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Review doc: ff
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‎.gitattributes‎

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This file was deleted.

‎.gitignore‎

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# Qt Creator
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CMakeLists.txt.user
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## Tinker9 Project
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# bin
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bin/*
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bin*/*
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# build
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build
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build/*
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build*/*
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# docker
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# Docker
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docker/Dockerfile*
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docker/*.dockerfile
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# macOS
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.DS_Store
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._.DS_Store
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# Example
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example/*.arc
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example/*.dyn
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# Manual
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doc/manual/_build/*
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# Wiki
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*.wiki
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*.wiki/*
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# example
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example/*.arc
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example/*.dyn
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# Manual
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doc/manual/_build/*
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## OS
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# macOS
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.DS_Store
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._.DS_Store
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## Text Editors and IDEs
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# CLion
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.idea
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.idea/*
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# gdb
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*.out
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# Nsight
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Debug/*
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.project
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.settings/*
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# CLion
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.idea
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.idea/*
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# Qt Creator
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CMakeLists.txt.user
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# VSCode
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.vscode
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.vscode/*
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# bin
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bin/*
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bin*/*
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# build
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build
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build/*
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build*/*
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# vi
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*.swp
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# gdb
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*.out

‎doc/doc.h‎

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* \defgroup egv Energy
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* \brief Energy, gradient, virial tensor, and number of interactions
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*
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* \defgroup ff Force Fields
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* \brief Shared modules across force fields calculation.
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*
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* \defgroup bonded Valence
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* \brief Valence potential energies
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*
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* \ingroup bonded
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* \brief Urey-Bradley term
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*
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* \defgroup torsion Torsion
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* \defgroup tors Torsion
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* \ingroup bonded
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* \brief Torsion, improper torsion, improper dihedral, Pi-orbital torsion coupling,
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* stretch-torsion coupling, angle-torsion coupling, and torsion-torsion coupling
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*
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* \defgroup geom Restraint
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* \ingroup bonded
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* \brief Geometric Restraints
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*
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* \defgroup vdw VDW
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* \brief Van der Waals
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*
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* \defgroup fft FFT
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* \brief Fast Fourier Transform
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*/
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/// \defgroup ff Force Fields
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/// \defgroup vdw Van der Waals (VDW)
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/// \ingroup ff
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/// \defgroup charge Partial Charge Electrostatics
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/// \ingroup ff
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/// \defgroup chglj Charge & LJ
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/// \ingroup ff
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/// \defgroup mpole AMOEBA Multipole Electrostatics
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/// \ingroup ff
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/// \defgroup polar AMOEBA Polarization Electrostatics
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/// \ingroup ff
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/// \defgroup mplar AMOEBA Multipole & Polarization
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/// \ingroup ff
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/// \defgroup pme Particle Mesh Ewald
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/// \ingroup ff
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/// \defgroup cflux Charge Flux
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/// \ingroup ff
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/// \defgroup disp HIPPO Dispersion
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/// \ingroup ff
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/// \defgroup repel HIPPO Repulsion
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/// \ingroup ff
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/// \defgroup chgtrn Charge Transfer
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/// \ingroup ff
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/// \defgroup hippompole HIPPO Multipole Electrostatics
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/// \ingroup ff
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/// \defgroup hippopolar HIPPO Polarization
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/// \ingroup ff
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/// \defgroup md Molecular Dynamics
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/// \defgroup mdpq Positions and Velocities
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/// \defgroup async Asynchronous Flow Control
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/// \defgroup rc Resource: Pointer, Allocation, Deallocation, Queue
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/// \defgroup fft Fast Fourier Transform
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/// \defgroup test Unit Tests
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//====================================================================//

