#include <string>
+#include "gromacs/gmxpreprocess/notset.h"
#include "gromacs/topology/atoms.h"
#include "gromacs/topology/block.h"
#include "gromacs/topology/idef.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/real.h"
-#define MAXSLEN 32
-
-struct t_param
+/*! \libinternal \brief
+ * Describes a single parameter in a force field.
+ */
+class InteractionType
{
- int a[MAXATOMLIST]; /* The atom list (eg. bonds: particle */
- /* i = a[0] (ai), j = a[1] (aj)) */
- real c[MAXFORCEPARAM]; /* Force parameters (eg. b0 = c[0]) */
- char s[MAXSLEN]; /* A string (instead of parameters), *
- * read from the .rtp file in pdb2gmx */
- const int &ai() const { return a[0]; }
- int &ai() { return a[0]; }
- const int &aj() const { return a[1]; }
- int &aj() { return a[1]; }
- const int &ak() const { return a[2]; }
- int &ak() { return a[2]; }
- const int &al() const { return a[3]; }
- int &al() { return a[3]; }
- const int &am() const { return a[4]; }
- int &am() { return a[4]; }
-
- const real &c0() const { return c[0]; }
- real &c0() { return c[0]; }
- const real &c1() const { return c[1]; }
- real &c1() { return c[1]; }
- const real &c2() const { return c[2]; }
- real &c2() { return c[2]; }
+ public:
+ //! Constructor that initializes vectors.
+ InteractionType(gmx::ArrayRef<const int> atoms,
+ gmx::ArrayRef<const real> params,
+ const std::string &name = "");
+ /*!@{*/
+ //! Access the individual elements set for the parameter.
+ const int &ai() const;
+ const int &aj() const;
+ const int &ak() const;
+ const int &al() const;
+ const int &am() const;
+
+ const real &c0() const;
+ const real &c1() const;
+ const real &c2() const;
+
+ const std::string &interactionTypeName() const;
+ /*!@}*/
+
+ /*! \brief Renumbers atom Ids.
+ *
+ * Enforces that ai() is less than the opposite terminal atom index,
+ * with the number depending on the interaction type.
+ */
+ void sortAtomIds();
+
+ //! Set single force field parameter.
+ void setForceParameter(int pos, real value);
+
+ //! View on all atoms numbers that are actually set.
+ gmx::ArrayRef<int> atoms() { return atoms_; }
+ //! Const view on all atoms numbers that are actually set.
+ gmx::ArrayRef<const int> atoms() const { return atoms_; }
+ //! View on all of the force field parameters
+ gmx::ArrayRef<const real> forceParam() const { return forceParam_; }
+ //! View on all of the force field parameters
+ gmx::ArrayRef<real> forceParam() { return forceParam_; }
+
+ private:
+ //! Return if we have a bond parameter, means two atoms right now.
+ bool isBond() const { return atoms_.size() == 2; }
+ //! Return if we have an angle parameter, means three atoms right now.
+ bool isAngle() const { return atoms_.size() == 3; }
+ //! Return if we have a dihedral parameter, means four atoms right now.
+ bool isDihedral() const { return atoms_.size() == 4; }
+ //! Return if we have a cmap parameter, means five atoms right now.
+ bool isCmap() const { return atoms_.size() == 5; }
+ //! Enforce that atom id ai() is less than aj().
+ void sortBondAtomIds();
+ //! Enforce that atom id ai() is less than ak(). Does not change aj().
+ void sortAngleAtomIds();
+ /*! \brief Enforce order of atoms in dihedral.
+ *
+ * Changes atom order if needed to enforce that ai() is less than al().
+ * If ai() and al() are swapped, aj() and ak() are swapped as well,
+ * independent of their previous order.
+ */
+ void sortDihedralAtomIds();
+ //! The atom list (eg. bonds: particle, i = atoms[0] (ai), j = atoms[1] (aj))
+ std::vector<int> atoms_;
+ //! Force parameters (eg. b0 = forceParam[0])
+ std::array<real, MAXFORCEPARAM> forceParam_;
+ //! Used with forcefields whose .rtp files name the interaction types (e.g. GROMOS), rather than look them up from the atom names.
+ std::string interactionTypeName_;
};
/*! \libinternal \brief
- * The parameters for a set of interactions of a given
- * (unspecified) type found in the enumeration in ifunc.h.
+ * A set of interactions of a given type
+ * (found in the enumeration in ifunc.h), complete with
+ * atom indices and force field function parameters.
*
* This is used for containing the data obtained from the
* lists of interactions of a given type in a [moleculetype]
* topology file definition.
- *
- * \todo Remove manual memory management.
*/
struct InteractionTypeParameters
{ // NOLINT (clang-analyzer-optin.performance.Padding)
- //! Number of parameters.
- int nr = 0;
- //! Maximum number of parameters.
- int maxnr = 0;
- //! The parameters of the interactions
- t_param *param;
+ //! The different parameters in the system.
+ std::vector<InteractionType> interactionTypes;
//! CMAP grid spacing.
- int cmakeGridSpacing = -1;
+ int cmakeGridSpacing = -1;
//! Number of cmap angles.
- int cmapAngles = -1;
+ int cmapAngles = -1;
//! CMAP grid data.
- std::vector<real> cmap;
+ std::vector<real> cmap;
//! The five atomtypes followed by a number that identifies the type.
- std::vector<int> cmapAtomTypes;
+ std::vector<int> cmapAtomTypes;
+ //! Number of parameters.
+ size_t size() const { return interactionTypes.size(); }
//! Elements in cmap grid data.
- int ncmap() const { return cmap.size(); }
+ int ncmap() const { return cmap.size(); }
//! Number of elements in cmapAtomTypes.
- int nct() const { return cmapAtomTypes.size(); }
+ int nct() const { return cmapAtomTypes.size(); }
};
struct t_excls
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