├── .DESCRIPTION.md ├── .files.txt ├── .generateREADME.sh ├── .gitattributes ├── .github └── workflows │ └── latexmk_yml ├── .gitignore ├── .gitmodules ├── LICENSE ├── Makefile ├── README.md ├── figures ├── CNT-breakable-stress-energy.png ├── CNT-deformed-breakable.png ├── CNT-deformed-unbreakable.png ├── CNT-energy-breakable.png ├── CNT-energy-unbreakable.png ├── CNT-lenght-unbreakable.png ├── CNT-stress-strain-breakable.png ├── CNT-stress-strain-unbreakable.png ├── CNT-unbreakable-length-energy.png ├── CNT-unbreakable-stress-strain.png ├── CNT-unbreakable.png ├── CNT-underformed-deleted.png ├── CNT-underformed.png ├── CNT.png ├── GCMC-cracked.png ├── GCMC-dimension.png ├── GCMC-generate.png ├── GCMC-number.png ├── GCMC-solvated.png ├── GCMC.png ├── GUI-1.png ├── LJ-avatar.png ├── LJ-coords.png ├── LJ-cylinder.png ├── LJ-energy.png ├── LJ-evolution.png ├── LJ-mixing.png ├── LJ.png ├── NANOSHEAR-equilibration.png ├── NANOSHEAR-minimization.png ├── NANOSHEAR-profiles.png ├── NANOSHEAR-system.png ├── NANOSHEAR.png ├── PEG-density.png ├── PEG-distance.png ├── PEG-in-vacuum.png ├── PEG-in-water.png ├── PEG-solvated.png ├── PEG-water.png ├── PEG.png ├── REACT-final.png ├── REACT-mixing.png ├── REACT-reacting.png ├── REACT.png ├── SIO-charge.png ├── SIO-decorated.png ├── SIO-deformed-charge.png ├── SIO-deformed.png ├── SIO-distribution-bis.png ├── SIO-distribution.png ├── SIO-slice.png ├── SIO-temperature.png ├── SIO-volume.png ├── SIO.png ├── US-density-evolution.png ├── US-density.png ├── US-free-energy.png ├── US-freenergy.png ├── US-freesampling.png ├── US-potential.png ├── US-system-biased.png ├── US-system-unbiased.png ├── US.png └── chart-and-output.png ├── files ├── tutorial1 │ ├── .manifest │ ├── improved.md.lmp │ ├── improved.min.lmp │ ├── initial.lmp │ └── solution │ │ ├── improved.md.dat │ │ ├── improved.md.ipynb │ │ ├── improved.md.lmp │ │ ├── improved.md.log │ │ ├── improved.md.mp4 │ │ ├── improved.md.png │ │ ├── improved.min.data │ │ ├── improved.min.lmp │ │ ├── improved.min.log │ │ ├── improved.min.png │ │ ├── initial.ipynb │ │ ├── initial.lmp │ │ ├── initial.log │ │ ├── initial.min.png │ │ ├── initial.mp4 │ │ └── initial.png ├── tutorial2 │ ├── .manifest │ ├── CH.airebo │ ├── breakable.data │ ├── breakable.lmp │ ├── solution │ │ ├── CH.airebo │ │ ├── breakable-with-tip.lmp │ │ ├── breakable-yaml-reader.py │ │ ├── breakable.dat │ │ ├── breakable.data │ │ ├── breakable.ipynb │ │ ├── breakable.lmp │ │ ├── breakable.log │ │ ├── breakable.png │ │ ├── breakable.yaml │ │ ├── unbreakable-yaml-reader.py │ │ ├── unbreakable.dat │ │ ├── unbreakable.data │ │ ├── unbreakable.inc │ │ ├── unbreakable.ipynb │ │ ├── unbreakable.lmp │ │ ├── unbreakable.log │ │ ├── unbreakable.png │ │ └── unbreakable.yaml │ ├── unbreakable-yaml-reader.py │ ├── unbreakable.data │ ├── unbreakable.inc │ └── unbreakable.lmp ├── tutorial3 │ ├── .manifest │ ├── merge.lmp │ ├── parameters.inc │ ├── peg.mol │ ├── pull.lmp │ ├── solution │ │ ├── merge.lmp │ │ ├── merge.log │ │ ├── merge.png │ │ ├── merge.restart │ │ ├── parameters.inc │ │ ├── peg.mol │ │ ├── pull-with-tip.lmp │ │ ├── pull.dat │ │ ├── pull.ipynb │ │ ├── pull.lammpstrj │ │ ├── pull.lmp │ │ ├── pull.log │ │ ├── pull.png │ │ ├── water.ipynb │ │ ├── water.lmp │ │ ├── water.log │ │ ├── water.mol │ │ ├── water.png │ │ └── water.restart │ ├── water.lmp │ └── water.mol ├── tutorial4 │ ├── .manifest │ ├── create.lmp │ ├── equilibrate.lmp │ ├── groups.inc │ ├── parameters.inc │ ├── shearing.lmp │ ├── solution │ │ ├── create.data │ │ ├── create.lmp │ │ ├── create.log │ │ ├── equilibrate.data │ │ ├── equilibrate.ipynb │ │ ├── equilibrate.lmp │ │ ├── equilibrate.log │ │ ├── groups.inc │ │ ├── parameters.inc │ │ ├── shearing-ions.dat │ │ ├── shearing-wall.dat │ │ ├── shearing-water.dat │ │ ├── shearing.ipynb │ │ ├── shearing.lmp │ │ ├── shearing.log │ │ ├── shearing.png │ │ └── water.mol │ └── water.mol ├── tutorial5 │ ├── .manifest │ ├── decorate.lmp │ ├── deform.lmp │ ├── ffield.reax.CHOFe │ ├── relax.lmp │ ├── silica.data │ └── solution │ │ ├── decorate-H.histo │ │ ├── decorate-O.histo │ │ ├── decorate-Si.histo │ │ ├── decorate.lmp │ │ ├── decorate.log │ │ ├── decorate.png │ │ ├── decorate.species │ │ ├── deform-O.histo │ │ ├── deform-Si.histo │ │ ├── deform-mod.data │ │ ├── deform.data │ │ ├── deform.ipynb │ │ ├── deform.lmp │ │ ├── deform.log │ │ ├── deform.png │ │ ├── deform.species │ │ ├── ffield.reax.CHOFe │ │ ├── relax-O.histo │ │ ├── relax-Si.histo │ │ ├── relax.data │ │ ├── relax.ipynb │ │ ├── relax.lmp │ │ ├── relax.log │ │ ├── relax.png │ │ ├── relax.species │ │ └── silica.data ├── tutorial6 │ ├── .manifest │ ├── H2O.mol │ ├── SiO.1990.vashishta │ ├── cracking.lmp │ ├── gcmc.lmp │ ├── generate.lmp │ └── solution │ │ ├── H2O.mol │ │ ├── SiO.1990.vashishta │ │ ├── cracking-mod.data │ │ ├── cracking.data │ │ ├── cracking.lmp │ │ ├── cracking.log │ │ ├── cracking.png │ │ ├── gcmc.ipynb │ │ ├── gcmc.lmp │ │ ├── gcmc.log │ │ ├── gcmc.png │ │ ├── generate.data │ │ ├── generate.ipynb │ │ ├── generate.lmp │ │ ├── generate.log │ │ └── generate.png ├── tutorial7 │ ├── .manifest │ ├── free-sampling.lmp │ ├── solution │ │ ├── free-sampling.dat │ │ ├── free-sampling.ipynb │ │ ├── free-sampling.lmp │ │ ├── free-sampling.log │ │ ├── free-sampling.png │ │ ├── umbrella-sampling.1.dat │ │ ├── umbrella-sampling.10.dat │ │ ├── umbrella-sampling.11.dat │ │ ├── umbrella-sampling.12.dat │ │ ├── umbrella-sampling.13.dat │ │ ├── umbrella-sampling.14.dat │ │ ├── umbrella-sampling.15.dat │ │ ├── umbrella-sampling.2.dat │ │ ├── umbrella-sampling.3.dat │ │ ├── umbrella-sampling.4.dat │ │ ├── umbrella-sampling.5.dat │ │ ├── umbrella-sampling.6.dat │ │ ├── umbrella-sampling.7.dat │ │ ├── umbrella-sampling.8.dat │ │ ├── umbrella-sampling.9.dat │ │ ├── umbrella-sampling.dat │ │ ├── umbrella-sampling.ipynb │ │ ├── umbrella-sampling.lmp │ │ ├── umbrella-sampling.log │ │ ├── umbrella-sampling.meta │ │ ├── umbrella-sampling.png │ │ └── wham │ ├── umbrella-sampling.lmp │ ├── umbrella-sampling.meta │ └── wham ├── tutorial8 │ ├── .manifest │ ├── CNT.data │ ├── M-M.rxnmap │ ├── M-M_post.mol │ ├── M-M_pre.mol │ ├── M-P.rxnmap │ ├── M-P_post.mol │ ├── M-P_pre.mol │ ├── P-P.rxnmap │ ├── P-P_post.mol │ ├── P-P_pre.mol │ ├── mixing.lmp │ ├── polymerize.lmp │ ├── solution │ │ ├── CNT.data │ │ ├── M-M.rxnmap │ │ ├── M-M_post.mol │ │ ├── M-M_pre.mol │ │ ├── M-P.rxnmap │ │ ├── M-P_post.mol │ │ ├── M-P_pre.mol │ │ ├── P-P.rxnmap │ │ ├── P-P_post.mol │ │ ├── P-P_pre.mol │ │ ├── mixing.data │ │ ├── mixing.ipynb │ │ ├── mixing.lmp │ │ ├── mixing.log │ │ ├── mixing.png │ │ ├── mixing.restart │ │ ├── polymerize.data │ │ ├── polymerize.ipynb │ │ ├── polymerize.lmp │ │ ├── polymerize.log │ │ ├── polymerize.png │ │ └── styrene.mol │ └── styrene.mol └── update_headers.py ├── journal-article.bib ├── lammps-tutorials.tex ├── livecoms.cls ├── releases ├── header_v1.0.png └── published-version-v1.0.pdf └── vancouver-livecoms.bst /.DESCRIPTION.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/.DESCRIPTION.md -------------------------------------------------------------------------------- /.files.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/.files.txt -------------------------------------------------------------------------------- /.generateREADME.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | .dependencies/.github/generateREADME.sh 4 | -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/workflows/latexmk_yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/.github/workflows/latexmk_yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/.gitmodules -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/LICENSE -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/README.md -------------------------------------------------------------------------------- /figures/CNT-breakable-stress-energy.