# | Line 4 | Line 4 | |
---|---|---|
4 | #include "Integrator.hpp" | |
5 | #include "Thermo.hpp" | |
6 | #include "ReadWrite.hpp" | |
7 | + | #include "ForceField.hpp" |
8 | + | #include "simError.h" |
9 | ||
8 | – | |
10 | extern "C"{ | |
11 | ||
12 | void v_constrain_a_( double &dt, int &n_atoms, double* mass, | |
# | Line 34 | Line 35 | Symplectic::Symplectic( SimInfo* the_entry_plug ){ | |
35 | isFirst = 1; | |
36 | ||
37 | srInteractions = entry_plug->sr_interactions; | |
37 | – | longRange = entry_plug->longRange; |
38 | nSRI = entry_plug->n_SRI; | |
39 | ||
40 | // give a little love back to the SimInfo object | |
# | Line 120 | Line 120 | void Symplectic::integrate( void ){ | |
120 | double dt2; // half the dt | |
121 | ||
122 | double vx, vy, vz; // the velocities | |
123 | < | double vx2, vy2, vz2; // the square of the velocities |
123 | > | // double vx2, vy2, vz2; // the square of the velocities |
124 | double rx, ry, rz; // the postitions | |
125 | ||
126 | double ji[3]; // the body frame angular momentum | |
# | Line 141 | Line 141 | void Symplectic::integrate( void ){ | |
141 | int sample_n = (int)( sampleTime / dt ); | |
142 | int status_n = (int)( statusTime / dt ); | |
143 | int vel_n = (int)( thermalTime / dt ); | |
144 | + | |
145 | + | ForceFields *ff = entry_plug-> |
146 | ||
147 | Thermo *tStats = new Thermo( entry_plug ); | |
148 | ||
149 | StatWriter* e_out = new StatWriter( entry_plug ); | |
150 | DumpWriter* dump_out = new DumpWriter( entry_plug ); | |
151 | ||
150 | – | |
152 | Atom** atoms = entry_plug->atoms; | |
153 | DirectionalAtom* dAtom; | |
154 | dt2 = 0.5 * dt; | |
155 | ||
156 | // initialize the forces the before the first step | |
157 | ||
158 | + | |
159 | ||
160 | for(i = 0; i < nAtoms; i++){ | |
161 | atoms[i]->zeroForces(); | |
# | Line 492 | Line 494 | void Symplectic::integrate( void ){ | |
494 | atoms[i]->set_vy( vy ); | |
495 | atoms[i]->set_vz( vz ); | |
496 | ||
497 | < | vx2 = vx * vx; |
498 | < | vy2 = vy * vy; |
499 | < | vz2 = vz * vz; |
497 | > | // vx2 = vx * vx; |
498 | > | // vy2 = vy * vy; |
499 | > | // vz2 = vz * vz; |
500 | ||
501 | if( atoms[i]->isDirectional() ){ | |
502 |
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