort 0 1
region dummyRegion block -100 -99 -1 1 -1 1 region dummyRegion block -100 -99 -1 1 -1 1
group dummy region dummyRegion group dummy region dummyRegion
# ID group atc PhysicsType ParameterFile # ID group atc PhysicsType ParameterFile
fix AtC dummy atc two_temperature Cu_ttm.mat fix AtC dummy atc two_temperature Cu_ttm.mat
timestep 0.002 timestep 0.002
thermo 20 thermo 20
# ID part keywords nx ny nz region # ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 feRegion f p p fix_modify AtC mesh create 12 1 1 feRegion f p p
# fix a temperature # fix a temperature
fix_modify AtC initial temperature all 20.0 fix_modify AtC initial temperature all 20.0
#fix_modify AtC initial electron_temperature all 30.0 #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 fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
# relaxation # relaxation
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] 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 output no_atomsFE 10 text
#fix_modify AtC extrinsic electron_integration subcycle 100 #fix_modify AtC extrinsic electron_integration subcycle 100
fix_modify AtC extrinsic electron_integration implicit fix_modify AtC extrinsic electron_integration implicit
run 400 run 400
# heating # heating
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF 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 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 lbc 20.
fix_modify AtC fix electron_temperature rbc 20. fix_modify AtC fix electron_temperature rbc 20.
#fix_modify AtC extrinsic exchange off #fix_modify AtC extrinsic exchange off
#fix_modify AtC fix temperature lbc 20. #fix_modify AtC fix temperature lbc 20.
#fix_modify AtC fix temperature rbc 20. #fix_modify AtC fix temperature rbc 20.
#fix_modify AtC extrinsic electron_integration lockstep #fix_modify AtC extrinsic electron_integration lockstep
#fix_modify AtC source electron_temperature all 1000.0 #fix_modify AtC source electron_temperature all 1000.0
fix_modify AtC source electron_temperature all 0.521981 fix_modify AtC source electron_temperature all 0.521981
run 400 run 400
# relaxation # relaxation
fix_modify AtC remove_source electron_temperature all fix_modify AtC remove_source electron_temperature all
run 400 run 400

132
examples/PACKAGES/atc/two_temperature/in.uniform_exchange
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@ -1,66 +1,66 @@
#AtC Two temperature Coupling #AtC Two temperature Coupling
# DESCRIPTION: # DESCRIPTION:
# full overlap of MD and FE regions with full periodic boundary conditions. # full overlap of MD and FE regions with full periodic boundary conditions.
# initial electron and phonon temperatures are different and then allowed to # initial electron and phonon temperatures are different and then allowed to
# relax. # relax.
# #
units real units real
atom_style atomic atom_style atomic
boundary p p p boundary p p p
# create domain # create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, #lattice type reduced density rho* = 4*(sigma/a)^3,
# where N = 4 for fcc, # where N = 4 for fcc,
# s = 3.405 A (Wagner) # s = 3.405 A (Wagner)
# a = 5.25 A (Ashcroft & Mermin, p. 70) # a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.405 origin 0.25 0.25 0.25 lattice fcc 5.405 origin 0.25 0.25 0.25
pair_style lj/cut 13.5 pair_style lj/cut 13.5
read_data uniform_exchange.init read_data uniform_exchange.init
region simRegion block -12 12 -3 3 -3 3 region simRegion block -12 12 -3 3 -3 3
region feRegion block -12 12 -3 3 -3 3 region feRegion block -12 12 -3 3 -3 3
# create atoms # create atoms
region mdRegion block -12 12 -3 3 -3 3 region mdRegion block -12 12 -3 3 -3 3
# specify interal/ghost atoms # specify interal/ghost atoms
region mdInternal block -12 12 -3 3 -3 3 region mdInternal block -12 12 -3 3 -3 3
group internal region mdInternal group internal region mdInternal
neighbor 5. bin neighbor 5. bin
neigh_modify every 10 delay 0 check no neigh_modify every 10 delay 0 check no
# ID group atc PhysicsType ParameterFile # ID group atc PhysicsType ParameterFile
fix AtC internal atc two_temperature Ar_ttm.mat fix AtC internal atc two_temperature Ar_ttm.mat
# ID part keywords nx ny nz region # ID part keywords nx ny nz region
fix_modify AtC mesh create 4 1 1 feRegion p p p fix_modify AtC mesh create 4 1 1 feRegion p p p
# fix a temperature # fix a temperature
fix_modify AtC fix temperature all 20.0 fix_modify AtC fix temperature all 20.0
fix_modify AtC fix electron_temperature all 30.0 fix_modify AtC fix electron_temperature all 30.0
timestep 5.0 timestep 5.0
# output # output
thermo_style custom step pe temp f_AtC[2] f_AtC[4] thermo_style custom step pe temp f_AtC[2] f_AtC[4]
thermo 10 thermo 10
# equilibrate MD field # equilibrate MD field
fix_modify AtC control thermal rescale 13 fix_modify AtC control thermal rescale 13
run 500 run 500
# relax # relax
fix_modify AtC output uniform_exchangeFE 100 text fix_modify AtC output uniform_exchangeFE 100 text
fix_modify AtC filter type exponential fix_modify AtC filter type exponential
fix_modify AtC filter scale 5.0e2 fix_modify AtC filter scale 5.0e2
fix_modify AtC filter on fix_modify AtC filter on
fix_modify AtC unfix temperature all fix_modify AtC unfix temperature all
fix_modify AtC unfix electron_temperature all fix_modify AtC unfix electron_temperature all
fix_modify AtC control thermal flux fix_modify AtC control thermal flux
# run with FE # run with FE
run 5000 run 5000

238
examples/PACKAGES/eff/Auger-Adamantane/data.adamantane
View File

@ -1,119 +1,119 @@
Created by AJB Created by AJB
102 atoms 102 atoms
3 atom types 3 atom types
-500.0 500.0 xlo xhi -500.0 500.0 xlo xhi
-500.0 500.0 ylo yhi -500.0 500.0 ylo yhi
-500.0 500.0 zlo zhi -500.0 500.0 zlo zhi
Masses Masses
1 12.01070 # C nuclei 1 12.01070 # C nuclei
2 1.000794 # H nuclei 2 1.000794 # H nuclei
3 1.000000 # electron 3 1.000000 # electron
Atoms Atoms
1 1 6.00 0 0.000000 0.223271 2.836177 0.99547 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 102 3 0.00 -1 1.543000 3.342182 2.816694 -0.986155

