Pressure calculation. More...

#include "utils.h"
#include "integrate.h"
#include "statistics.h"
#include "thermostat.h"
#include "adresso.h"
#include "forces.h"
#include "npt.h"

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Functions
Exported Functions
void	init_virials (Observable_stat *stat)
	Initializes a virials Observable stat.
void	init_virials_non_bonded (Observable_stat_non_bonded *stat_nb)
	Initializes a virials Observable stat.
void	init_p_tensor_non_bonded (Observable_stat_non_bonded *stat_nb)
	Initializes stat_nb to be used by pressure_calc.
void	init_p_tensor (Observable_stat *stat)
	Initializes stat to be used by pressure_calc.
void	master_pressure_calc (int v_comp)
	on the master node: calc energies only if necessary
void	pressure_calc (double result, double result_t, double result_nb, double result_t_nb, int v_comp)
	Calculates the pressure in the system from a virial expansion using the terms from calculate_verlet_virials or nsq_calculate_virials dependeing on the used cell system.
MDINLINE void	add_non_bonded_pair_virials (Particle p1, Particle p2, double d[3], double dist, double dist2)
	Calculate non bonded energies between a pair of particles.
MDINLINE void	calc_bonded_force (Particle p1, Particle p2, Bonded_ia_parameters iaparams, int i, double dx[3], double force[3])
MDINLINE void	calc_three_body_bonded_forces (Particle p1, Particle p2, Particle p3, Bonded_ia_parameters iaparams, double force1[3], double force2[3], double force3[3])
MDINLINE void	add_bonded_virials (Particle *p1)
	Calculate bonded virials for one particle.
MDINLINE void	add_three_body_bonded_stress (Particle *p1)
	Calculate the contribution to the stress tensor from angular potentials.
MDINLINE void	add_kinetic_virials (Particle *p1, int v_comp)
	Calculate kinetic pressure (aka energy) for one particle.
int	local_stress_tensor_calc (DoubleList *TensorInBin, int bins[3], int periodic[3], double range_start[3], double range[3])
	implementation of 'analyse local_stress_tensor
int	observable_compute_stress_tensor (int v_comp, double *A, unsigned int n_A)
	function to calculate stress tensor for the observables
Variables
Exported Variables
Observable_stat	virials
Observable_stat	total_pressure
Observable_stat	p_tensor
Observable_stat	total_p_tensor
Observable_stat_non_bonded	virials_non_bonded
Observable_stat_non_bonded	total_pressure_non_bonded
Observable_stat_non_bonded	p_tensor_non_bonded
Observable_stat_non_bonded	total_p_tensor_non_bonded

Detailed Description

Pressure calculation.

Really similar to energy.h.

Definition in file pressure.h.

Function Documentation

MDINLINE void add_bonded_virials ( Particle * p1 )

Calculate bonded virials for one particle.

For performance reasons the force routines add their values directly to the particles. So here we do some tricks to get the value out without changing the forces.

Parameters:

p1	particle for which to calculate virials

Definition at line 311 of file pressure.h.

References Particle::bl, BONDED_IA_HARMONIC, bonded_ia_params, calc_bonded_force(), IntList::e, ERROR_SPRINTF, ES_INTEGER_SPACE, get_mi_vector(), Bonded_ia_parameters::harmonic, i, ParticleProperties::identity, local_particles, obsstat_bonded(), ParticlePosition::p, Particle::p, Bonded_ia_parameters::p, Particle::r, and runtime_error().

Referenced by calculate_link_cell_virials(), calculate_verlet_virials(), layered_calculate_virials(), and nsq_calculate_virials().

MDINLINE void add_kinetic_virials	(	Particle *	p1,
		int	v_comp
	)

Calculate kinetic pressure (aka energy) for one particle.

Parameters:

p1	particle for which to calculate pressure
v_comp	flag which enables (1) compensation of the velocities required for deriving a pressure reflecting nptiso_struct::p_inst (hence it only works with domain decomposition); naturally it therefore doesn't make sense to use it without NpT.

Definition at line 508 of file pressure.h.

References Observable_stat::data, DoubleList::e, ParticleForce::f, Particle::f, Particle::m, PMASS, SQR(), and ParticleMomentum::v.

Referenced by calculate_link_cell_virials(), calculate_verlet_virials(), layered_calculate_virials(), and nsq_calculate_virials().

MDINLINE void add_non_bonded_pair_virials	(	Particle *	p1,
		Particle *	p2,
		double	d[3],
		double	dist,
		double	dist2
	)

Calculate non bonded energies between a pair of particles.

Parameters:

p1	pointer to particle 1.
p2	pointer to particle 2.
d	vector between p1 and p2.
dist	distance between p1 and p2.
dist2	distance squared between p1 and p2.

Definition at line 73 of file pressure.h.

