diff --git a/doc/src/fix_mscg.rst b/doc/src/fix_mscg.rst index 5e9bc520b5..3255f3fbe9 100644 --- a/doc/src/fix_mscg.rst +++ b/doc/src/fix_mscg.rst @@ -40,15 +40,15 @@ Description This fix applies the Multi-Scale Coarse-Graining (MSCG) method to snapshots from a dump file to generate potentials for coarse-grained -simulations from all-atom simulations, using a force-matching -technique (:ref:`Izvekov `, :ref:`Noid `). +simulations from all-atom simulations, using a force-matching technique +(:ref:`Izvekov `, :ref:`Noid `). -It makes use of the MS-CG library, written and maintained by Greg -Voth's group at the University of Chicago, which is freely available -on their `MS-CG GitHub site `_. See instructions -on obtaining and installing the MS-CG library in the src/MSCG/README -file, which must be done before you build LAMMPS with this fix command -and use the command in a LAMMPS input script. +It makes use of the MS-CG library, written and maintained by Greg Voth's +group at the University of Chicago, which is freely available on their +`MS-CG GitHub site `_. +See instructions on obtaining and installing the MS-CG library in the +src/MSCG/README file, which must be done before you build LAMMPS with +this fix command and use the command in a LAMMPS input script. An example script using this fix is provided the examples/mscg directory. @@ -65,15 +65,18 @@ simulations is as follows: 6. Check the results of the force matching. 7. Run coarse-grained simulations using the new coarse-grained potentials. -This fix can perform the range finding and force matching steps 4 and -5 of the above workflow when used in conjunction with the -:doc:`rerun ` command. It does not perform steps 1-3 and 6-7. +This fix can perform the range finding and force matching steps 4 and 5 +of the above workflow when used in conjunction with the :doc:`rerun +` command. It does not perform steps 1-3 and 6-7. -Step 2 can be performed using a Python script (what is the name?) -provided with the MS-CG library which defines the coarse-grained model -and converts a standard LAMMPS dump file for an all-atom simulation -(step 1) into a LAMMPS dump file which has the positions of and forces -on the coarse-grained beads. +Step 2 can be performed using a Python script (cgmap), which defines the +coarse-grained model and converts a standard LAMMPS dump file for an +all-atom simulation (step 1) into a LAMMPS dump file which has the +positions of and forces on the coarse-grained beads. To use cgmap the +following repositories need to be downloaded and installed. + +#. The custom lammpsdata branch of mdtraj from https://github.com/hockyg/mdtraj/tree/lammpsdata +#. The master branch of cgmap from https://github.com/uchicago-voth/cgmap In step 3, an input file named "control.in" is needed by the MS-CG library which sets parameters for the range finding and force matching @@ -83,12 +86,12 @@ info on this file. When this fix is used to perform steps 4 and 5, the MS-CG library also produces additional output files. The range finder functionality -(step 4) outputs files defining pair and bonded interaction ranges. -The force matching functionality (step 5) outputs tabulated force -files for every interaction in the system. Other diagnostic files can -also be output depending on the parameters in the MS-CG library input -script. Again, see the documentation provided with the MS-CG library -for more info. +(step 4) outputs files defining pair and bonded interaction ranges. The +force matching functionality (step 5) outputs tabulated force files for +every interaction in the system. Other diagnostic files can also be +output depending on the parameters in the MS-CG library input script. +Again, see the documentation provided with the MS-CG library for more +info. ---------- @@ -97,8 +100,8 @@ be invoked. If *on*, the step 4 range finder functionality is invoked. *off*, the step 5 force matching functionality is invoked. If the *name* keyword is used, string names are defined to associate -with the integer atom types in LAMMPS. *Ntype* names must be -provided, one for each atom type (1-Ntype). +with the integer atom types in LAMMPS. *Ntype* names must be provided, +one for each atom type (1-Ntype). The *max* keyword specifies the maximum number of bonds, angles, and dihedrals a bead can have in the coarse-grained model. @@ -107,16 +110,13 @@ Restrictions """""""""""" This fix is part of the MSCG package. It is only enabled if LAMMPS was -built with that package. See the :doc:`Build package ` -doc page for more info. +built with that package. Building the MSCG package also requires +external libraries. See the :doc:`Build_package` and :doc:`Build_extras` +pages for more info. -The MS-CG library uses C++11, which may not be supported by older -compilers. The MS-CG library also has some additional numeric library -dependencies, which are described in its documentation. - -Currently, the MS-CG library is not setup to run in parallel with MPI, -so this fix can only be used in a serial LAMMPS build and run -on a single processor. +Currently, the MS-CG library is not set up to run in parallel with MPI, +so this fix can only be used in a serial LAMMPS build and run on a +single processor. Related commands """"""""""""""""