baoabmd 1.0.0

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Files changed (50) hide show
  1. package/BaoabMD.js +928 -0
  2. package/CL/cl.h +1979 -0
  3. package/CL/cl_d3d10.h +268 -0
  4. package/CL/cl_d3d11.h +270 -0
  5. package/CL/cl_dx9_media_sharing.h +386 -0
  6. package/CL/cl_dx9_media_sharing_intel.h +18 -0
  7. package/CL/cl_egl.h +187 -0
  8. package/CL/cl_ext.h +4738 -0
  9. package/CL/cl_ext_intel.h +19 -0
  10. package/CL/cl_function_types.h +1199 -0
  11. package/CL/cl_gl.h +421 -0
  12. package/CL/cl_gl_ext.h +18 -0
  13. package/CL/cl_half.h +440 -0
  14. package/CL/cl_icd.h +349 -0
  15. package/CL/cl_layer.h +163 -0
  16. package/CL/cl_platform.h +1414 -0
  17. package/CL/cl_va_api_media_sharing_intel.h +220 -0
  18. package/CL/cl_version.h +85 -0
  19. package/CL/opencl.h +32 -0
  20. package/INSTRUCTIONS.txt +13 -0
  21. package/OpenCL.lib +0 -0
  22. package/binding.gyp +24 -0
  23. package/build/Release/forces.exp +0 -0
  24. package/build/Release/forces.iobj +0 -0
  25. package/build/Release/forces.ipdb +0 -0
  26. package/build/Release/forces.lib +0 -0
  27. package/build/Release/forces.node +0 -0
  28. package/build/Release/forces.pdb +0 -0
  29. package/build/Release/nothing.lib +0 -0
  30. package/build/Release/obj/forces/forces.node.recipe +11 -0
  31. package/build/Release/obj/forces/forces.obj +0 -0
  32. package/build/Release/obj/forces/forces.tlog/CL.command.1.tlog +0 -0
  33. package/build/Release/obj/forces/forces.tlog/CL.read.1.tlog +0 -0
  34. package/build/Release/obj/forces/forces.tlog/CL.write.1.tlog +0 -0
  35. package/build/Release/obj/forces/forces.tlog/Cl.items.tlog +2 -0
  36. package/build/Release/obj/forces/forces.tlog/forces.lastbuildstate +2 -0
  37. package/build/Release/obj/forces/forces.tlog/link.command.1.tlog +0 -0
  38. package/build/Release/obj/forces/forces.tlog/link.read.1.tlog +0 -0
  39. package/build/Release/obj/forces/forces.tlog/link.secondary.1.tlog +5 -0
  40. package/build/Release/obj/forces/forces.tlog/link.write.1.tlog +0 -0
  41. package/build/Release/obj/forces/win_delay_load_hook.obj +0 -0
  42. package/build/binding.sln +39 -0
  43. package/build/forces.vcxproj +156 -0
  44. package/build/forces.vcxproj.filters +46 -0
  45. package/extra xyz files/traj_GB1-10000s.xyz +451900 -0
  46. package/forces.cpp +194 -0
  47. package/package.json +26 -0
  48. package/pdb/1UBQ.pdb +970 -0
  49. package/pdb/1YRF.pdb +1467 -0
  50. package/pdb/input.pdb +4521 -0
@@ -0,0 +1,220 @@
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+ /*******************************************************************************
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+ * Copyright (c) 2008-2026 The Khronos Group Inc.
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+ *
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+ * Licensed under the Apache License, Version 2.0 (the "License");
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+ * you may not use this file except in compliance with the License.
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+ * You may obtain a copy of the License at
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+ *
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+ * http://www.apache.org/licenses/LICENSE-2.0
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+ *
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+ * Unless required by applicable law or agreed to in writing, software
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+ * distributed under the License is distributed on an "AS IS" BASIS,
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+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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+ * See the License for the specific language governing permissions and
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+ * limitations under the License.
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+ ******************************************************************************/
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+
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+ #ifndef OPENCL_CL_VA_API_MEDIA_SHARING_INTEL_H_
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+ #define OPENCL_CL_VA_API_MEDIA_SHARING_INTEL_H_
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+
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+ /*
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+ ** This header is generated from the Khronos OpenCL XML API Registry.
