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 Changes to be committed:
	modified:   hostdepend/ARM64MAC64
	modified:   include/eosStarFile.h
	deleted:    src/Objects/.DS_Store
	deleted:    src/Objects/.Source.org
	deleted:    src/Objects/DataExpress/.Source.org
	deleted:    src/Objects/DataExpress/Makefile.org
	deleted:    src/Objects/DataManip/.Source.org
	deleted:    src/Objects/DataManip/Makefile.org
	modified:   src/Objects/DataManip/eosStarFile/doc/eosStarFile.html
	modified:   src/Objects/DataManip/eosStarFile/inc/eosStarFile.h
	deleted:    src/Objects/General/Makefile.org
	modified:   src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/mrcImageAbnormalValueRemove.c
	modified:   src/Tools/mrcImage/mrcImageBlurByTemperatureFactor/src/mrcImageBlurByTemperatureFactor.c
	modified:   util/src/DataFormat/Makefile

 Changes not staged for commit:
	modified:   hostdepend/ARM64MAC64 (new commits)
	modified:   include/eosMATH.h

diff --git a/hostdepend/ARM64MAC64 b/hostdepend/ARM64MAC64
index b8745df..3f7dd8c 160000 (submodule)
--- a/hostdepend/ARM64MAC64
+++ b/hostdepend/ARM64MAC64
@@ -1 +1 @@
-Subproject commit b8745dfd26b78656350495ca523e2608ddcb3bfb
+Subproject commit 3f7dd8c2ccc4056ad9956e03de20fa4605de3ad4

diff --git a/include/eosStarFile.h b/include/eosStarFile.h
index 2bce2db..fb268be 100644 (file)
--- a/include/eosStarFile.h
+++ b/include/eosStarFile.h
@@ -83,15 +83,17 @@ extern int* eosStarFileDataGetIntegerP(eosStarFile* star, char* block, char* key
 extern int  eosStarFilDataGetInterger (eosStarFile* star, char* block, char* key, int* value, int mode);
 
 // Loop
-char** eosStarFileLoopDataGetStringP(eosStarFile* star, char* key, int mode);
-void eosStarFileLoopDataGetString(eosStarFile* star, char* key, char*** value, int mode);
+extern char** eosStarFileLoopDataGetStringP(eosStarFile* star, char* key, int mode);
+extern void eosStarFileLoopDataGetString(eosStarFile* star, char* key, char*** value, int mode);
 
-double* eosStarFileLoopDataGetRealP(eosStarFile* star, char* key, int mode);
-void eosStarFileLoopDataGetReal(eosStarFile* star, char* key, double** value, int mode);
+extern double* eosStarFileLoopDataGetRealP(eosStarFile* star, char* key, int mode);
+extern void eosStarFileLoopDataGetReal(eosStarFile* star, char* key, double** value, int mode);
 
-int* eosStarFileLoopDataGetIntergerP(eosStarFile* star, char* key, int mode);
-void eosStarFileLoopDataGetInterger(eosStarFile* star, char* key, int** value, int mode);
+extern int* eosStarFileLoopDataGetIntergerP(eosStarFile* star, char* key, int mode);
+extern void eosStarFileLoopDataGetInterger(eosStarFile* star, char* key, int** value, int mode);
 
+// Write
+extern void eosStarFileWrite(FILE* fpt, eosStarFile* star, int mode);
 /* prototype end */
 
 #ifdef __cplusplus

diff --git a/src/Objects/.DS_Store b/src/Objects/.DS_Store
deleted file mode 100644 (file)
index e401ed9..0000000
Binary files a/src/Objects/.DS_Store and /dev/null differ

diff --git a/src/Objects/.Source.org b/src/Objects/.Source.org
deleted file mode 100644 (file)
index f1269ba..0000000
--- a/src/Objects/.Source.org
+++ /dev/null
@@ -1,6 +0,0 @@
-SOURCE=\
-DataExpress \
-DataManip \
-General \
-MachineManip \
-#LastSource

diff --git a/src/Objects/DataExpress/.Source.org b/src/Objects/DataExpress/.Source.org
deleted file mode 100644 (file)
index c941e3d..0000000
--- a/src/Objects/DataExpress/.Source.org
+++ /dev/null
@@ -1,11 +0,0 @@
-SOURCE=\
-Contour \
-TclTk \
-avsFile \
-eosAlsa \
-eosOpenGL \
-eosRuby \
-gifFile \
-pngFile \
-psFile \
-#LastSource

