lammps_wrappers.h File Reference

Declarations for LAMMPS wrapper functions. More...

#include <string>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <iostream>
#include <mpi.h>
#include <vector>
#include <array>
#include <cmath>
#include "lammps.h"
#include "papreca_error.h"
#include "utilities.h"

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Namespaces
	PAPRECA

Functions
void	PAPRECA::initializeLMP (LAMMPS_NS::LAMMPS **lmp)
	Initialize LAMMPS. More...
void	PAPRECA::readLMPinput (const std::string &lmp_input, LAMMPS_NS::LAMMPS *lmp)
void	PAPRECA::runLammps (LAMMPS_NS::LAMMPS *lmp, const int &timesteps_num)
void	PAPRECA::MPIBcastAndExecuteCommand (LAMMPS_NS::LAMMPS *lmp, std::string &command)
void	PAPRECA::remap3DArrayInPeriodicBox (LAMMPS_NS::LAMMPS *lmp, double *arr)
void	PAPRECA::deleteAtoms (LAMMPS_NS::LAMMPS *lmp, LAMMPS_NS::tagint *atom_ids, const int &num_atoms, const std::string &delete_bonds, const std::string &delete_molecule)
void	PAPRECA::deleteAtoms (LAMMPS_NS::LAMMPS *lmp, std::vector< LAMMPS_NS::tagint > &atom_ids, const std::string &delete_bonds, const std::string &delete_molecule)
void	PAPRECA::deleteAtomsInBoxRegion (LAMMPS_NS::LAMMPS *lmp, double &boxxlo, double &boxxhi, double &boxylo, double &boxyhi, double &boxzlo, double &boxzhi, const std::string &delete_bonds, const std::string &delete_molecule)
void	PAPRECA::createAtom (LAMMPS_NS::LAMMPS *lmp, const double atom_pos[3], const int &atom_type)
void	PAPRECA::deleteBond (LAMMPS_NS::LAMMPS *lmp, const LAMMPS_NS::tagint &atom1id, const LAMMPS_NS::tagint &atom2id, const bool special)
void	PAPRECA::formBond (LAMMPS_NS::LAMMPS *lmp, const LAMMPS_NS::tagint &atom1id, const LAMMPS_NS::tagint &atom2id, const int &bond_type)
void	PAPRECA::resetMobileAtomsGroups (LAMMPS_NS::LAMMPS *lmp, const std::vector< int > &fluid_atomtypes)
void	PAPRECA::insertMolecule (LAMMPS_NS::LAMMPS *lmp, const double site_pos[3], const double rot_pos[3], const double &rot_theta, const int &type_offset, const char *mol_name)
void	PAPRECA::diffuseAtom (LAMMPS_NS::LAMMPS *lmp, const double vac_pos[3], const LAMMPS_NS::tagint &parent_id, const int &parent_type, const int &is_displacive, const int &diffused_type)
void	PAPRECA::initType2SigmaFromLammpsPairCoeffs (LAMMPS_NS::LAMMPS *lmp, INTPAIR2DOUBLE_MAP &type2sigma)
int	PAPRECA::getMaskedNeibIndex (int *neighbors, int &j)
void	PAPRECA::initAndGatherBondsList (LAMMPS_NS::LAMMPS *lmp, LAMMPS_NS::tagint **bonds_list, LAMMPS_NS::bigint &bonds_num)
const int	PAPRECA::getMolIndexFromMolName (LAMMPS_NS::LAMMPS *lmp, std::string mol_name)
void	PAPRECA::computeMolCenter (LAMMPS_NS::LAMMPS *lmp, std::string mol_name)
void	PAPRECA::dumpRestart (LAMMPS_NS::LAMMPS *lmp, const int &KMC_loopid, const int &dump_freq)
double	PAPRECA::get3DSqrDistWithPBC (LAMMPS_NS::LAMMPS *lmp, const double *x1, const double *x2)

Detailed Description

Declarations for LAMMPS wrapper functions.

Typically functions that calls lmp->input->one or lammps_command to execute a specific LAMMPS command with given inputs.