Merge remote-tracking branch 'github/kim-doc' into install-and-docs-reviewed

https://openkim.org/kim-items/models/by-model-drivers

See the list of example KIM models included by default here:

https://openkim.org/kim-api

in the "What is in the KIM API source package?" section

https://openkim.org/kim-api in the "What is in the KIM API source

package?" section

You can then install/un-install the package and build LAMMPS in the

usual manner:

double FixMSST::compute_scalar()

{

  // compute new pressure and volume.

  // compute new pressure and volume

  temperature->compute_vector();

  pressure->compute_vector();

  energy -= p0 * ( v0 - volume ) / nktv2p;

  // subtract off precomputed TS_int integral value

  // TS_int = 0 for non DFTB calculations

  if (dftb) { // TS_int == 0 for non DFTB calculations

    energy -= TS_int;

  }

  if (dftb) energy -= TS_int;

  return energy;

}

/* ----------------------------------------------------------------------

   Computes the deviation of the current point

   from the Hugoniot in Kelvin for the MSST.

   from the Hugoniot in Kelvin for the MSST

------------------------------------------------------------------------- */

double FixMSST::compute_hugoniot()

/* ----------------------------------------------------------------------

   Computes the deviation of the current point from the Rayleigh

   in pressure units for the MSST.

   in pressure units for the MSST

------------------------------------------------------------------------- */

double FixMSST::compute_rayleigh()

  double bytes = 3*atom->nmax * sizeof(double);

  return bytes;

}

  double memory_usage();

 private:

  double dtv,dtf,dthalf;           // Full and half step sizes

  double dtv,dtf,dthalf;           // full and half step sizes

  double boltz,nktv2p, mvv2e;      // Boltzmann factor and unit conversions

  double total_mass;               // Mass of the computational cell

  double total_mass;               // mass of the computational cell

  double omega[3];                 // Time derivative of the volume

  double omega[3];                 // time derivative of the volume

  double p_current[3],dilation[3];

  double qmass;                    // Effective cell mass

  double mu;                       // Effective cell viscosity

  double tscale;                   // Converts thermal energy to compressive

  double qmass;                    // effective cell mass

  double mu;                       // effective cell viscosity

  double tscale;                   // converts thermal energy to compressive

                                   // strain ke at simulation start

  int dftb;                        // flag for use with DFTB+

  double velocity_sum;             // Sum of the velocities squared

  double damping;                  // Damping function for TS force term at

  double velocity_sum;             // sum of the velocities squared

  double damping;                  // damping function for TS force term at

                                   //   small volume difference (v0 - vol)

  double T0S0;                     // Initial TS term for DFTB+ simulations

  double T0S0;                     // initial TS term for DFTB+ simulations

  double S_elec,S_elec_1,S_elec_2; // time history of electron entropy

                                   //   for DFTB+ simulaitons

  double TS_dot;                   // time derivative of TS term for

                                   //   DFTB+ simulations

  double **old_velocity;           // Saved velocities

  double **old_velocity;           // saved velocities

  int kspace_flag;                 // 1 if KSpace invoked, 0 if not

  int nrigid;                      // number of rigid fixes

  int *rfix;                       // indices of rigid fixes

  char *id_temp,*id_press;         // Strings with identifiers of

  char *id_temp,*id_press;         // strings with identifiers of

  char *id_pe;                     // created computes

  class Compute *temperature;      // Computes created to evaluate

  class Compute *temperature;      // computes created to evaluate

  class Compute *pressure;         // thermodynamic quantities

  class Compute *pe;

  int tflag,pflag,vsflag,peflag;   // Flags to keep track of computes that

  int tflag,pflag,vsflag,peflag;   // flags to keep track of computes that

                                   // were created

  // shock initial conditions

  double e0;                       // Initial energy

  double v0;                       // Initial volume

  double p0;                       // Initial pressure

  double velocity;                 // Velocity of the shock

  double e0;                       // initial energy

  double v0;                       // initial volume

  double p0;                       // initial pressure

  double velocity;                 // velocity of the shock

  double lagrangian_position;      // Lagrangian location of computational cell

  int direction;                   // Direction of shock

  int p0_set;                      // Is pressure set

  int v0_set;                      // Is volume set

  int e0_set;                      // Is energy set

  double TS_int;                   // Needed for conserved quantity

  int direction;                   // direction of shock

  int p0_set;                      // is pressure set

  int v0_set;                      // is volume set

  int e0_set;                      // is energy set

  double TS_int;                   // needed for conserved quantity

                                   //   with thermal electronic excitations

  double beta;                     // Energy conservation scaling factor

  double beta;                     // energy conservation scaling factor

  int maxold;                      // allocated size of old_velocity

  class FixExternal *fix_external; // ptr to fix external