diff --git a/src/Objects/DataExpress/Makefile.org b/src/Objects/DataExpress/Makefile.org
deleted file mode 100755 (executable)
index b69f906..0000000
--- a/src/Objects/DataExpress/Makefile.org
+++ /dev/null
@@ -1,6 +0,0 @@
-include ../../Config/Define.inc
-include ../Config/Define.inc
-include Config/Define.inc
-include .Source
-
-include Config/Target.inc

diff --git a/src/Objects/DataManip/.Source.org b/src/Objects/DataManip/.Source.org
deleted file mode 100644 (file)
index 8c4a3e7..0000000
--- a/src/Objects/DataManip/.Source.org
+++ /dev/null
@@ -1,25 +0,0 @@
-SOURCE=\
-DCDFile \
-IMAGIC \
-bildFile \
-bmpFile \
-ctfInfo \
-ctfforBayes \
-dmFile \
-dsn6File \
-emData \
-eosMATH \
-eosStarFile \
-khorosData \
-largeIP \
-llData \
-ltlgData \
-mapFile \
-mrcImage \
-mrcImageShape \
-pdbFile \
-rigakuImage \
-simulation \
-tgaFile \
-transform \
-#LastSource

diff --git a/src/Objects/DataManip/Makefile.org b/src/Objects/DataManip/Makefile.org
deleted file mode 100755 (executable)
index b69f906..0000000
--- a/src/Objects/DataManip/Makefile.org
+++ /dev/null
@@ -1,6 +0,0 @@
-include ../../Config/Define.inc
-include ../Config/Define.inc
-include Config/Define.inc
-include .Source
-
-include Config/Target.inc

diff --git a/src/Objects/DataManip/eosStarFile/doc/eosStarFile.html b/src/Objects/DataManip/eosStarFile/doc/eosStarFile.html
index db46102..ffd575c 100644 (file)
--- a/src/Objects/DataManip/eosStarFile/doc/eosStarFile.html
+++ b/src/Objects/DataManip/eosStarFile/doc/eosStarFile.html
@@ -3,13 +3,6 @@
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/eosStarFileDataGet.c:
-
-../src/eosStarFileLoopDataGet.c:
-
-../src/eosStarFileRead.c:
-
-../src/eosStarFileWrite.c:
 </PRE>
 <HR>
 <A NAME="include">
@@ -101,15 +94,17 @@ extern int* eosStarFileDataGetIntegerP(eosStarFile* star, char* block, char* key
 extern int  eosStarFilDataGetInterger (eosStarFile* star, char* block, char* key, int* value, int mode);
 
 // Loop
-char** eosStarFileLoopDataGetStringP(eosStarFile* star, char* key, int mode);
-void eosStarFileLoopDataGetString(eosStarFile* star, char* key, char*** value, int mode);
+extern char** eosStarFileLoopDataGetStringP(eosStarFile* star, char* key, int mode);
+extern void eosStarFileLoopDataGetString(eosStarFile* star, char* key, char*** value, int mode);
 
-double* eosStarFileLoopDataGetRealP(eosStarFile* star, char* key, int mode);
-void eosStarFileLoopDataGetReal(eosStarFile* star, char* key, double** value, int mode);
+extern double* eosStarFileLoopDataGetRealP(eosStarFile* star, char* key, int mode);
+extern void eosStarFileLoopDataGetReal(eosStarFile* star, char* key, double** value, int mode);
 
-int* eosStarFileLoopDataGetIntergerP(eosStarFile* star, char* key, int mode);
-void eosStarFileLoopDataGetInterger(eosStarFile* star, char* key, int** value, int mode);
+extern int* eosStarFileLoopDataGetIntergerP(eosStarFile* star, char* key, int mode);
+extern void eosStarFileLoopDataGetInterger(eosStarFile* star, char* key, int** value, int mode);
 
+// Write
+extern void eosStarFileWrite(FILE* fpt, eosStarFile* star, int mode);
 /* prototype end */
 
