AMBER-22: add patches used in easyconfig to the repo

Golden_Repo/a/AMBER/AmberTools-21_CMake-FlexiBLAS.patch

+make CMake scripts that picks BLAS/LAPACK library aware of FlexiBLAS
+author: Kenneth Hoste (HPC-UGent)
+--- cmake/patched-cmake-modules/FindBLASFixed.cmake.orig	2022-05-04 18:53:42.410384491 +0200
++++ cmake/patched-cmake-modules/FindBLASFixed.cmake	2022-05-04 18:54:39.034612008 +0200
+@@ -36,7 +36,7 @@
+ #   BLA_F95     if set on tries to find the f95 interfaces for BLAS/LAPACK
+ #
+ # ######### ## List of vendors (BLA_VENDOR) valid in this module #
+-# Goto,OpenBLAS,ATLAS PhiPACK,CXML,DXML,SunPerf,SCSL,SGIMATH,IBMESSL,
++# Goto,OpenBLAS,FlexiBLAS ATLAS PhiPACK,CXML,DXML,SunPerf,SCSL,SGIMATH,IBMESSL,
+ # ACML,ACML_MP,ACML_GPU,Apple, NAS, Generic
+ 
+ include(CMakePushCheckState)
+@@ -49,8 +49,8 @@
+ 	set(BLA_VENDOR_DEFAULT "All")
+ endif ()
+ 
+-set(BLA_VENDOR ${BLA_VENDOR_DEFAULT} CACHE STRING "BLAS vendor to use for BLAS and Lapack.  Valid values: All, Goto, OpenBLAS, ATLAS, PhiPACK, CXML, DXML, SunPerf, SCSL, SGIMATH, IBMESSL, ACML, ACML_MP, ACML_GPU, Apple, NAS, Generic")
+-validate_configuration_enum(BLA_VENDOR  All Goto OpenBLAS ATLAS PhiPACK CXML DXML SunPerf SCSL SGIMATH IBMESSL ACML ACML_MP ACML_GPU Apple NAS Generic)
++set(BLA_VENDOR ${BLA_VENDOR_DEFAULT} CACHE STRING "BLAS vendor to use for BLAS and Lapack.  Valid values: All, Goto, OpenBLAS, FlexiBLAS, ATLAS, PhiPACK, CXML, DXML, SunPerf, SCSL, SGIMATH, IBMESSL, ACML, ACML_MP, ACML_GPU, Apple, NAS, Generic")
++validate_configuration_enum(BLA_VENDOR  All Goto OpenBLAS FlexiBLAS ATLAS PhiPACK CXML DXML SunPerf SCSL SGIMATH IBMESSL ACML ACML_MP ACML_GPU Apple NAS Generic)
+ 
+ if(DEFINED BLAS_FIND_QUIETLY)
+ 	set(CMAKE_REQUIRED_QUIET ${BLAS_FIND_QUIETLY})
+@@ -159,6 +159,20 @@
+  endif()
+ endif ()
+ 
++if (BLA_VENDOR STREQUAL "FlexiBLAS" OR BLA_VENDOR STREQUAL "All")
++ if(NOT BLAS_LIBRARIES)
++	 # FlexiBLAS (https://github.com/mpimd-csc/flexiblas)
++	check_fortran_libraries(
++	BLAS_LIBRARIES
++	BLAS
++	sgemm
++	""
++	"flexiblas"
++	""
++	)
++ endif()
++endif ()
++
+ if (BLA_VENDOR STREQUAL "OpenBLAS" OR BLA_VENDOR STREQUAL "All")
+  if(NOT BLAS_LIBRARIES)
+ 	# OpenBLAS (http://www.openblas.net)
+@@ -524,4 +538,4 @@
+ endif()
+ 
+ cmake_pop_check_state()
+-set(CMAKE_FIND_LIBRARY_SUFFIXES ${_blas_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES})
+\ No newline at end of file
++set(CMAKE_FIND_LIBRARY_SUFFIXES ${_blas_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES})
+--- cmake/patched-cmake-modules/FindLAPACKFixed.cmake.orig	2022-05-04 18:56:14.315407989 +0200
++++ cmake/patched-cmake-modules/FindLAPACKFixed.cmake	2022-05-04 18:56:39.930772703 +0200
+@@ -36,7 +36,7 @@
+ #   BLA_F95     if set on tries to find the f95 interfaces for BLAS/LAPACK
+ #
+ # ## List of vendors (BLA_VENDOR) valid in this module:
+-# OpenBLAS, ACML,Apple, NAS, Generic
++# OpenBLAS, FlexiBLAS, ACML,Apple, NAS, Generic
+ 
+ set(_lapack_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES ${CMAKE_FIND_LIBRARY_SUFFIXES})
+ 
+@@ -173,6 +173,20 @@
+ 		endif()
+ 	endif ()
+ 	
++	if(BLA_VENDOR STREQUAL "FlexiBLAS" OR BLA_VENDOR STREQUAL "All")
++		if(NOT LAPACK_LIBRARIES)
++			check_lapack_libraries(
++			LAPACK_LIBRARIES
++			LAPACK
++			cheev
++			""
++			"flexiblas"
++			"${BLAS_LIBRARIES}"
++			""
++			)
++		endif()
++	endif()
++	
+ 	if(BLA_VENDOR STREQUAL "OpenBLAS" OR BLA_VENDOR STREQUAL "All")
+ 		if(NOT LAPACK_LIBRARIES)
+ 			check_lapack_libraries(
+@@ -289,4 +303,4 @@
+ endif()
+ 
+ cmake_pop_check_state()
+-set(CMAKE_FIND_LIBRARY_SUFFIXES ${_lapack_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES})
+\ No newline at end of file
++set(CMAKE_FIND_LIBRARY_SUFFIXES ${_lapack_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES})

Golden_Repo/a/AMBER/pmemd_xray_non_bulk_no_implicit_type.patch

+diff -ruN amber22_src/src/pmemd/src/xray/src/xray_non_bulk_impl_cpu.F90 amber22_src1/src/pmemd/src/xray/src/xray_non_bulk_impl_cpu.F90
+--- amber22_src/src/pmemd/src/xray/src/xray_non_bulk_impl_cpu.F90	2022-04-09 03:11:46.000000000 +0200
++++ amber22_src1/src/pmemd/src/xray/src/xray_non_bulk_impl_cpu.F90	2023-08-25 20:30:12.828529000 +0200
+@@ -90,7 +90,7 @@
+     call check_precondition(size(frac, 2) == size(scatter_type_index))
+     call check_precondition(size(hkl, 2) == size(atomic_scatter_factor, 1))
+     
+-    !$omp parallel do private(ihkl,i,f,angle)
++    !$omp parallel do private(ihkl,f,angle)
+     do ihkl = 1, size(hkl, 2)
+       
+       ! Fhkl = SUM( fj * exp(2 * M_PI * i * (h * xj + k * yj + l * zj)) ),
+@@ -127,4 +127,4 @@
+   end subroutine calc_f_non_bulk
+ 
+ 
+-end module xray_non_bulk_impl_cpu_module
+\ No newline at end of file
++end module xray_non_bulk_impl_cpu_module