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

This commit is contained in:
Axel Kohlmeyer 2017-07-26 19:35:15 -04:00
parent da7a5f55d3 934cbbbeca
commit 72419b6313
3 changed files with 31 additions and 33 deletions
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6
doc/src/Section_packages.txt
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@ -503,7 +503,7 @@ make lib-kim # print help message
make lib-kim args="-b . none" # install KIM API lib with only example models
make lib-kim args="-b . Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
make lib-kim args="-b . OpenKIM" # install KIM API lib with all models
make lib-kim args="-a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver :pre
make lib-kim args="-a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver :pre
Note that in LAMMPS lingo, a KIM model driver is a pair style
(e.g. EAM or Tersoff). A KIM model is a pair style for a particular
@ -519,8 +519,8 @@ See the list of all KIM models here:
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:

12
src/SHOCK/fix_msst.cpp
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@ -939,7 +939,7 @@ int FixMSST::modify_param(int narg, char **arg)
double FixMSST::compute_scalar()
{
// compute new pressure and volume.
// compute new pressure and volume
temperature->compute_vector();
pressure->compute_vector();
@ -958,10 +958,9 @@ double FixMSST::compute_scalar()
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;
}
@ -987,7 +986,7 @@ double FixMSST::compute_vector(int n)
/* ----------------------------------------------------------------------
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()
@ -1012,7 +1011,7 @@ 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()
@ -1108,4 +1107,3 @@ double FixMSST::memory_usage()
double bytes = 3*atom->nmax * sizeof(double);
return bytes;
}

46
src/SHOCK/fix_msst.h
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@ -41,56 +41,56 @@ class FixMSST : public Fix {
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