 #ifdef __cplusplus

diff --git a/src/Objects/DataManip/eosStarFile/inc/eosStarFile.h b/src/Objects/DataManip/eosStarFile/inc/eosStarFile.h
index 2bce2db..fb268be 100644 (file)
--- a/src/Objects/DataManip/eosStarFile/inc/eosStarFile.h
+++ b/src/Objects/DataManip/eosStarFile/inc/eosStarFile.h
@@ -83,15 +83,17 @@ extern int* eosStarFileDataGetIntegerP(eosStarFile* star, char* block, char* key
 extern int  eosStarFilDataGetInterger (eosStarFile* star, char* block, char* key, int* value, int mode);
 
 // Loop
-char** eosStarFileLoopDataGetStringP(eosStarFile* star, char* key, int mode);
-void eosStarFileLoopDataGetString(eosStarFile* star, char* key, char*** value, int mode);
+extern char** eosStarFileLoopDataGetStringP(eosStarFile* star, char* key, int mode);
+extern void eosStarFileLoopDataGetString(eosStarFile* star, char* key, char*** value, int mode);
 
-double* eosStarFileLoopDataGetRealP(eosStarFile* star, char* key, int mode);
-void eosStarFileLoopDataGetReal(eosStarFile* star, char* key, double** value, int mode);
+extern double* eosStarFileLoopDataGetRealP(eosStarFile* star, char* key, int mode);
+extern void eosStarFileLoopDataGetReal(eosStarFile* star, char* key, double** value, int mode);
 
-int* eosStarFileLoopDataGetIntergerP(eosStarFile* star, char* key, int mode);
-void eosStarFileLoopDataGetInterger(eosStarFile* star, char* key, int** value, int mode);
+extern int* eosStarFileLoopDataGetIntergerP(eosStarFile* star, char* key, int mode);
+extern void eosStarFileLoopDataGetInterger(eosStarFile* star, char* key, int** value, int mode);
 
+// Write
+extern void eosStarFileWrite(FILE* fpt, eosStarFile* star, int mode);
 /* prototype end */
 
 #ifdef __cplusplus

diff --git a/src/Objects/General/Makefile.org b/src/Objects/General/Makefile.org
deleted file mode 100755 (executable)
index b69f906..0000000
--- a/src/Objects/General/Makefile.org
+++ /dev/null
@@ -1,6 +0,0 @@
-include ../../Config/Define.inc
-include ../Config/Define.inc
-include Config/Define.inc
-include .Source
-
-include Config/Target.inc

diff --git a/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/mrcImageAbnormalValueRemove.c b/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/mrcImageAbnormalValueRemove.c
index 5d4c587..16a0ae2 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/mrcImageAbnormalValueRemove.c
+++ b/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/mrcImageAbnormalValueRemove.c
@@ -223,7 +223,10 @@ lmrcImageAbnormalValueRemoveAllArea(mrcImage* out,
                                                }
                                        }
                     fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); 
-                               }
+                               } else {
+                    dst = data;
+                }
+                               mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart);
                        }
                        }
                        }
@@ -282,7 +285,10 @@ lmrcImageAbnormalValueRemoveAllArea(mrcImage* out,
                                                }
                                        }
                     fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); 
-                               }
+                               } else {
+                    dst = data;
+                }
+                               mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart);
                        }
                        }
                        }
@@ -329,7 +335,10 @@ lmrcImageAbnormalValueRemoveAllArea(mrcImage* out,
                                                }
                                        }
                     fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); 
-                               }
+                               } else {
+                    dst = data;
+                }
+                               mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart);
                        }
                        }
                        }
@@ -395,7 +404,10 @@ lmrcImageAbnormalValueRemoveAllArea(mrcImage* out,
                                                }
                                        }
                     fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); 
-                               }
+                               } else {
+                    dst = data;
+                }
+                               mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart);
                        }
                        }
                        }
@@ -443,7 +455,10 @@ lmrcImageAbnormalValueRemoveHighValueArea(mrcImage* out,
                                                }
                                        }
                     fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); 
-                               }
+                               } else {
+                    dst = data;
+                }
+                               mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart);
                        }
                        }
                        }
@@ -483,7 +498,10 @@ lmrcImageAbnormalValueRemoveHighValueArea(mrcImage* out,
                                                }
                                        }
                     fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); 
-                               }
+                               } else {
+                    dst = data;
+                }
+                               mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart);
             }
             }
             }
@@ -548,7 +566,10 @@ lmrcImageAbnormalValueRemoveHighValueArea(mrcImage* out,
                                                }
                                        }
                     fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); 
-                               }
+                               } else {
+                    dst = data;
+                }
+                               mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart);
                        }
                        }
                        }
@@ -604,7 +625,10 @@ lmrcImageAbnormalValueRemoveHighValueArea(mrcImage* out,
                                                }
                                        }
                     fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); 
-                               }
+                               } else {
+                    dst = data;
+                }
+                               mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart);
                        }
                        }
                        }
@@ -652,7 +676,10 @@ lmrcImageAbnormalValueRemoveLowValueArea(mrcImage* out,
                                                }
                                        }
                     fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); 
-                               }
+                               } else {
+                    dst = data;
+                }
+                               mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart);
                        }
                        }
                        }
@@ -693,7 +720,10 @@ lmrcImageAbnormalValueRemoveLowValueArea(mrcImage* out,
                                                }
                                        }
                     fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); 
-                               }
+                               } else {
+                    dst = data;
+                }
+                               mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart);
                        }
                        }
                        }
@@ -759,7 +789,10 @@ lmrcImageAbnormalValueRemoveLowValueArea(mrcImage* out,
                                                }
                                        }
                     fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); 
-                               }
+                               } else {
+                    dst = data;
+                }
+                               mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart);
                        }
                        }
                        }
@@ -815,7 +848,10 @@ lmrcImageAbnormalValueRemoveLowValueArea(mrcImage* out,
                                                }
                                        }
                     fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); 
-                               }
+                               } else {
+                    dst = data;
+                }
+                   mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart);
                        }
                        }
                        }
@@ -827,7 +863,6 @@ lmrcImageAbnormalValueRemoveLowValueArea(mrcImage* out,
                        break;
                }
        }
-       mrcPixelDataSet(out, x, y, z, data, mrcPixelRePart);
        return; 
 }
 

