src/gromacs/mdlib/vcm.h

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  38 #ifndef GMX_MDLIB_VCM_H
  39 #define GMX_MDLIB_VCM_H
  40
  41 #include <stdio.h>
  42
  43 #include <vector>
  44
  45 #include "gromacs/math/vectypes.h"
  46 #include "gromacs/mdtypes/mdatom.h"
  47 #include "gromacs/utility/basedefinitions.h"
  48 #include "gromacs/utility/real.h"
  49
  50 struct SimulationGroups;
  51 struct t_inputrec;
  52 struct t_mdatoms;
  53
  54 struct t_vcm_thread
  55 {
  56     //! Linear momentum
  57     rvec p = { 0 };
  58     //! Center of mass
  59     rvec x = { 0 };
  60     //! Angular momentum
  61     rvec j = { 0 };
  62     //! Moment of inertia
  63     tensor i = { { 0 } };
  64     //! Mass
  65     real mass = 0;
  66 };
  67
  68 struct t_vcm
  69 {
  70     //! Number of groups
  71     int nr = 0;
  72     //! Size of group arrays
  73     int size = 0;
  74     //! Stride for thread data
  75     int stride = 0;
  76     //! One of the enums above
  77     int mode = 0;
  78     //! The number of dimensions for corr.
  79     int ndim = 0;
  80     //! The time step for COMM removal
  81     real timeStep = 0;
  82     //! Number of degrees of freedom
  83     std::vector<real> group_ndf;
  84     //! Mass per group
  85     std::vector<real> group_mass;
  86     //! Linear momentum per group
  87     std::vector<gmx::RVec> group_p;
  88     //! Linear velocity per group
  89     std::vector<gmx::RVec> group_v;
  90     //! Center of mass per group
  91     std::vector<gmx::RVec> group_x;
  92     //! Angular momentum per group
  93     std::vector<gmx::RVec> group_j;
  94     //! Angular velocity (omega)
  95     std::vector<gmx::RVec> group_w;
  96     //! Moment of inertia per group
  97     tensor* group_i = nullptr;
  98     //! These two are copies to pointers in
  99     std::vector<char*> group_name;
 100     //! Tells whether dimensions are frozen per freeze group
 101     ivec* nFreeze = nullptr;
 102     //! Temporary data per thread and group
 103     std::vector<t_vcm_thread> thread_vcm;
 104
 105     //! Tell whether the integrator conserves momentum
 106     bool integratorConservesMomentum = false;
 107
 108     t_vcm(const SimulationGroups& groups, const t_inputrec& ir);
 109     ~t_vcm();
 110 };
 111
 112 /* print COM removal info to log */
 113 void reportComRemovalInfo(FILE* fp, const t_vcm& vcm);
 114
 115
 116 /* Do a per group center of mass things */
 117 void calc_vcm_grp(const t_mdatoms& md, const rvec x[], const rvec v[], t_vcm* vcm);
 118
 119 /* Set the COM velocity to zero and potentially correct the COM position.
 120  *
 121  * Processes the kinetic energy reduced over MPI before removing COM motion.
 122  * With mode linear, nullptr can be passed for x.
 123  * With acceleration correction nullptr should be passed for x at initialization
 124  * and a pointer to the coordinates at normal MD steps.
 125  * When fplog != nullptr, a warning is printed to fplog with high COM velocity.
 126  */
 127 void process_and_stopcm_grp(FILE* fplog, t_vcm* vcm, const t_mdatoms& mdatoms, rvec x[], rvec v[]);
 128
 129 #endif