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/CNT-breakable-stress-energy.png -------------------------------------------------------------------------------- /figures/CNT-deformed-breakable.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/CNT-deformed-breakable.png -------------------------------------------------------------------------------- /figures/CNT-deformed-unbreakable.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/CNT-deformed-unbreakable.png -------------------------------------------------------------------------------- /figures/CNT-energy-breakable.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/CNT-energy-breakable.png -------------------------------------------------------------------------------- /figures/CNT-energy-unbreakable.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/CNT-energy-unbreakable.png -------------------------------------------------------------------------------- /figures/CNT-lenght-unbreakable.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/CNT-lenght-unbreakable.png -------------------------------------------------------------------------------- /figures/CNT-stress-strain-breakable.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/CNT-stress-strain-breakable.png -------------------------------------------------------------------------------- /figures/CNT-stress-strain-unbreakable.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/CNT-stress-strain-unbreakable.png -------------------------------------------------------------------------------- /figures/CNT-unbreakable-length-energy.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/CNT-unbreakable-length-energy.png -------------------------------------------------------------------------------- /figures/CNT-unbreakable-stress-strain.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/CNT-unbreakable-stress-strain.png -------------------------------------------------------------------------------- /figures/CNT-unbreakable.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/CNT-unbreakable.png -------------------------------------------------------------------------------- /figures/CNT-underformed-deleted.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/CNT-underformed-deleted.png -------------------------------------------------------------------------------- /figures/CNT-underformed.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/CNT-underformed.png -------------------------------------------------------------------------------- /figures/CNT.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/CNT.png -------------------------------------------------------------------------------- /figures/GCMC-cracked.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/GCMC-cracked.png -------------------------------------------------------------------------------- /figures/GCMC-dimension.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/GCMC-dimension.png -------------------------------------------------------------------------------- /figures/GCMC-generate.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/GCMC-generate.png -------------------------------------------------------------------------------- /figures/GCMC-number.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/GCMC-number.png -------------------------------------------------------------------------------- /figures/GCMC-solvated.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/GCMC-solvated.png -------------------------------------------------------------------------------- /figures/GCMC.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/GCMC.png -------------------------------------------------------------------------------- /figures/GUI-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/GUI-1.png -------------------------------------------------------------------------------- /figures/LJ-avatar.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/LJ-avatar.png -------------------------------------------------------------------------------- /figures/LJ-coords.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/LJ-coords.png -------------------------------------------------------------------------------- /figures/LJ-cylinder.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/LJ-cylinder.png -------------------------------------------------------------------------------- /figures/LJ-energy.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/LJ-energy.png -------------------------------------------------------------------------------- /figures/LJ-evolution.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/LJ-evolution.png -------------------------------------------------------------------------------- /figures/LJ-mixing.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/LJ-mixing.png -------------------------------------------------------------------------------- /figures/LJ.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/LJ.png -------------------------------------------------------------------------------- /figures/NANOSHEAR-equilibration.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/NANOSHEAR-equilibration.png -------------------------------------------------------------------------------- /figures/NANOSHEAR-minimization.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/NANOSHEAR-minimization.png -------------------------------------------------------------------------------- /figures/NANOSHEAR-profiles.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/NANOSHEAR-profiles.png -------------------------------------------------------------------------------- /figures/NANOSHEAR-system.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/NANOSHEAR-system.png -------------------------------------------------------------------------------- /figures/NANOSHEAR.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/NANOSHEAR.png -------------------------------------------------------------------------------- /figures/PEG-density.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/PEG-density.png -------------------------------------------------------------------------------- /figures/PEG-distance.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/PEG-distance.png -------------------------------------------------------------------------------- /figures/PEG-in-vacuum.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/PEG-in-vacuum.png -------------------------------------------------------------------------------- /figures/PEG-in-water.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/PEG-in-water.png -------------------------------------------------------------------------------- /figures/PEG-solvated.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/PEG-solvated.png -------------------------------------------------------------------------------- /figures/PEG-water.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/PEG-water.png -------------------------------------------------------------------------------- /figures/PEG.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/PEG.png -------------------------------------------------------------------------------- /figures/REACT-final.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/REACT-final.png -------------------------------------------------------------------------------- /figures/REACT-mixing.