diff --git a/src/Tools/mrcImage/mrcImageBlurByTemperatureFactor/src/mrcImageBlurByTemperatureFactor.c b/src/Tools/mrcImage/mrcImageBlurByTemperatureFactor/src/mrcImageBlurByTemperatureFactor.c
index c973322..40be221 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageBlurByTemperatureFactor/src/mrcImageBlurByTemperatureFactor.c
+++ b/src/Tools/mrcImage/mrcImageBlurByTemperatureFactor/src/mrcImageBlurByTemperatureFactor.c
@@ -19,9 +19,14 @@
 #include "genUtil.h"
 #include "mrcImage.h"
 
+typedef struct atomInfo {   
+    int nAtom;
+    mrcImageParaTypeRealCoord* coord;
+    mrcImageParaTypeReal* Temparature;
+} atomInfo;
+
 typedef struct lmrcImageBlurByTemperatureFactorInfo {
-       float a;
-       int   b;
+    atomInfo
 } lmrcImageBlurByTemperatureFactorInfo;
 
 typedef enum lmrcImageBlurByTemperatureFactorMode {

diff --git a/util/src/DataFormat/Makefile b/util/src/DataFormat/Makefile
index 4b6129b..ffa5e98 100644 (file)
--- a/util/src/DataFormat/Makefile
+++ b/util/src/DataFormat/Makefile
@@ -7,6 +7,7 @@ help::
        @echo "make pkg-config"
        @echo "make icu" 
        @echo "make cif_api" 
+       @echo "make libcif" 
 
 HDF5-VERSION=1.13.0
 HDF5-VERSION2=1-13-0
@@ -14,12 +15,12 @@ HDF5-VERSION3=1.12.1
 
 PKG-CONFIG-VERSION=0.29.2
 
-
 target::
        make pkg-config
        make icu
        make hdf5
        make cif_api
+       make libcif 
 
 
 init:: init-hdf5 init-cif_api init-icu
@@ -98,3 +99,12 @@ clean-hdf5::
 cleanAll-hdf5::
        rm -f hdf5-$(HDF5-VERSION3).tar.gz; rm -rf hdf5-$(HDF5-VERSION3)
 
+libcif: 
+       make init-libcif
+       make config-libcif
+       make all-libcif
+       make clean-libcif
+       make cleanAll-libcif
+
+init-libcif:
+       git clone https://github.com/ElectronicStructureLibrary/libcif.git