diff --git a/attic/group/2dgroups/CMakeLists.txt b/attic/group/2dgroups/CMakeLists.txt
index 7069ee7..ada1a0f 100644
--- a/attic/group/2dgroups/CMakeLists.txt
+++ b/attic/group/2dgroups/CMakeLists.txt
@@ -1,6 +1,6 @@
 add_executable(new_2dgroups
     ${BUILD_MACOSX_BUNDLE} WIN32
-	new_2dgroups.f
+	new_2dgroups.f90
 )
 target_link_libraries(new_2dgroups LINK_PUBLIC common io scf rpa)
 
diff --git a/attic/group/2dgroups/new_2dgroups.f b/attic/group/2dgroups/new_2dgroups.f90
similarity index 100%
rename from attic/group/2dgroups/new_2dgroups.f
rename to attic/group/2dgroups/new_2dgroups.f90
diff --git a/attic/group/Makefile b/attic/group/Makefile
index ee84684..5a434ff 100644
--- a/attic/group/Makefile
+++ b/attic/group/Makefile
@@ -13,10 +13,10 @@ NOPT=-Mfree=f90
 clean:
 	rm -f *.o *.mod 
 
-new_group:	new_group.f \
+new_group:	new_group.f90 \
         ../../unit_cell_mod.o ../../group_mod.o \
 	../../io_mod.o ../../const_mod.o
-	$(F90) $(FAST) -o $(BIN)/new_group new_group.f \
+	$(F90) $(FAST) -o $(BIN)/new_group new_group.f90 \
         ../../unit_cell_mod.o ../../group_mod.o \
 	../../io_mod.o ../../const_mod.o
 
diff --git a/attic/group/make_group.f b/attic/group/make_group.f90
similarity index 100%
rename from attic/group/make_group.f
rename to attic/group/make_group.f90
diff --git a/attic/group/new_group.f b/attic/group/new_group.f90
similarity index 100%
rename from attic/group/new_group.f
rename to attic/group/new_group.f90
diff --git a/attic/group/test.f b/attic/group/test.f90
similarity index 100%
rename from attic/group/test.f
rename to attic/group/test.f90
diff --git a/attic/rpa/test.f b/attic/rpa/test.f90
similarity index 100%
rename from attic/rpa/test.f
rename to attic/rpa/test.f90
diff --git a/attic/utility/CMakeLists.txt b/attic/utility/CMakeLists.txt
index efcd12a..67979be 100644
--- a/attic/utility/CMakeLists.txt
+++ b/attic/utility/CMakeLists.txt
@@ -2,19 +2,19 @@
 
 
 add_executable(nto2
-		nto2.f
+		nto2.f90
 )
 target_link_libraries(nto2 LINK_PUBLIC common )
 
 
 add_executable(nto3
-		nto3.f
+		nto3.f90
 )
 target_link_libraries(nto3 LINK_PUBLIC common )
 
 
 add_executable(switch
-		switch.f
+		switch.f90
 )
 target_link_libraries(switch LINK_PUBLIC common )
 
diff --git a/attic/utility/Makefile b/attic/utility/Makefile
index 7ba52a5..679c126 100644
--- a/attic/utility/Makefile
+++ b/attic/utility/Makefile
@@ -12,18 +12,18 @@ NOPT=-Mfree=f90
 clean:
 	rm -f *.o *.mod 
 
-switch:	switch.f \
+switch:	switch.f90 \
 	../build/const_mod.o
-	$(F90) $(FAST) -o $(BIN)/switch switch.f \
+	$(F90) $(FAST) -o $(BIN)/switch switch.f90 \
 	../build/const_mod.o
 
-nto2:	nto2.f \
+nto2:	nto2.f90 \
 	../build/const_mod.o
-	$(F90) $(FAST) -o $(BIN)/nto2 nto2.f \
+	$(F90) $(FAST) -o $(BIN)/nto2 nto2.f90 \
 	../build/const_mod.o
 
