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Update develop from main (grab hotfixes) #72

Merged
merged 11 commits into from
May 30, 2024
Merged

Update develop from main (grab hotfixes) #72

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8b5351c
Merge pull request #1 from RKLindsey/develop
RKLindsey Apr 7, 2024
5ae3e44
Merge branch 'LindseyLab-umich:main' into main
RKLindsey Apr 8, 2024
3fd18d2
Fix bug in serial_interface.cpp that led to massive memory requiremen…
RKLindsey May 17, 2024
c0ddef5
Merge branch 'main' of github.com:RKLindsey/chimes_calculator-myLLfork
RKLindsey May 17, 2024
961dd2a
Add CN parameter file from transfer learning paper
RKLindsey May 17, 2024
b2d7e25
Merge pull request #25 from RKLindsey/main
RKLindsey May 17, 2024
6683cfc
Merge pull request #71 from rk-lindsey/develop
rk-lindsey May 29, 2024
86ebc9b
Merge branch 'rk-lindsey:main' into main
RKLindsey May 30, 2024
5d3c21e
Hot fix: Add published parameter file
RKLindsey May 30, 2024
97b61c6
Merge pull request #26 from RKLindsey/main
RKLindsey May 30, 2024
3b9e38b
Merge pull request #69 from LindseyLab-umich/main
rk-lindsey May 30, 2024
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25 changes: 19 additions & 6 deletions serial_interface/src/serial_chimes_interface.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -177,11 +177,15 @@ void simulation_system::init(vector<string> & atmtyps, vector<double> & x_in, ve
n_ghost = n_atoms;
n_repl = n_atoms;

sys_atmtyp_indices.resize(0);
sys_atmtyp_indices .resize(0);

sys_x.resize(0);
sys_y.resize(0);
sys_z.resize(0);
sys_x .resize(0);
sys_y .resize(0);
sys_z .resize(0);
sys_parent .resize(0);
sys_rep_parent .resize(0);
atmtyps .erase(atmtyps.begin() + n_atoms, atmtyps.end());
sys_atmtyps .resize(0);

for (int a=0; a<n_atoms; a++)
{
Expand Down Expand Up @@ -529,8 +533,14 @@ void simulation_system::build_layered_system(vector<string> & atmtyps, vector<in
}
}

// Build the layers

// Build the layers. First clear out the associated vectors so you don't run into memory issues on multiple calls:

sys_atmtyps.erase(sys_atmtyps.begin() + n_atoms, sys_atmtyps.end());
sys_x .erase(sys_x .begin() + n_atoms, sys_x .end());
sys_y .erase(sys_y .begin() + n_atoms, sys_y .end());
sys_z .erase(sys_z .begin() + n_atoms, sys_z .end());
sys_parent .erase(sys_parent .begin() + n_atoms, sys_parent .end());

double tmp_x, tmp_y, tmp_z;

for (int i=-n_layers; i<=n_layers; i++) // x
Expand Down Expand Up @@ -567,10 +577,13 @@ void simulation_system::build_layered_system(vector<string> & atmtyps, vector<in
sys_z[n_ghost-1] = hmat[6]*tmp_x + hmat[7]*tmp_y + hmat[8]*tmp_z;

sys_parent.push_back(a);


}
}
}
}

}
void simulation_system::build_neigh_lists(vector<int> & poly_orders, vector<vector<int> > & neighlist_2b, vector<vector<int> > & neighlist_3b, vector<vector<int> > & neighlist_4b, double max_2b_cut, double max_3b_cut, double max_4b_cut)
{
Expand Down
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