236
examples/PACKAGES/eff/Auger-Adamantane/data.adamantane_ionized
View File

@ -1,118 +1,118 @@
Created by AJB Created by AJB
101 atoms 101 atoms
3 atom types 3 atom types
-50.0 50.0 xlo xhi -50.0 50.0 xlo xhi
-50.0 50.0 ylo yhi -50.0 50.0 ylo yhi
-50.0 50.0 zlo zhi -50.0 50.0 zlo zhi
Masses Masses
1 12.01070 # C nuclei 1 12.01070 # C nuclei
2 1.000794 # H nuclei 2 1.000794 # H nuclei
3 1.000000 # electron 3 1.000000 # electron
Atoms Atoms
1 1 6.00 0 0.000000 0.224230 2.918607 1.015812 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 101 3 0.00 1 1.558594 3.503398 3.047996 -1.264247

6944
examples/PACKAGES/eff/Li-dendritic/data.Li-dendritic
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12012
examples/PACKAGES/entropy/Na_MendelevM_2014.eam.fs
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126
examples/PACKAGES/interlayer/lebedeva/2particles.in
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@ -1,63 +1,63 @@
# After running LAMMPS with this input script a number of dump files is created. # After running LAMMPS with this input script a number of dump files is created.
# To extract the data from there I used grep script: # To extract the data from there I used grep script:
# grep '^2 ' *cfg > LammpsResult.dat # grep '^2 ' *cfg > LammpsResult.dat
# After that after removing some text from LammpsResult.dat, # After that after removing some text from LammpsResult.dat,
# the data can be viewed by lebedeva00.plot # the data can be viewed by lebedeva00.plot
# #
# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland # Author: Zbigniew Koziol, National Center for Nuclear Research, Poland
# Email: softquake@gmail.com # Email: softquake@gmail.com
# ---------- Start simulation --------------------- # ---------- Start simulation ---------------------
clear clear
units metal units metal
dimension 3 dimension 3
boundary f f f boundary f f f
atom_style atomic atom_style atomic
# ========================== Create Atomistic Structure =========================== # ========================== Create Atomistic Structure ===========================
region whole block 0 20 0 20 0 10 region whole block 0 20 0 20 0 10
create_box 2 whole create_box 2 whole
read_data 2particles.dat add append read_data 2particles.dat add append
region graphite block INF INF INF INF 0 10 units box region graphite block INF INF INF INF 0 10 units box
group graphite type 1 2 group graphite type 1 2
group graphene1 type 1 group graphene1 type 1
group graphene2 type 2 group graphene2 type 2
pair_style hybrid/overlay lebedeva/z 20 pair_style hybrid/overlay lebedeva/z 20
pair_coeff * * none pair_coeff * * none
pair_coeff 1 2 lebedeva/z CC.Lebedeva C C pair_coeff 1 2 lebedeva/z CC.Lebedeva C C
mass 1 12.01 # Carbon mass 1 12.01 # Carbon
mass 2 12.01 # Carbon mass 2 12.01 # Carbon
neighbor 0.3 bin neighbor 0.3 bin
neigh_modify delay 1 check yes neigh_modify delay 1 check yes
compute peratom all pe/atom compute peratom all pe/atom
dump 1 all custom 1 dump_lebedeva_*.cfg id x y z c_peratom fx fy fz dump 1 all custom 1 dump_lebedeva_*.cfg id x y z c_peratom fx fy fz
dump_modify 1 pad 3 dump_modify 1 pad 3
thermo 10 thermo 10
thermo_style custom step pe press temp thermo_style custom step pe press temp
thermo_modify lost ignore thermo_modify lost ignore
label STEP_LOOP label STEP_LOOP
variable MYSTEP loop 0 400 pad # in degrees variable MYSTEP loop 0 400 pad # in degrees
variable DELTA_STEP equal 0.05 variable DELTA_STEP equal 0.05
displace_atoms graphene2 move ${DELTA_STEP} ${DELTA_STEP} 0 displace_atoms graphene2 move ${DELTA_STEP} ${DELTA_STEP} 0
run 1 run 1
next MYSTEP next MYSTEP
jump SELF STEP_LOOP jump SELF STEP_LOOP
print "all done" print "all done"