-nto3:	nto3.f \
+nto3:	nto3.f90 \
 	../build/const_mod.o
-	$(F90) $(FAST) -o $(BIN)/nto3 nto3.f \
+	$(F90) $(FAST) -o $(BIN)/nto3 nto3.f90 \
 	../build/const_mod.o
 
diff --git a/attic/utility/nto2.f b/attic/utility/nto2.f90
similarity index 100%
rename from attic/utility/nto2.f
rename to attic/utility/nto2.f90
diff --git a/attic/utility/nto3.f b/attic/utility/nto3.f90
similarity index 100%
rename from attic/utility/nto3.f
rename to attic/utility/nto3.f90
diff --git a/attic/utility/switch.f b/attic/utility/switch.f90
similarity index 100%
rename from attic/utility/switch.f
rename to attic/utility/switch.f90
diff --git a/doc/Makefile b/doc/Makefile
index dc6a35d..9b2881b 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -18,13 +18,13 @@ user-man: user-man/*.rst
 .PHONY: devel-man 
 
 devel-man:	
-	cp $(BLD)/pscf.f $(SRC)/pscf.f
-	cp $(BLD)/scf_mod.f $(SRC)/scf_mod.f
-	cp $(BLD)/iterate_mod.f $(SRC)/iterate_mod.f
+	cp $(BLD)/pscf.f90 $(SRC)/pscf.f90
+	cp $(BLD)/scf_mod.f90 $(SRC)/scf_mod.f90
+	cp $(BLD)/iterate_mod.f90 $(SRC)/iterate_mod.f90
 	$(PYTHON) $(GDOC)
-	rm $(SRC)/pscf.f
-	rm $(SRC)/scf_mod.f
-	rm $(SRC)/iterate_mod.f
+	rm $(SRC)/pscf.f90
+	rm $(SRC)/scf_mod.f90
+	rm $(SRC)/iterate_mod.f90
 
 .PHONY: clean
 
diff --git a/doc/user-man/compile-make.rst b/doc/user-man/compile-make.rst
index c92b063..ed6bfa2 100644
--- a/doc/user-man/compile-make.rst
+++ b/doc/user-man/compile-make.rst
@@ -35,7 +35,7 @@ To compile the code in this way, proceed as follows:
    * The pscf/git/make directory will contain files named config.mk_r 
      and Makefile. Make a copy of the file config.mk_r, by entering::
 
-        cd config.mk_r config.mk
+        cp config.mk_r config.mk
 
    * Examine and edit the new config.mk file to reflect your environment, 
      and to specify an installation directory.  See below for further 
@@ -118,6 +118,10 @@ This will install:
 
    * python modules in $(INSTALL)/lib/python2.7/site-packages/pscf/
 
+   * matlab scripts in $(INSTALL)/lib/matlab
+
+   * text files in $(INSTALL)/share
+
 where $(INSTALL) denotes the value of the makefile variable defined in 
 the config.mk file.
 
diff --git a/make/.gitignore b/make/.gitignore
index 7c6209d..6108c5c 100644
--- a/make/.gitignore
+++ b/make/.gitignore
@@ -1,4 +1,5 @@
 *.f
+*.f90
 *.o
 *.mod
 pscf
diff --git a/make/INSTALL b/make/INSTALL
index 5aeb96b..167075d 100644
--- a/make/INSTALL
+++ b/make/INSTALL
@@ -31,7 +31,7 @@ FFTW fast fourier transform library.
 2. Change directory (cd) to the pscf/make directory (i.e., this 
 directory) and copy the file config.mk_r to config.mk, by entering
 
->  cp Makefile_r Makefile
+>  cp config.mk_r config.mk
 
 Explanation: The file config.mk_r is a default version of a 
 configuration file that is stored in the git repository. Users can 
diff --git a/make/Makefile b/make/Makefile
index 9e7b88c..2117d9a 100644
--- a/make/Makefile
+++ b/make/Makefile
@@ -23,7 +23,7 @@ all:
 	make pscf
 
 clean:
-	rm -f  *.o  *.mod  *.f  pscf
+	rm -f  *.o  *.mod  *.f90  pscf
 
 pscf:	pscf.o\
 	const_mod.o string_mod.o io_mod.o version_mod.o field_io_mod.o\
@@ -41,15 +41,15 @@ pscf:	pscf.o\
 	response_mod.o response_step_mod.o extrapolate_mod.o \
 	$(LIBDIRS) $(FFTWLIB) $(LAPACKLIB) -lm
 
-pscf.o: pscf.f const_mod.o io_mod.o version_mod.o\
+pscf.o: pscf.f90 const_mod.o io_mod.o version_mod.o\
 	unit_cell_mod.o chemistry_mod.o field_io_mod.o\
 	sweep_mod.o iterate_mod.o scf_mod.o basis_mod.o\
 	spinodal_mod.o\
 	response_mod.o $(FFT_FILE).o response_step_mod.o extrapolate_mod.o
-	$(F90) $(FAST) -c pscf.f
+	$(F90) $(FAST) -c pscf.f90
 
