├── .gitattributes ├── .github └── workflows │ ├── style.yaml │ ├── test-notebooks.yml │ └── test-projects.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .render_all_notebooks.sh ├── .update_project_readme.py ├── CODE_OF_CONDUCT.md ├── LICENSE.txt ├── README.md ├── contributors.txt ├── notebooks ├── idg ├── index.ipynb ├── signac_101_Getting_Started.ipynb ├── signac_102_Exploring_Data.ipynb ├── signac_103_A_Basic_Workflow.ipynb ├── signac_104_Modifying_the_Data_Space.ipynb ├── signac_105_signac-flow_Ideal_Gas_Example.ipynb ├── signac_106_signac-flow_HOOMD-blue_Example.ipynb ├── signac_107_Integration_with_Sacred.ipynb ├── signac_202_Integration_with_pandas.ipynb └── signac_301_Aggregation_Tutorial.ipynb ├── pixi.lock ├── pixi.toml ├── projects ├── LICENSE.txt ├── README.md ├── flow-test.py ├── flow.2D-random-walk │ ├── README.md │ └── src │ │ ├── dashboard.py │ │ ├── init.py │ │ └── project.py ├── flow.aggregation-mpi │ ├── .gitignore │ ├── README.md │ ├── init.py │ └── project.py ├── flow.aggregation-plotting │ ├── .gitignore │ ├── README.md │ └── src │ │ ├── init.py │ │ └── project.py ├── flow.gmx-lysozyme-in-water │ ├── .gitignore │ ├── .skipci │ ├── README.md │ ├── init.py │ └── project.py ├── flow.gmx-mtools │ ├── .skipci │ ├── LICENSE │ ├── README.md │ ├── mdp_files │ │ ├── em.mdp │ │ ├── equil.mdp │ │ └── sample.mdp │ └── src │ │ ├── calc_density.py │ │ ├── init.py │ │ └── project.py ├── flow.hello-world-optimization │ ├── README.md │ ├── init.py │ ├── project.py │ └── templates │ │ └── script.sh ├── flow.hello-world │ ├── README.md │ └── project.py ├── flow.hoomd.lj │ ├── .gitignore │ ├── .skipci │ ├── README.md │ ├── src │ │ ├── init.py │ │ ├── notebook.ipynb │ │ └── project.py │ └── test.sh ├── flow.minimal │ ├── README.md │ └── project.py ├── flow.qe-minimal │ ├── .skipci │ ├── README.md │ ├── init.py │ ├── project.py │ ├── pseudo │ │ ├── C.pw-mt_fhi.upf │ │ ├── Ge.pw-mt_fhi.upf │ │ ├── Pb.pw-mt_fhi.upf │ │ ├── Si.pw-mt_fhi.upf │ │ ├── Si.pz-hgh.upf │ │ ├── Si.pz-vbc.upf │ │ └── Sn.pw-mt_fhi.upf │ └── vc-relax.in ├── flow.sklearn.init-ParameterGrid │ ├── README.md │ ├── dashboard.py │ ├── init.py │ └── project.py ├── idg-minimal │ ├── README.md │ └── idg.py └── run-tests.sh └── renovate.json /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/workflows/style.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/.github/workflows/style.yaml -------------------------------------------------------------------------------- /.github/workflows/test-notebooks.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/.github/workflows/test-notebooks.yml -------------------------------------------------------------------------------- /.github/workflows/test-projects.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/.github/workflows/test-projects.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /.render_all_notebooks.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/.render_all_notebooks.sh -------------------------------------------------------------------------------- /.update_project_readme.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/.update_project_readme.py -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/CODE_OF_CONDUCT.md -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/README.md -------------------------------------------------------------------------------- /contributors.txt: -------------------------------------------------------------------------------- 1 | Carl Simon Adorf 2 | Vyas Ramasubramani 3 | Bradley Dice 4 | Ali Malek 5 | Hardik Ojha 6 | -------------------------------------------------------------------------------- /notebooks/idg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/notebooks/idg -------------------------------------------------------------------------------- /notebooks/index.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/notebooks/index.ipynb -------------------------------------------------------------------------------- /notebooks/signac_101_Getting_Started.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/notebooks/signac_101_Getting_Started.ipynb -------------------------------------------------------------------------------- /notebooks/signac_102_Exploring_Data.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/notebooks/signac_102_Exploring_Data.ipynb -------------------------------------------------------------------------------- /notebooks/signac_103_A_Basic_Workflow.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/notebooks/signac_103_A_Basic_Workflow.ipynb -------------------------------------------------------------------------------- /notebooks/signac_104_Modifying_the_Data_Space.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/notebooks/signac_104_Modifying_the_Data_Space.ipynb -------------------------------------------------------------------------------- /notebooks/signac_105_signac-flow_Ideal_Gas_Example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/notebooks/signac_105_signac-flow_Ideal_Gas_Example.ipynb -------------------------------------------------------------------------------- /notebooks/signac_106_signac-flow_HOOMD-blue_Example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/notebooks/signac_106_signac-flow_HOOMD-blue_Example.ipynb -------------------------------------------------------------------------------- /notebooks/signac_107_Integration_with_Sacred.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/notebooks/signac_107_Integration_with_Sacred.ipynb -------------------------------------------------------------------------------- /notebooks/signac_202_Integration_with_pandas.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/notebooks/signac_202_Integration_with_pandas.ipynb -------------------------------------------------------------------------------- /notebooks/signac_301_Aggregation_Tutorial.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/notebooks/signac_301_Aggregation_Tutorial.ipynb -------------------------------------------------------------------------------- /pixi.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/pixi.lock -------------------------------------------------------------------------------- /pixi.