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#include "Thermo.hpp" |
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#include "ExtendedSystem.hpp" |
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ExtendedSystem::ExtendedSystem( SimInfo &info ) { |
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ExtendedSystem::ExtendedSystem( SimInfo* the_entry_plug ) { |
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// get what information we need from the SimInfo object |
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entry_plug = &info; |
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entry_plug = the_entry_plug; |
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nAtoms = entry_plug->n_atoms; |
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atoms = entry_plug->atoms; |
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nMols = entry_plug->n_mol; |
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// amu*Ang^2*fs^-2/K |
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DirectionalAtom* dAtom; |
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ke_temp = ke * e_convert; |
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NkBT = (double)ndf * kB * targetTemp; |
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// qmass is set in the parameter file |
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zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass ); |
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std::cerr << "ke_temp = " << ke_temp << "\n"; |
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zetaScale = zeta * dt; |
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// perform thermostat scaling on linear velocities and angular momentum |
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for(i = 0; i < nAtoms; i++){ |
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