-pscf.f: $(SRC)/pscf.fp.f
-	$(FORPEDO) $(DEVEL) $(SRC)/pscf.fp.f > pscf.f
+pscf.f90: $(SRC)/pscf.fp.f90
+	$(FORPEDO) $(DEVEL) $(SRC)/pscf.fp.f90 > pscf.f90
 
 # ====== Install =================================================
 
@@ -66,5 +66,149 @@ install: pscf
 
 uninstall:
 	rm -rf $(BIN_DIR)/pscf*
-	rm -rf $(PYTHON_DIR)/p*
+	rm -rf $(PYTHON_DIR)/pscf/*
+
+# ====== Modules =================================================
+
+const_mod.o: $(SRC)/const_mod.f90
+	$(F90) $(FAST) -c $(SRC)/const_mod.f90
+
+# io Directory
+string_mod.o: $(SRC)/io/string_mod.f90
+	$(F90) $(FAST) -c $(SRC)/io/string_mod.f90
+
+io_mod.o: $(SRC)/io/io_mod.f90 const_mod.o string_mod.o
+	$(F90) $(FAST) -c $(SRC)/io/io_mod.f90
+
+version_mod.o: $(SRC)/io/version_mod.f90
+	$(F90) $(FAST) -c $(SRC)/io/version_mod.f90
+
+field_io_mod.o: $(SRC)/io/field_io_mod.f90 const_mod.o io_mod.o\
+	string_mod.o unit_cell_mod.o chemistry_mod.o basis_mod.o\
+	$(FFT_FILE).o grid_basis_mod.o
+	$(F90) $(FAST) -c $(SRC)/io/field_io_mod.f90
+
+# grid directory
+grid_mod.o: $(SRC)/grid/grid_mod.f90 const_mod.o\
+	group_mod.o unit_cell_mod.o
+	$(F90) $(FAST) -c $(SRC)/grid/grid_mod.f90
+
+$(FFT_FILE).o: $(SRC)/grid/$(FFT_FILE).f90 const_mod.o
+	$(F90) $(FAST) -c $(SRC)/grid/$(FFT_FILE).f90
+
+# crystal directory
+group_mod.o: $(SRC)/crystal/group_mod.f90 const_mod.o version_mod.o
+	$(F90) $(FAST) -c $(SRC)/crystal/group_mod.f90
+
+unit_cell_mod.o: $(SRC)/crystal/unit_cell_mod.f90 const_mod.o\
+	io_mod.o group_mod.o
+	$(F90) $(FAST) -c $(SRC)/crystal/unit_cell_mod.f90
+
+space_groups_mod.o: $(SRC)/crystal/space_groups_mod.f90 const_mod.o\
+	group_mod.o
+	$(F90) $(NOPT) -c $(SRC)/crystal/space_groups_mod.f90
+
+basis_mod.o: $(SRC)/crystal/basis_mod.f90\
+	const_mod.o string_mod.o io_mod.o\
+	group_mod.o space_groups_mod.o unit_cell_mod.o\
+	grid_mod.o
+	$(F90) $(FAST) -c $(SRC)/crystal/basis_mod.f90
+
+grid_basis_mod.o: $(SRC)/crystal/grid_basis_mod.f90 const_mod.o\
+	grid_mod.o basis_mod.o
+	$(F90) $(FAST) -c $(SRC)/crystal/grid_basis_mod.f90
+
+deform_mod.o: $(SRC)/crystal/deform_mod.f90\
+	const_mod.o string_mod.o io_mod.o\
+	group_mod.o space_groups_mod.o unit_cell_mod.o\
+	grid_mod.o basis_mod.o
+	$(F90) $(FAST) -c $(SRC)/crystal/deform_mod.f90
+
+# scf directory
+chemistry_mod.o: $(SRC)/scf/chemistry_mod.f90 const_mod.o io_mod.o
+	$(F90) $(FAST) -c $(SRC)/scf/chemistry_mod.f90
+
+chain_mod.o: $(SRC)/scf/chain_mod.f90 const_mod.o\
+	chemistry_mod.o $(FFT_FILE).o
+	$(F90) $(FAST) -c $(SRC)/scf/chain_mod.f90
+
+step_mod.o: $(SRC)/scf/step_mod.f90 const_mod.o\
+	$(FFT_FILE).o
+	$(F90) $(FAST) -c $(SRC)/scf/step_mod.f90
+
+scf_mod.f90: $(SRC)/scf/scf_mod.fp.f90
