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fix_rx.h
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Fri, May 31, 22:43

fix_rx.h
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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(rx,FixRX)
#else
#ifndef LMP_FIX_RX_H
#define LMP_FIX_RX_H
#include "fix.h"
typedef int (*fnptr)(double, const double *, double *, void *);
namespace LAMMPS_NS {
enum { ODE_LAMMPS_RK4, ODE_LAMMPS_RKF45 };
class FixRX : public Fix {
public:
FixRX(class LAMMPS *, int, char **);
~FixRX();
int setmask();
void post_constructor();
virtual void init();
void init_list(int, class NeighList *);
virtual void setup_pre_force(int);
virtual void pre_force(int);
protected:
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
int pack_forward_comm(int , int *, double *, int, int *);
void unpack_forward_comm(int , int , double *);
class NeighList *list;
double tmpArg;
int *mol2param; // mapping from molecule to parameters
int nreactions; // # of stored parameter sets
int maxparam; // max # of parameter sets
struct Param {
double cp;
int ispecies;
char *name; // names of unique molecules and interaction type
};
Param *params; // parameter set for an I-J-K interaction
int nspecies;
void read_file(char *);
void setupParams();
double *Arr, *nArr, *Ea, *tempExp;
double **stoich, **stoichReactants, **stoichProducts;
double *kR;
//!< Classic Runge-Kutta 4th-order stepper.
void rk4(int, double*, void*);
//!< Runge-Kutta-Fehlberg ODE Solver.
void rkf45(int, double*, void*, int ode_counter[]);
//!< Runge-Kutta-Fehlberg ODE stepper function.
void rkf45_step (const int neq, const double h, double y[], double y_out[],
double rwk[], void *);
//!< Initial step size estimation for the Runge-Kutta-Fehlberg ODE solver.
int rkf45_h0 (const int neq, const double t, const double t_stop,
const double hmin, const double hmax,
double& h0, double y[], double rwk[], void *v_params);
class PairDPDfdtEnergy *pairDPDE;
double *dpdThetaLocal;
double *sumWeights;
void computeLocalTemperature();
int localTempFlag,wtFlag,odeIntegrationFlag;
double sigFactor;
int rhs(double, const double *, double *, void *);
int rhs_dense (double, const double *, double *, void *);
// User-defined data container needed in rhs.
struct UserRHSData
{
double *kFor;
double *rxnRateLaw;
};
// Sparse stoichiometric matrix storage format and methods.
bool useSparseKinetics;
//SparseKinetics sparseKinetics;
void initSparse(void);
int rhs_sparse(double, const double *, double *, void *) const;
int sparseKinetics_maxReactants; //<! Max # of reactants species in any reaction
int sparseKinetics_maxProducts; //<! Max # of product species in any reaction
int sparseKinetics_maxSpecies; //<! Max # of species (maxReactants + maxProducts) in any reaction
//! Objects to hold the stoichiometric coefficients using a sparse matrix
//! format. Enables a sparse formulation for the reaction rates:
//! \f${\omega}_i = \Pi_{j=1}^{NS_i} K^{f}_i [x_j]^{\nu^{'}_{ij}} -
//! K^{r}_i x_j^{\nu^{''}_{ij}}\f$.
double **sparseKinetics_nu; //<! Stoichiometric matrix with FLT values.
int **sparseKinetics_nuk; //<! Index (base-0) of species ... this is the column sparse matrix.
int **sparseKinetics_inu; //<! Stoichiometric matrix with integral values.
bool *sparseKinetics_isIntegralReaction; //<! Flag indicating if a reaction has integer stoichiometric values.
// ODE Parameters
int minSteps; //!< Minimum # of steps for the ODE solver(s).
int maxIters; //!< Maximum # of iterations for the ODE solver(s).
double relTol, absTol; //!< Relative and absolute tolerances for the ODE solver(s).
// ODE Diagnostics
//int nSteps; //!< # of accepted steps taken over all atoms.
//int nIters; //!< # of attemped steps for all atoms.
//int nFuncs; //!< # of RHS evaluations for all atoms.
//int nFails; //!< # of ODE systems that failed (for some reason).
int diagnosticFrequency; //!< Frequency (LMP steps) that run-time diagnostics will be printed to the log.
enum { numDiagnosticCounters = 5 };
enum { StepSum=0, FuncSum, TimeSum, AtomSum, CountSum };
double diagnosticCounter[ numDiagnosticCounters ];
int *diagnosticCounterPerODE[ numDiagnosticCounters ];
//!< ODE Solver diagnostics.
void odeDiagnostics(void);
private:
char *kineticsFile;
char *id_fix_species,*id_fix_species_old;
class FixPropertyAtom *fix_species,*fix_species_old;
int restartFlag;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: fix rx cannot be combined with fix property/atom
Self-explanatory
E: Cannot open rx file %s
Self-explanatory
E: Exceeded the maximum number of species permitted in fix rx
Reduce the number of species in the fix rx reaction kinetics file
E: There are no rx species specified.
Self-explanatory
E: Must use pair_style dpd/fdt/energy with fix rx.
Self-explanatory
E: fix rx requires fix eos/table/rx to be specified.
Self-explanatory
W: in FixRX::pre_force, ODE solver failed for %d atoms.
Self-explanatory
E: Missing parameters in reaction kinetic equation.
Self-explanatory
E: Potential file has duplicate entry.
Self-explanatory
E: Computed concentration in RK4 (RKF45) solver is < -1.0e-10.
Self-explanatory: Adjust settings for the RK4 solver.
*/

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