References add_dh_coulomb_pair_force(), add_rf_coulomb_pair_force(), calc_non_bonded_pair_force_simple(), Observable_stat::coulomb, coulomb, COULOMB_DH, COULOMB_INTER_RF, COULOMB_NONE, COULOMB_P3M, COULOMB_P3M_GPU, COULOMB_RF, DIPOLAR_NONE, Coulomb_parameters::Dmethod, Coulomb_parameters::method, ParticleProperties::mol_id, obsstat_nonbonded(), obsstat_nonbonded_inter(), obsstat_nonbonded_intra(), Particle::p, p3m_pair_energy(), ParticleProperties::q, and ParticleProperties::type.

Referenced by calculate_link_cell_virials(), calculate_verlet_virials(), layered_calculate_virials(), and nsq_calculate_virials().

MDINLINE void add_three_body_bonded_stress ( Particle * p1 )

Calculate the contribution to the stress tensor from angular potentials.

The central particle of the three-particle interaction is responsible for the contribution of the entire interaction - this is the coding not the physics.

Definition at line 355 of file pressure.h.

References Particle::bl, BONDED_IA_ANGLE_COSINE, BONDED_IA_ANGLE_COSSQUARE, BONDED_IA_ANGLE_HARMONIC, BONDED_IA_ANGLEDIST, BONDED_IA_AREA_FORCE_GLOBAL, BONDED_IA_AREA_FORCE_LOCAL, BONDED_IA_BENDING_FORCE, BONDED_IA_DIHEDRAL, BONDED_IA_FENE, BONDED_IA_HARMONIC, bonded_ia_params, BONDED_IA_RIGID_BOND, BONDED_IA_STRETCHING_FORCE, BONDED_IA_SUBT_LJ, BONDED_IA_TABULATED, BONDED_IA_VIRTUAL_BOND, BONDED_IA_VOLUME_FORCE, calc_three_body_bonded_forces(), IntList::e, ERROR_SPRINTF, ES_INTEGER_SPACE, get_mi_vector(), i, ParticleProperties::identity, local_particles, obsstat_bonded(), ParticlePosition::p, Particle::p, Bonded_ia_parameters::p, Particle::r, runtime_error(), Bonded_ia_parameters::tab, TAB_BOND_ANGLE, TAB_BOND_DIHEDRAL, TAB_BOND_LENGTH, and Bonded_ia_parameters::type.

Referenced by calculate_link_cell_virials(), calculate_verlet_virials(), layered_calculate_virials(), and nsq_calculate_virials().

MDINLINE void calc_bonded_force	(	Particle *	p1,
		Particle *	p2,
		Bonded_ia_parameters *	iaparams,
		int *	i,
		double	dx[3],
		double	force[3]
	)

Definition at line 156 of file pressure.h.

References adress_non_bonded_force_weight(), BONDED_IA_ANGLE_COSINE, BONDED_IA_ANGLE_COSSQUARE, BONDED_IA_ANGLE_HARMONIC, BONDED_IA_ANGLEDIST, BONDED_IA_DIHEDRAL, BONDED_IA_FENE, BONDED_IA_HARMONIC, BONDED_IA_OVERLAPPED, BONDED_IA_RIGID_BOND, BONDED_IA_SUBT_LJ, BONDED_IA_TABULATED, BONDED_IA_VIRTUAL_BOND, calc_fene_pair_force(), calc_harmonic_pair_force(), calc_overlap_bond_force(), calc_subt_lj_pair_force(), calc_tab_bond_force(), ERROR_SPRINTF, ES_INTEGER_SPACE, get_mol_com_particle(), ParticleProperties::identity, Bonded_ia_parameters::overlap, OVERLAP_BOND_ANGLE, OVERLAP_BOND_DIHEDRAL, OVERLAP_BOND_LENGTH, Particle::p, Bonded_ia_parameters::p, ROUND_ERROR_PREC, runtime_error(), Bonded_ia_parameters::tab, TAB_BOND_ANGLE, TAB_BOND_DIHEDRAL, TAB_BOND_LENGTH, and Bonded_ia_parameters::type.

Referenced by add_bonded_virials(), and local_stress_tensor_calc().

MDINLINE void calc_three_body_bonded_forces	(	Particle *	p1,
		Particle *	p2,
		Particle *	p3,
		Bonded_ia_parameters *	iaparams,
		double	force1[3],
		double	force2[3],
		double	force3[3]
	)

void init_p_tensor ( Observable_stat * stat )

Initializes stat to be used by pressure_calc.

Definition at line 270 of file pressure.c.

References coulomb, COULOMB_NONE, COULOMB_P3M, COULOMB_P3M_GPU, DIPOLAR_ALL_WITH_ALL_AND_NO_REPLICA, DIPOLAR_DS, DIPOLAR_NONE, DIPOLAR_P3M, Coulomb_parameters::Dmethod, Observable_stat::init_status, Coulomb_parameters::method, n_bonded_ia, n_particle_types, and obsstat_realloc_and_clear().

Referenced by observable_compute_stress_tensor(), pressure_calc(), tclcommand_analyze_parse_and_print_pressure(), and tclcommand_analyze_parse_and_print_stress_tensor().

void init_p_tensor_non_bonded ( Observable_stat_non_bonded * stat_nb )

Initializes stat_nb to be used by pressure_calc.

Definition at line 303 of file pressure.c.