+	$(FORPEDO) $(DEVEL) $(SRC)/scf/scf_mod.fp.f90 > scf_mod.f90
+
+scf_mod.o: scf_mod.f90 const_mod.o io_mod.o\
+	basis_mod.o chemistry_mod.o step_mod.o\
+	grid_mod.o chain_mod.o $(FFT_FILE).o grid_basis_mod.o
+	$(F90) $(FAST) -c scf_mod.f90
+
+#rpa directory
+rpa_mod.o: $(SRC)/rpa/rpa_mod.f90\
+	chemistry_mod.o const_mod.o
+	$(F90) $(FAST) -c $(SRC)/rpa/rpa_mod.f90
+
+spinodal_mod.o: $(SRC)/rpa/spinodal_mod.f90 const_mod.o io_mod.o\
+	response_pd_mod.o chemistry_mod.o
+	$(F90) $(FAST) -c $(SRC)/rpa/spinodal_mod.f90
+
+# iterate directory
+iterate_mod.f90: $(SRC)/iterate/iterate_mod.fp.f90
+	$(FORPEDO) $(DEVEL) $(SRC)/iterate/iterate_mod.fp.f90 > iterate_mod.f90
+
+iterate_mod.o: iterate_mod.f90 const_mod.o\
+	scf_mod.o basis_mod.o chemistry_mod.o unit_cell_mod.o\
+	response_pd_mod.o
+	$(F90) $(FAST) -c iterate_mod.f90
+
+response_pd_mod.o: $(SRC)/iterate/response_pd_mod.f90 const_mod.o io_mod.o\
+	chemistry_mod.o basis_mod.o unit_cell_mod.o scf_mod.o\
+	grid_mod.o $(FFT_FILE).o
+	$(F90) $(FAST) -c $(SRC)/iterate/response_pd_mod.f90
+
+sweep_mod.o: $(SRC)/iterate/sweep_mod.f90 const_mod.o io_mod.o\
+	chemistry_mod.o unit_cell_mod.o basis_mod.o
+	$(F90) $(FAST) -c $(SRC)/iterate/sweep_mod.f90
+
+# response directory
+response_step_mod.o: $(SRC)/response/response_step_mod.f90\
+	chemistry_mod.o $(FFT_FILE).o
+	$(F90) $(FAST) -c $(SRC)/response/response_step_mod.f90
+
+extrapolate_mod.o: $(SRC)/response/extrapolate_mod.f90\
+	const_mod.o
+	$(F90) $(FAST) -c $(SRC)/response/extrapolate_mod.f90
+
+response_mod.o:	$(SRC)/response/response_mod.f90\
+	chemistry_mod.o const_mod.o chain_mod.o\
+	grid_mod.o $(FFT_FILE).o group_mod.o response_step_mod.o\
+	extrapolate_mod.o field_io_mod.o spinodal_mod.o
+	$(F90) $(FAST) -c $(SRC)/response/response_mod.f90
+
+# ========================================================
+# tests subdirectory 
+
+rpa_test.o: $(SRC)/tests/rpa/test.f90 rpa_mod.o\
+	chemistry_mod.o io_mod.o string_mod.o const_mod.o
+	$(F90) $(FAST) -o rpa_test.o -c $(SRC)/tests/rpa/test.f90
+
+rpa_test: rpa_test.o rpa_mod.o\
+	chemistry_mod.o io_mod.o string_mod.o const_mod.o
+	$(F90) $(LINK) -lm -o $(SRC)/tests/rpa/exc\
+	rpa_test.o rpa_mod.o\
+	chemistry_mod.o io_mod.o string_mod.o const_mod.o\
+	$(LAPACKLIB)
+
+# ========================================================
+# Code to convert 2D groups to Fortran
+ 
+new_2dgroups: $(SRC)/tests/group/2dgroups/new_2dgroups.f90\
+	const_mod.o io_mod.o version_mod.o string_mod.o\
+	group_mod.o unit_cell_mod.o
+	$(F90) $(LINK) -o $(SRC)/tests/group/2dgroups/new_2dgroups\
+	$(SRC)/tests/group/2dgroups/new_2dgroups.f90\
+	const_mod.o io_mod.o string_mod.o version_mod.o\
+	group_mod.o unit_cell_mod.o
+>>>>>>> master
 