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/REACT-mixing.png -------------------------------------------------------------------------------- /figures/REACT-reacting.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/REACT-reacting.png -------------------------------------------------------------------------------- /figures/REACT.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/REACT.png -------------------------------------------------------------------------------- /figures/SIO-charge.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/SIO-charge.png -------------------------------------------------------------------------------- /figures/SIO-decorated.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/SIO-decorated.png -------------------------------------------------------------------------------- /figures/SIO-deformed-charge.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/SIO-deformed-charge.png -------------------------------------------------------------------------------- /figures/SIO-deformed.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/SIO-deformed.png -------------------------------------------------------------------------------- /figures/SIO-distribution-bis.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/SIO-distribution-bis.png -------------------------------------------------------------------------------- /figures/SIO-distribution.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/SIO-distribution.png -------------------------------------------------------------------------------- /figures/SIO-slice.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/SIO-slice.png -------------------------------------------------------------------------------- /figures/SIO-temperature.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/SIO-temperature.png -------------------------------------------------------------------------------- /figures/SIO-volume.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/SIO-volume.png -------------------------------------------------------------------------------- /figures/SIO.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/SIO.png -------------------------------------------------------------------------------- /figures/US-density-evolution.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/US-density-evolution.png -------------------------------------------------------------------------------- /figures/US-density.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/US-density.png -------------------------------------------------------------------------------- /figures/US-free-energy.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/US-free-energy.png -------------------------------------------------------------------------------- /figures/US-freenergy.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/US-freenergy.png -------------------------------------------------------------------------------- /figures/US-freesampling.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/US-freesampling.png -------------------------------------------------------------------------------- /figures/US-potential.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/US-potential.png -------------------------------------------------------------------------------- /figures/US-system-biased.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/US-system-biased.png -------------------------------------------------------------------------------- /figures/US-system-unbiased.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/US-system-unbiased.png -------------------------------------------------------------------------------- /figures/US.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/US.png -------------------------------------------------------------------------------- /figures/chart-and-output.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/figures/chart-and-output.png -------------------------------------------------------------------------------- /files/tutorial1/.manifest: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/.manifest -------------------------------------------------------------------------------- /files/tutorial1/improved.md.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/improved.md.lmp -------------------------------------------------------------------------------- /files/tutorial1/improved.min.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/improved.min.lmp -------------------------------------------------------------------------------- /files/tutorial1/initial.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/initial.lmp -------------------------------------------------------------------------------- /files/tutorial1/solution/improved.md.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/solution/improved.md.dat -------------------------------------------------------------------------------- /files/tutorial1/solution/improved.md.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/solution/improved.md.ipynb -------------------------------------------------------------------------------- /files/tutorial1/solution/improved.md.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/solution/improved.md.lmp -------------------------------------------------------------------------------- /files/tutorial1/solution/improved.md.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/solution/improved.md.log -------------------------------------------------------------------------------- /files/tutorial1/solution/improved.md.mp4: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/solution/improved.md.mp4 -------------------------------------------------------------------------------- /files/tutorial1/solution/improved.md.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/solution/improved.md.png -------------------------------------------------------------------------------- /files/tutorial1/solution/improved.min.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/solution/improved.min.data -------------------------------------------------------------------------------- /files/tutorial1/solution/improved.min.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/solution/improved.min.lmp -------------------------------------------------------------------------------- /files/tutorial1/solution/improved.min.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/solution/improved.min.log -------------------------------------------------------------------------------- /files/tutorial1/solution/improved.min.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/solution/improved.min.png -------------------------------------------------------------------------------- /files/tutorial1/solution/initial.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/solution/initial.ipynb -------------------------------------------------------------------------------- /files/tutorial1/solution/initial.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/solution/initial.lmp -------------------------------------------------------------------------------- /files/tutorial1/solution/initial.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/solution/initial.log -------------------------------------------------------------------------------- /files/tutorial1/solution/initial.min.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/solution/initial.min.png -------------------------------------------------------------------------------- /files/tutorial1/solution/initial.mp4: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/solution/initial.mp4 -------------------------------------------------------------------------------- /files/tutorial1/solution/initial.