From a9a896c6779317fb6bbbfc5313085da6861ea12b Mon Sep 17 00:00:00 2001 From: jtclemm Date: Mon, 15 Jul 2024 17:19:51 -0600 Subject: [PATCH] Small doc changes, renaming status variable --- doc/src/Howto_rheo.rst | 33 ++++++++++++----------- examples/rheo/oxidation/in.rheo.oxidation | 3 +-- src/RHEO/atom_vec_rheo.cpp | 28 +++++++++---------- src/RHEO/atom_vec_rheo.h | 2 +- src/RHEO/atom_vec_rheo_thermal.cpp | 28 +++++++++---------- src/RHEO/atom_vec_rheo_thermal.h | 2 +- src/RHEO/bond_rheo_shell.cpp | 2 +- src/RHEO/compute_rheo_grad.cpp | 2 +- src/RHEO/compute_rheo_interface.cpp | 4 +-- src/RHEO/compute_rheo_kernel.cpp | 2 +- src/RHEO/compute_rheo_property_atom.cpp | 32 ++++++---------------- src/RHEO/compute_rheo_property_atom.h | 3 +-- src/RHEO/compute_rheo_surface.cpp | 10 +++---- src/RHEO/compute_rheo_vshift.cpp | 4 +-- src/RHEO/fix_rheo.cpp | 10 +++---- src/RHEO/fix_rheo_oxidation.cpp | 4 +-- src/RHEO/fix_rheo_thermal.cpp | 16 +++++------ src/RHEO/pair_rheo.cpp | 2 +- src/RHEO/pair_rheo_solid.cpp | 6 ++--- src/atom.cpp | 10 +++---- src/atom.h | 4 +-- src/set.cpp | 4 +-- 22 files changed, 97 insertions(+), 114 deletions(-) diff --git a/doc/src/Howto_rheo.rst b/doc/src/Howto_rheo.rst index 7c62d09ab1..34c0f7b6a1 100644 --- a/doc/src/Howto_rheo.rst +++ b/doc/src/Howto_rheo.rst @@ -2,25 +2,26 @@ Reproducing hydrodynamics and elastic objects (RHEO) ==================================================== The RHEO package is a hybrid implementation of smoothed particle -hydrodynamics (SPH) for fluid flow, coupled to the :doc:`BPM package ` -to model solid elements. RHEO combines these methods to enable mesh-free modeling -of multi-phase material systems. The SPH solver supports many advanced options -including reproducing kernels, particle shifting, free surface identification, -and solid surface reconstruction. To model fluid-solid systems, the status of -particles can dynamically change between a fluid and solid state, e.g. during -melting/solidification, which determines how they interact and their physical -behavior. The package is designed with modularity in mind, so one can easily -turn various features on/off, adjust physical details of the system, or -develop new capabilities. For instance, the numerics associated with -calculating gradients, reproducing kernels, etc. are separated into distinct -classes to simplify the development of new integration schemes which can call -these calculations. Additional numerical details can be found in +hydrodynamics (SPH) for fluid flow, which can couple to the :doc:`BPM package +` to model solid elements. RHEO combines these methods to enable +mesh-free modeling of multi-phase material systems. Its SPH solver supports +many advanced options including reproducing kernels, particle shifting, free +surface identification, and solid surface reconstruction. To model fluid-solid +systems, the status of particles can dynamically change between a fluid and +solid state, e.g. during melting/solidification, which determines how they +interact and their physical behavior. The package is designed with modularity +in mind, so one can easily turn various features on/off, adjust physical +details of the system, or develop new capabilities. For instance, the numerics +associated with calculating gradients, reproducing kernels, etc. are separated +into distinctclasses to simplify the development of new integration schemes +which can call these calculations. Additional numerical details can be found in :ref:`(Palermo) ` and :ref:`(Clemmer) `. -Note, if you simply want to run a traditional SPH simulation, the SPH package -is