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 15869b2..4e3c107 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,10 +1,10 @@
 # TODO: move these options to the top file
 
 if (USE_FFT3)
-    set (FFT_FILE fft3_mod.f)    
+    set (FFT_FILE fft3_mod.f90)    
     find_package(FFTW)
 else (USE_FFT3)
-    set (FFT_FILE fft2_mod.f)    
+    set (FFT_FILE fft2_mod.f90)    
     find_package(FFTW)
 endif (USE_FFT3)
 
@@ -22,43 +22,43 @@ set(FORPEDO ${CMAKE_SOURCE_DIR}/tools/python/preprocess-0.6.1/preprocess.py)
 find_package(LAPACK)
 
 add_custom_command(
-        OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/scf_mod.f
-	COMMAND	${FORPEDO} ${DEVEL} ${CMAKE_CURRENT_SOURCE_DIR}/scf_mod.fp.f > ${CMAKE_CURRENT_BINARY_DIR}/scf_mod.f
-	DEPENDS scf_mod.fp.f
+        OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/scf_mod.f90
+	COMMAND	${FORPEDO} ${DEVEL} ${CMAKE_CURRENT_SOURCE_DIR}/scf_mod.fp.f90 > ${CMAKE_CURRENT_BINARY_DIR}/scf_mod.f90
+	DEPENDS scf_mod.fp.f90
 )
 
 add_custom_command(
-   OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/iterate_mod.f 
-   COMMAND ${FORPEDO} ${DEVEL} ${CMAKE_CURRENT_SOURCE_DIR}/iterate_mod.fp.f > ${CMAKE_CURRENT_BINARY_DIR}/iterate_mod.f 
-   DEPENDS iterate_mod.fp.f
+   OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/iterate_mod.f90
+   COMMAND ${FORPEDO} ${DEVEL} ${CMAKE_CURRENT_SOURCE_DIR}/iterate_mod.fp.f90 > ${CMAKE_CURRENT_BINARY_DIR}/iterate_mod.f90
+   DEPENDS iterate_mod.fp.f90
 )
 
 # Create a library called "pscf_lib", which includes module source files.
 # The extension is already found. Any number of sources could be listed here.
 add_library(pscf_lib
-    const_mod.f
-    io_mod.f
-    string_mod.f
-    version_mod.f
-    field_io_mod.f
+    const_mod.f90
+    io_mod.f90
+    string_mod.f90
+    version_mod.f90
+    field_io_mod.f90
     ${FFT_FILE}
-    grid_mod.f
-    basis_mod.f
-    grid_basis_mod.f
-    group_mod.f
-    unit_cell_mod.f
-    space_groups_mod.f
-    chain_mod.f
-    chemistry_mod.f
-    step_mod.f
-    ${CMAKE_CURRENT_BINARY_DIR}/scf_mod.f
-    ${CMAKE_CURRENT_BINARY_DIR}/iterate_mod.f 
-    response_pd_mod.f
-    sweep_mod.f
-    extrapolate_mod.f
-    response_mod.f
-    response_step_mod.f
-    spinodal_mod.f
+    grid_mod.f90
+    basis_mod.f90
+    grid_basis_mod.f90
+    group_mod.f90
+    unit_cell_mod.f90
+    space_groups_mod.f90
+    chain_mod.f90
+    chemistry_mod.f90
+    step_mod.f90
+    ${CMAKE_CURRENT_BINARY_DIR}/scf_mod.f90
+    ${CMAKE_CURRENT_BINARY_DIR}/iterate_mod.f90 
+    response_pd_mod.f90
+    sweep_mod.f90
+    extrapolate_mod.f90
+    response_mod.f90
+    response_step_mod.f90
+    spinodal_mod.f90
 )
 
 # Ensure that linker can find any headers or fortram *.mod module files,
@@ -74,14 +74,14 @@ target_link_libraries(pscf_lib LINK_PUBLIC ${FFTW_LIBRARIES} ${LAPACK_LIBRARIES}
 
 ### PREPROCESS THE MAIN FILE ###
 add_custom_command(
-   OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/pscf.f 
-   COMMAND  ${FORPEDO} ${DEVEL} ${CMAKE_CURRENT_SOURCE_DIR}/pscf.fp.f > ${CMAKE_CURRENT_BINARY_DIR}/pscf.f 
-   DEPENDS pscf.fp.f
+   OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/pscf.f90 
+   COMMAND  ${FORPEDO} ${DEVEL} ${CMAKE_CURRENT_SOURCE_DIR}/pscf.fp.f90 > ${CMAKE_CURRENT_BINARY_DIR}/pscf.f90 
+   DEPENDS pscf.fp.f90
 )
 
 add_executable(pscf 
    ${BUILD_MACOSX_BUNDLE} WIN32
-   ${CMAKE_CURRENT_BINARY_DIR}/pscf.f 
+   ${CMAKE_CURRENT_BINARY_DIR}/pscf.f90 
 )
 
 set(APPS ${CMAKE_CURRENT_BINARY_DIR}/pscf${MACOSX_BUNDLE_EXT})
diff --git a/src/README b/src/README
index a8531bd..af1bcdd 100644
--- a/src/README
+++ b/src/README
@@ -1,29 +1,23 @@
 
