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38 #ifndef GMX_MDLIB_VCM_H
39 #define GMX_MDLIB_VCM_H
45 #include "gromacs/math/vectypes.h"
46 #include "gromacs/utility/basedefinitions.h"
47 #include "gromacs/utility/real.h"
49 struct SimulationGroups;
77 //! Size of group arrays
79 //! Stride for thread data
81 //! One of the enums above
83 //! The number of dimensions for corr.
85 //! The time step for COMM removal
87 //! Number of degrees of freedom
88 std::vector<real> group_ndf;
90 std::vector<real> group_mass;
91 //! Linear momentum per group
92 std::vector<gmx::RVec> group_p;
93 //! Linear velocity per group
94 std::vector<gmx::RVec> group_v;
95 //! Center of mass per group
96 std::vector<gmx::RVec> group_x;
97 //! Angular momentum per group
98 std::vector<gmx::RVec> group_j;
99 //! Angular velocity (omega)
100 std::vector<gmx::RVec> group_w;
101 //! Moment of inertia per group
102 tensor* group_i = nullptr;
103 //! These two are copies to pointers in
104 std::vector<char*> group_name;
105 //! Tells whether dimensions are frozen per freeze group
106 ivec* nFreeze = nullptr;
107 //! Temporary data per thread and group
108 std::vector<t_vcm_thread> thread_vcm;
110 //! Tell whether the integrator conserves momentum
111 bool integratorConservesMomentum = false;
113 t_vcm(const SimulationGroups& groups, const t_inputrec& ir);
117 /* print COM removal info to log */
118 void reportComRemovalInfo(FILE* fp, const t_vcm& vcm);
121 /* Do a per group center of mass things */
122 void calc_vcm_grp(const t_mdatoms& md,
123 gmx::ArrayRef<const gmx::RVec> x,
124 gmx::ArrayRef<const gmx::RVec> v,
127 /* Set the COM velocity to zero and potentially correct the COM position.
129 * Processes the kinetic energy reduced over MPI before removing COM motion.
130 * With mode linear, nullptr can be passed for x.
131 * With acceleration correction nullptr should be passed for x at initialization
132 * and a pointer to the coordinates at normal MD steps.
133 * When fplog != nullptr, a warning is printed to fplog with high COM velocity.
135 void process_and_stopcm_grp(FILE* fplog,
137 const t_mdatoms& mdatoms,
138 gmx::ArrayRef<gmx::RVec> x,
139 gmx::ArrayRef<gmx::RVec> v);