132612
examples/PACKAGES/machdyn/funnel_flow/boundary.stl
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260
examples/PACKAGES/meam_spline/TiO.meam.spline
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@ -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 # 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 meam/spline 2 Ti O
spline3eq spline3eq
13 13
-20 0 -20 0
1.742692837 3.744277175966 99.4865081627958 1.742692837 3.744277175966 99.4865081627958
2.05580176725 0.910839730906 10.8702523265355 2.05580176725 0.910839730906 10.8702523265355
2.3689106975 0.388045896634 -1.55322418749562 2.3689106975 0.388045896634 -1.55322418749562
2.68201962775 -0.018840906533 2.43630041329215 2.68201962775 -0.018840906533 2.43630041329215
2.995128558 -0.248098929639 2.67912713976835 2.995128558 -0.248098929639 2.67912713976835
3.30823748825 -0.264489550297 -0.125056384603077 3.30823748825 -0.264489550297 -0.125056384603077
3.6213464185 -0.227196189283 1.10662555360438 3.6213464185 -0.227196189283 1.10662555360438
3.93445534875 -0.129293090176 -0.592053676745914 3.93445534875 -0.129293090176 -0.592053676745914
4.247564279 -0.059685366933 -0.470123414607672 4.247564279 -0.059685366933 -0.470123414607672
4.56067320925 -0.031100025561 -0.0380739973059663 4.56067320925 -0.031100025561 -0.0380739973059663
4.8737821395 -0.013847363202 -0.0711547960695406 4.8737821395 -0.013847363202 -0.0711547960695406
5.18689106975 -0.003203412728 -0.081768292420175 5.18689106975 -0.003203412728 -0.081768292420175
5.5 0 -0.0571422964883619 5.5 0 -0.0571422964883619
spline3eq spline3eq
5 5
0.155001355787331 0 0.155001355787331 0
1.9 0.533321679606674 0 1.9 0.533321679606674 0
2.8 0.456402081843862 -1.60311717015859 2.8 0.456402081843862 -1.60311717015859
3.7 -0.324281383502201 1.19940299483249 3.7 -0.324281383502201 1.19940299483249
4.6 -0.474029826906675 1.47909794595154 4.6 -0.474029826906675 1.47909794595154
5.5 0 -2.49521499855605 5.5 0 -2.49521499855605
spline3eq spline3eq
13 13
0 0 0 0
1.742692837 0 0 1.742692837 0 0
2.05580176725 0 0 2.05580176725 0 0
2.3689106975 0 0 2.3689106975 0 0
2.68201962775 0 0 2.68201962775 0 0
2.995128558 0 0 2.995128558 0 0
3.30823748825 0 0 3.30823748825 0 0
3.6213464185 0 0 3.6213464185 0 0
3.93445534875 0 0 3.93445534875 0 0
4.247564279 0 0 4.247564279 0 0
4.56067320925 0 0 4.56067320925 0 0
4.8737821395 0 0 4.8737821395 0 0
5.18689106975 0 0 5.18689106975 0 0
5.5 0 0 5.5 0 0
spline3eq spline3eq
11 11
-1 0 -1 0
2.055801767 1.7475279661 -525.869786904802 2.055801767 1.7475279661 -525.869786904802
2.2912215903 -5.8677963945 252.796316927755 2.2912215903 -5.8677963945 252.796316927755
2.5266414136 -8.3376288737 71.7318388721015 2.5266414136 -8.3376288737 71.7318388721015
2.7620612369 -5.8398712842 -1.93587742753693 2.7620612369 -5.8398712842 -1.93587742753693
2.9974810602 -3.1140648231 -39.2999192667503 2.9974810602 -3.1140648231 -39.2999192667503
3.2329008835 -1.7257245065 14.3424136002004 3.2329008835 -1.7257245065 14.3424136002004
3.4683207068 -0.4428977017 -29.4925534559498 3.4683207068 -0.4428977017 -29.4925534559498
3.7037405301 -0.1466643003 -3.18010534572236 3.7037405301 -0.1466643003 -3.18010534572236
3.9391603534 -0.2095507945 3.33490838803603 3.9391603534 -0.2095507945 3.33490838803603
4.1745801767 -0.1442384563 3.71918691359508 4.1745801767 -0.1442384563 3.71918691359508
4.41 0 -9.66717019857564 4.41 0 -9.66717019857564
spline3eq spline3eq
5 5
-61.9827585211652 0 -61.9827585211652 0
1.9 11.2293641315584 0 1.9 11.2293641315584 0
2.8 -27.9976343076148 122.648031332411 2.8 -27.9976343076148 122.648031332411
3.7 -8.32979773113248 -54.3340881766381 3.7 -8.32979773113248 -54.3340881766381
4.6 -1.00863195297399 3.23150064581724 4.6 -1.00863195297399 3.23150064581724
5.5 0 -5.3514242228123 5.5 0 -5.3514242228123
spline3eq spline3eq
4 4
0.00776934946045395 0.105197706160344 0.00776934946045395 0.105197706160344
-55.14233165 -0.29745568008 0.00152870603877451 -55.14233165 -0.29745568008 0.00152870603877451
-44.7409899033333 -0.15449458722 0.00038933722543571 -44.7409899033333 -0.15449458722 0.00038933722543571
-34.3396481566667 0.05098657168 0.00038124926922248 -34.3396481566667 0.05098657168 0.00038124926922248
-23.93830641 0.57342694704 0.0156639264890892 -23.93830641 0.57342694704 0.0156639264890892
spline3eq spline3eq
5 5
-0.00676745157022662 -0.0159520381982146 -0.00676745157022662 -0.0159520381982146
-23.9928 0.297607384684645 0 -23.9928 0.297607384684645 0
-15.9241175 0.216691597077105 -0.0024248755353942 -15.9241175 0.216691597077105 -0.0024248755353942
-7.855435 0.0637598673719069 0.00306245895013358 -7.855435 0.0637598673719069 0.00306245895013358
0.213247499999998 -0.00183450621970427 -0.00177588407633909 0.213247499999998 -0.00183450621970427 -0.00177588407633909
8.28193 -0.111277018874367 0 8.28193 -0.111277018874367 0
spline3eq spline3eq
10 10
2.77327511656661 0 2.77327511656661 0
2.055801767 -0.1485215264 72.2010867146919 2.055801767 -0.1485215264 72.2010867146919
2.31737934844444 1.6845304918 -47.2744689053404 2.31737934844444 1.6845304918 -47.2744689053404
2.57895692988889 2.0113365977 -15.1859578405326 2.57895692988889 2.0113365977 -15.1859578405326
2.84053451133333 1.1444092747 3.33978204841873 2.84053451133333 1.1444092747 3.33978204841873
3.10211209277778 0.2861606803 2.587867603808 3.10211209277778 0.2861606803 2.587867603808
3.36368967422222 -0.3459281126 6.14070694084556 3.36368967422222 -0.3459281126 6.14070694084556
3.62526725566667 -0.6257480601 3.7397696717154 3.62526725566667 -0.6257480601 3.7397696717154
3.88684483711111 -0.6119510826 4.64749084871402 3.88684483711111 -0.6119510826 4.64749084871402
4.14842241855556 -0.3112059651 2.83275746415936 4.14842241855556 -0.3112059651 2.83275746415936
4.41 0 -15.0612086827734 4.41 0 -15.0612086827734
spline3eq spline3eq
5 5
12.3315547862781 0 12.3315547862781 0
1.9 2.62105440156724 0 1.9 2.62105440156724 0
2.8 10.2850803058354 -25.439802988016 2.8 10.2850803058354 -25.439802988016
3.7 3.23933763743897 -7.20203673434025 3.7 3.23933763743897 -7.20203673434025
4.6 -5.79049355858613 39.5509978688682 4.6 -5.79049355858613 39.5509978688682
5.5 0 -41.221771373642 5.5 0 -41.221771373642
spline3eq spline3eq
8 8
8.33642274810572 -60.4024574736564 8.33642274810572 -60.4024574736564
-1 0.07651409193 -110.652321293778 -1 0.07651409193 -110.652321293778
-0.724509054371429 0.14155824541 44.8853405500508 -0.724509054371429 0.14155824541 44.8853405500508
-0.449018108742857 0.75788697341 -25.3065115342002 -0.449018108742857 0.75788697341 -25.3065115342002
-0.173527163114286 0.63011570378 -2.48510144915082 -0.173527163114286 0.63011570378 -2.48510144915082
0.101963782514286 0.09049597305 2.68769386908235 0.101963782514286 0.09049597305 2.68769386908235
0.377454728142857 -0.35741586657 -1.01558570129633 0.377454728142857 -0.35741586657 -1.01558570129633
0.652945673771428 -0.65293217647 13.4224786001212 0.652945673771428 -0.65293217647 13.4224786001212
0.9284366194 -6.00912190653 -452.752542694929 0.9284366194 -6.00912190653 -452.752542694929
spline3eq spline3eq
5 5
0.137191606537625 -1.55094230968985 0.137191606537625 -1.55094230968985
-1 0.0513843442016519 0 -1 0.0513843442016519 0
-0.5 0.0179024412245673 -2.44986494990154 -0.5 0.0179024412245673 -2.44986494990154
0 -0.260650876879273 3.91774583656401 0 -0.260650876879273 3.91774583656401
0.5 -0.190163791764901 -4.84414871911743 0.5 -0.190163791764901 -4.84414871911743
1 -0.763795416646599 0 1 -0.763795416646599 0
spline3eq spline3eq
8 8
0 0 0 0
-1 0 0 -1 0 0
-0.724509054371429 0 0 -0.724509054371429 0 0
-0.449018108742857 0 0 -0.449018108742857 0 0
-0.173527163114286 0 0 -0.173527163114286 0 0
0.101963782514286 0 0 0.101963782514286 0 0
0.377454728142857 0 0 0.377454728142857 0 0
0.652945673771428 0 0 0.652945673771428 0 0
0.9284366194 0 0 0.9284366194 0 0