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+ */
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+
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+ #include <va/va.h>
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+
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+ #include <CL/cl.h>
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+
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+ /* CL_NO_PROTOTYPES implies CL_NO_EXTENSION_PROTOTYPES: */
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+ #if defined(CL_NO_PROTOTYPES) && !defined(CL_NO_EXTENSION_PROTOTYPES)
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+ #define CL_NO_EXTENSION_PROTOTYPES
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+ #endif
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+
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+ /* CL_NO_EXTENSION_PROTOTYPES implies
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+ CL_NO_ICD_DISPATCH_EXTENSION_PROTOTYPES and
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+ CL_NO_NON_ICD_DISPATCH_EXTENSION_PROTOTYPES: */
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+ #if defined(CL_NO_EXTENSION_PROTOTYPES) && \
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+ !defined(CL_NO_ICD_DISPATCH_EXTENSION_PROTOTYPES)
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+ #define CL_NO_ICD_DISPATCH_EXTENSION_PROTOTYPES
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+ #endif
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+ #if defined(CL_NO_EXTENSION_PROTOTYPES) && \
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+ !defined(CL_NO_NON_ICD_DISPATCH_EXTENSION_PROTOTYPES)
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+ #define CL_NO_NON_ICD_DISPATCH_EXTENSION_PROTOTYPES
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+ #endif
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+
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+ #ifdef __cplusplus
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+ extern "C" {
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+ #endif
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+
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+ /***************************************************************
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+ * cl_intel_sharing_format_query_va_api
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+ ***************************************************************/
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+ #define cl_intel_sharing_format_query_va_api 1
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+ #define CL_INTEL_SHARING_FORMAT_QUERY_VA_API_EXTENSION_NAME \
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+ "cl_intel_sharing_format_query_va_api"
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+
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+
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+ #define CL_INTEL_SHARING_FORMAT_QUERY_VA_API_EXTENSION_VERSION CL_MAKE_VERSION(0, 0, 0)
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+
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+ /* when cl_intel_va_api_media_sharing is supported */
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+
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+ typedef cl_int CL_API_CALL
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+ clGetSupportedVA_APIMediaSurfaceFormatsINTEL_t(
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+ cl_context context,
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+ cl_mem_flags flags,
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+ cl_mem_object_type image_type,
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+ cl_uint plane,
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+ cl_uint num_entries,
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+ VAImageFormat* va_api_formats,
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+ cl_uint* num_surface_formats);
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+
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+ typedef clGetSupportedVA_APIMediaSurfaceFormatsINTEL_t *
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+ clGetSupportedVA_APIMediaSurfaceFormatsINTEL_fn ;
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+
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+ #if !defined(CL_NO_NON_ICD_DISPATCH_EXTENSION_PROTOTYPES)
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+
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+ extern CL_API_ENTRY cl_int CL_API_CALL
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+ clGetSupportedVA_APIMediaSurfaceFormatsINTEL(
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+ cl_context context,
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+ cl_mem_flags flags,
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+ cl_mem_object_type image_type,
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+ cl_uint plane,
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+ cl_uint num_entries,
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+ VAImageFormat* va_api_formats,
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+ cl_uint* num_surface_formats) ;
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+
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+ #endif /* !defined(CL_NO_NON_ICD_DISPATCH_EXTENSION_PROTOTYPES) */
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+
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+ /***************************************************************
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+ * cl_intel_va_api_media_sharing
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+ ***************************************************************/
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+ #define cl_intel_va_api_media_sharing 1
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+ #define CL_INTEL_VA_API_MEDIA_SHARING_EXTENSION_NAME \
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+ "cl_intel_va_api_media_sharing"
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+
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+
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+ #define CL_INTEL_VA_API_MEDIA_SHARING_EXTENSION_VERSION CL_MAKE_VERSION(0, 0, 0)
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+
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+ typedef cl_uint cl_va_api_device_source_intel;
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+ typedef cl_uint cl_va_api_device_set_intel;
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+
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+ /* Error codes */
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+ #define CL_INVALID_VA_API_MEDIA_ADAPTER_INTEL -1098
