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/* |
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* Copyright (c) 2013 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include <cstdlib> |
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#include <cstdio> |
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#include <cstring> |
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#include <cmath> |
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#include <iostream> |
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#include <string> |
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#include <map> |
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#include <fstream> |
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#include <algorithm> |
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|
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#include "config.h" |
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#include "icosahedralBuilderCmd.h" |
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#include "utils/MoLocator.hpp" |
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#include "utils/Tuple.hpp" |
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#include "brains/Register.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "brains/SimCreator.hpp" |
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#include "io/DumpWriter.hpp" |
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#include "math/Vector3.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "utils/StringUtils.hpp" |
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|
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using namespace OpenMD; |
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using namespace std; |
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|
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// |
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// Create Mackay icosaheron structure. |
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// |
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// Heavily modified from a code created by: Yanting Wang 07/21/2003 |
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// |
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|
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vector<Vector3d> Points; |
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vector<std::pair<int, int> > Edges; |
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vector<tuple3<int, int, int> > Facets; |
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vector<Vector3d> Basis; // Basis vectors of the edges |
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|
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// |
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// function np |
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// |
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// Calculate number of particles on the nth layer. |
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// |
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|
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int np( int n ) { |
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if( n<0 ) return -1; |
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else if( n==0 ) return 1; |
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else if( n==1 ) return 12; |
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else if( n==2 ) return 42; |
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else { |
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int count = 0; |
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count += 12; // edge particles |
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count += (n-1)*30; // side particles |
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for( int i = 1; i <= n-2; i++ ) count += i*20; // body particles |
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return count; |
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} |
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} |
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|
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// |
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// function init |
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// |
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// Initialize some constants. |
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// |
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|
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void init() { |
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|
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Basis.clear(); |
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Edges.clear(); |
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Facets.clear(); |
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Points.clear(); |
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|
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// |
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// Initialize Basis vectors. |
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// |
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const RealType HT = ( sqrt(5.0) + 1.0 ) / 4.0; // half Tau |
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|
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Basis.push_back( Vector3d( HT, 0.0, 0.5 )); |
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Basis.push_back( Vector3d( HT, 0.0, -0.5 )); |
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Basis.push_back( Vector3d( 0.5, HT, 0.0 )); |
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Basis.push_back( Vector3d( -0.5, HT, 0.0 )); |
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Basis.push_back( Vector3d( 0.0, 0.5, HT )); |
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Basis.push_back( Vector3d( 0.0, -0.5, HT )); |
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Basis.push_back( Vector3d( 0.5, -HT, 0.0 )); |
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Basis.push_back( Vector3d( 0.0, 0.5, -HT )); |
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Basis.push_back( Vector3d( -HT, 0.0, 0.5 )); |
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Basis.push_back( Vector3d( 0.0, -0.5, -HT )); |
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Basis.push_back( Vector3d( -HT, 0.0, -0.5 )); |
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Basis.push_back( Vector3d( -0.5, -HT, 0.0 )); |
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|
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// |
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// Initialize 30 edges |
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// |
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|
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Edges.push_back(std::make_pair(0, 1)); |
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Edges.push_back(std::make_pair(0, 2)); |
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Edges.push_back(std::make_pair(0, 4)); |
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Edges.push_back(std::make_pair(0, 5)); |
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Edges.push_back(std::make_pair(0, 6)); |
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|
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Edges.push_back(std::make_pair(10, 3)); |
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Edges.push_back(std::make_pair(10, 7)); |
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Edges.push_back(std::make_pair(10, 8)); |
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Edges.push_back(std::make_pair(10, 9)); |
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Edges.push_back(std::make_pair(10, 11)); |
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|
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Edges.push_back(std::make_pair(1, 2)); |
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Edges.push_back(std::make_pair(1, 6)); |
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Edges.push_back(std::make_pair(1, 7)); |
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Edges.push_back(std::make_pair(1, 9)); |
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|
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Edges.push_back(std::make_pair(8, 3)); |
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Edges.push_back(std::make_pair(8, 4)); |
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Edges.push_back(std::make_pair(8, 5)); |
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Edges.push_back(std::make_pair(8, 11)); |
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|
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Edges.push_back(std::make_pair(2, 3)); |
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Edges.push_back(std::make_pair(2, 4)); |
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Edges.push_back(std::make_pair(2, 7)); |
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|
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Edges.push_back(std::make_pair(11, 5)); |
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Edges.push_back(std::make_pair(11, 6)); |
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Edges.push_back(std::make_pair(11, 9)); |
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|
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Edges.push_back(std::make_pair(6, 5)); |
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Edges.push_back(std::make_pair(6, 9)); |
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|
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Edges.push_back(std::make_pair(3, 4)); |
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Edges.push_back(std::make_pair(3, 7)); |
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|
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Edges.push_back(std::make_pair(7, 9)); |
