Merge pull request #104 from peastman/master

Fixed some compilation errors

platforms/cuda/tests/TestCudaCustomNonbondedForce.cpp

@@ -34,6 +34,9 @@
  * This tests all the different force terms in the CUDA implementation of CustomNonbondedForce.
  */
 
+#ifdef WIN32
+  #define _USE_MATH_DEFINES // Needed to get M_PI
+#endif
 #include "openmm/internal/AssertionUtilities.h"
 #include "sfmt/SFMT.h"
 #include "openmm/Context.h"
@@ -42,6 +45,7 @@
 #include "openmm/NonbondedForce.h"
 #include "openmm/System.h"
 #include "openmm/VerletIntegrator.h"
+#include <cmath>
 #include <iostream>
 #include <vector>
 

platforms/opencl/tests/TestOpenCLCustomNonbondedForce.cpp

@@ -34,6 +34,9 @@
  * This tests all the different force terms in the OpenCL implementation of CustomNonbondedForce.
  */
 
+#ifdef WIN32
+  #define _USE_MATH_DEFINES // Needed to get M_PI
+#endif
 #include "openmm/internal/AssertionUtilities.h"
 #include "sfmt/SFMT.h"
 #include "openmm/Context.h"
@@ -42,6 +45,7 @@
 #include "openmm/NonbondedForce.h"
 #include "openmm/System.h"
 #include "openmm/VerletIntegrator.h"
+#include <cmath>
 #include <iostream>
 #include <vector>
 

platforms/reference/tests/TestReferenceCustomNonbondedForce.cpp

@@ -34,6 +34,9 @@
  * This tests all the different force terms in the reference implementation of CustomNonbondedForce.
  */
 
+#ifdef WIN32
+  #define _USE_MATH_DEFINES // Needed to get M_PI
+#endif
 #include "openmm/internal/AssertionUtilities.h"
 #include "sfmt/SFMT.h"
 #include "openmm/Context.h"
@@ -42,6 +45,7 @@
 #include "openmm/NonbondedForce.h"
 #include "openmm/System.h"
 #include "openmm/VerletIntegrator.h"
+#include <cmath>
 #include <iostream>
 #include <set>
 #include <vector>

wrappers/CWrapper_Header.xslt

@@ -17,6 +17,7 @@
 <xsl:variable name="map_property_type_id" select="/GCC_XML/Class[starts-with(@name, 'map&lt;std::basic_string') and not(contains(@name, 'double'))]/@id"/>
 <xsl:variable name="vector_double_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;double')]/@id"/>
 <xsl:variable name="vector_int_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;int')]/@id"/>
+<xsl:variable name="set_int_type_id" select="/GCC_XML/Class[starts-with(@name, 'set&lt;int')]/@id"/>
 
 <!-- Do not generate functions for the following classes -->
 <xsl:variable name="skip_classes" select="('Vec3', 'Kernel', 'Stream', 'KernelImpl', 'StreamImpl', 'KernelFactory', 'StreamFactory')"/>
@@ -50,6 +51,7 @@ typedef struct OpenMM_ParameterArray_struct OpenMM_ParameterArray;
 typedef struct OpenMM_PropertyArray_struct OpenMM_PropertyArray;
 typedef struct OpenMM_DoubleArray_struct OpenMM_DoubleArray;
 typedef struct OpenMM_IntArray_struct OpenMM_IntArray;
+typedef struct OpenMM_IntSet_struct OpenMM_IntSet;
 typedef struct {double x, y, z;} OpenMM_Vec3;
 
 typedef enum {OpenMM_False = 0, OpenMM_True = 1} OpenMM_Boolean;
@@ -103,6 +105,10 @@ extern OPENMM_EXPORT const char* OpenMM_PropertyArray_get(const OpenMM_PropertyA
  <xsl:with-param name="element_type" select="'int'"/>
  <xsl:with-param name="name" select="'OpenMM_IntArray'"/>
 </xsl:call-template>
+<xsl:call-template name="primitive_set">
+ <xsl:with-param name="element_type" select="'int'"/>
+ <xsl:with-param name="name" select="'OpenMM_IntSet'"/>
+</xsl:call-template>
 