 File Name Conventions:
 
-  Files named <name>.f  are Fortran 90 files
-  Files named <name>.fp.f are Fortran 90 preprocessor input files.
-
-  Preprocessor input files are simply Fortran 90 files that contain 
-  blocks of code that is conditionally included and compiled only if 
-  particular environment variables are defined.  These files are 
-  converted by the build system into corresponding Fortran 90 files
-  by applying a python preprocessor script that is distributed with the
-  pscf source code.  There are only a few files that are treated in
-  this manner, but the main program is among them. See the comment 
-  at the end of this file for further discussion of the use of a 
-  preprocessor.
+  Files named <base>_mod.f90  are Fortran 90 modules
+  Files named <name>.fp.f90   are preprocessor input files. 
 
+  The un-preprocessed version of the main program is src/pscf.fp.f90. 
+  A corresponding compilable fortran program is generated by applying
+  a preprocessor script, which installs the resulting program in the 
+  build directory. See the end of this file for a discussion of the 
+  use of a preprocessor.
 
 Main Program:
 
-pscf.fp.f
-	Main program preprocessor input file. Used to generate the 
-	compilable fortran file pscf.f, which is installed in the 
-        build directory.
+pscf.fp.f90
+	Main program (preprocessor input file). Used to generate the 
+	compilable fortran file pscf.f90 in the build directory.
 
 Utility Modules:
-
+=======
 const_mod.f
 	Defines global variable dim (= # dimensions of space) and 
 	parameter long (=real kind for double precision). Used by
@@ -48,11 +42,11 @@ FFT grid Modules:
 
 fft3_mod.f
         Fortran 90 wrappers for FFTW Fourier transform functions, 
-	for FFTW version 3 (Either this or fft2_mod.f is linked)
+	for FFTW version 3 (Either this or fft2_mod.f90 is linked)
 
 fft2_mod.f
         Fortran 90 wrappers for FFTW Fourier transform functions,
-	for FFTW version 2 (Either this or fft3_mod.f is linked)
+	for FFTW version 2 (Either this or fft3_mod.f90 is linked)
 
 grid_mod.f
         Defines scf data structures on an FFT grid, and routines
@@ -111,10 +105,12 @@ chain_mod.f
 	destroy these arrays. 
 
 step_mod.f
-        Routines to integrate one time step of modified diffusion
-	equation, using the Rasmussen-Kaloskas pseudo-spectral
-	algorithm and extrapolation with respect to contour 
-	length step size.
+	Contains routines to solve diffusion equation by the
+	pseudo-spectral method, and to calculate monomer 
+        concentration fields, the free and energy, and stress.
+	Note: scf/scf_mod.fp.f90 is a preprocessor input file, which
+	is used to generate file scf_mod.f90 in the build directory.
+
 
 scf_mod.fp.f
 	Contains routines to solve diffusion equation by the
@@ -123,13 +119,20 @@ scf_mod.fp.f
 	Note: scf_mod.fp.f is a preprocessor input file, which
 	is used to generate file scf_mod.f in the build directory.
 
+scf/chain_mod.f90
+	Defines a derived type chain_type that contains the
+	q(r,s) =qf and q^{+}(r,s) =qr functions for a chain, and 
+	information about discretization in r and s. Also defines 
+	arrays of chain_types and subroutines to allocate and 
+	destroy these arrays. 
+
 Iteration Modules:
 
 iterate_mod.fp.f
 	Iterates scf equations to convergence. Currently contains
 	Newton-Raphson (NR) algorithm for both fixed and variable 
-	unit cells. Note: File iterate_mod.fp.f is a preprocessor
-	input file, which is used to generate file iterate_mod.f
+	unit cells. Note: File iterate_mod.fp.f90 is a preprocessor
+	input file, which is used to generate file iterate_mod.f90
         in the build directory.
 
 sweep_mod
@@ -167,9 +170,9 @@ extrapolate_mod.f
   
   The relevant preprocesor input files are:
 
-     src/pscf.fp.f 
-     src/iterate/iterate_mod.fp.f 
-     src/scf/scf_mod.fp.f 
+     src/pscf.fp.f90 
+     src/iterate_mod.fp.f90 
+     src/scf_mod.fp.f90 
 