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/pixi.toml -------------------------------------------------------------------------------- /projects/LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/LICENSE.txt -------------------------------------------------------------------------------- /projects/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/README.md -------------------------------------------------------------------------------- /projects/flow-test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow-test.py -------------------------------------------------------------------------------- /projects/flow.2D-random-walk/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.2D-random-walk/README.md -------------------------------------------------------------------------------- /projects/flow.2D-random-walk/src/dashboard.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.2D-random-walk/src/dashboard.py -------------------------------------------------------------------------------- /projects/flow.2D-random-walk/src/init.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.2D-random-walk/src/init.py -------------------------------------------------------------------------------- /projects/flow.2D-random-walk/src/project.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.2D-random-walk/src/project.py -------------------------------------------------------------------------------- /projects/flow.aggregation-mpi/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.aggregation-mpi/.gitignore -------------------------------------------------------------------------------- /projects/flow.aggregation-mpi/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.aggregation-mpi/README.md -------------------------------------------------------------------------------- /projects/flow.aggregation-mpi/init.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.aggregation-mpi/init.py -------------------------------------------------------------------------------- /projects/flow.aggregation-mpi/project.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.aggregation-mpi/project.py -------------------------------------------------------------------------------- /projects/flow.aggregation-plotting/.gitignore: -------------------------------------------------------------------------------- 1 | *.png 2 | -------------------------------------------------------------------------------- /projects/flow.aggregation-plotting/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.aggregation-plotting/README.md -------------------------------------------------------------------------------- /projects/flow.aggregation-plotting/src/init.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.aggregation-plotting/src/init.py -------------------------------------------------------------------------------- /projects/flow.aggregation-plotting/src/project.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.aggregation-plotting/src/project.py -------------------------------------------------------------------------------- /projects/flow.gmx-lysozyme-in-water/.gitignore: -------------------------------------------------------------------------------- 1 | mdp_files 2 | -------------------------------------------------------------------------------- /projects/flow.gmx-lysozyme-in-water/.skipci: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /projects/flow.gmx-lysozyme-in-water/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.gmx-lysozyme-in-water/README.md -------------------------------------------------------------------------------- /projects/flow.gmx-lysozyme-in-water/init.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.gmx-lysozyme-in-water/init.py -------------------------------------------------------------------------------- /projects/flow.gmx-lysozyme-in-water/project.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.gmx-lysozyme-in-water/project.py -------------------------------------------------------------------------------- /projects/flow.gmx-mtools/.skipci: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /projects/flow.gmx-mtools/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.gmx-mtools/LICENSE -------------------------------------------------------------------------------- /projects/flow.gmx-mtools/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.gmx-mtools/README.md -------------------------------------------------------------------------------- /projects/flow.gmx-mtools/mdp_files/em.mdp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.gmx-mtools/mdp_files/em.mdp -------------------------------------------------------------------------------- /projects/flow.gmx-mtools/mdp_files/equil.mdp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.gmx-mtools/mdp_files/equil.mdp -------------------------------------------------------------------------------- /projects/flow.gmx-mtools/mdp_files/sample.mdp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.gmx-mtools/mdp_files/sample.mdp -------------------------------------------------------------------------------- /projects/flow.gmx-mtools/src/calc_density.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.gmx-mtools/src/calc_density.py -------------------------------------------------------------------------------- /projects/flow.gmx-mtools/src/init.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.gmx-mtools/src/init.py -------------------------------------------------------------------------------- /projects/flow.gmx-mtools/src/project.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.gmx-mtools/src/project.py -------------------------------------------------------------------------------- /projects/flow.hello-world-optimization/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.hello-world-optimization/README.md -------------------------------------------------------------------------------- /projects/flow.hello-world-optimization/init.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.hello-world-optimization/init.py -------------------------------------------------------------------------------- /projects/flow.hello-world-optimization/project.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.hello-world-optimization/project.py -------------------------------------------------------------------------------- /projects/flow.hello-world-optimization/templates/script.