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial1/solution/initial.png -------------------------------------------------------------------------------- /files/tutorial2/.manifest: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/.manifest -------------------------------------------------------------------------------- /files/tutorial2/CH.airebo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/CH.airebo -------------------------------------------------------------------------------- /files/tutorial2/breakable.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/breakable.data -------------------------------------------------------------------------------- /files/tutorial2/breakable.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/breakable.lmp -------------------------------------------------------------------------------- /files/tutorial2/solution/CH.airebo: -------------------------------------------------------------------------------- 1 | ../CH.airebo -------------------------------------------------------------------------------- /files/tutorial2/solution/breakable-with-tip.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/solution/breakable-with-tip.lmp -------------------------------------------------------------------------------- /files/tutorial2/solution/breakable-yaml-reader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/solution/breakable-yaml-reader.py -------------------------------------------------------------------------------- /files/tutorial2/solution/breakable.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/solution/breakable.dat -------------------------------------------------------------------------------- /files/tutorial2/solution/breakable.data: -------------------------------------------------------------------------------- 1 | ../breakable.data -------------------------------------------------------------------------------- /files/tutorial2/solution/breakable.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/solution/breakable.ipynb -------------------------------------------------------------------------------- /files/tutorial2/solution/breakable.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/solution/breakable.lmp -------------------------------------------------------------------------------- /files/tutorial2/solution/breakable.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/solution/breakable.log -------------------------------------------------------------------------------- /files/tutorial2/solution/breakable.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/solution/breakable.png -------------------------------------------------------------------------------- /files/tutorial2/solution/breakable.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/solution/breakable.yaml -------------------------------------------------------------------------------- /files/tutorial2/solution/unbreakable-yaml-reader.py: -------------------------------------------------------------------------------- 1 | ../unbreakable-yaml-reader.py -------------------------------------------------------------------------------- /files/tutorial2/solution/unbreakable.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/solution/unbreakable.dat -------------------------------------------------------------------------------- /files/tutorial2/solution/unbreakable.data: -------------------------------------------------------------------------------- 1 | ../unbreakable.data -------------------------------------------------------------------------------- /files/tutorial2/solution/unbreakable.inc: -------------------------------------------------------------------------------- 1 | ../unbreakable.inc -------------------------------------------------------------------------------- /files/tutorial2/solution/unbreakable.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/solution/unbreakable.ipynb -------------------------------------------------------------------------------- /files/tutorial2/solution/unbreakable.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/solution/unbreakable.lmp -------------------------------------------------------------------------------- /files/tutorial2/solution/unbreakable.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/solution/unbreakable.log -------------------------------------------------------------------------------- /files/tutorial2/solution/unbreakable.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/solution/unbreakable.png -------------------------------------------------------------------------------- /files/tutorial2/solution/unbreakable.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/solution/unbreakable.yaml -------------------------------------------------------------------------------- /files/tutorial2/unbreakable-yaml-reader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/unbreakable-yaml-reader.py -------------------------------------------------------------------------------- /files/tutorial2/unbreakable.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/unbreakable.data -------------------------------------------------------------------------------- /files/tutorial2/unbreakable.inc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/unbreakable.inc -------------------------------------------------------------------------------- /files/tutorial2/unbreakable.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial2/unbreakable.lmp -------------------------------------------------------------------------------- /files/tutorial3/.manifest: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/.manifest -------------------------------------------------------------------------------- /files/tutorial3/merge.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/merge.lmp -------------------------------------------------------------------------------- /files/tutorial3/parameters.inc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/parameters.inc -------------------------------------------------------------------------------- /files/tutorial3/peg.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/peg.mol -------------------------------------------------------------------------------- /files/tutorial3/pull.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/pull.lmp -------------------------------------------------------------------------------- /files/tutorial3/solution/merge.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/solution/merge.lmp -------------------------------------------------------------------------------- /files/tutorial3/solution/merge.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/solution/merge.log -------------------------------------------------------------------------------- /files/tutorial3/solution/merge.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/solution/merge.png -------------------------------------------------------------------------------- /files/tutorial3/solution/merge.restart: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/solution/merge.restart -------------------------------------------------------------------------------- /files/tutorial3/solution/parameters.inc: -------------------------------------------------------------------------------- 1 | ../parameters.inc -------------------------------------------------------------------------------- /files/tutorial3/solution/peg.mol: -------------------------------------------------------------------------------- 1 | ../peg.mol -------------------------------------------------------------------------------- /files/tutorial3/solution/pull-with-tip.