 /* These methods need to be handled specially, since their C++ APIs cannot be directly translated to C.
    Unlike the C++ versions, the return value is allocated on the heap, and you must delete it yourself. */
@@ -135,6 +141,17 @@ extern OPENMM_EXPORT void <xsl:value-of select="$name"/>_set(<xsl:value-of selec
 extern OPENMM_EXPORT <xsl:value-of select="concat($element_type, ' ', $name)"/>_get(const <xsl:value-of select="$name"/>* array, int index);
 </xsl:template>
 
+<!-- Print out the declarations for a (Primitive)Set type -->
+<xsl:template name="primitive_set">
+ <xsl:param name="element_type"/>
+ <xsl:param name="name"/>
+/* <xsl:value-of select="$name"/> */
+extern OPENMM_EXPORT <xsl:value-of select="$name"/>* <xsl:value-of select="$name"/>_create();
+extern OPENMM_EXPORT void <xsl:value-of select="$name"/>_destroy(<xsl:value-of select="$name"/>* set);
+extern OPENMM_EXPORT int <xsl:value-of select="$name"/>_getSize(const <xsl:value-of select="$name"/>* set);
+extern OPENMM_EXPORT void <xsl:value-of select="$name"/>_insert(<xsl:value-of select="$name"/>* set, <xsl:value-of select="$element_type"/> value);
+</xsl:template>
+
 <!-- Print out information for a class -->
 <xsl:template name="class">
  <xsl:variable name="class_name" select="@name"/>
@@ -252,6 +269,9 @@ extern OPENMM_EXPORT <xsl:call-template name="wrap_type"><xsl:with-param name="t
   <xsl:when test="$type_id=$vector_int_type_id">
    <xsl:value-of select="'OpenMM_IntArray'"/>
   </xsl:when>
+  <xsl:when test="$type_id=$set_int_type_id">
+   <xsl:value-of select="'OpenMM_IntSet'"/>
+  </xsl:when>
   <xsl:when test="local-name($node)='ReferenceType' or local-name($node)='PointerType'">
    <xsl:call-template name="wrap_type">
     <xsl:with-param name="type_id" select="$node/@type"/>

wrappers/CWrapper_Source.xslt

@@ -19,6 +19,7 @@
 <xsl:variable name="map_property_type_id" select="/GCC_XML/Class[starts-with(@name, 'map&lt;std::basic_string') and not(contains(@name, 'double'))]/@id"/>
 <xsl:variable name="vector_double_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;double')]/@id"/>
 <xsl:variable name="vector_int_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;int')]/@id"/>
+<xsl:variable name="set_int_type_id" select="/GCC_XML/Class[starts-with(@name, 'set&lt;int')]/@id"/>
 <xsl:variable name="newline">
 <xsl:text>
 </xsl:text>
@@ -152,6 +153,10 @@ OPENMM_EXPORT const char* OpenMM_PropertyArray_get(const OpenMM_PropertyArray* a
  <xsl:with-param name="element_type" select="'int'"/>
  <xsl:with-param name="name" select="'OpenMM_IntArray'"/>
 </xsl:call-template>
+<xsl:call-template name="primitive_set">
+ <xsl:with-param name="element_type" select="'int'"/>
+ <xsl:with-param name="name" select="'OpenMM_IntSet'"/>
+</xsl:call-template>
 
 /* These methods need to be handled specially, since their C++ APIs cannot be directly translated to C.
    Unlike the C++ versions, the return value is allocated on the heap, and you must delete it yourself. */
@@ -200,6 +205,25 @@ OPENMM_EXPORT <xsl:value-of select="concat($element_type, ' ')"/> <xsl:value-of
 }
 </xsl:template>
 
