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/* |
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* Copyright (c) 2005 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. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. 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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* 3. 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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|
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <string.h> |
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|
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#include "io/node_list.h" |
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#include "io/make_nodes.h" |
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#include "utils/simError.h" |
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|
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/* |
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walks to to the top of a stmt_list. Needed when assigning the |
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statment list to a block of code. |
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*/ |
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|
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struct node_tag* walk_to_top( struct node_tag* walk_me ){ |
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|
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while( walk_me->prev_stmt != NULL ){ |
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walk_me = walk_me->prev_stmt; |
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} |
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return walk_me; |
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} |
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|
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/* |
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the next three functions are for creating and initializing the |
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assignment statements. |
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*/ |
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|
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struct node_tag* assign_i( char* lhs, int rhs ){ |
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|
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struct node_tag* the_node; |
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the_node = ( struct node_tag* )malloc( sizeof( node ) ); |
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|
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the_node->type = ASSIGNMENT_STMT; |
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the_node->index = 0; |
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the_node->next_stmt = NULL; |
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the_node->prev_stmt = NULL; |
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the_node->stmt_list = NULL; |
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|
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the_node->the_data.asmt.type = INT_ASSN; |
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the_node->the_data.asmt.identifier = lhs; |
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the_node->the_data.asmt.rhs.i_val = rhs; |
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|
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return the_node; |
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} |
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|
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struct node_tag* assign_d( char* lhs, double rhs ){ |
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|
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struct node_tag* the_node; |
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the_node = ( struct node_tag* )malloc( sizeof( node ) ); |
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|
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the_node->type = ASSIGNMENT_STMT; |
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the_node->index = 0; |
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the_node->next_stmt = NULL; |
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the_node->prev_stmt = NULL; |
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the_node->stmt_list = NULL; |
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|
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the_node->the_data.asmt.type = DOUBLE_ASSN; |
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the_node->the_data.asmt.identifier = lhs; |
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the_node->the_data.asmt.rhs.d_val = rhs; |
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|
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return the_node; |
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} |
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|
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struct node_tag* assign_s( char* lhs, char* rhs ){ |
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|
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struct node_tag* the_node; |
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the_node = ( struct node_tag* )malloc( sizeof( node ) ); |
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|
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the_node->type = ASSIGNMENT_STMT; |
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the_node->index = 0; |
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the_node->next_stmt = NULL; |
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the_node->prev_stmt = NULL; |
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the_node->stmt_list = NULL; |
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|
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the_node->the_data.asmt.type = STR_ASSN; |
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the_node->the_data.asmt.identifier = lhs; |
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the_node->the_data.asmt.rhs.str_ptr = rhs; |
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|
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return the_node; |
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} |
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|
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/* |
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The next function deals with creating and initializing of the |
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members statements used by the bonds, bends, torsions, rigid bodies, |
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and cutoff groups. |
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*/ |
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|
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struct node_tag* members( char* list_str ){ |
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|
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int nTokens, i; |
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char *foo; |
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|
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struct node_tag* the_node; |
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the_node = ( struct node_tag* )malloc( sizeof( node ) ); |
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|
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the_node->type = MEMBERS_STMT; |
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the_node->index = 0; |
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the_node->next_stmt = NULL; |
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the_node->prev_stmt = NULL; |
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the_node->stmt_list = NULL; |
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|
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nTokens = count_tokens(list_str, " ,;\t"); |
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|
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if (nTokens < 1) { |
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yyerror("can't find any members in this members statement"); |
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} |
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|
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the_node->the_data.mbrs.nMembers = nTokens; |
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|
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the_node->the_data.mbrs.memberList = (int *) calloc(nTokens, sizeof(int)); |
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|
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foo = strtok(list_str, " ,;\t"); |
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the_node->the_data.mbrs.memberList[0] = atoi( foo ); |
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|
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for (i = 1; i < nTokens; i++) { |
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foo = strtok(NULL, " ,;\t"); |
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the_node->the_data.mbrs.memberList[i] = atoi( foo ); |
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} |
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|
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return the_node; |
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} |
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|
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/* |