80
examples/PACKAGES/mop/in.compute_stress_mop
View File

@ -1,40 +1,40 @@
variable T equal 0.8 variable T equal 0.8
variable p_solid equal 0.05 variable p_solid equal 0.05
read_data data.mop read_data data.mop
pair_style lj/cut 2.5 pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 pair_coeff * * 1.0 1.0
pair_coeff 1 2 0.5 1.0 pair_coeff 1 2 0.5 1.0
pair_coeff 2 2 0.0 0.0 pair_coeff 2 2 0.0 0.0
neigh_modify delay 0 neigh_modify delay 0
group liquid type 1 group liquid type 1
group solid type 2 group solid type 2
region bottom block INF INF INF INF INF 7.0 region bottom block INF INF INF INF INF 7.0
group bottom region bottom group bottom region bottom
group solid_bottom intersect solid bottom group solid_bottom intersect solid bottom
group solid_up subtract solid solid_bottom group solid_up subtract solid solid_bottom
variable faSolid equal ${p_solid}*lx*ly/count(solid_up) variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
fix piston_up solid_up aveforce NULL NULL -${faSolid} fix piston_up solid_up aveforce NULL NULL -${faSolid}
fix freeze_up solid_up setforce 0.0 0.0 NULL fix freeze_up solid_up setforce 0.0 0.0 NULL
fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0 fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
fix nvesol solid nve fix nvesol solid nve
compute Tliq liquid temp compute Tliq liquid temp
fix nvtliq liquid nvt temp $T $T 0.5 fix nvtliq liquid nvt temp $T $T 0.5
fix_modify nvtliq temp Tliq fix_modify nvtliq temp Tliq
thermo 1000 thermo 1000
thermo_modify flush yes temp Tliq thermo_modify flush yes temp Tliq
fix fxbal all balance 1000 1.05 shift z 10 1.05 fix fxbal all balance 1000 1.05 shift z 10 1.05
compute mopz0 all stress/mop z center kin conf compute mopz0 all stress/mop z center kin conf
fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time 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 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 fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
run 0 run 0

132
examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene.map
View File

@ -1,66 +1,66 @@
map file: styrene growth map file: styrene growth
1 edgeIDs 1 edgeIDs
30 equivalences 30 equivalences
16 createIDs 16 createIDs
InitiatorIDs InitiatorIDs
4 4
13 13
EdgeIDs EdgeIDs
30 30
CreateIDs CreateIDs
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15
16 16
Equivalences Equivalences
1 45 1 45
2 46 2 46
3 44 3 44
4 43 4 43
5 42 5 42
6 41 6 41
7 40 7 40
8 39 8 39
9 38 9 38
10 37 10 37
11 36 11 36
12 35 12 35
13 34 13 34
14 33 14 33
15 32 15 32
16 31 16 31
17 17 17 17
18 18 18 18
19 19 19 19
20 20 20 20
21 21 21 21
22 22 22 22
23 23 23 23
24 24 24 24
25 25 25 25
26 26 26 26
27 27 27 27
28 28 28 28
29 29 29 29
30 30 30 30

912
examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_post.data_template
View File