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/solution/pull-with-tip.lmp -------------------------------------------------------------------------------- /files/tutorial3/solution/pull.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/solution/pull.dat -------------------------------------------------------------------------------- /files/tutorial3/solution/pull.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/solution/pull.ipynb -------------------------------------------------------------------------------- /files/tutorial3/solution/pull.lammpstrj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/solution/pull.lammpstrj -------------------------------------------------------------------------------- /files/tutorial3/solution/pull.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/solution/pull.lmp -------------------------------------------------------------------------------- /files/tutorial3/solution/pull.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/solution/pull.log -------------------------------------------------------------------------------- /files/tutorial3/solution/pull.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/solution/pull.png -------------------------------------------------------------------------------- /files/tutorial3/solution/water.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/solution/water.ipynb -------------------------------------------------------------------------------- /files/tutorial3/solution/water.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/solution/water.lmp -------------------------------------------------------------------------------- /files/tutorial3/solution/water.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/solution/water.log -------------------------------------------------------------------------------- /files/tutorial3/solution/water.mol: -------------------------------------------------------------------------------- 1 | ../water.mol -------------------------------------------------------------------------------- /files/tutorial3/solution/water.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/solution/water.png -------------------------------------------------------------------------------- /files/tutorial3/solution/water.restart: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/solution/water.restart -------------------------------------------------------------------------------- /files/tutorial3/water.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/water.lmp -------------------------------------------------------------------------------- /files/tutorial3/water.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial3/water.mol -------------------------------------------------------------------------------- /files/tutorial4/.manifest: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/.manifest -------------------------------------------------------------------------------- /files/tutorial4/create.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/create.lmp -------------------------------------------------------------------------------- /files/tutorial4/equilibrate.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/equilibrate.lmp -------------------------------------------------------------------------------- /files/tutorial4/groups.inc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/groups.inc -------------------------------------------------------------------------------- /files/tutorial4/parameters.inc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/parameters.inc -------------------------------------------------------------------------------- /files/tutorial4/shearing.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/shearing.lmp -------------------------------------------------------------------------------- /files/tutorial4/solution/create.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/solution/create.data -------------------------------------------------------------------------------- /files/tutorial4/solution/create.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/solution/create.lmp -------------------------------------------------------------------------------- /files/tutorial4/solution/create.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/solution/create.log -------------------------------------------------------------------------------- /files/tutorial4/solution/equilibrate.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/solution/equilibrate.data -------------------------------------------------------------------------------- /files/tutorial4/solution/equilibrate.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/solution/equilibrate.ipynb -------------------------------------------------------------------------------- /files/tutorial4/solution/equilibrate.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/solution/equilibrate.lmp -------------------------------------------------------------------------------- /files/tutorial4/solution/equilibrate.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/solution/equilibrate.log -------------------------------------------------------------------------------- /files/tutorial4/solution/groups.inc: -------------------------------------------------------------------------------- 1 | ../groups.inc -------------------------------------------------------------------------------- /files/tutorial4/solution/parameters.inc: -------------------------------------------------------------------------------- 1 | ../parameters.inc -------------------------------------------------------------------------------- /files/tutorial4/solution/shearing-ions.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/solution/shearing-ions.dat -------------------------------------------------------------------------------- /files/tutorial4/solution/shearing-wall.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/solution/shearing-wall.dat -------------------------------------------------------------------------------- /files/tutorial4/solution/shearing-water.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/solution/shearing-water.dat -------------------------------------------------------------------------------- /files/tutorial4/solution/shearing.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/solution/shearing.ipynb -------------------------------------------------------------------------------- /files/tutorial4/solution/shearing.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/solution/shearing.lmp -------------------------------------------------------------------------------- /files/tutorial4/solution/shearing.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/solution/shearing.log -------------------------------------------------------------------------------- /files/tutorial4/solution/shearing.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/solution/shearing.png -------------------------------------------------------------------------------- /files/tutorial4/solution/water.mol: -------------------------------------------------------------------------------- 1 | ../water.mol -------------------------------------------------------------------------------- /files/tutorial4/water.