likely better suited for your application. It has fewer advanced features -and therefore benefits from improved performance. +Note, if you simply want to run a traditional SPH simulation, the :ref:`SPH package +` package is likely better suited for your application. It has fewer advanced +features and therefore benefits from improved performance. The :ref:`MACHDYN +` package for solids may also be relevant for fluid-solid problems. ---------- diff --git a/examples/rheo/oxidation/in.rheo.oxidation b/examples/rheo/oxidation/in.rheo.oxidation index d8b4b1a464..57bd71b917 100644 --- a/examples/rheo/oxidation/in.rheo.oxidation +++ b/examples/rheo/oxidation/in.rheo.oxidation @@ -87,7 +87,6 @@ fix 11 all enforce2d compute surf all rheo/property/atom surface compute rho all rheo/property/atom rho compute phase all rheo/property/atom phase -compute status all rheo/property/atom status compute temp all rheo/property/atom temperature compute eng all rheo/property/atom energy compute nbond_shell all rheo/property/atom nbond/shell @@ -98,6 +97,6 @@ compute nbond_solid all nbond/atom bond/type 1 thermo 200 thermo_style custom step time ke press atoms -#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond_solid c_nbond_shell c_rho c_surf c_status +#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond_solid c_nbond_shell c_rho c_surf run 40000 diff --git a/src/RHEO/atom_vec_rheo.cpp b/src/RHEO/atom_vec_rheo.cpp index 92f5ca05a4..0cbebff008 100644 --- a/src/RHEO/atom_vec_rheo.cpp +++ b/src/RHEO/atom_vec_rheo.cpp @@ -33,7 +33,7 @@ AtomVecRHEO::AtomVecRHEO(LAMMPS *lmp) : AtomVec(lmp) mass_type = PER_TYPE; forceclearflag = 1; - atom->status_flag = 1; + atom->rheo_status_flag = 1; atom->pressure_flag = 1; atom->rho_flag = 1; atom->viscosity_flag = 1; @@ -43,17 +43,17 @@ AtomVecRHEO::AtomVecRHEO(LAMMPS *lmp) : AtomVec(lmp) // order of fields in a string does not matter // except: fields_data_atom & fields_data_vel must match data file - fields_grow = {"status", "rho", "drho", "pressure", "viscosity"}; - fields_copy = {"status", "rho", "drho", "pressure", "viscosity"}; - fields_comm = {"status", "rho"}; - fields_comm_vel = {"status", "rho"}; + fields_grow = {"rheo_status", "rho", "drho", "pressure", "viscosity"}; + fields_copy = {"rheo_status", "rho", "drho", "pressure", "viscosity"}; + fields_comm = {"rheo_status", "rho"}; + fields_comm_vel = {"rheo_status", "rho"}; fields_reverse = {"drho"}; - fields_border = {"status", "rho"}; - fields_border_vel = {"status", "rho"}; - fields_exchange = {"status", "rho"}; - fields_restart = {"status", "rho"}; - fields_create = {"status", "rho", "drho", "pressure", "viscosity"}; - fields_data_atom = {"id", "type", "status", "rho", "x"}; + fields_border = {"rheo_status", "rho"}; + fields_border_vel = {"rheo_status", "rho"}; + fields_exchange = {"rheo_status", "rho"}; + fields_restart = {"rheo_status", "rho"}; + fields_create = {"rheo_status", "rho", "drho", "pressure", "viscosity"}; + fields_data_atom = {"id", "type", "rheo_status", "rho", "x"}; fields_data_vel = {"id", "v"}; setup_fields(); @@ -66,7 +66,7 @@ AtomVecRHEO::AtomVecRHEO(LAMMPS *lmp) : AtomVec(lmp) void AtomVecRHEO::grow_pointers() { - status = atom->status; + rheo_status = atom->rheo_status; pressure = atom->pressure; rho = atom->rho; drho = atom->drho; @@ -111,7 +111,7 @@ void AtomVecRHEO::data_atom_post(int ilocal) int AtomVecRHEO::property_atom(const std::string &name) { - if (name == "status") return 0; + if (name == "rheo_status") return 0; if (name == "pressure") return 1; if (name == "rho") return 2; if (name == "drho") return 3; @@ -133,7 +133,7 @@ void