@ -1,456 +1,456 @@
molecule template: end of chain plus polymerized styrene molecule template: end of chain plus polymerized styrene
46 atoms 46 atoms
48 bonds 48 bonds
81 angles 81 angles
121 dihedrals 121 dihedrals
35 impropers 35 impropers
1 fragments 1 fragments
Fragments Fragments
create_fit 34 44 create_fit 34 44
Types Types
1 1 1 1
2 2 2 2
3 1 3 1
4 5 4 5
5 1 5 1
6 2 6 2
7 1 7 1
8 2 8 2
9 1 9 1
10 2 10 2
11 1 11 1
12 2 12 2
13 2 13 2
14 6 14 6
15 2 15 2
16 2 16 2
17 1 17 1
18 2 18 2
19 1 19 1
20 5 20 5
21 1 21 1
22 2 22 2
23 1 23 1
24 2 24 2
25 1 25 1
26 2 26 2
27 1 27 1
28 2 28 2
29 2 29 2
30 6 30 6
31 1 31 1
32 2 32 2
33 1 33 1
34 5 34 5
35 1 35 1
36 2 36 2
37 1 37 1
38 2 38 2
39 1 39 1
40 2 40 2
41 1 41 1
42 2 42 2
43 2 43 2
44 6 44 6
45 2 45 2
46 2 46 2
Charges Charges
1 -0.129000 1 -0.129000
2 0.123700 2 0.123700
3 0.026600 3 0.026600
4 -0.018200 4 -0.018200
5 -0.129000 5 -0.129000
6 0.123700 6 0.123700
7 -0.173400 7 -0.173400
8 0.140300 8 0.140300
9 -0.113400 9 -0.113400
10 0.128800 10 0.128800
11 -0.173400 11 -0.173400
12 0.140300 12 0.140300
13 0.051600 13 0.051600
14 -0.069600 14 -0.069600
15 0.035400 15 0.035400
16 0.035400 16 0.035400
17 -0.129000 17 -0.129000
18 0.123700 18 0.123700
19 0.026600 19 0.026600
20 -0.018200 20 -0.018200
21 -0.129000 21 -0.129000
22 0.123700 22 0.123700
23 -0.173400 23 -0.173400
24 0.140300 24 0.140300
25 -0.113400 25 -0.113400
26 0.128800 26 0.128800
27 -0.173400 27 -0.173400
28 0.140300 28 0.140300
29 0.051600 29 0.051600
30 -0.069600 30 -0.069600
31 -0.129000 31 -0.129000
32 0.123700 32 0.123700
33 0.026600 33 0.026600
34 -0.018200 34 -0.018200
35 -0.129000 35 -0.129000
36 0.123700 36 0.123700
37 -0.173400 37 -0.173400
38 0.140300 38 0.140300
39 -0.113400 39 -0.113400
40 0.128800 40 0.128800
41 -0.173400 41 -0.173400
42 0.140300 42 0.140300
43 0.051600 43 0.051600
44 -0.069600 44 -0.069600
45 0.035400 45 0.035400
46 0.035400 46 0.035400
Coords Coords
1 24.130699 1.043900 -1.309300 1 24.130699 1.043900 -1.309300
2 25.062700 1.582900 -1.309300 2 25.062700 1.582900 -1.309300
3 22.900700 1.753900 -1.309300 3 22.900700 1.753900 -1.309300
4 22.900700 3.253900 -1.309300 4 22.900700 3.253900 -1.309300
5 21.670700 1.043900 -1.309300 5 21.670700 1.043900 -1.309300
6 20.738701 1.582900 -1.309300 6 20.738701 1.582900 -1.309300
7 21.670700 -0.376100 -1.309300 7 21.670700 -0.376100 -1.309300
8 20.738701 -0.915100 -1.309300 8 20.738701 -0.915100 -1.309300
9 22.900700 -1.086100 -1.309300 9 22.900700 -1.086100 -1.309300
10 22.900700 -2.163100 -1.309300 10 22.900700 -2.163100 -1.309300
11 24.130699 -0.376100 -1.309300 11 24.130699 -0.376100 -1.309300
12 25.062700 -0.915100 -1.309300 12 25.062700 -0.915100 -1.309300
13 23.766701 3.658900 -0.952300 13 23.766701 3.658900 -0.952300
14 21.622700 3.802900 -1.871300 14 21.622700 3.802900 -1.871300
15 21.672701 4.544900 -1.970300 15 21.672701 4.544900 -1.970300
16 20.979700 2.979900 -2.165300 16 20.979700 2.979900 -2.165300
17 13.465800 0.682500 -1.658900 17 13.465800 0.682500 -1.658900
18 14.397800 1.221500 -1.658900 18 14.397800 1.221500 -1.658900
19 12.235800 1.392500 -1.658900 19 12.235800 1.392500 -1.658900
20 12.235800 2.892500 -1.658900 20 12.235800 2.892500 -1.658900
21 11.005800 0.682500 -1.658900 21 11.005800 0.682500 -1.658900
22 10.073800 1.221500 -1.658900 22 10.073800 1.221500 -1.658900
23 11.005800 -0.737500 -1.658900 23 11.005800 -0.737500 -1.658900
24 10.073800 -1.276500 -1.658900 24 10.073800 -1.276500 -1.658900
25 12.235800 -1.447500 -1.658900 25 12.235800 -1.447500 -1.658900
26 12.235800 -2.524500 -1.658900 26 12.235800 -2.524500 -1.658900
27 13.465800 -0.737500 -1.658900 27 13.465800 -0.737500 -1.658900
28 14.397800 -1.276500 -1.658900 28 14.397800 -1.276500 -1.658900
29 13.101800 3.297500 -1.301900 29 13.101800 3.297500 -1.301900
30 10.957800 3.441500 -2.220900 30 10.957800 3.441500 -2.220900
31 18.663500 0.855500 -1.372100 31 18.663500 0.855500 -1.372100
32 19.595501 1.394500 -1.372100 32 19.595501 1.394500 -1.372100
33 17.433500 1.565500 -1.372100 33 17.433500 1.565500 -1.372100
34 17.433500 3.065500 -1.372100 34 17.433500 3.065500 -1.372100
35 16.203501 0.855500 -1.372100 35 16.203501 0.855500 -1.372100
36 15.271500 1.394500 -1.372100 36 15.271500 1.394500 -1.372100
37 16.203501 -0.564500 -1.372100 37 16.203501 -0.564500 -1.372100
38 15.271500 -1.103500 -1.372100 38 15.271500 -1.103500 -1.372100
39 17.433500 -1.274500 -1.372100 39 17.433500 -1.274500 -1.372100
40 17.433500 -2.351500 -1.372100 40 17.433500 -2.351500 -1.372100
41 18.663500 -0.564500 -1.372100 41 18.663500 -0.564500 -1.372100
42 19.595501 -1.103500 -1.372100 42 19.595501 -1.103500 -1.372100
43 18.299500 3.470500 -1.015100 43 18.299500 3.470500 -1.015100
44 16.155500 3.614500 -1.934100 44 16.155500 3.614500 -1.934100
45 16.205500 4.356500 -2.033100 45 16.205500 4.356500 -2.033100
46 15.512500 2.791500 -2.228100 46 15.512500 2.791500 -2.228100
Bonds Bonds
1 1 1 2 1 1 1 2
2 2 1 3 2 2 1 3
3 2 1 11 3 2 1 11
4 11 3 4 4 11 3 4
5 2 3 5 5 2 3 5
6 12 13 4 6 12 13 4
7 13 4 14 7 13 4 14
8 1 5 6 8 1 5 6
9 2 5 7 9 2 5 7
10 1 7 8 10 1 7 8
11 2 7 9 11 2 7 9
12 1 9 10 12 1 9 10
13 2 9 11 13 2 9 11
14 1 11 12 14 1 11 12
15 10 15 14 15 10 15 14
16 10 16 14 16 10 16 14
17 9 14 34 17 9 14 34
18 1 17 18 18 1 17 18
19 2 17 19 19 2 17 19
20 2 17 27 20 2 17 27
21 7 19 20 21 7 19 20
22 2 19 21 22 2 19 21
23 8 29 20 23 8 29 20
24 9 30 20 24 9 30 20
25 9 44 20 25 9 44 20
26 1 21 22 26 1 21 22
27 2 21 23 27 2 21 23
28 1 23 24 28 1 23 24
29 2 23 25 29 2 23 25
30 1 25 26 30 1 25 26
31 2 25 27 31 2 25 27
32 1 27 28 32 1 27 28
33 1 31 32 33 1 31 32
34 2 31 33 34 2 31 33
35 2 31 41 35 2 31 41
36 7 33 34 36 7 33 34
37 2 33 35 37 2 33 35
38 8 43 34 38 8 43 34
39 9 44 34 39 9 44 34
40 1 35 36 40 1 35 36
41 2 35 37 41 2 35 37
42 1 37 38 42 1 37 38
43 2 37 39 43 2 37 39
44 1 39 40 44 1 39 40
45 2 39 41 45 2 39 41
46 1 41 42 46 1 41 42
47 10 45 44 47 10 45 44
48 10 46 44 48 10 46 44
Angles Angles
1 1 3 1 2 1 1 3 1 2
2 1 11 1 2 2 1 11 1 2
3 2 3 1 11 3 2 3 1 11
4 17 1 3 4 4 17 1 3 4
5 2 1 3 5 5 2 1 3 5
6 17 5 3 4 6 17 5 3 4
7 18 3 4 13 7 18 3 4 13
8 19 3 4 14 8 19 3 4 14
9 20 13 4 14 9 20 13 4 14
10 1 3 5 6 10 1 3 5 6
11 2 3 5 7 11 2 3 5 7
12 1 7 5 6 12 1 7 5 6
13 1 5 7 8 13 1 5 7 8
14 2 5 7 9 14 2 5 7 9
15 1 9 7 8 15 1 9 7 8
16 1 7 9 10 16 1 7 9 10
17 2 7 9 11 17 2 7 9 11
18 1 11 9 10 18 1 11 9 10
19 2 1 11 9 19 2 1 11 9
20 1 1 11 12 20 1 1 11 12
21 1 9 11 12 21 1 9 11 12
22 21 15 14 4 22 21 15 14 4
23 21 16 14 4 23 21 16 14 4
24 22 4 14 34 24 22 4 14 34
25 15 15 14 16 25 15 15 14 16
26 14 15 14 34 26 14 15 14 34
27 14 16 14 34 27 14 16 14 34
28 1 19 17 18 28 1 19 17 18
29 1 27 17 18 29 1 27 17 18
30 2 19 17 27 30 2 19 17 27