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+ #define CL_INVALID_VA_API_MEDIA_SURFACE_INTEL -1099
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+ #define CL_VA_API_MEDIA_SURFACE_ALREADY_ACQUIRED_INTEL -1100
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+ #define CL_VA_API_MEDIA_SURFACE_NOT_ACQUIRED_INTEL -1101
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+
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+ /* cl_va_api_device_source_intel */
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+ #define CL_VA_API_DISPLAY_INTEL 0x4094
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+
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+ /* cl_va_api_device_set_intel */
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+ #define CL_PREFERRED_DEVICES_FOR_VA_API_INTEL 0x4095
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+ #define CL_ALL_DEVICES_FOR_VA_API_INTEL 0x4096
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+
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+ /* cl_context_info */
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+ #define CL_CONTEXT_VA_API_DISPLAY_INTEL 0x4097
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+
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+ /* cl_mem_info */
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+ #define CL_MEM_VA_API_MEDIA_SURFACE_INTEL 0x4098
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+
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+ /* cl_image_info */
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+ #define CL_IMAGE_VA_API_PLANE_INTEL 0x4099
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+
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+ /* cl_command_type */
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+ #define CL_COMMAND_ACQUIRE_VA_API_MEDIA_SURFACES_INTEL 0x409A
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+ #define CL_COMMAND_RELEASE_VA_API_MEDIA_SURFACES_INTEL 0x409B
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+
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+
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+ typedef cl_int CL_API_CALL
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+ clGetDeviceIDsFromVA_APIMediaAdapterINTEL_t(
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+ cl_platform_id platform,
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+ cl_va_api_device_source_intel media_adapter_type,
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+ void* media_adapter,
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+ cl_va_api_device_set_intel media_adapter_set,
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+ cl_uint num_entries,
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+ cl_device_id* devices,
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+ cl_uint* num_devices);
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+
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+ typedef clGetDeviceIDsFromVA_APIMediaAdapterINTEL_t *
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+ clGetDeviceIDsFromVA_APIMediaAdapterINTEL_fn CL_API_SUFFIX__VERSION_1_2;
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+
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+ typedef cl_mem CL_API_CALL
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+ clCreateFromVA_APIMediaSurfaceINTEL_t(
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+ cl_context context,
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+ cl_mem_flags flags,
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+ VASurfaceID* surface,
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+ cl_uint plane,
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+ cl_int* errcode_ret);
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+
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+ typedef clCreateFromVA_APIMediaSurfaceINTEL_t *
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+ clCreateFromVA_APIMediaSurfaceINTEL_fn CL_API_SUFFIX__VERSION_1_2;
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+
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+ typedef cl_int CL_API_CALL
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+ clEnqueueAcquireVA_APIMediaSurfacesINTEL_t(
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+ cl_command_queue command_queue,
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+ cl_uint num_objects,
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+ const cl_mem* mem_objects,
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+ cl_uint num_events_in_wait_list,
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+ const cl_event* event_wait_list,
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+ cl_event* event);
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+
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+ typedef clEnqueueAcquireVA_APIMediaSurfacesINTEL_t *
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+ clEnqueueAcquireVA_APIMediaSurfacesINTEL_fn CL_API_SUFFIX__VERSION_1_2;
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+
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+ typedef cl_int CL_API_CALL
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+ clEnqueueReleaseVA_APIMediaSurfacesINTEL_t(
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+ cl_command_queue command_queue,
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+ cl_uint num_objects,
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+ const cl_mem* mem_objects,
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+ cl_uint num_events_in_wait_list,
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+ const cl_event* event_wait_list,
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+ cl_event* event);
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+
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+ typedef clEnqueueReleaseVA_APIMediaSurfacesINTEL_t *
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+ clEnqueueReleaseVA_APIMediaSurfacesINTEL_fn CL_API_SUFFIX__VERSION_1_2;
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+
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+ #if !defined(CL_NO_NON_ICD_DISPATCH_EXTENSION_PROTOTYPES)
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+
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+ extern CL_API_ENTRY cl_int CL_API_CALL
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+ clGetDeviceIDsFromVA_APIMediaAdapterINTEL(
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+ cl_platform_id platform,
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+ cl_va_api_device_source_intel media_adapter_type,
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+ void* media_adapter,
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+ cl_va_api_device_set_intel media_adapter_set,
