Loading doc/src/Python_examples.rst +4 −4 Original line number Diff line number Diff line Loading @@ -61,12 +61,12 @@ from a Python script. See the PyMol WWW pages `here <pymolhome_>`_ or .. parsed-literal:: http://www.pymol.org http://sourceforge.net/scm/?type=svn&group_id=4546 https://www.pymol.org https://github.com/schrodinger/pymol-open-source .. _pymolhome: http://www.pymol.org .. _pymolhome: https://www.pymol.org .. _pymolopen: http://sourceforge.net/scm/?type=svn&group\_id=4546 .. _pymolopen: https://github.com/schrodinger/pymol-open-source The latter link is to the open-source version. Loading doc/src/Tools.rst +6 −6 Original line number Diff line number Diff line Loading @@ -6,17 +6,17 @@ molecular dynamics computations. Additional pre- and post-processing steps are often necessary to setup and analyze a simulation. A list of such tools can be found on the `LAMMPS webpage <lws_>`_ at these links: * `Pre/Post processing <http://lammps.sandia.gov/prepost.html>`_ * `Offsite LAMMPS packages & tools <http://lammps.sandia.gov/offsite.html>`_ * `Pre/Post processing <https://lammps.sandia.gov/prepost.html>`_ * `Offsite LAMMPS packages & tools <https://lammps.sandia.gov/offsite.html>`_ * `Pizza.py toolkit <pizza_>`_ The last link for `Pizza.py <pizza_>`_ is a Python-based tool developed at Sandia which provides tools for doing setup, analysis, plotting, and visualization for LAMMPS simulations. .. _lws: http://lammps.sandia.gov .. _lws: https://lammps.sandia.gov .. _pizza: https://pizza.sandia.gov .. _python: http://www.python.org .. _python: https://www.python.org Additional tools included in the LAMMPS distribution are described on this page. Loading Loading @@ -519,9 +519,9 @@ The pymol\_asphere sub-directory contains a tool for converting a LAMMPS dump file that contains orientation info for ellipsoidal particles into an input file for the `PyMol visualization package <pymolhome_>`_ or its `open source variant <pymolopen_>`_. .. _pymolhome: http://www.pymol.org .. _pymolhome: https://www.pymol.org .. _pymolopen: http://sourceforge.net/scm/?type=svn&group\_id=4546 .. _pymolopen: https://github.com/schrodinger/pymol-open-source Specifically, the tool triangulates the ellipsoids so they can be viewed as true ellipsoidal particles within PyMol. See the README and Loading Loading
doc/src/Python_examples.rst +4 −4 Original line number Diff line number Diff line Loading @@ -61,12 +61,12 @@ from a Python script. See the PyMol WWW pages `here <pymolhome_>`_ or .. parsed-literal:: http://www.pymol.org http://sourceforge.net/scm/?type=svn&group_id=4546 https://www.pymol.org https://github.com/schrodinger/pymol-open-source .. _pymolhome: http://www.pymol.org .. _pymolhome: https://www.pymol.org .. _pymolopen: http://sourceforge.net/scm/?type=svn&group\_id=4546 .. _pymolopen: https://github.com/schrodinger/pymol-open-source The latter link is to the open-source version. Loading
doc/src/Tools.rst +6 −6 Original line number Diff line number Diff line Loading @@ -6,17 +6,17 @@ molecular dynamics computations. Additional pre- and post-processing steps are often necessary to setup and analyze a simulation. A list of such tools can be found on the `LAMMPS webpage <lws_>`_ at these links: * `Pre/Post processing <http://lammps.sandia.gov/prepost.html>`_ * `Offsite LAMMPS packages & tools <http://lammps.sandia.gov/offsite.html>`_ * `Pre/Post processing <https://lammps.sandia.gov/prepost.html>`_ * `Offsite LAMMPS packages & tools <https://lammps.sandia.gov/offsite.html>`_ * `Pizza.py toolkit <pizza_>`_ The last link for `Pizza.py <pizza_>`_ is a Python-based tool developed at Sandia which provides tools for doing setup, analysis, plotting, and visualization for LAMMPS simulations. .. _lws: http://lammps.sandia.gov .. _lws: https://lammps.sandia.gov .. _pizza: https://pizza.sandia.gov .. _python: http://www.python.org .. _python: https://www.python.org Additional tools included in the LAMMPS distribution are described on this page. Loading Loading @@ -519,9 +519,9 @@ The pymol\_asphere sub-directory contains a tool for converting a LAMMPS dump file that contains orientation info for ellipsoidal particles into an input file for the `PyMol visualization package <pymolhome_>`_ or its `open source variant <pymolopen_>`_. .. _pymolhome: http://www.pymol.org .. _pymolhome: https://www.pymol.org .. _pymolopen: http://sourceforge.net/scm/?type=svn&group\_id=4546 .. _pymolopen: https://github.com/schrodinger/pymol-open-source Specifically, the tool triangulates the ellipsoids so they can be viewed as true ellipsoidal particles within PyMol. See the README and Loading
