src/gromacs/mdtypes/group.h

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  37 #ifndef GMX_MDTYPES_GROUP_H
  38 #define GMX_MDTYPES_GROUP_H
  39
  40 #include <vector>
  41
  42 #include "gromacs/math/vectypes.h"
  43 #include "gromacs/utility/basedefinitions.h"
  44 #include "gromacs/utility/real.h"
  45 #include "gromacs/utility/smalloc.h"
  46
  47 struct t_grp_tcstat
  48 {
  49     //! Temperature at half step
  50     real Th = 0;
  51     //! Temperature at full step
  52     real T = 0;
  53     //! Kinetic energy at half step
  54     tensor ekinh = { { 0 } };
  55     //! Kinetic energy at old half step
  56     tensor ekinh_old = { { 0 } };
  57     //! Kinetic energy at full step
  58     tensor ekinf = { { 0 } };
  59     //! Berendsen coupling lambda
  60     real lambda = 0;
  61     //! Scaling factor for NHC- full step
  62     double ekinscalef_nhc = 0;
  63     //! Scaling factor for NHC- half step
  64     double ekinscaleh_nhc = 0;
  65     //! Scaling factor for NHC- velocity
  66     double vscale_nhc = 0;
  67 };
  68
  69 struct t_grp_acc
  70 {
  71     //! Number of atoms in this group
  72     int nat = 0;
  73     //! Mean velocities of home particles
  74     rvec u = { 0 };
  75     //! Previous mean velocities of home particles
  76     rvec uold = { 0 };
  77     //! Mass for topology A
  78     double mA = 0;
  79     //! Mass for topology B
  80     double mB = 0;
  81 };
  82
  83 struct t_cos_acc
  84 {
  85     //! The acceleration for the cosine profile
  86     real cos_accel = 0;
  87     //! The cos momenta of home particles
  88     real mvcos = 0;
  89     //! The velocity of the cosine profile
  90     real vcos = 0;
  91 };
  92
  93 struct gmx_ekindata_t
  94 {
  95     //! Whether non-equilibrium MD is active (ie. constant or cosine acceleration)
  96     gmx_bool bNEMD;
  97     //! The number of T-coupling groups
  98     int ngtc = 0;
  99     //! For size of ekin_work
 100     int nthreads = 0;
 101     //! T-coupling data
 102     std::vector<t_grp_tcstat> tcstat;
 103     //! Allocated locations for *_work members
 104     tensor** ekin_work_alloc = nullptr;
 105     //! Work arrays for tcstat per thread
 106     tensor** ekin_work = nullptr;
 107     //! Work location for dekindl per thread
 108     real** dekindl_work = nullptr;
 109     //! The number of acceleration groups
 110     int ngacc = 0;
 111     //! Acceleration data
 112     std::vector<t_grp_acc> grpstat;
 113     //! overall kinetic energy
 114     tensor ekin = { { 0 } };
 115     //! overall 1/2 step kinetic energy
 116     tensor ekinh = { { 0 } };
 117     //! dEkin/dlambda at half step
 118     real dekindl = 0;
 119     //! dEkin/dlambda at old half step
 120     real dekindl_old = 0;
 121     //! Cosine acceleration data
 122     t_cos_acc cosacc;
 123
 124     ~gmx_ekindata_t();
 125 };
 126
 127 #define GID(igid, jgid, gnr) \
 128     (((igid) < (jgid)) ? ((igid) * (gnr) + (jgid)) : ((jgid) * (gnr) + (igid)))
 129
 130 #endif