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial4/water.mol -------------------------------------------------------------------------------- /files/tutorial5/.manifest: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/.manifest -------------------------------------------------------------------------------- /files/tutorial5/decorate.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/decorate.lmp -------------------------------------------------------------------------------- /files/tutorial5/deform.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/deform.lmp -------------------------------------------------------------------------------- /files/tutorial5/ffield.reax.CHOFe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/ffield.reax.CHOFe -------------------------------------------------------------------------------- /files/tutorial5/relax.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/relax.lmp -------------------------------------------------------------------------------- /files/tutorial5/silica.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/silica.data -------------------------------------------------------------------------------- /files/tutorial5/solution/decorate-H.histo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/decorate-H.histo -------------------------------------------------------------------------------- /files/tutorial5/solution/decorate-O.histo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/decorate-O.histo -------------------------------------------------------------------------------- /files/tutorial5/solution/decorate-Si.histo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/decorate-Si.histo -------------------------------------------------------------------------------- /files/tutorial5/solution/decorate.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/decorate.lmp -------------------------------------------------------------------------------- /files/tutorial5/solution/decorate.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/decorate.log -------------------------------------------------------------------------------- /files/tutorial5/solution/decorate.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/decorate.png -------------------------------------------------------------------------------- /files/tutorial5/solution/decorate.species: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/decorate.species -------------------------------------------------------------------------------- /files/tutorial5/solution/deform-O.histo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/deform-O.histo -------------------------------------------------------------------------------- /files/tutorial5/solution/deform-Si.histo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/deform-Si.histo -------------------------------------------------------------------------------- /files/tutorial5/solution/deform-mod.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/deform-mod.data -------------------------------------------------------------------------------- /files/tutorial5/solution/deform.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/deform.data -------------------------------------------------------------------------------- /files/tutorial5/solution/deform.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/deform.ipynb -------------------------------------------------------------------------------- /files/tutorial5/solution/deform.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/deform.lmp -------------------------------------------------------------------------------- /files/tutorial5/solution/deform.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/deform.log -------------------------------------------------------------------------------- /files/tutorial5/solution/deform.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/deform.png -------------------------------------------------------------------------------- /files/tutorial5/solution/deform.species: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/deform.species -------------------------------------------------------------------------------- /files/tutorial5/solution/ffield.reax.CHOFe: -------------------------------------------------------------------------------- 1 | ../ffield.reax.CHOFe -------------------------------------------------------------------------------- /files/tutorial5/solution/relax-O.histo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/relax-O.histo -------------------------------------------------------------------------------- /files/tutorial5/solution/relax-Si.histo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/relax-Si.histo -------------------------------------------------------------------------------- /files/tutorial5/solution/relax.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/relax.data -------------------------------------------------------------------------------- /files/tutorial5/solution/relax.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/relax.ipynb -------------------------------------------------------------------------------- /files/tutorial5/solution/relax.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/relax.lmp -------------------------------------------------------------------------------- /files/tutorial5/solution/relax.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/relax.log -------------------------------------------------------------------------------- /files/tutorial5/solution/relax.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/relax.png -------------------------------------------------------------------------------- /files/tutorial5/solution/relax.species: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial5/solution/relax.species -------------------------------------------------------------------------------- /files/tutorial5/solution/silica.data: -------------------------------------------------------------------------------- 1 | ../silica.data -------------------------------------------------------------------------------- /files/tutorial6/.manifest: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/.manifest -------------------------------------------------------------------------------- /files/tutorial6/H2O.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/H2O.mol -------------------------------------------------------------------------------- /files/tutorial6/SiO.1990.vashishta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/SiO.1990.vashishta -------------------------------------------------------------------------------- /files/tutorial6/cracking.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/cracking.lmp -------------------------------------------------------------------------------- /files/tutorial6/gcmc.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/gcmc.lmp -------------------------------------------------------------------------------- /files/tutorial6/generate.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/generate.lmp -------------------------------------------------------------------------------- /files/tutorial6/solution/H2O.mol: -------------------------------------------------------------------------------- 1 | ../H2O.mol -------------------------------------------------------------------------------- /files/tutorial6/solution/SiO.1990.vashishta: -------------------------------------------------------------------------------- 1 | ../SiO.1990.vashishta -------------------------------------------------------------------------------- /files/tutorial6/solution/cracking-mod.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/solution/cracking-mod.data -------------------------------------------------------------------------------- /files/tutorial6/solution/cracking.