| 6 |  | * redistribute this software in source and binary code form, provided | 
| 7 |  | * that the following conditions are met: | 
| 8 |  | * | 
| 9 | < | * 1. Acknowledgement of the program authors must be made in any | 
| 10 | < | *    publication of scientific results based in part on use of the | 
| 11 | < | *    program.  An acceptable form of acknowledgement is citation of | 
| 12 | < | *    the article in which the program was described (Matthew | 
| 13 | < | *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher | 
| 14 | < | *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented | 
| 15 | < | *    Parallel Simulation Engine for Molecular Dynamics," | 
| 16 | < | *    J. Comput. Chem. 26, pp. 252-271 (2005)) | 
| 17 | < | * | 
| 18 | < | * 2. Redistributions of source code must retain the above copyright | 
| 9 | > | * 1. Redistributions of source code must retain the above copyright | 
| 10 |  | *    notice, this list of conditions and the following disclaimer. | 
| 11 |  | * | 
| 12 | < | * 3. Redistributions in binary form must reproduce the above copyright | 
| 12 | > | * 2. Redistributions in binary form must reproduce the above copyright | 
| 13 |  | *    notice, this list of conditions and the following disclaimer in the | 
| 14 |  | *    documentation and/or other materials provided with the | 
| 15 |  | *    distribution. | 
| 28 |  | * arising out of the use of or inability to use software, even if the | 
| 29 |  | * University of Notre Dame has been advised of the possibility of | 
| 30 |  | * such damages. | 
| 31 | + | * | 
| 32 | + | * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your | 
| 33 | + | * research, please cite the appropriate papers when you publish your | 
| 34 | + | * work.  Good starting points are: | 
| 35 | + | * | 
| 36 | + | * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). | 
| 37 | + | * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). | 
| 38 | + | * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). | 
| 39 | + | * [4]  Vardeman & Gezelter, in progress (2009). | 
| 40 |  | */ | 
| 41 |  |  | 
| 42 |  | #ifndef SELECTION_TOKEN_HPP | 
| 47 |  | #include <utility> | 
| 48 |  | #include "utils/any.hpp" | 
| 49 |  |  | 
| 50 | < | namespace oopse { | 
| 50 | > | namespace OpenMD { | 
| 51 |  |  | 
| 52 |  |  | 
| 53 |  | /** | 
| 102 |  | const static int endofline         = 9; | 
| 103 |  | const static int endofstatement    = 10; | 
| 104 |  |  | 
| 105 | < | const static int command           = (1 <<  8); | 
| 106 | < | const static int expressionCommand = (1 <<  9); // expression command | 
| 107 | < | const static int expression        = (1 << 10); /// expression term | 
| 105 | > | const static int command           = (1 <<  11); | 
| 106 | > | const static int expressionCommand = (1 <<  12); // expression command | 
| 107 | > | const static int expression        = (1 << 13); /// expression term | 
| 108 |  |  | 
| 109 |  | // generally, the minus sign is used to denote atom ranges | 
| 110 |  | // this property is used for the few commands which allow negative integers | 
| 111 | < | const static int negnums      = (1 << 11); | 
| 111 | > | const static int negnums      = (1 << 14); | 
| 112 |  |  | 
| 113 |  | //expression involves coordinates which will change every frame, such as withins | 
| 114 | < | const static int dynamic        = (1 << 12); | 
| 114 | > | const static int dynamic        = (1 << 15); | 
| 115 |  |  | 
| 116 |  | // every property is also valid in an expression context | 
| 117 | < | const static int atomproperty      = (1 << 12) | expression | negnums; | 
| 117 | > | const static int atomproperty      = (1 << 16) | expression | negnums; | 
| 118 |  | // every predefined is also valid in an expression context | 
| 119 | < | const static int comparator        = (1 << 13) | expression; | 
| 120 | < | const static int predefinedset     = (1 << 14) | expression; | 
| 121 | < | const  static int embeddedExpression= (1 << 15); // embedded expression | 
| 122 | < | const static int index = (1 << 16) | expression; | 
| 119 | > | const static int comparator        = (1 << 17) | expression; | 
| 120 | > | const static int predefinedset     = (1 << 18) | expression; | 
| 121 | > | const  static int embeddedExpression= (1 << 19); // embedded expression | 
| 122 | > | const static int index = (1 << 20) | expression; | 
| 123 |  | // rasmol commands | 
| 124 |  | const static int define       = command | expressionCommand |1; | 
| 125 |  | const static int select       = command |expressionCommand |2 ; | 
| 130 |  | // atom expression operators | 
| 131 |  | const static int leftparen    = expression |  0; | 
| 132 |  | const static int rightparen   = expression |  1; | 
| 133 | < | const static int to                = expression | 2; | 
| 133 | > | const static int to           = expression |  2; | 
| 134 |  | const static int opAnd        = expression |  3; | 
| 135 |  | const static int opOr         = expression |  4; | 
| 136 |  | const static int opNot        = expression |  5; | 
| 138 |  | const static int asterisk     = expression |  7; | 
| 139 |  | const static int dot          = expression | 8; | 
| 140 |  | const static int all          = expression | 9 ; | 
| 141 | < | const static int none      = expression | 10; | 
| 142 | < | const static int name      = expression | 11; | 
| 141 | > | const static int none         = expression | 10; | 
| 142 | > | const static int name         = expression | 11; | 
| 143 | > | const static int hull         = expression | dynamic | 12; | 
| 144 |  | // miguel 2005 01 01 | 
| 145 |  | // these are used to demark the beginning and end of expressions | 
| 146 |  | // they do not exist in the source code, but are emitted by the | 
| 150 |  |  | 
| 151 |  | const static int mass         = atomproperty | 0; | 
| 152 |  | const static int charge       = atomproperty | 1; | 
| 153 | + | const static int x            = atomproperty | dynamic | 2; | 
| 154 | + | const static int y            = atomproperty | dynamic | 3; | 
| 155 | + | const static int z            = atomproperty | dynamic | 4; | 
| 156 | + | const static int r            = atomproperty | dynamic | 5; | 
| 157 |  |  | 
| 158 | < | const static int opGT         = comparator |  0; | 
| 159 | < | const static int opGE         = comparator |  1; | 
| 160 | < | const static int opLE         = comparator |  2; | 
| 161 | < | const static int opLT         = comparator |  3; | 
| 162 | < | const static int opEQ         = comparator |  4; | 
| 163 | < | const static int opNE         = comparator |  5; | 
| 158 | > | const static int opGT         = comparator |  dynamic | 0; | 
| 159 | > | const static int opGE         = comparator |  dynamic | 1; | 
| 160 | > | const static int opLE         = comparator |  dynamic | 2; | 
| 161 | > | const static int opLT         = comparator |  dynamic | 3; | 
| 162 | > | const static int opEQ         = comparator |  dynamic | 4; | 
| 163 | > | const static int opNE         = comparator |  dynamic | 5; | 
| 164 |  |  | 
| 165 |  | static Token tokenExpressionBegin; | 
| 166 |  | static Token tokenExpressionEnd; |