   These are fortran files that contain preprocessor directives that
   control conditional compilation of some sections of code. The 
@@ -179,9 +182,9 @@ extrapolate_mod.f
   a Fortran file with the same name as the preprocessor input file 
   without the .fp. string. The resulting fortran files are thus named:
      
-     build/scf.f 
-     build/iterate_mod.f 
-     build/scf_mod.f 
+     build/scf.f90 
+     build/iterate_mod.f90 
+     build/scf_mod.f90 
   
   These preprocessed fortran files installed in the build directory 
   from which make is invoked, rather than in the src/ directory. If 
@@ -202,10 +205,10 @@ extrapolate_mod.f
   conditional compilation directives and are excluded from release
   versions of the corresponding fortran files. 
 
-  If the *.fp.f preprocessor files are modified, and the program 
+  If the *.fp.f90 preprocessor files are modified, and the program 
   is then recompiled using either cmake or the make file in the 
-  pscf/make directory, then the *.f fortran files will be regenerated
+  pscf/make directory, then the *.f90 fortran files will be regenerated
   regenerated as part of the build process. When compiled with make
-  in the src/make directory, the src/make/*.f fortran files are also
+  in the src/make directory, the src/make/*.f90 fortran files are also
   removed by the 'make clean' command.
 
diff --git a/src/basis_mod.f b/src/basis_mod.f90
similarity index 100%
rename from src/basis_mod.f
rename to src/basis_mod.f90
diff --git a/src/chain_mod.f b/src/chain_mod.f90
similarity index 100%
rename from src/chain_mod.f
rename to src/chain_mod.f90
diff --git a/src/chemistry_mod.f b/src/chemistry_mod.f90
similarity index 100%
rename from src/chemistry_mod.f
rename to src/chemistry_mod.f90
diff --git a/src/const_mod.f b/src/const_mod.f90
similarity index 100%
rename from src/const_mod.f
rename to src/const_mod.f90
diff --git a/attic/deform/deform_mod.f b/src/deform_mod.f90
similarity index 100%
rename from attic/deform/deform_mod.f
rename to src/deform_mod.f90
diff --git a/src/extrapolate_mod.f b/src/extrapolate_mod.f90
similarity index 100%
rename from src/extrapolate_mod.f
rename to src/extrapolate_mod.f90
diff --git a/src/fft2_mod.f b/src/fft2_mod.f90
similarity index 100%
rename from src/fft2_mod.f
rename to src/fft2_mod.f90
diff --git a/src/fft3_mod.f b/src/fft3_mod.f90
similarity index 100%
rename from src/fft3_mod.f
rename to src/fft3_mod.f90
diff --git a/src/field_io_mod.f b/src/field_io_mod.f90
similarity index 100%
rename from src/field_io_mod.f
rename to src/field_io_mod.f90
diff --git a/src/grid_basis_mod.f b/src/grid_basis_mod.f90
similarity index 100%
rename from src/grid_basis_mod.f
rename to src/grid_basis_mod.f90
diff --git a/src/grid_mod.f b/src/grid_mod.f90
similarity index 100%
rename from src/grid_mod.f
rename to src/grid_mod.f90
diff --git a/src/group_mod.f b/src/group_mod.f90
similarity index 100%
rename from src/group_mod.f
rename to src/group_mod.f90
diff --git a/src/io_mod.f b/src/io_mod.f90
similarity index 100%
rename from src/io_mod.f
rename to src/io_mod.f90
diff --git a/src/iterate_mod.fp.f b/src/iterate_mod.fp.f90
similarity index 100%
rename from src/iterate_mod.fp.f
rename to src/iterate_mod.fp.f90
diff --git a/src/pscf.fp.f b/src/pscf.fp.f90
similarity index 100%
rename from src/pscf.fp.f
rename to src/pscf.fp.f90
diff --git a/src/response_mod.f b/src/response_mod.f90
similarity index 100%
rename from src/response_mod.f
rename to src/response_mod.f90
diff --git a/src/response_pd_mod.f b/src/response_pd_mod.f90
similarity index 100%
rename from src/response_pd_mod.f
rename to src/response_pd_mod.f90
diff --git a/src/response_step_mod.f b/src/response_step_mod.f90
similarity index 100%
rename from src/response_step_mod.f
rename to src/response_step_mod.f90
diff --git a/attic/rpa/rpa_mod.f b/src/rpa_mod.f90
similarity index 100%
rename from attic/rpa/rpa_mod.f
rename to src/rpa_mod.f90
diff --git a/src/scf_mod.fp.f b/src/scf_mod.fp.f90
similarity index 100%
rename from src/scf_mod.fp.f
rename to src/scf_mod.fp.f90
diff --git a/src/space_groups_mod.f b/src/space_groups_mod.f90
