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43 * This file contains datatypes and function declarations for internal
49 #ifndef GMX_PULLING_PULL_INTERNAL_H
50 #define GMX_PULLING_PULL_INTERNAL_H
57 #include "gromacs/domdec/localatomset.h"
58 #include "gromacs/mdtypes/pull_params.h"
59 #include "gromacs/utility/gmxmpi.h"
61 /*! \brief Determines up to what local atom count a pull group gets processed single-threaded.
63 * We set this limit to 1 with debug to catch bugs.
64 * On Haswell with GCC 5 the cross-over point is around 400 atoms,
65 * independent of thread count and hyper-threading.
68 static const int c_pullMaxNumLocalAtomsSingleThreaded = 100;
70 static const int c_pullMaxNumLocalAtomsSingleThreaded = 1;
74 enum class PbcType : int;
85 * \brief Pull group data used during pulling
87 struct pull_group_work_t
89 /*! \brief Constructor
91 * \param[in] params The group parameters set by the user
92 * \param[in] atomSet The global to local atom set manager
93 * \param[in] setPbcRefToPrevStepCOM Does this pull group use the COM from the previous step as reference position?
94 * \param[in] maxNumThreads Use either this number of threads of 1 for operations on x and f
96 pull_group_work_t(const t_pull_group& params,
97 gmx::LocalAtomSet atomSet,
98 bool setPbcRefToPrevStepCOM,
101 //! Returns the number of threads to use for local atom operations based on the local atom count
102 int numThreads() const
104 return atomSet.numAtomsLocal() <= c_pullMaxNumLocalAtomsSingleThreaded ? 1 : maxNumThreads;
107 /* Data only modified at initialization */
108 const t_pull_group params; /**< The pull group parameters */
109 const int epgrppbc; /**< The type of pbc for this pull group, see enum above */
110 const int maxNumThreads; /**< The maximum number of threads to use for operations on x and f */
111 bool needToCalcCom; /**< Do we need to calculate the COM? (Not for group 0 or if only used as cylinder group) */
112 std::vector<real> globalWeights; /**< Weights per atom set by the user and/or mass/friction coefficients, if empty all weights are equal */
114 /* Data modified only at init or at domain decomposition */
115 gmx::LocalAtomSet atomSet; /**< Global to local atom set mapper */
116 std::vector<real> localWeights; /**< Weights for the local atoms */
117 std::unique_ptr<gmx::LocalAtomSet> pbcAtomSet; /**< Keeps index of the pbc reference atom.
118 The stored LocalAtomSet consists of exactly one atom when pbc reference atom is required.
119 When no pbc refence atom is used, this pointer shall be null. */
121 /* Data, potentially, changed at every pull call */
122 real mwscale; /**< mass*weight scaling factor 1/sum w m */
123 real wscale; /**< scaling factor for the weights: sum w m/sum w w m */
124 real invtm; /**< inverse total mass of the group: 1/wscale sum w m */
125 std::vector<gmx::BasicVector<double>> mdw; /**< mass*gradient(weight) for atoms */
126 std::vector<double> dv; /**< distance to the other group(s) along vec */
127 dvec x; /**< COM before update */
128 dvec xp; /**< COM after update before constraining */
129 dvec x_prev_step; /**< center of mass of the previous step */
132 /* Struct describing the instantaneous spatial layout of a pull coordinate */
133 struct PullCoordSpatialData
135 dvec dr01; /* The direction vector of group 1 relative to group 0 */
136 dvec dr23; /* The direction vector of group 3 relative to group 2 */
137 dvec dr45; /* The direction vector of group 5 relative to group 4 */
138 dvec vec; /* The pull direction */
139 double vec_len; /* Length of vec for direction-relative */
140 dvec ffrad; /* conversion factor from vec to radial force */
141 double cyl_dev; /* The deviation from the reference position */
142 dvec planevec_m; /* Normal of plane for groups 0, 1, 2, 3 for geometry dihedral */
143 dvec planevec_n; /* Normal of plane for groups 2, 3, 4, 5 for geometry dihedral */
145 double value; /* The current value of the coordinate, units of nm or rad */
148 /* Struct with parameters and force evaluation local data for a pull coordinate */
149 struct pull_coord_work_t
152 pull_coord_work_t(const t_pull_coord& params) :
157 bExternalPotentialProviderHasBeenRegistered(false)
161 const t_pull_coord params; /* Pull coordinate parameters */
163 /* Dynamic pull group 0 for this coordinate with dynamic weights, only present when needed */
164 std::unique_ptr<pull_group_work_t> dynamicGroup0;
166 double value_ref; /* The reference value, usually init+rate*t, units of nm or rad */
168 PullCoordSpatialData spatialData; /* Data defining the current geometry */
170 double scalarForce; /* Scalar force for this cooordinate */
172 /* For external-potential coordinates only, for checking if a provider has been registered */
173 bool bExternalPotentialProviderHasBeenRegistered;
176 /* Struct for storing vectorial forces for a pull coordinate */
177 struct PullCoordVectorForces
179 dvec force01; /* Force due to the pulling/constraining for groups 0, 1 */
180 dvec force23; /* Force for groups 2 and 3 */
181 dvec force45; /* Force for groups 4 and 5 */
184 /* Struct for sums over (local) atoms in a pull group */
187 /* For normal weighting */
188 double sum_wm; /* Sum of weight*mass */
189 double sum_wwm; /* Sum of weight*weight*mass */
190 dvec sum_wmx; /* Sum of weight*mass*x */
191 dvec sum_wmxp; /* Sum of weight*mass*xp */
193 /* For cosine weighting */
194 double sum_cm; /* Sum of cos(x)*mass */
195 double sum_sm; /* Sum of sin(x)*mass */
196 double sum_ccm; /* Sum of cos(x)*cos(x)*mass */
197 double sum_csm; /* Sum of cos(x)*sin(x)*mass */
198 double sum_ssm; /* Sum of sin(x)*sin(x)*mass */
199 double sum_cmp; /* Sum of cos(xp)*sin(xp)*mass */
200 double sum_smp; /* Sum of sin(xp)*sin(xp)*mass */
202 /* Dummy data to ensure adjacent elements in an array are separated
203 * by a cache line size, max 128 bytes.
