Gromacs  2023.2
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
Classes | Functions
pull_rotation.h File Reference
#include <cstdio>
#include <memory>
#include "gromacs/math/vectypes.h"
+ Include dependency graph for pull_rotation.h:


Declares functions to enforce rotational motion upon a group of particles.

Carsten Kutzner


class  gmx::ArrayRef< typename >
 STL-like interface to a C array of T (or part of a std container of T). More...


< gmx::EnforcedRotation > 
init_rot (FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[], const t_commrec *cr, gmx::LocalAtomSetManager *atomSets, const t_state *globalState, const gmx_mtop_t &mtop, const gmx_output_env_t *oenv, const gmx::MdrunOptions &mdrunOptions, gmx::StartingBehavior startingBehavior)
 Initializes the enforced rotation groups. More...
void do_rotation (const t_commrec *cr, gmx_enfrot *er, const matrix box, gmx::ArrayRef< const gmx::RVec > coords, real t, int64_t step, bool bNS)
 Calculates the enforced rotation potential(s). More...
real add_rot_forces (gmx_enfrot *er, gmx::ArrayRef< gmx::RVec > force, const t_commrec *cr, int64_t step, real t)
 Add the enforced rotation forces to the official force array. More...

Function Documentation

real add_rot_forces ( gmx_enfrot *  er,
gmx::ArrayRef< gmx::RVec force,
const t_commrec *  cr,
int64_t  step,
real  t 

Add the enforced rotation forces to the official force array.

Adds the forces from enforced rotation potential to the local forces and sums up the contributions to the rotation potential from all the nodes. Since this needs communication, this routine should be called after the short range forces have been evaluated (in order not to spoil cycle counts). This routine also outputs data to the rotation output files (e.g. the potential, the angle of the group(s), and torques).

erPointer to the enforced rotation working data.
forceThe local forces to which the rotational forces have to be added.
crPointer to MPI communication data.
stepThe time step, used for output.
tTime, used for output.
The potential energy of the rotation potentials.
void do_rotation ( const t_commrec *  cr,
gmx_enfrot *  er,
const matrix  box,
gmx::ArrayRef< const gmx::RVec coords,
real  t,
int64_t  step,
bool  bNS 

Calculates the enforced rotation potential(s).

This is the main enforced rotation module which is called during every time step. Here the rotation potential as well as the resulting forces are calculated.

crPointer to MPI communication data.
erPointer to the enforced rotation working data.
boxSimulation box, needed to make group whole.
coordsThe positions of all the local particles.
stepThe time step.
bNSAfter domain decomposition / neighbor searching several local arrays have to be updated (masses, shifts)
std::unique_ptr<gmx::EnforcedRotation> init_rot ( FILE *  fplog,
t_inputrec *  ir,
int  nfile,
const t_filenm  fnm[],
const t_commrec *  cr,
gmx::LocalAtomSetManager atomSets,
const t_state globalState,
const gmx_mtop_t &  mtop,
const gmx_output_env_t *  oenv,
const gmx::MdrunOptions &  mdrunOptions,
gmx::StartingBehavior  startingBehavior 

Initializes the enforced rotation groups.

This routine does the memory allocation for various helper arrays, opens the output files etc.

fplogGeneral output file, normally md.log.
irStruct containing MD input parameters, among those also the enforced rotation parameters.
nfileNumber of entries in the fnm structure.
fnmThe filenames struct containing also the names of the rotation output files.
atomSetsTracks indices of atoms subject to enforced rotation for each DD rank.
crPointer to MPI communication data.
globalStateThe global state, only used on the main rank.
mtopMolecular topology.
oenvNeeded to open the rotation output xvgr file.
mdrunOptionsOptions for mdrun.
startingBehaviorDescribes whether this is a restart appending to output files
An enforced rotation module.