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thermo.h
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thermo.h
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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_THERMO_H
#define LMP_THERMO_H
#include "pointers.h"
namespace LAMMPS_NS {
class DumpNetCDF;
class DumpNetCDFMPIIO;
class Thermo : protected Pointers {
friend class MinCG; // accesses compute_pe
friend class DumpNetCDF; // accesses thermo properties
friend class DumpNetCDFMPIIO; // accesses thermo properties
public:
char *style;
int normflag; // 0 if do not normalize by atoms, 1 if normalize
int modified; // 1 if thermo_modify has been used, else 0
int lostflag; // IGNORE,WARN,ERROR
int lostbond; // ditto for atoms in bonds
Thermo(class LAMMPS *, int, char **);
~Thermo();
void init();
bigint lost_check();
void modify_params(int, char **);
void header();
void compute(int);
int evaluate_keyword(char *, double *);
private:
char *line;
char **keyword;
int *vtype;
int nfield,nfield_initial;
int me;
char **format;
char *format_line_user;
char *format_float_user,*format_int_user,*format_bigint_user;
char **format_column_user;
char *format_float_one_def,*format_float_multi_def;
char *format_int_one_def,*format_int_multi_def;
char format_multi[128];
char format_bigint_one_def[8],format_bigint_multi_def[8];
int normvalue; // use this for normflag unless natoms = 0
int normuserflag; // 0 if user has not set, 1 if has
int normuser;
int firststep;
int lostbefore;
int flushflag,lineflag;
double last_tpcpu,last_spcpu;
double last_time;
bigint last_step;
bigint natoms;
// data used by routines that compute single values
int ivalue; // integer value to print
double dvalue; // double value to print
bigint bivalue; // big integer value to print
int ifield; // which field in thermo output is being computed
int *field2index; // which compute,fix,variable calcs this field
int *argindex1; // indices into compute,fix scalar,vector
int *argindex2;
// data for keyword-specific Compute objects
// index = where they are in computes list
// id = ID of Compute objects
// Compute * = ptrs to the Compute objects
int index_temp,index_press_scalar,index_press_vector,index_pe;
char *id_temp,*id_press,*id_pe;
class Compute *temperature,*pressure,*pe;
int ncompute; // # of Compute objects called by thermo
char **id_compute; // their IDs
int *compute_which; // 0/1/2 if should call scalar,vector,array
class Compute **computes; // list of ptrs to the Compute objects
int nfix; // # of Fix objects called by thermo
char **id_fix; // their IDs
class Fix **fixes; // list of ptrs to the Fix objects
int nvariable; // # of variables evaluated by thermo
char **id_variable; // list of variable names
int *variables; // list of Variable indices
// private methods
void allocate();
void deallocate();
void parse_fields(char *);
int add_compute(const char *, int);
int add_fix(const char *);
int add_variable(const char *);
typedef void (Thermo::*FnPtr)();
void addfield(const char *, FnPtr, int);
FnPtr *vfunc; // list of ptrs to functions
void call_vfunc(int ifield);
void compute_compute(); // functions that compute a single value
void compute_fix(); // via calls to Compute,Fix,Variable classes
void compute_variable();
// functions that compute a single value
// customize a new keyword by adding a method prototype
void compute_step();
void compute_elapsed();
void compute_elapsed_long();
void compute_dt();
void compute_time();
void compute_cpu();
void compute_tpcpu();
void compute_spcpu();
void compute_cpuremain();
void compute_part();
void compute_timeremain();
void compute_atoms();
void compute_temp();
void compute_press();
void compute_pe();
void compute_ke();
void compute_etotal();
void compute_enthalpy();
void compute_evdwl();
void compute_ecoul();
void compute_epair();
void compute_ebond();
void compute_eangle();
void compute_edihed();
void compute_eimp();
void compute_emol();
void compute_elong();
void compute_etail();
void compute_vol();
void compute_density();
void compute_lx();
void compute_ly();
void compute_lz();
void compute_xlo();
void compute_xhi();
void compute_ylo();
void compute_yhi();
void compute_zlo();
void compute_zhi();
void compute_xy();
void compute_xz();
void compute_yz();
void compute_xlat();
void compute_ylat();
void compute_zlat();
void compute_bonds();
void compute_angles();
void compute_dihedrals();
void compute_impropers();
void compute_pxx();
void compute_pyy();
void compute_pzz();
void compute_pxy();
void compute_pyz();
void compute_pxz();
void compute_fmax();
void compute_fnorm();
void compute_nbuild();
void compute_ndanger();
void compute_cella();
void compute_cellb();
void compute_cellc();
void compute_cellalpha();
void compute_cellbeta();
void compute_cellgamma();
};
}
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Could not find thermo compute ID
Compute ID specified in thermo_style command does not exist.