+<!-- Print out the definitions for a (Primitive)Set type -->
+<xsl:template name="primitive_set">
+ <xsl:param name="element_type"/>
+ <xsl:param name="name"/>
+/* <xsl:value-of select="$name"/> */
+OPENMM_EXPORT <xsl:value-of select="$name"/>* <xsl:value-of select="$name"/>_create() {
+    return reinterpret_cast&lt;<xsl:value-of select="$name"/>*&gt;(new set&lt;<xsl:value-of select="$element_type"/>&gt;());
+}
+OPENMM_EXPORT void <xsl:value-of select="$name"/>_destroy(<xsl:value-of select="$name"/>* s) {
+    delete reinterpret_cast&lt;set&lt;<xsl:value-of select="$element_type"/>&gt;*&gt;(s);
+}
+OPENMM_EXPORT int <xsl:value-of select="$name"/>_getSize(const <xsl:value-of select="$name"/>* s) {
+    return reinterpret_cast&lt;const set&lt;<xsl:value-of select="$element_type"/>&gt;*&gt;(s)->size();
+}
+OPENMM_EXPORT void <xsl:value-of select="$name"/>_insert(<xsl:value-of select="$name"/>* s, <xsl:value-of select="$element_type"/> value) {
+    reinterpret_cast&lt;set&lt;<xsl:value-of select="$element_type"/>&gt;*&gt;(s)->insert(value);
+}
+</xsl:template>
+
 <!-- Print out information for a class -->
 <xsl:template name="class">
  <xsl:variable name="class_name" select="@name"/>
@@ -355,6 +379,9 @@ OPENMM_EXPORT <xsl:call-template name="wrap_type"><xsl:with-param name="type_id"
   <xsl:when test="$type_id=$vector_int_type_id">
    <xsl:value-of select="'OpenMM_IntArray'"/>
   </xsl:when>
+  <xsl:when test="$type_id=$set_int_type_id">
+   <xsl:value-of select="'OpenMM_IntSet'"/>
+  </xsl:when>
   <xsl:when test="local-name($node)='ReferenceType' or local-name($node)='PointerType'">
    <xsl:call-template name="wrap_type">
     <xsl:with-param name="type_id" select="$node/@type"/>

wrappers/FortranWrapper_Header.xslt

@@ -21,6 +21,7 @@
 <xsl:variable name="map_property_type_id" select="/GCC_XML/Class[starts-with(@name, 'map&lt;std::basic_string') and not(contains(@name, 'double'))]/@id"/>
 <xsl:variable name="vector_double_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;double')]/@id"/>
 <xsl:variable name="vector_int_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;int')]/@id"/>
+<xsl:variable name="set_int_type_id" select="/GCC_XML/Class[starts-with(@name, 'set&lt;int')]/@id"/>
 <xsl:variable name="newline">
 <xsl:text>
 </xsl:text>
@@ -514,6 +515,9 @@ END MODULE OpenMM
   <xsl:when test="$type_id=$vector_int_type_id">
    <xsl:value-of select="concat('type (OpenMM_IntArray) ', $value)"/>
   </xsl:when>
+  <xsl:when test="$type_id=$set_int_type_id">
+   <xsl:value-of select="concat('type (OpenMM_IntSet) ', $value)"/>
+  </xsl:when>
   <xsl:when test="local-name($node)='ReferenceType' or local-name($node)='PointerType'">
    <xsl:call-template name="declare_argument">
     <xsl:with-param name="type_id" select="$node/@type"/>

wrappers/FortranWrapper_Source.xslt

@@ -23,6 +23,7 @@
 <xsl:variable name="map_property_type_id" select="/GCC_XML/Class[starts-with(@name, 'map&lt;std::basic_string') and not(contains(@name, 'double'))]/@id"/>
 <xsl:variable name="vector_double_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;double')]/@id"/>
 <xsl:variable name="vector_int_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;int')]/@id"/>
+<xsl:variable name="set_int_type_id" select="/GCC_XML/Class[starts-with(@name, 'set&lt;int')]/@id"/>
 <xsl:variable name="newline">
 <xsl:text>
 </xsl:text>
@@ -243,6 +244,14 @@ OPENMM_EXPORT const char* OPENMM_PROPERTYARRAY_GET(const OpenMM_PropertyArray* c
  <xsl:with-param name="element_type" select="'double'"/>
  <xsl:with-param name="name" select="'OpenMM_DoubleArray'"/>
 </xsl:call-template>
+<xsl:call-template name="primitive_array">
+ <xsl:with-param name="element_type" select="'int'"/>
+ <xsl:with-param name="name" select="'OpenMM_IntArray'"/>
+</xsl:call-template>
+<xsl:call-template name="primitive_set">
+ <xsl:with-param name="element_type" select="'int'"/>
+ <xsl:with-param name="name" select="'OpenMM_IntSet'"/>
+</xsl:call-template>
 