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/solution/cracking.data -------------------------------------------------------------------------------- /files/tutorial6/solution/cracking.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/solution/cracking.lmp -------------------------------------------------------------------------------- /files/tutorial6/solution/cracking.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/solution/cracking.log -------------------------------------------------------------------------------- /files/tutorial6/solution/cracking.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/solution/cracking.png -------------------------------------------------------------------------------- /files/tutorial6/solution/gcmc.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/solution/gcmc.ipynb -------------------------------------------------------------------------------- /files/tutorial6/solution/gcmc.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/solution/gcmc.lmp -------------------------------------------------------------------------------- /files/tutorial6/solution/gcmc.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/solution/gcmc.log -------------------------------------------------------------------------------- /files/tutorial6/solution/gcmc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/solution/gcmc.png -------------------------------------------------------------------------------- /files/tutorial6/solution/generate.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/solution/generate.data -------------------------------------------------------------------------------- /files/tutorial6/solution/generate.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/solution/generate.ipynb -------------------------------------------------------------------------------- /files/tutorial6/solution/generate.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/solution/generate.lmp -------------------------------------------------------------------------------- /files/tutorial6/solution/generate.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/solution/generate.log -------------------------------------------------------------------------------- /files/tutorial6/solution/generate.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial6/solution/generate.png -------------------------------------------------------------------------------- /files/tutorial7/.manifest: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/.manifest -------------------------------------------------------------------------------- /files/tutorial7/free-sampling.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/free-sampling.lmp -------------------------------------------------------------------------------- /files/tutorial7/solution/free-sampling.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/free-sampling.dat -------------------------------------------------------------------------------- /files/tutorial7/solution/free-sampling.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/free-sampling.ipynb -------------------------------------------------------------------------------- /files/tutorial7/solution/free-sampling.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/free-sampling.lmp -------------------------------------------------------------------------------- /files/tutorial7/solution/free-sampling.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/free-sampling.log -------------------------------------------------------------------------------- /files/tutorial7/solution/free-sampling.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/free-sampling.png -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.1.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.1.dat -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.10.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.10.dat -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.11.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.11.dat -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.12.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.12.dat -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.13.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.13.dat -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.14.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.14.dat -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.15.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.15.dat -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.2.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.2.dat -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.3.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.3.dat -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.4.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.4.dat -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.5.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.5.dat -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.6.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.6.dat -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.7.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.7.dat -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.8.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.8.dat -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.9.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.9.dat -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.dat -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.ipynb -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.lmp -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.log -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.meta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.meta -------------------------------------------------------------------------------- /files/tutorial7/solution/umbrella-sampling.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/solution/umbrella-sampling.png -------------------------------------------------------------------------------- /files/tutorial7/solution/wham: -------------------------------------------------------------------------------- 1 | ../wham -------------------------------------------------------------------------------- /files/tutorial7/umbrella-sampling.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/umbrella-sampling.lmp -------------------------------------------------------------------------------- /files/tutorial7/umbrella-sampling.meta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/umbrella-sampling.meta -------------------------------------------------------------------------------- /files/tutorial7/wham: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial7/wham -------------------------------------------------------------------------------- /files/tutorial8/.manifest: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/.manifest -------------------------------------------------------------------------------- /files/tutorial8/CNT.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/CNT.data -------------------------------------------------------------------------------- /files/tutorial8/M-M.rxnmap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/M-M.rxnmap -------------------------------------------------------------------------------- /files/tutorial8/M-M_post.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/M-M_post.mol -------------------------------------------------------------------------------- /files/tutorial8/M-M_pre.