AtomVecRHEO::pack_property_atom(int index, double *buf, int nvalues, int gr if (index == 0) { for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) - buf[n] = status[i]; + buf[n] = rheo_status[i]; else buf[n] = 0.0; n += nvalues; diff --git a/src/RHEO/atom_vec_rheo.h b/src/RHEO/atom_vec_rheo.h index 62a7b1a630..8eaa01f7be 100644 --- a/src/RHEO/atom_vec_rheo.h +++ b/src/RHEO/atom_vec_rheo.h @@ -36,7 +36,7 @@ class AtomVecRHEO : virtual public AtomVec { void pack_property_atom(int, double *, int, int) override; private: - int *status; + int *rheo_status; double *pressure, *rho, *drho, *viscosity; }; diff --git a/src/RHEO/atom_vec_rheo_thermal.cpp b/src/RHEO/atom_vec_rheo_thermal.cpp index f541e2a0cb..426c059570 100644 --- a/src/RHEO/atom_vec_rheo_thermal.cpp +++ b/src/RHEO/atom_vec_rheo_thermal.cpp @@ -33,7 +33,7 @@ AtomVecRHEOThermal::AtomVecRHEOThermal(LAMMPS *lmp) : AtomVec(lmp) mass_type = PER_TYPE; forceclearflag = 1; - atom->status_flag = 1; + atom->rheo_status_flag = 1; atom->conductivity_flag = 1; atom->temperature_flag = 1; atom->esph_flag = 1; @@ -47,17 +47,17 @@ AtomVecRHEOThermal::AtomVecRHEOThermal(LAMMPS *lmp) : AtomVec(lmp) // order of fields in a string does not matter // except: fields_data_atom & fields_data_vel must match data file - fields_grow = {"status", "rho", "drho", "temperature", "esph", "heatflow", "conductivity", "pressure", "viscosity"}; - fields_copy = {"status", "rho", "drho", "temperature", "esph", "heatflow", "conductivity", "pressure", "viscosity"}; - fields_comm = {"status", "rho", "esph"}; - fields_comm_vel = {"status", "rho", "esph"}; + fields_grow = {"rheo_status", "rho", "drho", "temperature", "esph", "heatflow", "conductivity", "pressure", "viscosity"}; + fields_copy = {"rheo_status", "rho", "drho", "temperature", "esph", "heatflow", "conductivity", "pressure", "viscosity"}; + fields_comm = {"rheo_status", "rho", "esph"}; + fields_comm_vel = {"rheo_status", "rho", "esph"}; fields_reverse = {"drho", "heatflow"}; - fields_border = {"status", "rho", "esph"}; - fields_border_vel = {"status", "rho", "esph"}; - fields_exchange = {"status", "rho", "esph"}; - fields_restart = {"status", "rho", "esph"}; - fields_create = {"status", "rho", "drho", "temperature", "esph", "heatflow", "conductivity", "pressure", "viscosity"}; - fields_data_atom = {"id", "type", "status", "rho", "esph", "x"}; + fields_border = {"rheo_status", "rho", "esph"}; + fields_border_vel = {"rheo_status", "rho", "esph"}; + fields_exchange = {"rheo_status", "rho", "esph"}; + fields_restart = {"rheo_status", "rho", "esph"}; + fields_create = {"rheo_status", "rho", "drho", "temperature", "esph", "heatflow", "conductivity", "pressure", "viscosity"}; + fields_data_atom = {"id", "type", "rheo_status", "rho", "esph", "x"}; fields_data_vel = {"id", "v"}; setup_fields(); @@ -70,7 +70,7 @@ AtomVecRHEOThermal::AtomVecRHEOThermal(LAMMPS *lmp) : AtomVec(lmp) void AtomVecRHEOThermal::grow_pointers() { - status = atom->status; + rheo_status = atom->rheo_status; conductivity = atom->conductivity; temperature = atom->temperature; esph = atom->esph; @@ -123,7 +123,7 @@ void AtomVecRHEOThermal::data_atom_post(int ilocal) int AtomVecRHEOThermal::property_atom(const std::string &name) { - if (name == "status") return 0; + if (name == "rheo_status") return 0; if (name == "rho") return 1; if (name == "drho") return 2; if (name == "temperature") return 3; @@ -149,7 +149,7 @@ void AtomVecRHEOThermal::pack_property_atom(int index, double *buf, int nvalues, if (index == 0) { for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) - buf[n] = status[i]; + buf[n] = rheo_status[i]; else