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+ cl_uint num_entries,
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+ cl_device_id* devices,
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+ cl_uint* num_devices) CL_API_SUFFIX__VERSION_1_2;
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+
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+ extern CL_API_ENTRY cl_mem CL_API_CALL
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+ clCreateFromVA_APIMediaSurfaceINTEL(
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+ cl_context context,
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+ cl_mem_flags flags,
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+ VASurfaceID* surface,
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+ cl_uint plane,
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+ cl_int* errcode_ret) CL_API_SUFFIX__VERSION_1_2;
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+
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+ extern CL_API_ENTRY cl_int CL_API_CALL
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+ clEnqueueAcquireVA_APIMediaSurfacesINTEL(
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+ cl_command_queue command_queue,
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+ cl_uint num_objects,
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+ const cl_mem* mem_objects,
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+ cl_uint num_events_in_wait_list,
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+ const cl_event* event_wait_list,
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+ cl_event* event) CL_API_SUFFIX__VERSION_1_2;
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+
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+ extern CL_API_ENTRY cl_int CL_API_CALL
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+ clEnqueueReleaseVA_APIMediaSurfacesINTEL(
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+ cl_command_queue command_queue,
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+ cl_uint num_objects,
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+ const cl_mem* mem_objects,
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+ cl_uint num_events_in_wait_list,
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+ const cl_event* event_wait_list,
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+ cl_event* event) CL_API_SUFFIX__VERSION_1_2;
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+
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+ #endif /* !defined(CL_NO_NON_ICD_DISPATCH_EXTENSION_PROTOTYPES) */
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+
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+ #ifdef __cplusplus
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+ }
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+ #endif
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+
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+ #endif /* OPENCL_CL_VA_API_MEDIA_SHARING_INTEL_H_ */
@@ -0,0 +1,85 @@
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+ /*******************************************************************************
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+ * Copyright (c) 2018-2026 The Khronos Group Inc.
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+ *
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+ * Licensed under the Apache License, Version 2.0 (the "License");
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+ * you may not use this file except in compliance with the License.
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+ * You may obtain a copy of the License at
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+ *
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+ * http://www.apache.org/licenses/LICENSE-2.0
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+ *
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+ * Unless required by applicable law or agreed to in writing, software
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+ * distributed under the License is distributed on an "AS IS" BASIS,
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+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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+ * See the License for the specific language governing permissions and
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+ * limitations under the License.
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+ ******************************************************************************/
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+
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+ #ifndef __CL_VERSION_H
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+ #define __CL_VERSION_H
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+
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+ /* Detect which version to target */
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+ #if !defined(CL_TARGET_OPENCL_VERSION)
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+ #pragma message("cl_version.h: CL_TARGET_OPENCL_VERSION is not defined. Defaulting to 310 (OpenCL 3.1)")
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+ #define CL_TARGET_OPENCL_VERSION 310
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+ #endif
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+ #if CL_TARGET_OPENCL_VERSION != 100 && \
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+ CL_TARGET_OPENCL_VERSION != 110 && \
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+ CL_TARGET_OPENCL_VERSION != 120 && \
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+ CL_TARGET_OPENCL_VERSION != 200 && \
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+ CL_TARGET_OPENCL_VERSION != 210 && \
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+ CL_TARGET_OPENCL_VERSION != 220 && \
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+ CL_TARGET_OPENCL_VERSION != 300 && \
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+ CL_TARGET_OPENCL_VERSION != 310
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+ #pragma message("cl_version: CL_TARGET_OPENCL_VERSION is not a valid value (100, 110, 120, 200, 210, 220, 300, 310). Defaulting to 310 (OpenCL 3.1)")
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+ #undef CL_TARGET_OPENCL_VERSION
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+ #define CL_TARGET_OPENCL_VERSION 310
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+ #endif
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+
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+
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+ /* OpenCL Version */
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+ #if CL_TARGET_OPENCL_VERSION >= 310 && !defined(CL_VERSION_3_1)