204 * TODO: Replace this by some automated mechanism.
209 /*! \brief The normal COM buffer needs 3 elements per group */
210 static constexpr int c_comBufferStride = 3;
212 /*! \brief The cylinder buffer needs 9 elements per group */
213 static constexpr int c_cylinderBufferStride = 9;
217 gmx_bool bParticipateAll; /* Do all ranks always participate in pulling? */
218 gmx_bool bParticipate; /* Does our rank participate in pulling? */
220 MPI_Comm mpi_comm_com; /* Communicator for pulling */
222 int nparticipate; /* The number of ranks participating */
223 bool isMasterRank; /* Tells whether our rank is the master rank and thus should add the pull virial */
225 int64_t setup_count; /* The number of decomposition calls */
226 int64_t must_count; /* The last count our rank needed to be part */
228 /* Buffers for parallel reductions */
229 std::vector<gmx::RVec> pbcAtomBuffer; /* COM calculation buffer */
230 std::vector<gmx::BasicVector<double>> comBuffer; /* COM calculation buffer */
231 std::vector<double> cylinderBuffer; /* cylinder ref. groups calculation buffer */
234 // The COM pull force calculation data structure
235 // TODO Convert this into a ForceProvider
238 /* Global parameters */
239 pull_params_t params; /* The pull parameters, from inputrec */
241 gmx_bool bPotential; /* Are there coordinates with potential? */
242 gmx_bool bConstraint; /* Are there constrained coordinates? */
243 gmx_bool bAngle; /* Are there angle geometry coordinates? */
245 PbcType pbcType; /* the boundary conditions */
246 int npbcdim; /* do pbc in dims 0 <= dim < npbcdim */
247 gmx_bool bRefAt; /* do we need reference atoms for a group COM ? */
248 int cosdim; /* dimension for cosine weighting, -1 if none */
249 gmx_bool bCylinder; /* Is group 0 a cylinder group? */
251 /* Parameters + dynamic data for groups */
252 std::vector<pull_group_work_t> group; /* The pull group param and work data */
254 /* Parameters + dynamic data for coordinates */
255 std::vector<pull_coord_work_t> coord; /* The pull group param and work data */
257 /* Global dynamic data */
258 gmx_bool bSetPBCatoms; /* Do we need to set x_pbc for the groups? */
260 std::vector<ComSums> comSums; /* Work array for summing for COM, 1 entry per thread */
262 pull_comm_t comm; /* Communication parameters, communicator and buffers */
264 FILE* out_x; /* Output file for pull data */
265 FILE* out_f; /* Output file for pull data */
267 bool bXOutAverage; /* Output average pull coordinates */
268 bool bFOutAverage; /* Output average pull forces */
270 PullHistory* coordForceHistory; /* Pull coordinate and force history */
272 /* The number of coordinates using an external potential */
273 int numCoordinatesWithExternalPotential;
274 /* Counter for checking external potential registration */
275 int numUnregisteredExternalPotentials;
277 int numExternalPotentialsStillToBeAppliedThisStep;
280 /*! \brief Copies the pull group COM of the previous step from the checkpoint state to the pull state
282 * \param[in] pull The COM pull force calculation data structure
283 * \param[in] state The global state container
285 void setPrevStepPullComFromState(struct pull_t* pull, const t_state* state);
287 /*! \brief Resizes the vector, in the state container, containing the COMs from the previous step
289 * \param[in] state The global state container
290 * \param[in] pull The COM pull force calculation data structure
292 void allocStatePrevStepPullCom(t_state* state, const pull_t* pull);