buf[n] = 0.0; n += nvalues; diff --git a/src/RHEO/atom_vec_rheo_thermal.h b/src/RHEO/atom_vec_rheo_thermal.h index 29a764bea9..eaf944ca96 100644 --- a/src/RHEO/atom_vec_rheo_thermal.h +++ b/src/RHEO/atom_vec_rheo_thermal.h @@ -36,7 +36,7 @@ class AtomVecRHEOThermal : virtual public AtomVec { void pack_property_atom(int, double *, int, int) override; private: - int *status; + int *rheo_status; double *conductivity, *temperature, *heatflow, *esph; double *pressure, *rho, *drho, *viscosity; }; diff --git a/src/RHEO/bond_rheo_shell.cpp b/src/RHEO/bond_rheo_shell.cpp index 81e5ba02d1..258d047086 100644 --- a/src/RHEO/bond_rheo_shell.cpp +++ b/src/RHEO/bond_rheo_shell.cpp @@ -182,7 +182,7 @@ void BondRHEOShell::compute(int eflag, int vflag) double **v = atom->v; double **f = atom->f; tagint *tag = atom->tag; - int *status = atom->status; + int *status = atom->rheo_status; int **bondlist = neighbor->bondlist; int nbondlist = neighbor->nbondlist; int nlocal = atom->nlocal; diff --git a/src/RHEO/compute_rheo_grad.cpp b/src/RHEO/compute_rheo_grad.cpp index 216fcb1978..cdf90e1dc5 100644 --- a/src/RHEO/compute_rheo_grad.cpp +++ b/src/RHEO/compute_rheo_grad.cpp @@ -144,7 +144,7 @@ void ComputeRHEOGrad::compute_peratom() double *rho = atom->rho; double *energy = atom->esph; double *viscosity = atom->viscosity; - int *status = atom->status; + int *status = atom->rheo_status; int *type = atom->type; double *mass = atom->mass; int newton = force->newton; diff --git a/src/RHEO/compute_rheo_interface.cpp b/src/RHEO/compute_rheo_interface.cpp index ec8c10f276..8ccd4e6a3b 100644 --- a/src/RHEO/compute_rheo_interface.cpp +++ b/src/RHEO/compute_rheo_interface.cpp @@ -120,7 +120,7 @@ void ComputeRHEOInterface::compute_peratom() double **x = atom->x; int *type = atom->type; int newton = force->newton; - int *status = atom->status; + int *status = atom->rheo_status; double *rho = atom->rho; inum = list->inum; @@ -290,7 +290,7 @@ void ComputeRHEOInterface::unpack_reverse_comm(int n, int *list, double *buf) { int i, k, j, m; double *rho = atom->rho; - int *status = atom->status; + int *status = atom->rheo_status; m = 0; for (i = 0; i < n; i++) { j = list[i]; diff --git a/src/RHEO/compute_rheo_kernel.cpp b/src/RHEO/compute_rheo_kernel.cpp index a5865b894a..4558ddccc8 100644 --- a/src/RHEO/compute_rheo_kernel.cpp +++ b/src/RHEO/compute_rheo_kernel.cpp @@ -586,7 +586,7 @@ void ComputeRHEOKernel::compute_peratom() int *type = atom->type; double *mass = atom->mass; double *rho = atom->rho; - int *status = atom->status; + int *status = atom->rheo_status; tagint *tag = atom->tag; int *ilist, *jlist, *numneigh, **firstneigh; diff --git a/src/RHEO/compute_rheo_property_atom.cpp b/src/RHEO/compute_rheo_property_atom.cpp index 533822bbdd..7a450e7708 100644 --- a/src/RHEO/compute_rheo_property_atom.cpp +++ b/src/RHEO/compute_rheo_property_atom.cpp @@ -92,8 +92,9 @@ ComputeRHEOPropertyAtom::ComputeRHEOPropertyAtom(LAMMPS *lmp, int narg, char **a for (int iarg = 3; iarg < narg; iarg++) { if (strcmp(arg[iarg], "phase") == 0) { pack_choice[i] = &ComputeRHEOPropertyAtom::pack_phase; - } else if (strcmp(arg[iarg], "rho") == 0) { - pack_choice[i] = &ComputeRHEOPropertyAtom::pack_rho; + } else if (strcmp(arg[iarg], "status") == 0) { + // Short hand for "rheo_status" + pack_choice[i] = &ComputeRHEOPropertyAtom::pack_status; } else if (strcmp(arg[iarg], "chi") == 0) { interface_flag = 1; pack_choice[i] = &ComputeRHEOPropertyAtom::pack_chi; @@ -111,8 +112,6 @@ ComputeRHEOPropertyAtom::ComputeRHEOPropertyAtom(LAMMPS *lmp, int narg, char **a } else if (strcmp(arg[iarg], "pressure") == 