Changeset d067d45 for src/helpers.cpp

Timestamp:

Jul 23, 2009, 1:45:24 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, Candidate_v1.7.0, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

51c910

Parents:

ce5ac3 (diff), 437922 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

git-author:

Frederik Heber <heber@…> (07/23/09 12:34:47)

git-committer:

Frederik Heber <heber@…> (07/23/09 13:45:24)

Message:

Merge branch 'MultipleMolecules'

Conflicts:

molecuilder/src/analyzer.cpp
molecuilder/src/atom.cpp
molecuilder/src/boundary.cpp
molecuilder/src/boundary.hpp
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/datacreator.hpp
molecuilder/src/helpers.cpp
molecuilder/src/joiner.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/molecules.cpp
molecuilder/src/molecules.hpp
molecuilder/src/parser.cpp
molecuilder/src/parser.hpp
molecuilder/src/vector.cpp
molecuilder/src/verbose.cpp

merges:

• analyzer.cpp: all from HEAD, Hessian stuff
• atom.cpp: ostream & operator << (ostream &ost, const atom &a), 2nd param is const
• boundary.cpp: DoSingleStepOutput, VRMLSUffix, HULLEPSILON, Get_center_of_sphere(), Find_next_suitable_point_via_Angle_of_Sphere() and all of tesselation stuff from MultipleMolecules; DoRaster3DOutput, ~BoundaryLineSet(), ~Tesselation() from HEAD; write_raster3d_file with some changes from MultipleMolecules
• boundary.hpp: all from MultipleMolecules
• builder.cpp: all in ParseCommandLineOptions() from MultipleMolecules
• config.cpp: all from HEAD, is stuff from ThermoStat and ConstrainedMD
• datacreator.hpp: all from HEAD, Hessian stuff
• helpers.cpp: all from HEAD, ReAlloc() differed just by indentation
• moleculelist.cpp: all from MultipleMolecules, has to do with introduced molecule centers
• molecules.cpp: all from HEAD, was ConstrainedMD stuff
• molecules.hpp: ConstrainedMD and VerletForceIntegration from HEAD, moleculelist stuff from MultipleMolecules
• parser.cpp: all from HEAD, ColumnCounter is *ColumnCounter there
• parser.hpp: all from HEAD
• vector.cpp: completely from MultipleMolecules (more lines)
• verbose.cpp: all from HEAD

compilation fixes:

• CheckPresenceOfTriangle() from MultipleMolecules
• MoleculeListClass::ListOfMolecules has changed to STL list, hence use insert(), ReturnIndex() and MoleculeListClass::OutputConfigForListOfFragments
• MoleculeListClass::OutputConfigForListOfFragments() had fragmentprefix instead of FRAGMENTPREFIX
• parser.hpp: EnergyMatrix::ParseIndices() declaration was missing

File:

• src/helpers.cpp (modified) (13 diffs)

src/helpers.cpp

@@ -1 +1 @@
 /** \file helpers.cpp
  *
- * Implementation of some auxiliary functions for memory dis-/allocation and so on 
+ * Implementation of some auxiliary functions for memory dis-/allocation and so on
  */
 
@@ -15 +15 @@
 double ask_value(const char *text)
 {
-  double test = 0.1439851348959832147598734598273456723948652983045928346598365;
-  do {
-    cout << Verbose(0) << text;
-    cin >> test;
-  } while (test == 0.1439851348959832147598734598273456723948652983045928346598365);
-  return test;   
+        double test = 0.1439851348959832147598734598273456723948652983045928346598365;
+        do {
+                cout << Verbose(0) << text;
+                cin >> test;
+        } while (test == 0.1439851348959832147598734598273456723948652983045928346598365);
+        return test;
 };
 
@@ -29 +29 @@
 #ifdef HAVE_DEBUG
 void debug_in(const char *output, const char *file, const int line) {
-  if (output) fprintf(stderr,"DEBUG: in %s at line %i: %s\n", file, line, output);
+        if (output) fprintf(stderr,"DEBUG: in %s at line %i: %s\n", file, line, output);
 }
 #else
-void debug_in(const char *output, const char *file, const int line) {}  // print nothing
+void debug_in(const char *output, const char *file, const int line) {}  // print nothing
 #endif
 
@@ -40 +40 @@
  * \return pointer to memory range
  */
-void * Malloc(size_t size, const char* output) 
+void * Malloc(size_t size, const char* output)
 {
-  void *buffer = NULL;
-  buffer = (void *)malloc(size); // alloc
-  if (buffer == NULL)
-    cout << Verbose(0) << "Malloc failed - pointer is NULL: " << output << endl;
-  return(buffer);
+        void *buffer = NULL;
+        buffer = (void *)malloc(size); // alloc
+        if (buffer == NULL)
+                cout << Verbose(0) << "Malloc failed - pointer is NULL: " << output << endl;
+        return(buffer);
 };
 
@@ -54 +54 @@
  * \return pointer to memory range
  */
-void * Calloc(size_t size, const char* output) 
+void * Calloc(size_t size, const char* output)
 {
-  void *buffer = NULL;
-  buffer = (void *)calloc(size, (size_t)0); // alloc
-  if (buffer == NULL)
-    cout << Verbose(0) << "Calloc failed - pointer is NULL: " << output << endl;
-  return(buffer);
+        void *buffer = NULL;
+        buffer = (void *)calloc(size, (size_t)0); // alloc
+        if (buffer == NULL)
+                cout << Verbose(0) << "Calloc failed - pointer is NULL: " << output << endl;
+        return(buffer);
 };
 