E: Could not find thermo fix ID
Fix ID specified in thermo_style command does not exist.
E: Thermo and fix not computed at compatible times
Fixes generate values on specific timesteps. The thermo output
does not match these timesteps.
E: Could not find thermo variable name
Self-explanatory.
E: Too many total atoms
See the setting for bigint in the src/lmptype.h file.
E: Lost atoms: original %ld current %ld
Lost atoms are checked for each time thermo output is done. See the
thermo_modify lost command for options. Lost atoms usually indicate
bad dynamics, e.g. atoms have been blown far out of the simulation
box, or moved further than one processor's sub-domain away before
reneighboring.
W: Lost atoms: original %ld current %ld
Lost atoms are checked for each time thermo output is done. See the
thermo_modify lost command for options. Lost atoms usually indicate
bad dynamics, e.g. atoms have been blown far out of the simulation
box, or moved further than one processor's sub-domain away before
reneighboring.
E: Thermo style does not use temp
Cannot use thermo_modify to set this parameter since the thermo_style
is not computing this quantity.
E: Could not find thermo_modify temperature ID
The compute ID needed by thermo style custom to compute temperature does
not exist.
E: Thermo_modify temperature ID does not compute temperature
The specified compute ID does not compute temperature.
W: Temperature for thermo pressure is not for group all
User-assigned temperature to thermo via the thermo_modify command does
not compute temperature for all atoms. Since thermo computes a global
pressure, the kinetic energy contribution from the temperature is
assumed to also be for all atoms. Thus the pressure printed by thermo
could be inaccurate.
E: Pressure ID for thermo does not exist
The compute ID needed to compute pressure for thermodynamics does not
exist.
E: Thermo style does not use press
Cannot use thermo_modify to set this parameter since the thermo_style
is not computing this quantity.
E: Could not find thermo_modify pressure ID
The compute ID needed by thermo style custom to compute pressure does
not exist.
E: Thermo_modify pressure ID does not compute pressure
The specified compute ID does not compute pressure.
E: Thermo_modify int format does not contain d character
Self-explanatory.
E: Could not find thermo custom compute ID
The compute ID needed by thermo style custom to compute a requested
quantity does not exist.
E: Thermo compute does not compute scalar
Self-explanatory.
E: Thermo compute does not compute vector
Self-explanatory.
E: Thermo compute vector is accessed out-of-range
Self-explanatory.
E: Thermo compute does not compute array
Self-explanatory.
E: Thermo compute array is accessed out-of-range
Self-explanatory.
E: Could not find thermo custom fix ID
The fix ID needed by thermo style custom to compute a requested
quantity does not exist.
E: Thermo fix does not compute scalar
Self-explanatory.
E: Thermo fix does not compute vector
Self-explanatory.
E: Thermo fix vector is accessed out-of-range
Self-explanatory.
E: Thermo fix does not compute array
Self-explanatory.
E: Thermo fix array is accessed out-of-range
Self-explanatory.
E: Could not find thermo custom variable name
Self-explanatory.
E: Thermo custom variable is not equal-style variable
Only equal-style variables can be output with thermodynamics, not
atom-style variables.
E: Thermo custom variable cannot be indexed
Self-explanatory.
E: Unknown keyword in thermo_style custom command
One or more specified keywords are not recognized.
E: This variable thermo keyword cannot be used between runs
Keywords that refer to time (such as cpu, elapsed) do not
make sense in between runs.
E: Thermo keyword in variable requires thermo to use/init temp
You are using a thermo keyword in a variable that requires temperature
to be calculated, but your thermo output does not use it. Add it to
your thermo output.
E: Compute used in variable thermo keyword between runs is not current
Some thermo keywords rely on a compute to calculate their value(s).
Computes cannot be invoked by a variable in between runs. Thus they
must have been evaluated on the last timestep of the previous run in
order for their value(s) to be accessed. See the doc page for the
variable command for more info.
E: Thermo keyword in variable requires thermo to use/init press
You are using a thermo keyword in a variable that requires pressure to
be calculated, but your thermo output does not use it. Add it to your
thermo output.
E: Thermo keyword in variable requires thermo to use/init pe
You are using a thermo keyword in a variable that requires
potential energy to be calculated, but your thermo output
does not use it. Add it to your thermo output.
E: Energy was not tallied on needed timestep
You are using a thermo keyword that requires potentials to
have tallied energy, but they didn't on this timestep. See the
variable doc page for ideas on how to make this work.
*/

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