 /* These methods need to be handled specially, since their C++ APIs cannot be directly translated to C.
    Unlike the C++ versions, the return value is allocated on the heap, and you must delete it yourself. */
@@ -320,6 +329,41 @@ OPENMM_EXPORT void <xsl:value-of select="$name_upper"/>_GET(const <xsl:value-of
 }
 </xsl:template>
 
+<!-- Print out the definitions for a (Primitive)Set type -->
+<xsl:template name="primitive_set">
+ <xsl:param name="element_type"/>
+ <xsl:param name="name"/>
+ <xsl:variable name="name_lower" select="lower-case($name)"/>
+ <xsl:variable name="name_upper" select="upper-case($name)"/>
+/* <xsl:value-of select="$name"/> */
+OPENMM_EXPORT void <xsl:value-of select="$name_lower"/>_create_(<xsl:value-of select="$name"/>*&amp; result) {
+    result = <xsl:value-of select="$name"/>_create();
+}
+OPENMM_EXPORT void <xsl:value-of select="$name_upper"/>_CREATE(<xsl:value-of select="$name"/>*&amp; result) {
+    result = <xsl:value-of select="$name"/>_create();
+}
+OPENMM_EXPORT void <xsl:value-of select="$name_lower"/>_destroy_(<xsl:value-of select="$name"/>*&amp; array) {
+    <xsl:value-of select="$name"/>_destroy(array);
+    array = 0;
+}
+OPENMM_EXPORT void <xsl:value-of select="$name_upper"/>_DESTROY(<xsl:value-of select="$name"/>*&amp; array) {
+    <xsl:value-of select="$name"/>_destroy(array);
+    array = 0;
+}
+OPENMM_EXPORT int <xsl:value-of select="$name_lower"/>_getsize_(const <xsl:value-of select="$name"/>* const&amp; array) {
+    return <xsl:value-of select="$name"/>_getSize(array);
+}
+OPENMM_EXPORT int <xsl:value-of select="$name_upper"/>_GETSIZE(const <xsl:value-of select="$name"/>* const&amp; array) {
+    return <xsl:value-of select="$name"/>_getSize(array);
+}
+OPENMM_EXPORT void <xsl:value-of select="$name_lower"/>_insert_(<xsl:value-of select="$name"/>* const&amp; array, const <xsl:value-of select="$element_type"/>&amp; value) {
+    <xsl:value-of select="$name"/>_insert(array, value);
+}
+OPENMM_EXPORT void <xsl:value-of select="$name_upper"/>_INSERT(<xsl:value-of select="$name"/>* const&amp; array, const <xsl:value-of select="$element_type"/>&amp; value) {
+    <xsl:value-of select="$name"/>_insert(array, value);
+}
+</xsl:template>
+
 <!-- Print out information for a class -->
 <xsl:template name="class">
  <xsl:variable name="class_name" select="@name"/>
@@ -565,6 +609,9 @@ OPENMM_EXPORT <xsl:if test="$has_return">
   <xsl:when test="$type_id=$vector_int_type_id">
    <xsl:value-of select="'OpenMM_IntArray'"/>
   </xsl:when>
+  <xsl:when test="$type_id=$set_int_type_id">
+   <xsl:value-of select="'OpenMM_IntSet'"/>
+  </xsl:when>
   <xsl:when test="local-name($node)='ReferenceType' or local-name($node)='PointerType'">
    <xsl:call-template name="wrap_type">
     <xsl:with-param name="type_id" select="$node/@type"/>
@@ -605,6 +652,7 @@ OPENMM_EXPORT <xsl:if test="$has_return">
   <xsl:when test="$type_id=$vector_double_type_id">1</xsl:when>
   <xsl:when test="$type_id=$vector_int_type_id">1</xsl:when>
   <xsl:when test="$type_id=$vector_string_type_id">1</xsl:when>
+  <xsl:when test="$type_id=$set_int_type_id">1</xsl:when>
   <xsl:when test="local-name($node)='Class' and $node/@context=$openmm_namespace_id">1</xsl:when>
   <xsl:when test="local-name($node)='ReferenceType' or local-name($node)='PointerType'">
    <xsl:call-template name="is_handle_type">