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.hello-world-optimization/templates/script.sh -------------------------------------------------------------------------------- /projects/flow.hello-world/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.hello-world/README.md -------------------------------------------------------------------------------- /projects/flow.hello-world/project.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.hello-world/project.py -------------------------------------------------------------------------------- /projects/flow.hoomd.lj/.gitignore: -------------------------------------------------------------------------------- 1 | src/notebook.html 2 | -------------------------------------------------------------------------------- /projects/flow.hoomd.lj/.skipci: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /projects/flow.hoomd.lj/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.hoomd.lj/README.md -------------------------------------------------------------------------------- /projects/flow.hoomd.lj/src/init.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.hoomd.lj/src/init.py -------------------------------------------------------------------------------- /projects/flow.hoomd.lj/src/notebook.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.hoomd.lj/src/notebook.ipynb -------------------------------------------------------------------------------- /projects/flow.hoomd.lj/src/project.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.hoomd.lj/src/project.py -------------------------------------------------------------------------------- /projects/flow.hoomd.lj/test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.hoomd.lj/test.sh -------------------------------------------------------------------------------- /projects/flow.minimal/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.minimal/README.md -------------------------------------------------------------------------------- /projects/flow.minimal/project.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.minimal/project.py -------------------------------------------------------------------------------- /projects/flow.qe-minimal/.skipci: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /projects/flow.qe-minimal/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.qe-minimal/README.md -------------------------------------------------------------------------------- /projects/flow.qe-minimal/init.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.qe-minimal/init.py -------------------------------------------------------------------------------- /projects/flow.qe-minimal/project.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.qe-minimal/project.py -------------------------------------------------------------------------------- /projects/flow.qe-minimal/pseudo/C.pw-mt_fhi.upf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.qe-minimal/pseudo/C.pw-mt_fhi.upf -------------------------------------------------------------------------------- /projects/flow.qe-minimal/pseudo/Ge.pw-mt_fhi.upf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.qe-minimal/pseudo/Ge.pw-mt_fhi.upf -------------------------------------------------------------------------------- /projects/flow.qe-minimal/pseudo/Pb.pw-mt_fhi.upf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.qe-minimal/pseudo/Pb.pw-mt_fhi.upf -------------------------------------------------------------------------------- /projects/flow.qe-minimal/pseudo/Si.pw-mt_fhi.upf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.qe-minimal/pseudo/Si.pw-mt_fhi.upf -------------------------------------------------------------------------------- /projects/flow.qe-minimal/pseudo/Si.pz-hgh.upf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.qe-minimal/pseudo/Si.pz-hgh.upf -------------------------------------------------------------------------------- /projects/flow.qe-minimal/pseudo/Si.pz-vbc.upf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.qe-minimal/pseudo/Si.pz-vbc.upf -------------------------------------------------------------------------------- /projects/flow.qe-minimal/pseudo/Sn.pw-mt_fhi.upf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.qe-minimal/pseudo/Sn.pw-mt_fhi.upf -------------------------------------------------------------------------------- /projects/flow.qe-minimal/vc-relax.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.qe-minimal/vc-relax.in -------------------------------------------------------------------------------- /projects/flow.sklearn.init-ParameterGrid/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.sklearn.init-ParameterGrid/README.md -------------------------------------------------------------------------------- /projects/flow.sklearn.init-ParameterGrid/dashboard.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.sklearn.init-ParameterGrid/dashboard.py -------------------------------------------------------------------------------- /projects/flow.sklearn.init-ParameterGrid/init.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.sklearn.init-ParameterGrid/init.py -------------------------------------------------------------------------------- /projects/flow.sklearn.init-ParameterGrid/project.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/flow.sklearn.init-ParameterGrid/project.py -------------------------------------------------------------------------------- /projects/idg-minimal/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/idg-minimal/README.md -------------------------------------------------------------------------------- /projects/idg-minimal/idg.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/idg-minimal/idg.py -------------------------------------------------------------------------------- /projects/run-tests.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/projects/run-tests.sh -------------------------------------------------------------------------------- /renovate.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glotzerlab/signac-examples/HEAD/renovate.json --------------------------------------------------------------------------------