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This function does the C & I of the constraint statements |
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*/ |
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|
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struct node_tag* constraint( char* list_str ){ |
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|
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int nTokens; |
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char *foo; |
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|
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struct node_tag* the_node; |
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the_node = ( struct node_tag* )malloc( sizeof( node ) ); |
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|
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the_node->type = CONSTRAINT_STMT; |
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the_node->index = 0; |
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the_node->next_stmt = NULL; |
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the_node->prev_stmt = NULL; |
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the_node->stmt_list = NULL; |
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|
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nTokens = count_tokens(list_str, " ,;\t"); |
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if (nTokens != 1) { |
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yyerror("wrong number of arguments given in constraint statement"); |
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} |
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|
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foo = strtok(list_str, " ,;\t"); |
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the_node->the_data.cnstr.constraint_val = atof( foo ); |
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|
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return the_node; |
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} |
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|
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/* |
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This function does the C & I for the orientation statements |
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*/ |
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|
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struct node_tag* orientation( char* list_str ){ |
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|
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int nTokens; |
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char *foo; |
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|
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struct node_tag* the_node; |
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the_node = ( struct node_tag* )malloc( sizeof( node ) ); |
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|
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the_node->type = ORIENTATION_STMT; |
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the_node->index = 0; |
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the_node->next_stmt = NULL; |
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the_node->prev_stmt = NULL; |
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the_node->stmt_list = NULL; |
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|
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nTokens = count_tokens(list_str, " ,;\t"); |
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if (nTokens != 3) { |
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yyerror("wrong number of arguments given in orientation"); |
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} |
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|
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foo = strtok(list_str, " ,;\t"); |
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the_node->the_data.ort.phi = atof( foo ); |
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|
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foo = strtok(NULL, " ,;\t"); |
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the_node->the_data.ort.theta = atof( foo ); |
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|
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foo = strtok(NULL, " ,;\t"); |
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the_node->the_data.ort.psi = atof( foo ); |
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|
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return the_node; |
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} |
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|
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/* |
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This function does the C & I for the position statements |
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*/ |
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|
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struct node_tag* position( char* list_str ){ |
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|
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int nTokens; |
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char *foo; |
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|
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struct node_tag* the_node; |
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the_node = ( struct node_tag* )malloc( sizeof( node ) ); |
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|
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the_node->type = POSITION_STMT; |
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the_node->index = 0; |
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the_node->next_stmt = NULL; |
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the_node->prev_stmt = NULL; |
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the_node->stmt_list = NULL; |
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|
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nTokens = count_tokens(list_str, " ,;\t"); |
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if (nTokens != 3) { |
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yyerror("wrong number of arguments given in position"); |
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} |
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|
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foo = strtok(list_str, " ,;\t"); |
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the_node->the_data.pos.x = atof( foo ); |
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|
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foo = strtok(NULL, " ,;\t"); |
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the_node->the_data.pos.y = atof( foo ); |
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|
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foo = strtok(NULL, " ,;\t"); |
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the_node->the_data.pos.z = atof( foo ); |
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|
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|
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return the_node; |
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} |
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|
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/* |
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The following six functions initialize the statement nodes |
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coresponding to the different code block types. |
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*/ |
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|
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struct node_tag* molecule_blk( struct node_tag* stmt_list ){ |
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|
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struct node_tag* the_node; |
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the_node = ( struct node_tag* )malloc( sizeof( node ) ); |
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|
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the_node->type = MOLECULE_HEAD; |
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the_node->index = 0; |
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the_node->next_stmt = NULL; |
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the_node->prev_stmt = NULL; |
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the_node->stmt_list = walk_to_top( stmt_list ); |
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|
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return the_node; |
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} |
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|
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struct node_tag* rigidbody_blk( int index, struct node_tag* stmt_list ){ |
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|
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struct node_tag* the_node; |
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the_node = ( struct node_tag* )malloc( sizeof( node ) ); |
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|
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the_node->type = RIGIDBODY_HEAD; |
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the_node->index = index; |
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the_node->next_stmt = NULL; |
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the_node->prev_stmt = NULL; |
