--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2012,2014,2015,2016,2017 by the GROMACS development team.
+ * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
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+ */
+#ifndef GMX_PBCUTIL_PBC_H
+#define GMX_PBCUTIL_PBC_H
+
+#include <stdio.h>
+
+#include <string>
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/enumerationhelpers.h"
+#include "gromacs/utility/real.h"
+
+struct gmx_domdec_t;
+struct gmx_mtop_t;
+
+//! Enumeration that contains all supported periodic boundary setups.
+enum class PbcType : int
+{
+ Xyz = 0, //!< Periodic boundaries in all dimensions.
+ No = 1, //!< No periodic boundaries.
+ XY = 2, //!< Only two dimensions are periodic.
+ Screw = 3, //!< Screw.
+ Unset = 4, //!< The type of PBC is not set or invalid.
+ Count = 5
+};
+
+//! Names for all values in PBC types enumeration
+extern const gmx::EnumerationArray<PbcType, std::string> c_pbcTypeNames;
+
+/* Maximum number of combinations of single triclinic box vectors
+ * required to shift atoms that are within a brick of the size of
+ * the diagonal of the box to within the maximum cut-off distance.
+ */
+#define MAX_NTRICVEC 12
+
+/*! \brief Structure containing info on periodic boundary conditions */
+typedef struct t_pbc
+{
+ //! The PBC type
+ PbcType pbcType;
+ //! Number of dimensions in which PBC is exerted
+ int ndim_ePBC;
+ /*! \brief Determines how to compute distance vectors.
+ *
+ * Indicator of how to compute distance vectors, depending
+ * on PBC type (depends on pbcType and dimensions with(out) DD)
+ * and the box angles.
+ */
+ int pbcTypeDX;
+ /*! \brief Used for selecting which dimensions to use in PBC.
+ *
+ * In case of 1-D PBC this indicates which dimension is used,
+ * in case of 2-D PBC this indicates the opposite
+ */
+ int dim;
+ //! The simulation box
+ matrix box;
+ //! The lengths of the diagonal of the full box
+ rvec fbox_diag;
+ //! Halve of the above
+ rvec hbox_diag;
+ //! Negative of the above
+ rvec mhbox_diag;
+ //! Maximum allowed cutoff squared for the box and PBC used
+ real max_cutoff2;
+ /*! \brief Number of triclinic shift vectors.
+ *
+ * Number of triclinic shift vectors depends on the skewedness
+ * of the box, that is mostly on the angles. For triclinic boxes
+ * we first take the closest image along each Cartesian dimension
+ * independently. When the resulting distance^2 is larger than
+ * max_cutoff2, up to ntric_vec triclinic shift vectors need to
+ * be tried. Because of the restrictions imposed on the unit-cell
+ * by GROMACS, ntric_vec <= MAX_NTRICVEC = 12.
+ */
+ int ntric_vec;
+ //! The triclinic shift vectors in grid cells. Internal use only.
+ ivec tric_shift[MAX_NTRICVEC];
+ //! The triclinic shift vectors in length units
+ rvec tric_vec[MAX_NTRICVEC];
+} t_pbc;
+
+#define TRICLINIC(box) ((box)[YY][XX] != 0 || (box)[ZZ][XX] != 0 || (box)[ZZ][YY] != 0)
+
+#define NTRICIMG 14
+#define NCUCVERT 24
+#define NCUCEDGE 36
+
+enum
+{
+ ecenterTRIC, /* 0.5*(a+b+c) */
+ ecenterRECT, /* (0.5*a[x],0.5*b[y],0.5*c[z]) */
+ ecenterZERO, /* (0,0,0) */
+ ecenterDEF = ecenterTRIC
+};
+
+/*! \brief Returns the number of dimensions that use pbc
+ *
+ * \param[in] pbcType The periodic boundary condition type
+ * \return the number of dimensions that use pbc, starting at X
+ */
+int numPbcDimensions(PbcType pbcType);
+
+/*! \brief Dump the contents of the pbc structure to the file
+ *
+ * \param[in] fp The file pointer to write to
+ * \param[in] pbc The periodic boundary condition information structure
+ */
+void dump_pbc(FILE* fp, t_pbc* pbc);
+
+/*! \brief Check the box for consistency
+ *
+ * When \p pbcType=PbcTypes::Unset, the type of pbc is guessed from the box matrix.
+ *
+ * \param[in] pbcType The pbc identifier
+ * \param[in] box The box matrix
+ * \return NULL if the box is supported by Gromacs.
+ * Otherwise returns a string with the problem.
+ */
+const char* check_box(PbcType pbcType, const matrix box);
+
+/*! \brief Creates box matrix from edge lengths and angles.