31 9 17 19 20 31 9 17 19 20
32 2 17 19 21 32 2 17 19 21
33 9 21 19 20 33 9 21 19 20
34 10 19 20 29 34 10 19 20 29
35 11 19 20 30 35 11 19 20 30
36 11 19 20 44 36 11 19 20 44
37 12 29 20 30 37 12 29 20 30
38 12 29 20 44 38 12 29 20 44
39 13 30 20 44 39 13 30 20 44
40 1 19 21 22 40 1 19 21 22
41 2 19 21 23 41 2 19 21 23
42 1 23 21 22 42 1 23 21 22
43 1 21 23 24 43 1 21 23 24
44 2 21 23 25 44 2 21 23 25
45 1 25 23 24 45 1 25 23 24
46 1 23 25 26 46 1 23 25 26
47 2 23 25 27 47 2 23 25 27
48 1 27 25 26 48 1 27 25 26
49 2 17 27 25 49 2 17 27 25
50 1 17 27 28 50 1 17 27 28
51 1 25 27 28 51 1 25 27 28
52 1 33 31 32 52 1 33 31 32
53 1 41 31 32 53 1 41 31 32
54 2 33 31 41 54 2 33 31 41
55 9 31 33 34 55 9 31 33 34
56 2 31 33 35 56 2 31 33 35
57 9 35 33 34 57 9 35 33 34
58 11 33 34 14 58 11 33 34 14
59 12 43 34 14 59 12 43 34 14
60 13 14 34 44 60 13 14 34 44
61 10 33 34 43 61 10 33 34 43
62 11 33 34 44 62 11 33 34 44
63 12 43 34 44 63 12 43 34 44
64 1 33 35 36 64 1 33 35 36
65 2 33 35 37 65 2 33 35 37
66 1 37 35 36 66 1 37 35 36
67 1 35 37 38 67 1 35 37 38
68 2 35 37 39 68 2 35 37 39
69 1 39 37 38 69 1 39 37 38
70 1 37 39 40 70 1 37 39 40
71 2 37 39 41 71 2 37 39 41
72 1 41 39 40 72 1 41 39 40
73 2 31 41 39 73 2 31 41 39
74 1 31 41 42 74 1 31 41 42
75 1 39 41 42 75 1 39 41 42
76 16 20 44 34 76 16 20 44 34
77 14 45 44 20 77 14 45 44 20
78 14 46 44 20 78 14 46 44 20
79 14 45 44 34 79 14 45 44 34
80 14 46 44 34 80 14 46 44 34
81 15 45 44 46 81 15 45 44 46
Dihedrals Dihedrals
1 20 2 1 3 4 1 20 2 1 3 4
2 2 5 3 1 2 2 2 5 3 1 2
3 21 11 1 3 4 3 21 11 1 3 4
4 4 11 1 3 5 4 4 11 1 3 5
5 2 9 11 1 2 5 2 9 11 1 2
6 5 2 1 11 12 6 5 2 1 11 12
7 4 3 1 11 9 7 4 3 1 11 9
8 2 3 1 11 12 8 2 3 1 11 12
9 22 1 3 4 13 9 22 1 3 4 13
10 23 1 3 4 14 10 23 1 3 4 14
11 22 5 3 4 13 11 22 5 3 4 13
12 23 5 3 4 14 12 23 5 3 4 14
13 2 1 3 5 6 13 2 1 3 5 6
14 4 1 3 5 7 14 4 1 3 5 7
15 20 6 5 3 4 15 20 6 5 3 4
16 21 7 5 3 4 16 21 7 5 3 4
17 24 3 4 14 15 17 24 3 4 14 15
18 24 3 4 14 16 18 24 3 4 14 16
19 25 3 4 14 34 19 25 3 4 14 34
20 26 13 4 14 15 20 26 13 4 14 15
21 26 13 4 14 16 21 26 13 4 14 16
22 27 13 4 14 34 22 27 13 4 14 34
23 2 3 5 7 8 23 2 3 5 7 8
24 4 3 5 7 9 24 4 3 5 7 9
25 5 6 5 7 8 25 5 6 5 7 8
26 2 9 7 5 6 26 2 9 7 5 6
27 2 5 7 9 10 27 2 5 7 9 10
28 4 5 7 9 11 28 4 5 7 9 11
29 5 8 7 9 10 29 5 8 7 9 10
30 2 11 9 7 8 30 2 11 9 7 8
31 4 7 9 11 1 31 4 7 9 11 1
32 2 7 9 11 12 32 2 7 9 11 12
33 2 1 11 9 10 33 2 1 11 9 10
34 5 10 9 11 12 34 5 10 9 11 12
35 28 4 14 34 33 35 28 4 14 34 33
36 29 4 14 34 43 36 29 4 14 34 43
37 30 4 14 34 44 37 30 4 14 34 44
38 31 15 14 34 33 38 31 15 14 34 33
39 32 15 14 34 43 39 32 15 14 34 43
40 33 15 14 34 44 40 33 15 14 34 44
41 31 16 14 34 33 41 31 16 14 34 33
42 32 16 14 34 43 42 32 16 14 34 43
43 33 16 14 34 44 43 33 16 14 34 44
44 10 18 17 19 20 44 10 18 17 19 20
45 2 21 19 17 18 45 2 21 19 17 18
46 11 27 17 19 20 46 11 27 17 19 20
47 4 27 17 19 21 47 4 27 17 19 21
48 2 25 27 17 18 48 2 25 27 17 18
49 5 18 17 27 28 49 5 18 17 27 28
50 4 19 17 27 25 50 4 19 17 27 25
51 2 19 17 27 28 51 2 19 17 27 28
52 12 17 19 20 29 52 12 17 19 20 29
53 13 17 19 20 30 53 13 17 19 20 30
54 13 17 19 20 44 54 13 17 19 20 44
55 12 21 19 20 29 55 12 21 19 20 29
56 13 21 19 20 30 56 13 21 19 20 30
57 13 21 19 20 44 57 13 21 19 20 44
58 2 17 19 21 22 58 2 17 19 21 22
59 4 17 19 21 23 59 4 17 19 21 23
60 10 22 21 19 20 60 10 22 21 19 20
61 11 23 21 19 20 61 11 23 21 19 20
62 34 34 44 20 19 62 34 34 44 20 19
63 31 45 44 20 19 63 31 45 44 20 19
64 31 46 44 20 19 64 31 46 44 20 19
65 35 34 44 20 29 65 35 34 44 20 29
66 32 45 44 20 29 66 32 45 44 20 29
67 32 46 44 20 29 67 32 46 44 20 29
68 36 34 44 20 30 68 36 34 44 20 30
69 33 45 44 20 30 69 33 45 44 20 30
70 33 46 44 20 30 70 33 46 44 20 30
71 2 19 21 23 24 71 2 19 21 23 24
72 4 19 21 23 25 72 4 19 21 23 25
73 5 22 21 23 24 73 5 22 21 23 24
74 2 25 23 21 22 74 2 25 23 21 22
75 2 21 23 25 26 75 2 21 23 25 26
76 4 21 23 25 27 76 4 21 23 25 27
77 5 24 23 25 26 77 5 24 23 25 26
78 2 27 25 23 24 78 2 27 25 23 24
79 4 23 25 27 17 79 4 23 25 27 17
80 2 23 25 27 28 80 2 23 25 27 28
81 2 17 27 25 26 81 2 17 27 25 26
82 5 26 25 27 28 82 5 26 25 27 28
83 10 32 31 33 34 83 10 32 31 33 34
84 2 35 33 31 32 84 2 35 33 31 32
85 11 41 31 33 34 85 11 41 31 33 34
86 4 41 31 33 35 86 4 41 31 33 35
87 2 39 41 31 32 87 2 39 41 31 32
88 5 32 31 41 42 88 5 32 31 41 42
89 4 33 31 41 39 89 4 33 31 41 39
90 2 33 31 41 42 90 2 33 31 41 42
91 13 31 33 34 14 91 13 31 33 34 14
92 12 31 33 34 43 92 12 31 33 34 43
93 13 31 33 34 44 93 13 31 33 34 44
94 13 35 33 34 14 94 13 35 33 34 14
95 12 35 33 34 43 95 12 35 33 34 43
96 13 35 33 34 44 96 13 35 33 34 44
97 2 31 33 35 36 97 2 31 33 35 36
98 4 31 33 35 37 98 4 31 33 35 37
99 10 36 35 33 34 99 10 36 35 33 34
100 11 37 35 33 34 100 11 37 35 33 34
101 36 20 44 34 14 101 36 20 44 34 14
102 33 45 44 34 14 102 33 45 44 34 14
103 33 46 44 34 14 103 33 46 44 34 14
104 34 20 44 34 33 104 34 20 44 34 33
105 31 45 44 34 33 105 31 45 44 34 33
106 31 46 44 34 33 106 31 46 44 34 33
107 35 20 44 34 43 107 35 20 44 34 43
108 32 45 44 34 43 108 32 45 44 34 43
109 32 46 44 34 43 109 32 46 44 34 43
110 2 33 35 37 38 110 2 33 35 37 38
111 4 33 35 37 39 111 4 33 35 37 39
112 5 36 35 37 38 112 5 36 35 37 38
113 2 39 37 35 36 113 2 39 37 35 36
114 2 35 37 39 40 114 2 35 37 39 40
115 4 35 37 39 41 115 4 35 37 39 41
116 5 38 37 39 40 116 5 38 37 39 40
117 2 41 39 37 38 117 2 41 39 37 38
118 4 37 39 41 31 118 4 37 39 41 31
119 2 37 39 41 42 119 2 37 39 41 42
120 2 31 41 39 40 120 2 31 41 39 40
121 5 40 39 41 42 121 5 40 39 41 42
Impropers Impropers
1 1 3 1 11 2 1 1 3 1 11 2
2 8 1 3 5 4 2 8 1 3 5 4
3 9 3 4 13 14 3 9 3 4 13 14
4 1 3 5 7 6 4 1 3 5 7 6
5 1 5 7 9 8 5 1 5 7 9 8
6 1 7 9 11 10 6 1 7 9 11 10
7 1 1 11 9 12 7 1 1 11 9 12
8 1 19 17 27 18 8 1 19 17 27 18
9 5 17 19 21 20 9 5 17 19 21 20
10 1 19 21 23 22 10 1 19 21 23 22
11 1 21 23 25 24 11 1 21 23 25 24
12 1 23 25 27 26 12 1 23 25 27 26
13 1 17 27 25 28 13 1 17 27 25 28
14 1 33 31 41 32 14 1 33 31 41 32
15 5 31 33 35 34 15 5 31 33 35 34
16 1 33 35 37 36 16 1 33 35 37 36
17 1 35 37 39 38 17 1 35 37 39 38
18 1 37 39 41 40 18 1 37 39 41 40
19 1 31 41 39 42 19 1 31 41 39 42
20 1 15 14 16 4 20 1 15 14 16 4
21 1 15 14 4 34 21 1 15 14 4 34
22 1 16 14 4 34 22 1 16 14 4 34
23 1 15 14 16 34 23 1 15 14 16 34
24 1 19 20 29 30 24 1 19 20 29 30
25 1 19 20 29 44 25 1 19 20 29 44
26 1 19 20 30 44 26 1 19 20 30 44
27 1 29 20 30 44 27 1 29 20 30 44
28 1 33 34 43 14 28 1 33 34 43 14
29 1 33 34 14 44 29 1 33 34 14 44
30 1 43 34 14 44 30 1 43 34 14 44
31 1 33 34 43 44 31 1 33 34 43 44
32 1 45 44 34 20 32 1 45 44 34 20
33 1 46 44 34 20 33 1 46 44 34 20
34 1 45 44 46 20 34 1 45 44 46 20
35 1 45 44 46 34 35 1 45 44 46 34