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the_node->stmt_list = walk_to_top( stmt_list ); |
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|
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return the_node; |
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} |
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|
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struct node_tag* cutoffgroup_blk( int index, struct node_tag* stmt_list ){ |
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|
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struct node_tag* the_node; |
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the_node = ( struct node_tag* )malloc( sizeof( node ) ); |
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|
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// The guillotine statement: |
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the_node->type = CUTOFFGROUP_HEAD; |
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the_node->index = index; |
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the_node->next_stmt = NULL; |
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the_node->prev_stmt = NULL; |
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the_node->stmt_list = walk_to_top( stmt_list ); |
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|
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return the_node; |
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} |
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|
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struct node_tag* atom_blk( int index, struct node_tag* stmt_list ){ |
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|
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struct node_tag* the_node; |
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the_node = ( struct node_tag* )malloc( sizeof( node ) ); |
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|
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the_node->type = ATOM_HEAD; |
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the_node->index = index; |
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the_node->next_stmt = NULL; |
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the_node->prev_stmt = NULL; |
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the_node->stmt_list = walk_to_top( stmt_list ); |
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|
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return the_node; |
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} |
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|
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struct node_tag* bond_blk( int index, struct node_tag* stmt_list ){ |
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|
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struct node_tag* the_node; |
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the_node = ( struct node_tag* )malloc( sizeof( node ) ); |
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|
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the_node->type = BOND_HEAD; |
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the_node->index = index; |
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the_node->next_stmt = NULL; |
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the_node->prev_stmt = NULL; |
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the_node->stmt_list = walk_to_top( stmt_list ); |
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|
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return the_node; |
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} |
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|
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struct node_tag* bend_blk( int index, struct node_tag* stmt_list ){ |
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|
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struct node_tag* the_node; |
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the_node = ( struct node_tag* )malloc( sizeof( node ) ); |
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|
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the_node->type = BEND_HEAD; |
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the_node->index = index; |
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the_node->next_stmt = NULL; |
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the_node->prev_stmt = NULL; |
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the_node->stmt_list = walk_to_top( stmt_list ); |
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|
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return the_node; |
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} |
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|
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struct node_tag* torsion_blk( int index, struct node_tag* stmt_list ){ |
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|
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struct node_tag* the_node; |
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the_node = ( struct node_tag* )malloc( sizeof( node ) ); |
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|
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the_node->type = TORSION_HEAD; |
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the_node->index = index; |
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the_node->next_stmt = NULL; |
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the_node->prev_stmt = NULL; |
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the_node->stmt_list = walk_to_top( stmt_list ); |
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|
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return the_node; |
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} |
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|
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struct node_tag* zconstraint_blk( int index, struct node_tag* stmt_list ){ |
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|
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struct node_tag* the_node; |
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the_node = ( struct node_tag* )malloc( sizeof( node ) ); |
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|
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the_node->type = ZCONSTRAINT_HEAD; |
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the_node->index = index; |
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the_node->next_stmt = NULL; |
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the_node->prev_stmt = NULL; |
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the_node->stmt_list = walk_to_top( stmt_list ); |
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|
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return the_node; |
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} |
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|
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struct node_tag* component_blk( struct node_tag* stmt_list ){ |
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|
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struct node_tag* the_node; |
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the_node = ( struct node_tag* )malloc( sizeof( node ) ); |
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|
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the_node->type = COMPONENT_HEAD; |
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the_node->index = 0; |
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the_node->next_stmt = NULL; |
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the_node->prev_stmt = NULL; |
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the_node->stmt_list = walk_to_top( stmt_list ); |
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|
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return the_node; |
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} |
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|
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|
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int count_tokens(char *line, char *delimiters) { |
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/* PURPOSE: RETURN A COUNT OF THE NUMBER OF TOKENS ON THE LINE. */ |
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|
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char *working_line; /* WORKING COPY OF LINE. */ |
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int ntokens; /* NUMBER OF TOKENS FOUND IN LINE. */ |
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char *strtok_ptr; /* POINTER FOR STRTOK. */ |
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|
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strtok_ptr= working_line= strdup(line); |
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|
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ntokens=0; |
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while (strtok(strtok_ptr,delimiters)!=NULL) |
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{ |
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ntokens++; |
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strtok_ptr=NULL; |
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} |
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|
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free(working_line); |
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return(ntokens); |
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} |