@@ -69 +69 @@
  * \return pointer to memory range
  */
-void * ReAlloc(void * OldPointer, size_t size, const char* output) 
+void * ReAlloc(void * OldPointer, size_t size, const char* output)
 {
   void *buffer = NULL;
@@ -86 +86 @@
  * \param *output message if free fails
  */
-void Free(void ** buffer, const char* output) 
+void Free(void ** buffer, const char* output)
 {
-  if (*buffer == NULL) {
-    //cout << Verbose(5) << "Free not necesary: " << output << endl;
-  } else {
-    free(*buffer);
-    *buffer = NULL;
-  }
+        if (*buffer == NULL) {
+                //cout << Verbose(5) << "Free not necesary: " << output << endl;
+        } else {
+                free(*buffer);
+                *buffer = NULL;
+        }
 };
 
@@ -101 +101 @@
  * \return pointer to string array
  */
-char* MallocString(size_t size, const char* output) 
+char* MallocString(size_t size, const char* output)
 {
-  size_t i;
-  char *buffer;
-  buffer = (char *)malloc(sizeof(char) * (size+1)); // alloc
-  if (buffer == NULL)
-    cout << Verbose(0) << output << endl;
-  for (i=size;i--;)  // reset
-    buffer[i] = i % 2 == 0 ? 'p': 'c';
-  buffer[size] = '\0'; // and set length marker on its end
-  return(buffer);
+        size_t i;
+        char *buffer;
+        buffer = (char *)malloc(sizeof(char) * (size+1)); // alloc
+        if (buffer == NULL)
+                cout << Verbose(0) << output << endl;
+        for (i=size;i--;)       // reset
+                buffer[i] = i % 2 == 0 ? 'p': 'c';
+        buffer[size] = '\0'; // and set length marker on its end
+        return(buffer);
 }
 
@@ -121 +121 @@
 void bound(double *b, double lower_bound, double upper_bound)
 {
-  double step = (upper_bound - lower_bound);
-  while (*b >= upper_bound)
-    *b -= step;    
-  while (*b < lower_bound)
-    *b += step;    
-}; 
+        double step = (upper_bound - lower_bound);
+        while (*b >= upper_bound)
+                *b -= step;
+        while (*b < lower_bound)
+                *b += step;
+};
 
 /** Flips two doubles.
@@ -134 +134 @@
 void flip(double *x, double *y)
 {
-  double tmp;
-  tmp = *x;
-  *x = *y;
-  *y = tmp;
+        double tmp;
+        tmp = *x;
+        *x = *y;
+        *y = tmp;
 };
 
@@ -147 +147 @@
 int pot(int base, int n)
 {
-  int res = 1;
-  int j;
-  for (j=n;j--;)
-    res *= base;
-  return res;
+        int res = 1;
+        int j;
+        for (j=n;j--;)
+                res *= base;
+        return res;
 };
 
@@ -161 +161 @@
 char *FixedDigitNumber(const int FragmentNumber, const int digits)
 {
-  char *returnstring;
-  int number = FragmentNumber;
-  int order = 0;
-  while (number != 0) { // determine number of digits needed
-    number = (int)floor(((double)number / 10.));
-    order++;
-    //cout << "Number is " << number << ", order is " << order << "." << endl;
-  }
-  // allocate string
-  returnstring = (char *) Malloc(sizeof(char)*(order+2), "MoleculeListClass::CreateFragmentNumberForOutput: *returnstring");
-  // terminate  and fill string array from end backward
-  returnstring[order] = '\0';
-  number = digits;
-  for (int i=order;i--;) {
-    returnstring[i] = '0' + (char)(number % 10);
-    number = (int)floor(((double)number / 10.));
-  }
-  //cout << returnstring << endl;
-  return returnstring;
+        char *returnstring;
+        int number = FragmentNumber;
+        int order = 0;
+        while (number != 0) { // determine number of digits needed
+                number = (int)floor(((double)number / 10.));
+                order++;
+                //cout << "Number is " << number << ", order is " << order << "." << endl;
+        }
+        // allocate string
+        returnstring = (char *) Malloc(sizeof(char)*(order+2), "FixedDigitNumber: *returnstring");
+        // terminate    and fill string array from end backward
+        returnstring[order] = '\0';
+        number = digits;
+        for (int i=order;i--;) {
+                returnstring[i] = '0' + (char)(number % 10);
+                number = (int)floor(((double)number / 10.));
+        }
+        //cout << returnstring << endl;
+        return returnstring;
 };
 
@@ -186 +186 @@
  * \return true - is a number, false - is not a valid number
  */
-bool IsValidNumber( const char *string) 
+bool IsValidNumber( const char *string)
 {
-  int ptr = 0;
-  if ((string[ptr] == '.') || (string[ptr] == '-')) // number may be negative or start with dot
-    ptr++;
-  if ((string[ptr] >= '0') && (string[ptr] <= '9'))
-    return true;
-  return false;
+        int ptr = 0;
+        if ((string[ptr] == '.') || (string[ptr] == '-')) // number may be negative or start with dot
+                ptr++;
+        if ((string[ptr] >= '0') && (string[ptr] <= '9'))
+                return true;
+        return false;
 };