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