96
examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene
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# use bond/react 'create atoms' feature to add 30 new styrene monomers to chain # use bond/react 'create atoms' feature to add 30 new styrene monomers to chain
units real units real
boundary p p p boundary p p p
atom_style full atom_style full
kspace_style pppm 1.0e-4 kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5 pair_style lj/class2/coul/long 8.5
angle_style class2 angle_style class2
bond_style class2 bond_style class2
dihedral_style class2 dihedral_style class2
improper_style class2 improper_style class2
variable T equal 530 variable T equal 530
read_data trimer.data & read_data trimer.data &
extra/bond/per/atom 5 & extra/bond/per/atom 5 &
extra/angle/per/atom 15 & extra/angle/per/atom 15 &
extra/dihedral/per/atom 15 & extra/dihedral/per/atom 15 &
extra/improper/per/atom 25 & extra/improper/per/atom 25 &
extra/special/per/atom 25 extra/special/per/atom 25
molecule mol1 grow_styrene_pre.data_template molecule mol1 grow_styrene_pre.data_template
molecule mol2 grow_styrene_post.data_template molecule mol2 grow_styrene_post.data_template
fix myrxns all bond/react stabilization yes statted_grp .03 & fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map & react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map &
modify_create fit create_fit overlap 2.0 & modify_create fit create_fit overlap 2.0 &
stabilize_steps 100 max_rxn 30 stabilize_steps 100 max_rxn 30
fix 1 statted_grp_REACT nvt temp $T $T 100 fix 1 statted_grp_REACT nvt temp $T $T 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1 fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
thermo_style custom step temp press density f_myrxns[1] thermo_style custom step temp press density f_myrxns[1]
thermo 100 thermo 100
run 8000 run 8000
# write_data final.data nofix # write_data final.data nofix