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/M-M_pre.mol -------------------------------------------------------------------------------- /files/tutorial8/M-P.rxnmap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/M-P.rxnmap -------------------------------------------------------------------------------- /files/tutorial8/M-P_post.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/M-P_post.mol -------------------------------------------------------------------------------- /files/tutorial8/M-P_pre.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/M-P_pre.mol -------------------------------------------------------------------------------- /files/tutorial8/P-P.rxnmap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/P-P.rxnmap -------------------------------------------------------------------------------- /files/tutorial8/P-P_post.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/P-P_post.mol -------------------------------------------------------------------------------- /files/tutorial8/P-P_pre.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/P-P_pre.mol -------------------------------------------------------------------------------- /files/tutorial8/mixing.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/mixing.lmp -------------------------------------------------------------------------------- /files/tutorial8/polymerize.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/polymerize.lmp -------------------------------------------------------------------------------- /files/tutorial8/solution/CNT.data: -------------------------------------------------------------------------------- 1 | ../CNT.data -------------------------------------------------------------------------------- /files/tutorial8/solution/M-M.rxnmap: -------------------------------------------------------------------------------- 1 | ../M-M.rxnmap -------------------------------------------------------------------------------- /files/tutorial8/solution/M-M_post.mol: -------------------------------------------------------------------------------- 1 | ../M-M_post.mol -------------------------------------------------------------------------------- /files/tutorial8/solution/M-M_pre.mol: -------------------------------------------------------------------------------- 1 | ../M-M_pre.mol -------------------------------------------------------------------------------- /files/tutorial8/solution/M-P.rxnmap: -------------------------------------------------------------------------------- 1 | ../M-P.rxnmap -------------------------------------------------------------------------------- /files/tutorial8/solution/M-P_post.mol: -------------------------------------------------------------------------------- 1 | ../M-P_post.mol -------------------------------------------------------------------------------- /files/tutorial8/solution/M-P_pre.mol: -------------------------------------------------------------------------------- 1 | ../M-P_pre.mol -------------------------------------------------------------------------------- /files/tutorial8/solution/P-P.rxnmap: -------------------------------------------------------------------------------- 1 | ../P-P.rxnmap -------------------------------------------------------------------------------- /files/tutorial8/solution/P-P_post.mol: -------------------------------------------------------------------------------- 1 | ../P-P_post.mol -------------------------------------------------------------------------------- /files/tutorial8/solution/P-P_pre.mol: -------------------------------------------------------------------------------- 1 | ../P-P_pre.mol -------------------------------------------------------------------------------- /files/tutorial8/solution/mixing.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/solution/mixing.data -------------------------------------------------------------------------------- /files/tutorial8/solution/mixing.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/solution/mixing.ipynb -------------------------------------------------------------------------------- /files/tutorial8/solution/mixing.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/solution/mixing.lmp -------------------------------------------------------------------------------- /files/tutorial8/solution/mixing.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/solution/mixing.log -------------------------------------------------------------------------------- /files/tutorial8/solution/mixing.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/solution/mixing.png -------------------------------------------------------------------------------- /files/tutorial8/solution/mixing.restart: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/solution/mixing.restart -------------------------------------------------------------------------------- /files/tutorial8/solution/polymerize.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/solution/polymerize.data -------------------------------------------------------------------------------- /files/tutorial8/solution/polymerize.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/solution/polymerize.ipynb -------------------------------------------------------------------------------- /files/tutorial8/solution/polymerize.lmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/solution/polymerize.lmp -------------------------------------------------------------------------------- /files/tutorial8/solution/polymerize.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/solution/polymerize.log -------------------------------------------------------------------------------- /files/tutorial8/solution/polymerize.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/solution/polymerize.png -------------------------------------------------------------------------------- /files/tutorial8/solution/styrene.mol: -------------------------------------------------------------------------------- 1 | ../styrene.mol -------------------------------------------------------------------------------- /files/tutorial8/styrene.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/tutorial8/styrene.mol -------------------------------------------------------------------------------- /files/update_headers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/files/update_headers.py -------------------------------------------------------------------------------- /journal-article.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/journal-article.bib -------------------------------------------------------------------------------- /lammps-tutorials.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/lammps-tutorials.tex -------------------------------------------------------------------------------- /livecoms.cls: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/livecoms.cls -------------------------------------------------------------------------------- /releases/header_v1.0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/releases/header_v1.0.png -------------------------------------------------------------------------------- /releases/published-version-v1.0.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/releases/published-version-v1.0.pdf -------------------------------------------------------------------------------- /vancouver-livecoms.bst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-article/HEAD/vancouver-livecoms.bst --------------------------------------------------------------------------------