--- trunk/src/selection/SelectionToken.hpp 2005/12/02 15:38:03 770 +++ trunk/src/selection/SelectionToken.hpp 2012/08/22 02:28:28 1782 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,6 +28,16 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #ifndef SELECTION_TOKEN_HPP @@ -47,7 +48,7 @@ #include #include "utils/any.hpp" -namespace oopse { +namespace OpenMD { /** @@ -102,24 +103,24 @@ namespace oopse { const static int endofline = 9; const static int endofstatement = 10; - const static int command = (1 << 8); - const static int expressionCommand = (1 << 9); // expression command - const static int expression = (1 << 10); /// expression term + const static int command = (1 << 11); + const static int expressionCommand = (1 << 12); // expression command + const static int expression = (1 << 13); /// expression term // generally, the minus sign is used to denote atom ranges // this property is used for the few commands which allow negative integers - const static int negnums = (1 << 11); + const static int negnums = (1 << 14); //expression involves coordinates which will change every frame, such as withins - const static int dynamic = (1 << 12); + const static int dynamic = (1 << 15); // every property is also valid in an expression context - const static int atomproperty = (1 << 12) | expression | negnums; + const static int atomproperty = (1 << 16) | expression | negnums; // every predefined is also valid in an expression context - const static int comparator = (1 << 13) | expression; - const static int predefinedset = (1 << 14) | expression; - const static int embeddedExpression= (1 << 15); // embedded expression - const static int index = (1 << 16) | expression; + const static int comparator = (1 << 17) | expression; + const static int predefinedset = (1 << 18) | expression; + const static int embeddedExpression= (1 << 19); // embedded expression + const static int index = (1 << 20) | expression; // rasmol commands const static int define = command | expressionCommand |1; const static int select = command |expressionCommand |2 ; @@ -130,7 +131,7 @@ namespace oopse { // atom expression operators const static int leftparen = expression | 0; const static int rightparen = expression | 1; - const static int to = expression | 2; + const static int to = expression | 2; const static int opAnd = expression | 3; const static int opOr = expression | 4; const static int opNot = expression | 5; @@ -138,8 +139,9 @@ namespace oopse { const static int asterisk = expression | 7; const static int dot = expression | 8; const static int all = expression | 9 ; - const static int none = expression | 10; - const static int name = expression | 11; + const static int none = expression | 10; + const static int name = expression | 11; + const static int hull = expression | dynamic | 12; // miguel 2005 01 01 // these are used to demark the beginning and end of expressions // they do not exist in the source code, but are emitted by the @@ -149,13 +151,17 @@ namespace oopse { const static int mass = atomproperty | 0; const static int charge = atomproperty | 1; + const static int x = atomproperty | dynamic | 2; + const static int y = atomproperty | dynamic | 3; + const static int z = atomproperty | dynamic | 4; + const static int r = atomproperty | dynamic | 5; - const static int opGT = comparator | 0; - const static int opGE = comparator | 1; - const static int opLE = comparator | 2; - const static int opLT = comparator | 3; - const static int opEQ = comparator | 4; - const static int opNE = comparator | 5; + const static int opGT = comparator | dynamic | 0; + const static int opGE = comparator | dynamic | 1; + const static int opLE = comparator | dynamic | 2; + const static int opLT = comparator | dynamic | 3; + const static int opEQ = comparator | dynamic | 4; + const static int opNE = comparator | dynamic | 5; static Token tokenExpressionBegin; static Token tokenExpressionEnd;