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examples/SPIN/cobalt_fcc/Co_PurjaPun_2012.eam.alloy
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examples/SPIN/iron/Fe_Mishin2006.eam.alloy
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examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy
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examples/SPIN/test_problems/validation_nve/Fe_Mishin2006.eam.alloy
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examples/SPIN/test_problems/validation_nvt/Fe_Mishin2006.eam.alloy
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examples/SPIN/vmd/vmd_nano.vmd
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proc vmd_draw_arrow {mol start end} { proc vmd_draw_arrow {mol start end} {
set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]] set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]]
graphics $mol cylinder $start $middle radius 0.05 graphics $mol cylinder $start $middle radius 0.05
graphics $mol cone $middle $end radius 0.01 color 3 graphics $mol cone $middle $end radius 0.01 color 3
} }
proc vmd_draw_vector {args} { proc vmd_draw_vector {args} {
set usage {"draw vector {x1 y1 z1} {x2 y2 z2} [scale <s>] [resolution <res>] [radius <r>] [filled <yes/no>]"} set usage {"draw vector {x1 y1 z1} {x2 y2 z2} [scale <s>] [resolution <res>] [radius <r>] [filled <yes/no>]"}
# defaults # defaults
set scale 2.0 set scale 2.0
set res 50 set res 50
set radius 0.1 set radius 0.1
set filled yes set filled yes
if {[llength $args] < 3} { if {[llength $args] < 3} {
error "wrong # args: should be $usage" error "wrong # args: should be $usage"
} }
set mol [lindex $args 0] set mol [lindex $args 0]
set center [lindex $args 1] set center [lindex $args 1]
set vector [lindex $args 2] set vector [lindex $args 2]
if {[llength $center] != 3 || [llength $vector] != 3} { if {[llength $center] != 3 || [llength $vector] != 3} {
error "wrong type of args: should be $usage" error "wrong type of args: should be $usage"
} }
foreach {flag value} [lrange $args 3 end] { foreach {flag value} [lrange $args 3 end] {
switch -glob $flag { switch -glob $flag {
scale {set scale $value} scale {set scale $value}
res* {set res $value} res* {set res $value}
rad* {set radius $value} rad* {set radius $value}
fill* {set filled $value} fill* {set filled $value}
default {error "unknown option '$flag': should be $usage" } default {error "unknown option '$flag': should be $usage" }
} }
} }
set vechalf [vecscale [expr $scale * 0.5] $vector] set vechalf [vecscale [expr $scale * 0.5] $vector]
return [list \ return [list \
[graphics $mol color yellow]\ [graphics $mol color yellow]\
[graphics $mol cylinder [vecsub $center $vechalf]\ [graphics $mol cylinder [vecsub $center $vechalf]\
[vecadd $center [vecscale 0.7 $vechalf]] \ [vecadd $center [vecscale 0.7 $vechalf]] \
radius $radius resolution $res filled $filled] \ radius $radius resolution $res filled $filled] \
[graphics $mol color orange]\ [graphics $mol color orange]\
[graphics $mol cone [vecadd $center [vecscale 0.6 $vechalf]] \ [graphics $mol cone [vecadd $center [vecscale 0.6 $vechalf]] \
[vecadd $center $vechalf] radius [expr $radius * 2.5] \ [vecadd $center $vechalf] radius [expr $radius * 2.5] \
resolution $res]] resolution $res]]
} }
proc vmd_draw_spin {args} { proc vmd_draw_spin {args} {
global molid global molid
graphics $molid delete all graphics $molid delete all
set frame [molinfo $molid get frame] set frame [molinfo $molid get frame]
set natoms [molinfo $molid get numatoms] set natoms [molinfo $molid get numatoms]
for {set i 0} {$i < $natoms} {incr i} { for {set i 0} {$i < $natoms} {incr i} {
set sel [atomselect top "index $i"] set sel [atomselect top "index $i"]
# set sel [atomselect top "index 1200"] # set sel [atomselect top "index 1200"]
set coords [lindex [$sel get {x y z}] $molid] set coords [lindex [$sel get {x y z}] $molid]
set velocities [lindex [$sel get {vx vy vz}] $molid] set velocities [lindex [$sel get {vx vy vz}] $molid]
draw vector $coords $velocities draw vector $coords $velocities
set uvx [lindex [$sel get {vx}] $molid] set uvx [lindex [$sel get {vx}] $molid]
set uvy [lindex [$sel get {vy}] $molid] set uvy [lindex [$sel get {vy}] $molid]
set uvz [lindex [$sel get {vz}] $molid] set uvz [lindex [$sel get {vz}] $molid]
$sel set user [vecadd [vecadd [vecscale $uvy $uvy] [vecscale $uvz $uvz] ] [vecscale $uvx $uvx]] $sel set user [vecadd [vecadd [vecscale $uvy $uvy] [vecscale $uvz $uvz] ] [vecscale $uvx $uvx]]
$sel set user $uvy $sel set user $uvy
#draw vector $coords {0.0 uvy 0.0} #draw vector $coords {0.0 uvy 0.0}
} }
#pbc box -color 3 #pbc box -color 3
} }
proc enable_trace {} { proc enable_trace {} {
global vmd_frame global vmd_frame
trace variable vmd_frame([molinfo top]) w vmd_draw_spin 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] 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 scale by 0.5
animate style Loop animate style Loop
enable_trace enable_trace

24
examples/mscg/control.in
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block_size 1 block_size 1
start_frame 1 start_frame 1
n_frames 19 n_frames 19
nonbonded_cutoff 10.0 nonbonded_cutoff 10.0
basis_type 0 basis_type 0
primary_output_style 0 primary_output_style 0
output_solution_flag 1 output_solution_flag 1
output_spline_coeffs_flag 1 output_spline_coeffs_flag 1
pair_nonbonded_bspline_basis_order 6 pair_nonbonded_bspline_basis_order 6
pair_nonbonded_basis_set_resolution 0.7 pair_nonbonded_basis_set_resolution 0.7
pair_nonbonded_output_binwidth 0.1 pair_nonbonded_output_binwidth 0.1
matrix_type 0 matrix_type 0

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examples/relres/Data.22DMH.in.real
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tools/msi2lmp/test/PyAC_bulk-clayff.car
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tools/msi2lmp/test/PyAC_bulk-clayff.mdf
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tools/polybond/lmpsdata.py
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