‎include/ff/atom.h‎

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#include <istream>
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namespace tinker {
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/// \ingroup ff
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/// \addtogroup ff
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/// \{
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void nData(RcOp);
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/// \ingroup ff
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void massData(RcOp);
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/// \ingroup ff
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void xyzData(RcOp);
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/// \ingroup ff
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/// \brief Update #x, #y, #z by #xpos, #ypos, and #zpos.
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/// Update #x, #y, #z by #xpos, #ypos, and #zpos.
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/// If #xpos etc. are only aliases, return directly.
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void copyPosToXyz();
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/// \ingroup ff
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/// \brief Update #x, #y, #z by #xpos, #ypos, and #zpos.
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/// Update #x, #y, #z by #xpos, #ypos, and #zpos.
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/// If #xpos etc. are only aliases, return directly.
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/// \param refreshNBList If `true`, refresh the neighbor lists by the end.
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/// \param refreshNBList If `true`, refresh the neighbor lists at the end.
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void copyPosToXyz(bool refreshNBList);
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/// \ingroup ff
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/// \brief Finds the geometric center of each molecule and translate any stray
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/// Finds the geometric center of each molecule and translate any stray
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/// molecules back into the periodic box on GPU.
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/// \note
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/// - Updating #x, #y, #z is the goal.
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/// - Tinker uses centers of mass.
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void bounds();
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/// \ingroup ff
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void readFrameCopyinToXyz(std::istream& input, int& done);
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}
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//====================================================================//
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// //
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// Global Variables //
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// //
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//====================================================================//
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namespace tinker {
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/// \ingroup ff
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/// \brief Number of atoms.
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TINKER_EXTERN int padded_n;
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/// \ingroup ff
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/// \brief Number of atoms padded by #WARP_SIZE.
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/// \see WARP_SIZE
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TINKER_EXTERN int n;
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/// \ingroup ff
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/// \brief Number of the trajectory frames.
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TINKER_EXTERN int trajn;
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TINKER_EXTERN int padded_n; /// \brief Number of atoms padded by #WARP_SIZE.
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TINKER_EXTERN int n; /// \brief Number of atoms.
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TINKER_EXTERN int trajn; /// \brief Number of the trajectory frames.
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TINKER_EXTERN real* x; ///< Current coordinates used in energy evaluation and neighbor lists.
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TINKER_EXTERN real* y; ///< Current coordinates used in energy evaluation and neighbor lists.
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TINKER_EXTERN real* z; ///< Current coordinates used in energy evaluation and neighbor lists.
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TINKER_EXTERN real* trajx; ///< Coordinates of all the trajectory frames.
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TINKER_EXTERN real* trajy; ///< Coordinates of all the trajectory frames.
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TINKER_EXTERN real* trajz; ///< Coordinates of all the trajectory frames.
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/// \ingroup ff
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/// \{
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/// \var x
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/// \brief Current coordinates used in energy evaluation and neighbor lists.
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/// \var y
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/// \copydoc x
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/// \var z
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/// \copydoc x
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///
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/// \var trajx
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/// \brief Coordinates of all the trajectory frames.
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/// \var trajy
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/// \copydoc trajx
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/// \var trajz
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/// \copydoc trajx
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///
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/// \var xpos
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/// \brief Coordinates used in integrators.
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/// Coordinates used in integrators.
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/// \note
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/// - New arrays will be allocated only if `sizeof(pos_prec) > sizeof(real)`,
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/// otherwise, they will be aliases of #x, #y, and #z.
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/// - Whenever #xpos, #ypos, #zpos get updated by integrators, barostats etc.,
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/// - Whenever #xpos, #ypos, #zpos get updated by the integrator,
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/// #x, #y, #z must be updated immediately.
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/// \see pos_prec
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/// \see real
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/// \var ypos
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/// \copydoc xpos
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/// \var zpos
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/// \copydoc xpos
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/// \}
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TINKER_EXTERN real *x, *y, *z;
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TINKER_EXTERN real *trajx, *trajy, *trajz;
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TINKER_EXTERN pos_prec *xpos, *ypos, *zpos;
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static_assert(sizeof(pos_prec) >= sizeof(real), "Type pos_prec cannot be shorter than type real.");
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/// \ingroup ff
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/// \brief Atomic mass.
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TINKER_EXTERN double* mass;
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/// \ingroup ff
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/// \brief Inversed atomic mass.
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TINKER_EXTERN double* massinv;
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TINKER_EXTERN double* mass; ///< Atomic mass.
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TINKER_EXTERN double* massinv; ///< Inversed atomic mass.
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/// \}
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}

‎include/ff/elec.h‎

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}
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namespace tinker {
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/// \ingroup ff
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/// \addtogroup ff
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/// \{
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bool useEwald();
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/// \ingroup ff
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void elecData(RcOp);
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}
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//====================================================================//
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// //
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// Global Variables //
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// //
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//====================================================================//
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namespace tinker {
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/// \ingroup ff
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TINKER_EXTERN real electric;
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/// \ingroup ff
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TINKER_EXTERN real dielec;
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/// \}
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}

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