References Observable_stat_non_bonded::init_status_nb, n_particle_types, and obsstat_realloc_and_clear_non_bonded().

Referenced by observable_compute_stress_tensor(), pressure_calc(), tclcommand_analyze_parse_and_print_pressure(), and tclcommand_analyze_parse_and_print_stress_tensor().

void init_virials ( Observable_stat * stat )

Initializes a virials Observable stat.

Definition at line 225 of file pressure.c.

References coulomb, COULOMB_NONE, COULOMB_P3M, COULOMB_P3M_GPU, DIPOLAR_ALL_WITH_ALL_AND_NO_REPLICA, DIPOLAR_DS, DIPOLAR_NONE, DIPOLAR_P3M, Coulomb_parameters::Dmethod, Observable_stat::init_status, Coulomb_parameters::method, n_bonded_ia, n_particle_types, and obsstat_realloc_and_clear().

Referenced by observable_compute_stress_tensor(), pressure_calc(), tclcommand_analyze_parse_and_print_pressure(), and tclcommand_analyze_parse_and_print_stress_tensor().

void init_virials_non_bonded ( Observable_stat_non_bonded * stat_nb )

Initializes a virials Observable stat.

Definition at line 258 of file pressure.c.

References Observable_stat_non_bonded::init_status_nb, n_particle_types, and obsstat_realloc_and_clear_non_bonded().

Referenced by observable_compute_stress_tensor(), pressure_calc(), tclcommand_analyze_parse_and_print_pressure(), and tclcommand_analyze_parse_and_print_stress_tensor().

int local_stress_tensor_calc	(	DoubleList *	TensorInBin,
		int	bins[3],
		int	periodic[3],
		double	range_start[3],
		double	range[3]
	)

implementation of 'analyse local_stress_tensor

Definition at line 877 of file pressure.c.

References Particle::bl, bonded_ia_params, box_l, calc_bonded_force(), CellPList::cell, DomainDecomposition::cell_inter, dd, distribute_tensors(), drem_down(), IntList::e, DoubleList::e, ERROR_SPRINTF, ES_INTEGER_SPACE, get_mi_vector(), get_nonbonded_interaction(), i, ParticleProperties::identity, incubewithskin(), local_cells, local_particles, Particle::m, max_cut, PairList::n, CellPList::n, ParticleList::n, IA_Neighbor_List::n_neighbors, IA_Neighbor_List::nList, ParticlePosition::p, Particle::p, PairList::pair, ParticleList::part, PMASS, PTENSOR_TRACE, Particle::r, runtime_error(), skin, this_node, time_step, ParticleMomentum::v, IA_Neighbor::vList, and whichbin().

Referenced by mpi_local_stress_tensor(), and mpi_local_stress_tensor_slave().

void master_pressure_calc ( int v_comp )

on the master node: calc energies only if necessary

Parameters:

v_comp flag which enables (1) compensation of the velocities required for deriving a pressure reflecting nptiso_struct::p_inst (hence it only works with domain decomposition); naturally it therefore doesn't make sense to use it without NpT.

Definition at line 313 of file pressure.c.

References Observable_stat::data, Observable_stat_non_bonded::data_nb, DoubleList::e, Observable_stat::init_status, Observable_stat_non_bonded::init_status_nb, and mpi_gather_stats().

Referenced by observable_compute_stress_tensor(), tclcommand_analyze_parse_and_print_pressure(), and tclcommand_analyze_parse_and_print_stress_tensor().

int observable_compute_stress_tensor	(	int	v_comp,
		double *	A,
		unsigned int	n_A
	)

function to calculate stress tensor for the observables

Definition at line 1008 of file pressure.c.

References Observable_stat::data, nptiso_struct::dimension, DoubleList::e, nptiso_struct::geometry, i, init_p_tensor(), init_p_tensor_non_bonded(), Observable_stat::init_status, init_virials(), init_virials_non_bonded(), INTEG_METHOD_NPT_ISO, integ_switch, nptiso_struct::invalidate_p_vel, master_pressure_calc(), MPI_COMM_WORLD, MPI_DOUBLE, MPI_Reduce(), MPI_SUM, DoubleList::n, nptiso_struct::nptgeom_dir, nptiso_struct::p_vel, and nptiso_struct::volume.

Referenced by observable_stress_tensor(), and observable_stress_tensor_acf_obs().

void pressure_calc	(	double *	result,
		double *	result_t,
		double *	result_nb,
		double *	result_t_nb,
		int	v_comp
	)

Calculates the pressure in the system from a virial expansion using the terms from calculate_verlet_virials or nsq_calculate_virials dependeing on the used cell system.

Parameters:

result	here the data about the scalar pressure are stored
result_t	here the data about the stress tensor are stored
result_nb	here the data about the intra- and inter- molecular nonbonded contributions to scalar pressure are stored
result_t_nb	here the data about the intra- and inter- molecular nonbonded contributions to stress tensor are stored
v_comp	flag which enables (1) compensation of the velocities required for deriving a pressure reflecting nptiso_struct::p_inst (hence it only works with domain decomposition); naturally it therefore doesn't make sense to use it without NpT.