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37 * \brief Implementation of the AdResS method.
42 #include "gromacs/legacyheaders/types/simple.h"
43 #include "gromacs/legacyheaders/typedefs.h"
52 /** \brief calculates the AdResS weight of a particle
54 * \param[in] x position of the particle
55 * \param[in] adresstype type of address weight function
56 * eAdressOff - explicit simulation
57 * eAdressConst - constant weight all over the box
58 * eAdressXSplit - split in x direction with ref as center
59 * eAdressSphere - spherical splitting with ref as center
60 * else - weight = 1 - explicit simulation
61 * \param[in] adressr radius/size of the explicit zone
62 * \param[in] adressw size of the hybrid zone
63 * \param[in] ref center of the explicit zone
64 * for adresstype 1 - unused
65 * for adresstype 2 - only ref[0] is used
66 * \param[in] pbc pbc struct for calculating shortest distance
67 * \param[in] fr the forcerec containing all the parameters
69 * \return weight of the particle
81 /** \brief update the weight of all coarse-grained particles in several charge groups for com vsites
83 * \param[in,out] fplog log file in case of debug
84 * \param[in] cg0 first charge group to update
85 * \param[in] cg1 last+1 charge group to update
86 * \param[in] cgs block containing the cg index
87 * \param[in] x array with all the particle positions
88 * \param[in] fr the forcerec containing all the parameters
89 * \param[in,out] mdatoms the struct containing all the atoms properties
90 * \param[in] pbc for shortest distance in adress_weight
93 update_adress_weights_com(FILE * fplog,
102 /** \brief update the weight of all coarse-grained particles for cog vsites
104 * \param[in] ip contains interaction parameters, in this case the number of constructing atoms n for vsitesn
105 * \param[in] ilist list of interaction types, in this case the virtual site types are what's important
106 * \param[in] x array with all the particle positions
107 * \param[in] fr the forcerec containing all the parameters
108 * \param[in,out] mdatoms the struct containing all the atoms properties
109 * \param[in] pbc for shortest distance in adress_weight
112 update_adress_weights_cog(t_iparams ip[],
119 /** \brief update the weight of all coarse-grained particles in several charge groups for atom vsites
121 * \param[in] cg0 first charge group to update
122 * \param[in] cg1 last+1 charge group to update
123 * \param[in] cgs block containing the cg index
124 * \param[in] x array with all the particle positions
125 * \param[in] fr the forcerec containing all the parameters
126 * \param[in,out] mdatoms the struct containing all the atoms properties
127 * \param[in] pbc for shortest distance in adress_weight
130 update_adress_weights_atom(int cg0,
138 /** \brief update the weight on per atom basis of all coarse-grained particles in several charge groups for atom vsites
140 * \param[in] cg0 first charge group to update
141 * \param[in] cg1 last+1 charge group to update
142 * \param[in] cgs block containing the cg index
143 * \param[in] x array with all the particle positions
144 * \param[in] fr the forcerec containing all the parameters
145 * \param[in,out] mdatoms the struct containing all the atoms properties
146 * \param[in] pbc for shortest distance in adress_weight
149 update_adress_weights_atom_per_atom(int cg0,
157 /** \brief add AdResS IC thermodynamic force to f_novirsum
159 * \param[in] cg0 first charge group to update
160 * \param[in] cg1 last+1 charge group to update
161 * \param[in] cgs block containing the cg index
162 * \param[in] x array with all the particle positions
163 * \param[in,out] f the force array pointing at f_novirsum from sim_util.c
164 * \param[in] fr the forcerec containing all the parameters
165 * \param[in] mdatoms the struct containing all the atoms properties
166 * \param[in] pbc for shortest distance to fr->adress_refs
169 adress_thermo_force(int cg0,
179 /** \brief checks weather a cpu calculates only coarse-grained or explicit interactions
181 * \param[in] n_ex number of explicit particles
182 * \param[in] n_hyb number of hybrid particles
183 * \param[in] n_cg number of coarse-grained particles
184 * \param[in,out] mdatoms the struct containing all the atoms properties
186 void adress_set_kernel_flags(int n_ex, int n_hyb, int n_cg, t_mdatoms * mdatoms);
188 /** \brief looks up if a energy group is explicit
189 * \param[in] fr the forcerec containing all the parameters
190 * \param[in] egp_nr energy group number
191 * \return boolean if explicit or not
193 gmx_bool egp_explicit(t_forcerec * fr, int egp_nr);
195 /** \brief looks up if a energy group is coarse-grained
196 * \param[in] fr the forcerec containing all the parameters
197 * \param[in] egp_nr energy group number
198 * \return boolean if coarse-grained or not
200 gmx_bool egp_coarsegrained(t_forcerec * fr, int egp_nr);