Loading doc/src/Section_commands.txt +2 −2 Original line number Diff line number Diff line Loading @@ -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 Loading doc/src/Section_packages.txt +32 −8 Original line number Diff line number Diff line Loading @@ -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. Once that process is complete, you can then install/un-install the package and build LAMMPS in the usual manner: 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. 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 Loading src/SHOCK/fix_msst.cpp +5 −7 Original line number Diff line number Diff line Loading @@ -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(); Loading @@ -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; } Loading @@ -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() Loading @@ -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() Loading Loading @@ -1108,4 +1107,3 @@ double FixMSST::memory_usage() double bytes = 3*atom->nmax * sizeof(double); return bytes; } src/SHOCK/fix_msst.h +23 −23 Original line number Diff line number Diff line Loading @@ -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 Loading Loading
doc/src/Section_commands.txt +2 −2 Original line number Diff line number Diff line Loading @@ -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 Loading
doc/src/Section_packages.txt +32 −8 Original line number Diff line number Diff line Loading @@ -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. Once that process is complete, you can then install/un-install the package and build LAMMPS in the usual manner: 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. 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 Loading
src/SHOCK/fix_msst.cpp +5 −7 Original line number Diff line number Diff line Loading @@ -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(); Loading @@ -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; } Loading @@ -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() Loading @@ -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() Loading Loading @@ -1108,4 +1107,3 @@ double FixMSST::memory_usage() double bytes = 3*atom->nmax * sizeof(double); return bytes; }
src/SHOCK/fix_msst.h +23 −23 Original line number Diff line number Diff line Loading @@ -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 Loading
