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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 . 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 . 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="-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 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 (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 https://openkim.org/kim-items/models/by-model-drivers
See the list of example KIM models included by default here: See the list of example KIM models included by default here:
https://openkim.org/kim-api https://openkim.org/kim-api in the "What is in the KIM API source
in the "What is in the KIM API source package?" section package?" section
You can then install/un-install the package and build LAMMPS in the You can then install/un-install the package and build LAMMPS in the
usual manner: 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() double FixMSST::compute_scalar()
{ {
// compute new pressure and volume. // compute new pressure and volume
temperature->compute_vector(); temperature->compute_vector();
pressure->compute_vector(); pressure->compute_vector();
@ -958,10 +958,9 @@ double FixMSST::compute_scalar()
energy -= p0 * ( v0 - volume ) / nktv2p; energy -= p0 * ( v0 - volume ) / nktv2p;
// subtract off precomputed TS_int integral value // subtract off precomputed TS_int integral value
// TS_int = 0 for non DFTB calculations
if (dftb) { // TS_int == 0 for non DFTB calculations if (dftb) energy -= TS_int;
energy -= TS_int;
}
return energy; return energy;
} }
@ -987,7 +986,7 @@ double FixMSST::compute_vector(int n)
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
Computes the deviation of the current point 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() double FixMSST::compute_hugoniot()
@ -1012,7 +1011,7 @@ double FixMSST::compute_hugoniot()
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
Computes the deviation of the current point from the Rayleigh 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 FixMSST::compute_rayleigh()
@ -1108,4 +1107,3 @@ double FixMSST::memory_usage()
double bytes = 3*atom->nmax * sizeof(double); double bytes = 3*atom->nmax * sizeof(double);
return bytes; return bytes;
} }

46
src/SHOCK/fix_msst.h
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@ -41,56 +41,56 @@ class FixMSST : public Fix {
double memory_usage(); double memory_usage();
private: 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 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 p_current[3],dilation[3];
double qmass; // Effective cell mass double qmass; // effective cell mass
double mu; // Effective cell viscosity double mu; // effective cell viscosity
double tscale; // Converts thermal energy to compressive double tscale; // converts thermal energy to compressive
// strain ke at simulation start // strain ke at simulation start
int dftb; // flag for use with DFTB+ int dftb; // flag for use with DFTB+
double velocity_sum; // Sum of the velocities squared double velocity_sum; // sum of the velocities squared
double damping; // Damping function for TS force term at double damping; // damping function for TS force term at
// small volume difference (v0 - vol) // 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 double S_elec,S_elec_1,S_elec_2; // time history of electron entropy
// for DFTB+ simulaitons // for DFTB+ simulaitons
double TS_dot; // time derivative of TS term for double TS_dot; // time derivative of TS term for
// DFTB+ simulations // DFTB+ simulations
double **old_velocity; // Saved velocities double **old_velocity; // saved velocities
int kspace_flag; // 1 if KSpace invoked, 0 if not int kspace_flag; // 1 if KSpace invoked, 0 if not
int nrigid; // number of rigid fixes int nrigid; // number of rigid fixes
int *rfix; // indices 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 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 *pressure; // thermodynamic quantities
class Compute *pe; 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 // were created
// shock initial conditions // shock initial conditions
double e0; // Initial energy double e0; // initial energy
double v0; // Initial volume double v0; // initial volume
double p0; // Initial pressure double p0; // initial pressure
double velocity; // Velocity of the shock double velocity; // velocity of the shock
double lagrangian_position; // Lagrangian location of computational cell double lagrangian_position; // Lagrangian location of computational cell
int direction; // Direction of shock int direction; // direction of shock
int p0_set; // Is pressure set int p0_set; // is pressure set
int v0_set; // Is volume set int v0_set; // is volume set
int e0_set; // Is energy set int e0_set; // is energy set
double TS_int; // Needed for conserved quantity double TS_int; // needed for conserved quantity
// with thermal electronic excitations // with thermal electronic excitations
double beta; // Energy conservation scaling factor double beta; // energy conservation scaling factor
int maxold; // allocated size of old_velocity int maxold; // allocated size of old_velocity
class FixExternal *fix_external; // ptr to fix external class FixExternal *fix_external; // ptr to fix external