0) { pressure_flag = 1; pack_choice[i] = &ComputeRHEOPropertyAtom::pack_pressure; - } else if (strcmp(arg[iarg], "viscosity") == 0) { - pack_choice[i] = &ComputeRHEOPropertyAtom::pack_viscosity; } else if (strcmp(arg[iarg], "cv") == 0) { thermal_flag = 1; pack_choice[i] = &ComputeRHEOPropertyAtom::pack_cv; @@ -265,7 +264,7 @@ double ComputeRHEOPropertyAtom::memory_usage() void ComputeRHEOPropertyAtom::pack_phase(int n) { - int *status = atom->status; + int *status = atom->rheo_status; int *mask = atom->mask; int nlocal = atom->nlocal; @@ -278,14 +277,14 @@ void ComputeRHEOPropertyAtom::pack_phase(int n) /* ---------------------------------------------------------------------- */ -void ComputeRHEOPropertyAtom::pack_rho(int n) +void ComputeRHEOPropertyAtom::pack_status(int n) { - double *rho = atom->rho; + int *status = atom->rheo_status; int *mask = atom->mask; int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = rho[i]; + if (mask[i] & groupbit) buf[n] = status[i]; else buf[n] = 0.0; n += nvalues; } @@ -310,7 +309,7 @@ void ComputeRHEOPropertyAtom::pack_chi(int n) void ComputeRHEOPropertyAtom::pack_surface(int n) { - int *status = atom->status; + int *status = atom->rheo_status; int *mask = atom->mask; int nlocal = atom->nlocal; @@ -420,21 +419,6 @@ void ComputeRHEOPropertyAtom::pack_pressure(int n) /* ---------------------------------------------------------------------- */ -void ComputeRHEOPropertyAtom::pack_viscosity(int n) -{ - int *mask = atom->mask; - double *viscosity = atom->viscosity; - int nlocal = atom->nlocal; - - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) buf[n] = viscosity[i]; - else buf[n] = 0.0; - n += nvalues; - } -} - -/* ---------------------------------------------------------------------- */ - void ComputeRHEOPropertyAtom::pack_viscous_stress(int n) { double **gradv = compute_grad->gradv; diff --git a/src/RHEO/compute_rheo_property_atom.h b/src/RHEO/compute_rheo_property_atom.h index b3d247b102..4b1ebf2313 100644 --- a/src/RHEO/compute_rheo_property_atom.h +++ b/src/RHEO/compute_rheo_property_atom.h @@ -45,7 +45,7 @@ class ComputeRHEOPropertyAtom : public Compute { FnPtrPack *pack_choice; // ptrs to pack functions void pack_phase(int); - void pack_rho(int); + void pack_status(int); void pack_chi(int); void pack_surface(int); void pack_surface_r(int); @@ -56,7 +56,6 @@ class ComputeRHEOPropertyAtom : public Compute { void pack_shift_v(int); void pack_gradv(int); void pack_pressure(int); - void pack_viscosity(int); void pack_viscous_stress(int); void pack_total_stress(int); void pack_nbond_shell(int); diff --git a/src/RHEO/compute_rheo_surface.cpp b/src/RHEO/compute_rheo_surface.cpp index 69b0ebd108..c3a3774cdc 100644 --- a/src/RHEO/compute_rheo_surface.cpp +++ b/src/RHEO/compute_rheo_surface.cpp @@ -106,7 +106,7 @@ void ComputeRHEOSurface::compute_peratom() int nlocal = atom->nlocal; double **x = atom->x; - int *status = atom->status; + int *status = atom->rheo_status; int newton = force->newton; int dim = domain->dimension; int *mask = atom->mask; @@ -312,7 +312,7 @@ int ComputeRHEOSurface::pack_reverse_comm(int n, int first, double *buf) { int i,a,b,k,m,last; int dim = domain->dimension; - int *status = atom->status; + int *status = atom->rheo_status; m = 0; last = first + n; @@ -336,7 +336,7 @@ void ComputeRHEOSurface::unpack_reverse_comm(int n, int *list, double *buf) { int i,a,b,k,j,m; int dim = domain->dimension; - int *status = atom->status; + int *status = atom->rheo_status; int tmp1; double tmp2; @@ -367,7 +367,7 @@ int ComputeRHEOSurface::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int