+ *
+ * \param[in,out] box The box matrix
+ * \param[in] vec The edge lengths
+ * \param[in] angleInDegrees The angles
+ */
+void matrix_convert(matrix box, const rvec vec, const rvec angleInDegrees);
+
+/*! \brief Compute the maximum cutoff for the box
+
+ * Returns the square of the maximum cut-off allowed for the box,
+ * taking into account that the grid neighborsearch code and pbc_dx
+ * only check combinations of single box-vector shifts.
+ *
+ * \param[in] pbcType The pbc identifier
+ * \param[in] box The box matrix
+ * \return the maximum cut-off.
+ */
+real max_cutoff2(PbcType pbcType, const matrix box);
+
+/*! \brief Guess PBC type
+ *
+ * Guesses the type of periodic boundary conditions using the box
+ *
+ * \param[in] box The box matrix
+ * \return The pbc type identifier
+ */
+PbcType guessPbcType(const matrix box);
+
+/*! \brief Corrects the box if necessary
+ *
+ * Checks for un-allowed box angles and corrects the box.
+ *
+ * \param[in] fplog File for debug output
+ * \param[in] step The MD step number
+ * \param[in] box The simulation cell
+ * \return TRUE when the box was corrected.
+ */
+gmx_bool correct_box(FILE* fplog, int step, tensor box);
+
+/*! \brief Initiate the periodic boundary condition algorithms.
+ *
+ * pbc_dx will not use pbc and return the normal difference vector
+ * when one or more of the diagonal elements of box are zero.
+ * When \p pbcType=PbcType::Unset, the type of pbc is guessed from the box matrix.
+ *
+ * \param[in,out] pbc The pbc information structure
+ * \param[in] pbcType The PBC identifier
+ * \param[in] box The box tensor
+ */
+void set_pbc(t_pbc* pbc, PbcType pbcType, const matrix box);
+
+/*! \brief Initiate the periodic boundary condition algorithms.
+ *
+ * As set_pbc, but additionally sets that correct distances can
+ * be obtained using (combinations of) single box-vector shifts.
+ * Should be used with pbc_dx_aiuc.
+ * If domdecCells!=NULL pbc is not used for directions
+ * with dd->nc[i]==1 with bSingleDir==TRUE or
+ * with dd->nc[i]<=2 with bSingleDir==FALSE.
+ * Note that when no PBC is required only pbc->pbcType is set,
+ * the rest of the struct will be invalid.
+ *
+ * \param[in,out] pbc The pbc information structure
+ * \param[in] pbcType The PBC identifier
+ * \param[in] domdecCells 3D integer vector describing the number of DD cells
+ * or nullptr if not using DD.
+ * \param[in] bSingleDir TRUE if DD communicates only in one direction along dimensions
+ * \param[in] box The box tensor
+ * \return the pbc structure when pbc operations are required, NULL otherwise.
+ */
+t_pbc* set_pbc_dd(t_pbc* pbc, PbcType pbcType, const ivec domdecCells, gmx_bool bSingleDir, const matrix box);
+
+/*! \brief Compute distance with PBC
+ *
+ * Calculate the correct distance vector from x2 to x1 and put it in dx.
+ * set_pbc must be called before ever calling this routine.
+ *
+ * Note that for triclinic boxes that do not obey the GROMACS unit-cell
+ * restrictions, pbc_dx and pbc_dx_aiuc will not correct for PBC.
+ * \param[in,out] pbc The pbc information structure
+ * \param[in] x1 Coordinates for particle 1
+ * \param[in] x2 Coordinates for particle 2
+ * \param[out] dx Distance vector
+ */
+void pbc_dx(const t_pbc* pbc, const rvec x1, const rvec x2, rvec dx);
+
+/*! \brief Compute distance vector for simple PBC types
+ *
+ * Calculate the correct distance vector from x2 to x1 and put it in dx,
+ * This function can only be used when all atoms are in the rectangular
+ * or triclinic unit-cell.
+ * set_pbc_dd or set_pbc must be called before ever calling this routine.
+ * \param[in,out] pbc The pbc information structure
+ * \param[in] x1 Coordinates for particle 1
+ * \param[in] x2 Coordinates for particle 2
+ * \param[out] dx Distance vector
+ * \return the ishift required to shift x1 at closest distance to x2;
+ * i.e. if 0<=ishift<SHIFTS then x1 - x2 + shift_vec[ishift] = dx
+ * (see calc_shifts below on how to obtain shift_vec)
+ */
+int pbc_dx_aiuc(const t_pbc* pbc, const rvec x1, const rvec x2, rvec dx);
+
+/*! \brief Compute distance with PBC
+ *
+ * As pbc_dx, but for double precision vectors.
+ * set_pbc must be called before ever calling this routine.