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|
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Edges.push_back(std::make_pair(5, 4)); |
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|
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// |
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// Initialize 20 facets |
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// |
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|
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Facets.push_back(make_tuple3(0, 1, 2)); |
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Facets.push_back(make_tuple3(0, 2, 4)); |
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Facets.push_back(make_tuple3(0, 4, 5)); |
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Facets.push_back(make_tuple3(0, 5, 6)); |
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Facets.push_back(make_tuple3(0, 1, 6)); |
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|
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Facets.push_back(make_tuple3(10, 3, 7)); |
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Facets.push_back(make_tuple3(10, 3, 8)); |
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Facets.push_back(make_tuple3(10, 8, 11)); |
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Facets.push_back(make_tuple3(10, 9, 11)); |
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Facets.push_back(make_tuple3(10, 7, 9)); |
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|
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Facets.push_back(make_tuple3(1, 2, 7)); |
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Facets.push_back(make_tuple3(1, 7, 9)); |
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Facets.push_back(make_tuple3(1, 6, 9)); |
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|
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Facets.push_back(make_tuple3(8, 5, 11)); |
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Facets.push_back(make_tuple3(8, 4, 5)); |
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Facets.push_back(make_tuple3(8, 3, 4)); |
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|
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Facets.push_back(make_tuple3(2, 3, 7)); |
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Facets.push_back(make_tuple3(2, 3, 4)); |
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|
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Facets.push_back(make_tuple3(11, 5, 6)); |
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Facets.push_back(make_tuple3(11, 6, 9)); |
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} |
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|
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// |
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// function ih |
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// |
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// Create nth layer particles. |
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// The distance between nearest neighbors has the unit length of 1. |
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|
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vector<Vector3d> ih( int n ) { |
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|
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if( n < 0 ) return Points; |
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|
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if( n==0 ) { |
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// center particle only |
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Points.push_back(Vector3d( 0.0, 0.0, 0.0 )); |
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return Points; |
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} |
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|
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// |
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// Generate edge particles |
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// |
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for( vector<Vector3d>::iterator i = Basis.begin(); i != Basis.end(); ++i ) { |
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|
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Points.push_back( (*i) * RealType(n) ); |
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} |
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|
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// |
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// Generate side particles |
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// |
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|
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if( n<2 ) return Points; |
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|
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for( vector<pair<int,int> >::iterator i=Edges.begin(); |
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i != Edges.end(); ++i ) { |
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|
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Vector3d e1 = Basis[ (*i).first ] * RealType(n); |
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Vector3d e2 = Basis[ (*i).second ] * RealType(n); |
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|
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for( int j = 1; j <= n-1; j++ ) { |
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Points.push_back( e1 + (e2-e1) * RealType(j) / RealType(n)); |
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} |
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} |
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|
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// |
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// Generate body particles |
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// |
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|
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if( n<3 ) return Points; |
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|
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for( vector<tuple3<int,int,int> >::iterator i = Facets.begin(); |
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i != Facets.end(); ++i) { |
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|
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Vector3d e1 = Basis[ (*i).first ] * RealType(n); |
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Vector3d e2 = Basis[ (*i).second ] * RealType(n); |
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Vector3d e3 = Basis[ (*i).third ] * RealType(n); |
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|
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for( int j=1; j<=n-2; j++ ) { |
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|
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Vector3d v1 = e1 + (e2-e1) * RealType(j+1) / RealType(n); |
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Vector3d v2 = e1 + (e3-e1) * RealType(j+1) / RealType(n); |
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|
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for( int k=1; k<=j; k++ ) { |
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Points.push_back(v1 + (v2-v1) * RealType(k) / RealType(j+1)); |
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} |
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} |
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} |
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return Points; |
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} |
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|
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|
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void createMdFile(const std::string&oldMdFileName, |
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const std::string&newMdFileName, |
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int nMol) { |
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ifstream oldMdFile; |
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ofstream newMdFile; |
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const int MAXLEN = 65535; |
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char buffer[MAXLEN]; |
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|
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//create new .md file based on old .md file |
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oldMdFile.open(oldMdFileName.c_str()); |
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newMdFile.open(newMdFileName.c_str()); |
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oldMdFile.getline(buffer, MAXLEN); |
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|
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unsigned int i = 0; |
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while (!oldMdFile.eof()) { |
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|
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//correct molecule number |
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if (strstr(buffer, "nMol") != NULL) { |
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sprintf(buffer, "\tnMol = %i;", nMol); |
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newMdFile << buffer << std::endl; |
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} else { |
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newMdFile << buffer << std::endl; |
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} |
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|
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oldMdFile.getline(buffer, MAXLEN); |
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} |
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|
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oldMdFile.close(); |
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newMdFile.close(); |