similarity index 100%
rename from src/space_groups_mod.f
rename to src/space_groups_mod.f90
diff --git a/src/spinodal_mod.f b/src/spinodal_mod.f90
similarity index 100%
rename from src/spinodal_mod.f
rename to src/spinodal_mod.f90
diff --git a/src/step_mod.f b/src/step_mod.f90
similarity index 100%
rename from src/step_mod.f
rename to src/step_mod.f90
diff --git a/src/string_mod.f b/src/string_mod.f90
similarity index 100%
rename from src/string_mod.f
rename to src/string_mod.f90
diff --git a/src/sweep_mod.f b/src/sweep_mod.f90
similarity index 100%
rename from src/sweep_mod.f
rename to src/sweep_mod.f90
diff --git a/src/unit_cell_mod.f b/src/unit_cell_mod.f90
similarity index 100%
rename from src/unit_cell_mod.f
rename to src/unit_cell_mod.f90
diff --git a/src/version_mod.f b/src/version_mod.f90
similarity index 100%
rename from src/version_mod.f
rename to src/version_mod.f90
diff --git a/tools/python/preprocess-0.6.1/preprocess.py b/tools/python/preprocess-0.6.1/preprocess.py
index 2e0be75..f92b43c 100755
--- a/tools/python/preprocess-0.6.1/preprocess.py
+++ b/tools/python/preprocess-0.6.1/preprocess.py
@@ -133,7 +133,7 @@ def __init__(self, name, level=None, streamOrFileName=sys.stderr):
             self._level = self.WARN
         else:
             self._level = level
-        if type(streamOrFileName) == types.StringType:
+        if isinstance(streamOrFileName, str):
             self.stream = open(streamOrFileName, 'w')
             self._opennedStream = 1
         else:
@@ -190,7 +190,7 @@ def _evaluate(expr, defines):
     #interpolated = _interpolate(s, defines)
     try:
         rv = eval(expr, {'defined':lambda v: v in defines}, defines)
-    except Exception, ex:
+    except Exception as ex:
         msg = str(ex)
         if msg.startswith("name '") and msg.endswith("' is not defined"):
             # A common error (at least this is presumed:) is to have
@@ -276,7 +276,7 @@ def getContentType(filename):
     basename = os.path.basename(filename)
     contentType = None
     # Try to determine from the filename.
-    if not contentType and filenameMap.has_key(basename):
+    if not contentType and basename in filenameMap:
         contentType = filenameMap[basename]
         log.debug("Content type of '%s' is '%s' (determined from full "\
                   "filename).", filename, contentType)
@@ -286,7 +286,7 @@ def getContentType(filename):
         if sys.platform.startswith("win"):
             # Suffix patterns are case-insensitive on Windows.
             suffix = suffix.lower()
-        if suffixMap.has_key(suffix):
+        if suffix in suffixMap:
             contentType = suffixMap[suffix]
             log.debug("Content type of '%s' is '%s' (determined from "\
                       "suffix '%s').", filename, contentType, suffix)
@@ -378,9 +378,9 @@ def preprocess(infile, outfile=sys.stdout, defines={}, force=0, keepLines=0,
     # (Would be helpful if I knew anything about lexing and parsing
     # simple grammars.)
     fin = open(infile, 'r')
-    if type(outfile) in types.StringTypes:
+    if isinstance(outfile, str):
         if force and os.path.exists(outfile):
-            os.chmod(outfile, 0777)
+            os.chmod(outfile, 0o777)
             os.remove(outfile)
         fout = open(outfile, 'w')
     else:
@@ -541,7 +541,7 @@ def main(argv):
         optlist, args = getopt.getopt(argv[1:], 'hVvo:D:fkI:s',
             ['help', 'version', 'verbose', 'force', 'keep-lines',
              'substitute'])
-    except getopt.GetoptError, msg:
+    except getopt.GetoptError as msg:
         sys.stderr.write("preprocess: error: %s. Your invocation was: %s\n"\
                          % (msg, argv))
         sys.stderr.write("See 'preprocess --help'.\n")
@@ -594,7 +594,7 @@ def main(argv):
     try:
         preprocess(infile, outfile, defines, force, keepLines, includePath,
                    substitute)
-    except PreprocessError, ex:
+    except PreprocessError as ex:
         if verbose:
             import traceback
             traceback.print_exc(file=sys.stderr)