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+ #define CL_VERSION_3_1 1
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+ #endif
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+ #if CL_TARGET_OPENCL_VERSION >= 300 && !defined(CL_VERSION_3_0)
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+ #define CL_VERSION_3_0 1
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+ #endif
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+ #if CL_TARGET_OPENCL_VERSION >= 220 && !defined(CL_VERSION_2_2)
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+ #define CL_VERSION_2_2 1
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+ #endif
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+ #if CL_TARGET_OPENCL_VERSION >= 210 && !defined(CL_VERSION_2_1)
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+ #define CL_VERSION_2_1 1
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+ #endif
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+ #if CL_TARGET_OPENCL_VERSION >= 200 && !defined(CL_VERSION_2_0)
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+ #define CL_VERSION_2_0 1
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+ #endif
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+ #if CL_TARGET_OPENCL_VERSION >= 120 && !defined(CL_VERSION_1_2)
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+ #define CL_VERSION_1_2 1
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+ #endif
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+ #if CL_TARGET_OPENCL_VERSION >= 110 && !defined(CL_VERSION_1_1)
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+ #define CL_VERSION_1_1 1
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+ #endif
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+ #if CL_TARGET_OPENCL_VERSION >= 100 && !defined(CL_VERSION_1_0)
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+ #define CL_VERSION_1_0 1
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+ #endif
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+
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+ /* Allow deprecated APIs for older OpenCL versions. */
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+ #if CL_TARGET_OPENCL_VERSION <= 220 && !defined(CL_USE_DEPRECATED_OPENCL_2_2_APIS)
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+ #define CL_USE_DEPRECATED_OPENCL_2_2_APIS
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+ #endif
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+ #if CL_TARGET_OPENCL_VERSION <= 210 && !defined(CL_USE_DEPRECATED_OPENCL_2_1_APIS)
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+ #define CL_USE_DEPRECATED_OPENCL_2_1_APIS
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+ #endif
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+ #if CL_TARGET_OPENCL_VERSION <= 200 && !defined(CL_USE_DEPRECATED_OPENCL_2_0_APIS)
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+ #define CL_USE_DEPRECATED_OPENCL_2_0_APIS
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+ #endif
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+ #if CL_TARGET_OPENCL_VERSION <= 120 && !defined(CL_USE_DEPRECATED_OPENCL_1_2_APIS)
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+ #define CL_USE_DEPRECATED_OPENCL_1_2_APIS
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+ #endif
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+ #if CL_TARGET_OPENCL_VERSION <= 110 && !defined(CL_USE_DEPRECATED_OPENCL_1_1_APIS)
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+ #define CL_USE_DEPRECATED_OPENCL_1_1_APIS
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+ #endif
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+ #if CL_TARGET_OPENCL_VERSION <= 100 && !defined(CL_USE_DEPRECATED_OPENCL_1_0_APIS)
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+ #define CL_USE_DEPRECATED_OPENCL_1_0_APIS
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+ #endif
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+
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+ #endif /* __CL_VERSION_H */
package/CL/opencl.h ADDED
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+ /*******************************************************************************
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+ * Copyright (c) 2008-2026 The Khronos Group Inc.
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+ *
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+ * Licensed under the Apache License, Version 2.0 (the "License");
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+ * you may not use this file except in compliance with the License.
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+ * You may obtain a copy of the License at
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+ *
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+ * http://www.apache.org/licenses/LICENSE-2.0
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+ *
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+ * Unless required by applicable law or agreed to in writing, software
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+ * distributed under the License is distributed on an "AS IS" BASIS,
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+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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+ * See the License for the specific language governing permissions and
14
+ * limitations under the License.
15
+ ******************************************************************************/
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+
17
+ #ifndef __OPENCL_H
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+ #define __OPENCL_H
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+
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+ #ifdef __cplusplus
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+ extern "C" {
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+ #endif
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+
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+ #include <CL/cl.h>
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+ #include <CL/cl_gl.h>
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+ #include <CL/cl_ext.h>
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+
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+ #ifdef __cplusplus
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+ }
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+ #endif
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+
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+ #endif /* __OPENCL_H */
@@ -0,0 +1,13 @@
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+ 1. To run the program you have to go into the main folder "BaoabMD", then click the directory and type in cmd and then click enter to open cmd at the location of the folder. You can also just use cd to navigate to it.
