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Merge pull request #599 from lammps/kim-doc

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restore lost KIM doc section in Section packages
This commit is contained in:
sjplimp
2017-07-27 10:34:44 -06:00
committed by GitHub
parent 2806f070a4 934cbbbeca
commit 6d0a228624
4 changed files with 61 additions and 39 deletions
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4
doc/src/Section_commands.txt
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@ -734,8 +734,8 @@ package"_Section_start.html#start_3.
"smd/wall/surface"_fix_smd_wall_surface.html,
"temp/rescale/eff"_fix_temp_rescale_eff.html,
"ti/spring"_fix_ti_spring.html,
"ttm/mod"_fix_ttm.html
"wall/ees"_fix_wall_ees.html
"ttm/mod"_fix_ttm.html,
"wall/ees"_fix_wall_ees.html,
"wall/region/ees"_fix_wall_ees.html :tb(c=6,ea=c)
:line

38
doc/src/Section_packages.txt
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@ -492,14 +492,38 @@ Minnesota).
[Install or un-install:]
Using this package requires the KIM library and its models
(interatomic potentials) to be downloaded and installed on your
system. The library can be downloaded and built in lib/kim or
elsewhere on your system. Details of the download, build, and install
process for KIM are given in the lib/kim/README file.
Before building LAMMPS with this package, you must first download and
build the KIM library and include the KIM models that you want to
use. You can do this manually if you prefer; follow the instructions
in lib/kim/README. You can also do it in one step from the lammps/src
dir, using a command like these, which simply invoke the
lib/kim/Install.py script with the specified args.
Once that process is complete, you can then install/un-install the
package and build LAMMPS in the usual manner:
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
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
element or alloy and set of parameters, e.g. EAM for Cu with a
specific EAM potential file. Also note that installing the KIM API
library with all its models, may take around 30 min to build. Of
course you only need to do that once.
See the list of KIM model drivers here:
https://openkim.org/kim-items/model-drivers/alphabetical
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
You can then install/un-install the package and build LAMMPS in the
usual manner:
make yes-kim
make machine :pre

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