i,j,a,b,k,m; - int *status = atom->status; + int *status = atom->rheo_status; m = 0; for (i = 0; i < n; i++) { @@ -387,7 +387,7 @@ int ComputeRHEOSurface::pack_forward_comm(int n, int *list, double *buf, void ComputeRHEOSurface::unpack_forward_comm(int n, int first, double *buf) { int i, k, a, b, m, last; - int *status = atom->status; + int *status = atom->rheo_status; m = 0; last = first + n; diff --git a/src/RHEO/compute_rheo_vshift.cpp b/src/RHEO/compute_rheo_vshift.cpp index b01912111f..c06ef533ac 100644 --- a/src/RHEO/compute_rheo_vshift.cpp +++ b/src/RHEO/compute_rheo_vshift.cpp @@ -102,7 +102,7 @@ void ComputeRHEOVShift::compute_peratom() int inum, *ilist, *numneigh, **firstneigh; int *type = atom->type; - int *status = atom->status; + int *status = atom->rheo_status; int *mask = atom->mask; double **x = atom->x; double **v = atom->v; @@ -231,7 +231,7 @@ void ComputeRHEOVShift::correct_surfaces() int i, a, b; - int *status = atom->status; + int *status = atom->rheo_status; int *mask = atom->mask; double **nsurface = compute_surface->nsurface; diff --git a/src/RHEO/fix_rheo.cpp b/src/RHEO/fix_rheo.cpp index cd0ca1069a..f70b9e121f 100644 --- a/src/RHEO/fix_rheo.cpp +++ b/src/RHEO/fix_rheo.cpp @@ -86,7 +86,7 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR, "fix rheo command requires atom_style with density"); if (atom->viscosity_flag != 1) error->all(FLERR, "fix rheo command requires atom_style with viscosity"); - if (atom->status_flag != 1) + if (atom->rheo_status_flag != 1) error->all(FLERR, "fix rheo command requires atom_style with status"); if (narg < 5) @@ -235,7 +235,7 @@ void FixRHEO::init() if (modify->get_fix_by_style("^rheo$").size() > 1) error->all(FLERR, "Can only specify one instance of fix rheo"); - if (atom->status_flag != 1) + if (atom->rheo_status_flag != 1) error->all(FLERR,"fix rheo command requires atom property status"); if (atom->rho_flag != 1) error->all(FLERR,"fix rheo command requires atom property rho"); @@ -309,7 +309,7 @@ void FixRHEO::initial_integrate(int /*vflag*/) int *type = atom->type; int *mask = atom->mask; - int *status = atom->status; + int *status = atom->rheo_status; double **x = atom->x; double **v = atom->v; double **f = atom->f; @@ -432,7 +432,7 @@ void FixRHEO::pre_force(int /*vflag*/) // Remove temporary options int *mask = atom->mask; - int *status = atom->status; + int *status = atom->rheo_status; int nall = atom->nlocal + atom->nghost; for (int i = 0; i < nall; i++) if (mask[i] & groupbit) @@ -467,7 +467,7 @@ void FixRHEO::final_integrate() double *rmass = atom->rmass; int *type = atom->type; int *mask = atom->mask; - int *status = atom->status; + int *status = atom->rheo_status; int rmass_flag = atom->rmass_flag; int dim = domain->dimension; diff --git a/src/RHEO/fix_rheo_oxidation.cpp b/src/RHEO/fix_rheo_oxidation.cpp index 74d1bbab57..a51f2feb95 100644 --- a/src/RHEO/fix_rheo_oxidation.cpp +++ b/src/RHEO/fix_rheo_oxidation.cpp @@ -163,7 +163,7 @@ void FixRHEOOxidation::post_integrate() int **bond_type = atom->bond_type; int *num_bond = atom->num_bond; int *mask = atom->mask; - int *status = atom->status; + int *status = atom->rheo_status; double *rsurface = compute_surface->rsurface; double **x = atom->x; @@ -255,7 +255,7 @@ void FixRHEOOxidation::post_integrate() void FixRHEOOxidation::post_force(int /*vflag*/) { - int *status = atom->status; + int *status = atom->rheo_status; int *num_bond = atom->num_bond; for (int i = 0; i < atom->nlocal; i++) if (num_bond[i] != 0) diff --git a/src/RHEO/fix_rheo_thermal.cpp b/src/RHEO/fix_rheo_thermal.cpp index dbb59f12f7..daa5b347a7 100644 --- a/src/RHEO/fix_rheo_thermal.cpp +++ b/src/RHEO/fix_rheo_thermal.cpp @@ -326,7 +326,7 @@ void FixRHEOThermal::initial_integrate(int /*vflag*/) if (!fix_rheo->shift_flag) return; int i, a; - int *status = atom->status; + int *status = atom->rheo_status; double *energy = atom->esph; double **grade = compute_grad->grade; double **vshift = compute_vshift->vshift; @@ -351,7 +351,7 @@ void FixRHEOThermal::post_integrate() int i, itype; double cvi, Tci, Ti, Li; - int *status = atom->status; + int *status = atom->rheo_status; double *energy = atom->esph; double *temperature = atom->temperature; double *heatflow = atom->heatflow; @@ -466,7 +466,7 @@ void FixRHEOThermal::pre_force(int /*vflag*/) double *energy = atom->esph; double *temperature = atom->temperature; int *type = atom->type; - int *status = atom->status; + int *status = atom->rheo_status; int nlocal = atom->nlocal; int nall = nlocal + atom->nghost; @@ -494,7 +494,7 @@ void FixRHEOThermal::pre_force(int /*vflag*/) void FixRHEOThermal::final_integrate() { - int *status = atom->status; + int *status = atom->rheo_status; double *energy = atom->esph; double *heatflow = atom->heatflow; @@ -520,7 +520,7 @@ void FixRHEOThermal::break_bonds() int m, n, nmax, i, j, melti, meltj; tagint *tag = atom->tag; - int *status = atom->status; + int *status = atom->rheo_status; int **bond_type = atom->bond_type; tagint **bond_atom = atom->bond_atom; int *num_bond = atom->num_bond; @@ -649,7 +649,7 @@ void FixRHEOThermal::create_bonds() tagint *tag = atom->tag; tagint **bond_atom = atom->bond_atom; - int *status = atom->status; + int *status = atom->rheo_status; int **bond_type = atom->bond_type; int *num_bond = atom->num_bond; double **x = atom->x; @@ -754,7 +754,7 @@ int FixRHEOThermal::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int i, j, k, m; - int *status = atom->status; + int *status = atom->rheo_status; double **x = atom->x; m = 0; @@ -773,7 +773,7 @@ int FixRHEOThermal::pack_forward_comm(int n, int *list, double *buf, void FixRHEOThermal::unpack_forward_comm(int n, int first, double *buf) { int i, k, m, last; - int *status = atom->status; + int *status = atom->rheo_status; double **x = atom->x; m = 0; last = first + n; diff --git a/src/RHEO/pair_rheo.cpp b/src/RHEO/pair_rheo.cpp index b9beaf8383..9ebf884b6e 100644 --- a/src/RHEO/pair_rheo.cpp +++ b/src/RHEO/pair_rheo.cpp @@ -110,7 +110,7 @@ void PairRHEO::compute(int eflag, int vflag) double *heatflow = atom->heatflow; double *special_lj = force->special_lj; int *type = atom->type; - int *status = atom->status; + int *status = atom->rheo_status; tagint *tag = atom->tag; double **fp_store, *chi; diff --git a/src/RHEO/pair_rheo_solid.cpp b/src/RHEO/pair_rheo_solid.cpp index 1c8654b3c4..070cabaf86 100644 --- a/src/RHEO/pair_rheo_solid.cpp +++ b/src/RHEO/pair_rheo_solid.cpp @@ -74,7 +74,7 @@ void PairRHEOSolid::compute(int eflag, int vflag) double **v = atom->v; double **f = atom->f; int *type = atom->type; - int *status = atom->status; + int *status = atom->rheo_status; int nlocal = atom->nlocal; int newton_pair = force->newton_pair; double *special_lj = force->special_lj; @@ -223,7 +223,7 @@ void PairRHEOSolid::init_style() if (comm->ghost_velocity == 0) error->all(FLERR,"Pair rheo/solid requires ghost atoms store velocity"); - if (!atom->status_flag) + if (!atom->rheo_status_flag) error->all(FLERR,"Pair rheo/solid requires atom_style rheo"); neighbor->add_request(this); @@ -328,7 +328,7 @@ double PairRHEOSolid::single(int i, int j, int itype, int jtype, double rsq, dou if (rsq > cutsq[itype][jtype]) return 0.0; - int *status = atom->status; + int *status = atom->rheo_status; if (!