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+
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+
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+ 2. Once in terminal you just need to type "node BaoabMD.js" and run it, if there are any errors you probably just have missing dependencies that you need to download.
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+
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+
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+ 3. Now once it is showing you can put your pdb files in the pdb folder and then use "pdb/input.pdb", replace input with your file name if you want to use a custom one.
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+
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+
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+ 4. Now run the simulation for however long you want. I recommend a 100/1 ratio so if you do a 1000 step simulation log it every 10 steps to make 100 frames in total.
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+
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+
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+ 5. Now just wait for it to finish and then your traj.xyz file will apear in the main folder. You can view it with PyMol or OVITO.
package/OpenCL.lib ADDED
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package/binding.gyp ADDED
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+ {
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+ "targets": [
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+ {
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+ "target_name": "forces",
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+ "sources": [ "forces.cpp" ],
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+ "include_dirs": [
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+ "<(module_root_dir)",
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+ "<!@(node -p \"require('node-addon-api').include\")"
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+ ],
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+ "dependencies": [
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+ "<!(node -p \"require('node-addon-api').gyp\")"
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+ ],
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+ "library_dirs": [
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+ "<(module_root_dir)"
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+ ],
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+ "libraries": [
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+ "OpenCL.lib"
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+ ],
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+ "cflags!": [ "-fno-exceptions" ],
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+ "cflags_cc!": [ "-fno-exceptions" ],
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+ "defines": [ "NAPI_DISABLE_CPP_EXCEPTIONS" ]
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+ }
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+ ]
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+ }
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+ <?xml version="1.0" encoding="utf-8"?>
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+ <Project>
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+ <ProjectOutputs>
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+ <ProjectOutput>
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+ <FullPath>C:\Users\Zander Champion\Desktop\BaoabMD\build\Release\forces.node</FullPath>
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+ </ProjectOutput>
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+ </ProjectOutputs>
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+ <ContentFiles />
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+ <SatelliteDlls />
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+ <NonRecipeFileRefs />
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+ </Project>
@@ -0,0 +1,2 @@
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+ C:\Users\Zander Champion\Desktop\BaoabMD\forces.cpp;C:\Users\Zander Champion\Desktop\BaoabMD\build\Release\obj\forces\forces.obj
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+ C:\Program Files\nodejs\node_modules\npm\node_modules\node-gyp\src\win_delay_load_hook.cc;C:\Users\Zander Champion\Desktop\BaoabMD\build\Release\obj\forces\win_delay_load_hook.obj
@@ -0,0 +1,2 @@
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+ PlatformToolSet=v145:VCToolArchitecture=Native64Bit:VCToolsVersion=14.51.36231:VCServicingVersionATL=14.51.36244:VCServicingVersionCrtHeaders=14.51.36244:VCServicingVersionCompilers=14.51.36256:TargetPlatformVersion=10.0.26100.0:
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+ Release|x64|C:\Users\Zander Champion\Desktop\BaoabMD\build\|
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+ ^C:\USERS\ZANDER CHAMPION\DESKTOP\BAOABMD\BUILD\RELEASE\NOTHING.LIB|C:\USERS\ZANDER CHAMPION\DESKTOP\BAOABMD\BUILD\RELEASE\OBJ\FORCES\FORCES.OBJ|C:\USERS\ZANDER CHAMPION\DESKTOP\BAOABMD\BUILD\RELEASE\OBJ\FORCES\WIN_DELAY_LOAD_HOOK.OBJ
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+ C:\Users\Zander Champion\Desktop\BaoabMD\build\Release\forces.LIB
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+ C:\Users\Zander Champion\Desktop\BaoabMD\build\Release\forces.EXP
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+ C:\Users\Zander Champion\Desktop\BaoabMD\build\Release\forces.IPDB
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+ C:\Users\Zander Champion\Desktop\BaoabMD\build\Release\forces.IOBJ
@@ -0,0 +1,39 @@
1
+ Microsoft Visual Studio Solution File, Format Version 12.00
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