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} |
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|
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int main(int argc, char *argv []) { |
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|
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gengetopt_args_info args_info; |
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std::string inputFileName; |
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std::string outputFileName; |
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|
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MoLocator* locator; |
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RealType latticeConstant; |
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int nShells; |
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|
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DumpWriter *writer; |
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|
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init(); |
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|
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// Parse Command Line Arguments |
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if (cmdline_parser(argc, argv, &args_info) != 0) |
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exit(1); |
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|
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/* get input file name */ |
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if (args_info.inputs_num) |
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inputFileName = args_info.inputs[0]; |
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else { |
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sprintf(painCave.errMsg, "No input .md file name was specified " |
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"on the command line"); |
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painCave.isFatal = 1; |
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cmdline_parser_print_help(); |
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simError(); |
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} |
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|
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if (args_info.shells_given) { |
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nShells = args_info.shells_arg; |
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if( nShells < 0 ) { |
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sprintf(painCave.errMsg, "icosahedralBuilder: The number of shells\n" |
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"\tmust be greater than or equal to zero."); |
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painCave.isFatal = 1; |
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cmdline_parser_print_help(); |
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simError(); |
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} |
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} else { |
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sprintf(painCave.errMsg, "icosahedralBuilder: The number of shells\n" |
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"\tis required to build a Mackay Icosahedron."); |
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painCave.isFatal = 1; |
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cmdline_parser_print_help(); |
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simError(); |
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} |
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|
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if (args_info.latticeConstant_given) { |
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latticeConstant = args_info.latticeConstant_arg; |
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} else { |
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|
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int count=0; |
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for( int i = 0; i <= nShells; i++ ) count += np( i ); |
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sprintf(painCave.errMsg, "icosahedralBuilder: No lattice constant\n" |
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"\tgiven. Total number of atoms in a Mackay Icosahedron with\n" |
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"\t%d shells is %d.", nShells, count); |
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painCave.isFatal = 1; |
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cmdline_parser_print_help(); |
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simError(); |
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} |
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|
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/* parse md file and set up the system */ |
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SimCreator oldCreator; |
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SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
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|
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Globals* simParams = oldInfo->getSimParams(); |
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|
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//generate the coordinates |
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for( int i = 0; i <= nShells; i++ ) ih( i ); |
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|
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outputFileName = args_info.output_arg; |
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|
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//creat new .md file on fly which corrects the number of molecule |
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|
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createMdFile(inputFileName, outputFileName, Points.size()); |
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|
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if (oldInfo != NULL) |
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delete oldInfo; |
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|
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SimCreator newCreator; |
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SimInfo* NewInfo = newCreator.createSim(outputFileName, false); |
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|
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// Place molecules |
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Molecule* mol; |
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SimInfo::MoleculeIterator mi; |
| 388 |
mol = NewInfo->beginMolecule(mi); |
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|
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int l = 0; |
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|
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locator = new MoLocator(NewInfo->getMoleculeStamp(0), |
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NewInfo->getForceField()); |
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|
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Vector3d boxMax; |
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Vector3d boxMin; |
| 397 |
|
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for (int n = 0; n < Points.size(); n++) { |
| 399 |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
| 400 |
Vector3d location = Points[n] * latticeConstant; |
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Vector3d orientation = Vector3d(0, 0, 1.0); |
| 402 |
|
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if (n == 0) { |
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boxMax = location; |
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boxMin = location; |
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} else { |
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for (int i = 0; i < 3; i++) { |
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boxMax[i] = max(boxMax[i], location[i]); |
| 409 |
boxMin[i] = min(boxMin[i], location[i]); |
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} |
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} |
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|
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locator->placeMol(location, orientation, mol); |
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l++; |
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} |
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|
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Mat3x3d boundingBox; |
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boundingBox(0,0) = 10.0*(boxMax[0] - boxMin[0]); |
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boundingBox(1,1) = 10.0*(boxMax[1] - boxMin[1]); |
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boundingBox(2,2) = 10.0*(boxMax[2] - boxMin[2]); |
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|
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//set Hmat |
| 423 |
NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat( boundingBox ); |
| 424 |
|
| 425 |
//create dumpwriter and write out the coordinates |
| 426 |
writer = new DumpWriter(NewInfo, outputFileName); |
| 427 |
|
| 428 |
if (writer == NULL) { |
| 429 |
sprintf(painCave.errMsg, "Error in creating dumpwriter object "); |
| 430 |
painCave.isFatal = 1; |
| 431 |
simError(); |
| 432 |
} |
| 433 |
|
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writer->writeDump(); |
| 435 |
|
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// deleting the writer will put the closing at the end of the dump file |
| 437 |
|
| 438 |
delete writer; |
| 439 |
|
| 440 |
// cleanup a by calling sim error..... |
| 441 |
sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been " |
| 442 |
"generated.\n", outputFileName.c_str()); |
| 443 |
painCave.isFatal = 0; |
| 444 |
painCave.severity = OPENMD_INFO; |
| 445 |
simError(); |
| 446 |
return 0; |
| 447 |
} |