(status[i] & STATUS_SOLID)) return 0.0; if (!(status[j] & STATUS_SOLID)) return 0.0; diff --git a/src/atom.cpp b/src/atom.cpp index 09aaa4f1d8..9af945367b 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -200,7 +200,7 @@ Atom::Atom(LAMMPS *_lmp) : Pointers(_lmp), atom_style(nullptr), avec(nullptr), a // RHEO package - status = nullptr; + rheo_status = nullptr; conductivity = nullptr; pressure = nullptr; viscosity = nullptr; @@ -538,7 +538,7 @@ void Atom::peratom_create() // RHEO package - add_peratom("status",&status,INT,0); + add_peratom("rheo_status",&rheo_status,INT,0); add_peratom("conductivity",&conductivity,DOUBLE,0); add_peratom("pressure",&pressure,DOUBLE,0); add_peratom("viscosity",&viscosity,DOUBLE,0); @@ -648,7 +648,7 @@ void Atom::set_atomflag_defaults() temperature_flag = heatflow_flag = 0; vfrac_flag = spin_flag = eradius_flag = ervel_flag = erforce_flag = 0; cs_flag = csforce_flag = vforce_flag = ervelforce_flag = etag_flag = 0; - status_flag = conductivity_flag = pressure_flag = viscosity_flag = 0; + rheo_status_flag = conductivity_flag = pressure_flag = viscosity_flag = 0; rho_flag = esph_flag = cv_flag = vest_flag = 0; dpd_flag = edpd_flag = tdpd_flag = 0; sp_flag = 0; @@ -3065,7 +3065,7 @@ void *Atom::extract(const char *name) // RHEO package - if (strcmp(name,"status") == 0) return (void *) status; + if (strcmp(name,"rheo_status") == 0) return (void *) rheo_status; if (strcmp(name,"conductivity") == 0) return (void *) conductivity; if (strcmp(name,"pressure") == 0) return (void *) pressure; if (strcmp(name,"viscosity") == 0) return (void *) viscosity; @@ -3194,7 +3194,7 @@ int Atom::extract_datatype(const char *name) // RHEO package - if (strcmp(name,"status") == 0) return LAMMPS_INT; + if (strcmp(name,"rheo_status") == 0) return LAMMPS_INT; if (strcmp(name,"conductivity") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"pressure") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"viscosity") == 0) return LAMMPS_DOUBLE; diff --git a/src/atom.h b/src/atom.h index 568d78afb2..bd5b352cd0 100644 --- a/src/atom.h +++ b/src/atom.h @@ -157,7 +157,7 @@ class Atom : protected Pointers { // RHEO package - int *status; + int *rheo_status; double *conductivity; double *pressure; double *viscosity; @@ -197,7 +197,7 @@ class Atom : protected Pointers { int temperature_flag, heatflow_flag; int vfrac_flag, spin_flag, eradius_flag, ervel_flag, erforce_flag; int cs_flag, csforce_flag, vforce_flag, ervelforce_flag, etag_flag; - int status_flag, conductivity_flag, pressure_flag, viscosity_flag; + int rheo_status_flag, conductivity_flag, pressure_flag, viscosity_flag; int rho_flag, esph_flag, cv_flag, vest_flag; int dpd_flag, edpd_flag, tdpd_flag; int mesont_flag; diff --git a/src/set.cpp b/src/set.cpp index cd48ba2bfe..93d5068ef3 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -526,7 +526,7 @@ void Set::command(int narg, char **arg) if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "set rheo/status", error); if (utils::strmatch(arg[iarg+1],"^v_")) varparse(arg[iarg+1],1); else ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp); - if (!atom->status_flag) + if (!atom->rheo_status_flag) error->all(FLERR,"Cannot set attribute {} for atom style {}", arg[iarg], atom->get_style()); set(RHEO_STATUS); iarg += 2; @@ -901,7 +901,7 @@ void Set::set(int keyword) else if (keyword == RHEO_STATUS) { if (ivalue != 0 && ivalue != 1) error->one(FLERR,"Invalid value {} in set command for rheo/status", ivalue); - atom->status[i] = ivalue; + atom->rheo_status[i] = ivalue; } else if (keyword == SPH_E) atom->esph[i] = dvalue;