+ * \param[in,out] pbc The pbc information structure
+ * \param[in] x1 Coordinates for particle 1
+ * \param[in] x2 Coordinates for particle 2
+ * \param[out] dx Distance vector
+ */
+void pbc_dx_d(const t_pbc* pbc, const dvec x1, const dvec x2, dvec dx);
+
+/*! \brief Computes shift vectors
+ *
+ * This routine calculates ths shift vectors necessary to use the
+ * neighbor searching routine.
+ * \param[in] box The simulation box
+ * \param[out] shift_vec The shifting vectors
+ */
+void calc_shifts(const matrix box, rvec shift_vec[]);
+
+/*! \brief Calculates the center of the box.
+ *
+ * See the description for the enum ecenter above.
+ * \param[in] ecenter Description of center type
+ * \param[in] box The simulation box
+ * \param[out] box_center The center of the box
+ */
+void calc_box_center(int ecenter, const matrix box, rvec box_center);
+
+/*! \brief Calculates the NTRICIMG box images
+ *
+ * \param[in] box The simulation box
+ * \param[out] img The triclinic box images
+ */
+void calc_triclinic_images(const matrix box, rvec img[]);
+
+/*! \brief Calculates the NCUCVERT vertices of a compact unitcell
+ *
+ * \param[in] ecenter The center type
+ * \param[in] box The simulation box
+ * \param[out] vert The vertices
+ */
+void calc_compact_unitcell_vertices(int ecenter, const matrix box, rvec vert[]);
+
+/*! \brief Compute unitcell edges
+ *
+ * \return an array of unitcell edges of length NCUCEDGE*2,
+ * this is an index in vert[], which is calculated by calc_unitcell_vertices.
+ * The index consists of NCUCEDGE pairs of vertex indices.
+ * The index does not change, so it needs to be retrieved only once.
+ */
+int* compact_unitcell_edges();
+
+/*! \brief Put atoms inside the simulations box
+ *
+ * These routines puts ONE or ALL atoms in the box, not caring
+ * about charge groups!
+ * Also works for triclinic cells.
+ *
+ * \param[in] pbcType The pbc type
+ * \param[in] box The simulation box
+ * \param[in,out] x The coordinates of the atoms
+ */
+void put_atoms_in_box(PbcType pbcType, const matrix box, gmx::ArrayRef<gmx::RVec> x);
+
+/*! \brief Parallellizes put_atoms_in_box()
+ *
+ * This wrapper function around put_atoms_in_box() with the ugly manual
+ * workload splitting is needed to avoid silently introducing multithreading
+ * in tools.
+ *
+ * \param[in] pbcType The pbc type
+ * \param[in] box The simulation box
+ * \param[in,out] x The coordinates of the atoms
+ * \param[in] nth number of threads to be used in the given module
+ */
+void put_atoms_in_box_omp(PbcType pbcType, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_unused int nth);
+
+/*! \brief Put atoms inside triclinic box
+ *
+ * This puts ALL atoms in the triclinic unit cell, centered around the
+ * box center as calculated by calc_box_center.
+ * \param[in] ecenter The pbc center type
+ * \param[in] box The simulation box
+ * \param[in,out] x The coordinates of the atoms
+ */
+void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x);
+
+/*! \brief Put atoms inside the unitcell
+ *
+ * This puts ALL atoms at the closest distance for the center of the box
+ * as calculated by calc_box_center.
+ * When \p pbcType=PbcType::Unset, the type of pbc is guessed from the box matrix.
+ *
+ * \param[in] pbcType The pbc type
+ * \param[in] ecenter The pbc center type
+ * \param[in] box The simulation box
+ * \param[in,out] x The coordinates of the atoms
+ */
+void put_atoms_in_compact_unitcell(PbcType pbcType, int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x);
+
+/*! \brief Make all molecules whole by shifting positions
+ *
+ * \param[in] fplog Log file
+ * \param[in] pbcType The PBC type
+ * \param[in] box The simulation box
+ * \param[in] mtop System topology definition
+ * \param[in,out] x The coordinates of the atoms
+ */
+void do_pbc_first_mtop(FILE* fplog, PbcType pbcType, const matrix box, const gmx_mtop_t* mtop, rvec x[]);
+
+/*! \brief Make molecules consisting of multiple charge groups whole by shifting positions
+ *
+ * \param[in] pbcType The PBC type
+ * \param[in] box The simulation box
+ * \param[in] mtop System topology definition
+ * \param[in,out] x The coordinates of the atoms
+ */
+void do_pbc_mtop(PbcType pbcType, const matrix box, const gmx_mtop_t* mtop, rvec x[]);
+
+#endif
biod.pnpi.spb.ru / alexxy / gromacs-colorvec.git / blobdiff