doc updates and hmcode tidies (thanks Alex Mead, Minh Nguyen)

Author: cmbant

.travis.yml

@@ -13,51 +13,27 @@ branches:
 
 jobs:
   include:
-    - name: "GCC6 + Python 3.7"
-      addons:
-        apt:
-          packages:
-            - gfortran-6
-      env:
-        - GCC_VERSION="6"
-        - CHANNEL="defaults"
-        - PYDIST="ANACONDA"
-        - FORTRAN="test"
-      python: "3.7"
-    - name: "GCC9 + Python 3.9 (anaconda)"
-      addons:
-        apt:
-          sources:
-            - sourceline: "ppa:ubuntu-toolchain-r/test"
-          packages:
-            - gfortran-9
-      env:
-        - GCC_VERSION="9"
-        - PYDIST="ANACONDA"
-        - CHANNEL="defaults"
-        - FORTRAN="test"
-      python: "3.9"
-    - name: "Ubuntu 20.04 + Python 3.8"
+    - name: "Ubuntu 20.04 + Python 3.7"
       dist: focal
       addons:
         apt:
           packages:
             - gfortran
-      python: "3.10"
+      python: "3.7"
       env:
         - PYPI_DIST="true"
-    - name: "GCC10 + Python 3.9 (conda-forge)"
+    - name: "GCC10 + Python 3.10 anaconda"
       dist: focal
       addons:
         apt:
           packages:
             - gfortran-10
       env:
         - GCC_VERSION="10"
-        - FORTRAN="test"
-        - CHANNEL="conda-forge"
+        - CHANNEL="defaults"
         - PYDIST="ANACONDA"
-      python: "3.9"
+        - FORTRAN="test"
+      python: "3.10"
     - name: "GCC trunk cosmobox"
       language: shell
       services:

README.rst

@@ -35,13 +35,9 @@ To install from source, clone from github using::
 
     git clone --recursive https://github.com/cmbant/CAMB
 
-Then in the project source root directory use::
+Then install using::
 
-    python setup.py install [--user]
-
-If you want to work on the code, you can also just install in place without copying anything using::
-
-    pip install -e . [--user]
+    pip install -e ./CAMB [--user]
 
 You will need gfortran 6 or higher installed to compile. Binary files for Windows are also provided, so these are used instead if no
 gfortran installation is found on Windows machines. If you have gfortran installed, "python setup.py make"

camb/cambdll.dll

@@ -17,7 +17,7 @@ If you do not have a suitable Fortran compiler, you can get one as follows:
 :Mac:
     Download the `binary installation <https://gcc.gnu.org/wiki/GFortranBinaries>`_
 :Windows:
-    Download gfortran as part of `MinGW-w64 <https://sourceforge.net/projects/mingw-w64/>`_ (select x86_64 option in the installation program)
+    Download gfortran as part of `MinGW-w64 <https://sourceforge.net/projects/mingw-w64/files>`_ (select x86_64 option in the installation program)
 :Linux:
     To install from the standard repository use:
 
@@ -74,4 +74,3 @@ If you want to automamatically rebuild the library from Jupyter you can do somet
 
     except subprocess.CalledProcessError as E:
         print(E.output.decode())
-

docs/source/fortran_compilers.rst

@@ -17,31 +17,36 @@ For a standard non-editable installation use::
 The --user is optional and only required if you don't have write permission to your main python installation.
 If you want to work on the code from `GitHub <https://github.com/cmbant/camb>`_, you can also just install in place without copying anything using::
 
-    pip install -e /path/to/CAMB [--user]
+    git clone --recursive https://github.com/cmbant/CAMB.git
+    pip install -e ./CAMB [--user]
 
 You will need ifort or gfortran 6 or higher installed (and on your path) to compile; see :ref:`fortran-compilers` for
 compiler installation details if needed. A compiled library for Windows is also provided, and is used if no
-gfortran installation is found on Windows machines. If you have gfortrand installed, "python setup.py make" will build
+gfortran installation is found on Windows machines. If you have gfortran installed, "python setup.py make" will build
 the Fortran library on all systems (including Windows without directly using a Makefile), and can be used to update
 a source installation after changes or pulling an updated version.
 
-Anaconda users can also install from conda-forge using::
+Anaconda users can also install from conda-forge, best making a new clean environment using::
 
-  conda install -c conda-forge camb
+  conda create -n camb -c conda-forge python=3.9 camb
+  activate camb
 
 with no need for a Fortran compiler (unless you want to use custom sources/symbolic compilation features).
-Check that conda installs the latest version, if not try installing in a new clean conda environment.
+Check that conda installs the latest version, if not try installing
+in a new clean conda environment as above.
 
 After installation the camb python module can be loaded from your scripts using "import camb".
+
 You can also run CAMB from the command line reading parameters from a .ini file, e.g.::
 
   camb inifiles/planck_2018.ini
 
-You may need to check your python scripts directory is in your path for this to work.
-Alternatively from the source package root directory (after make but without installation) use::
+You may need to check your python scripts directory is in your path for this to work. Alternatively from the source package root directory (after make but without installation) use::
 
   python camb.py inifiles/planck_2018.ini
 
+Sample .ini files can be obtained from the `repository <https://github.com/cmbant/CAMB/tree/master/inifiles>`_. You can load parameters programmatically from an .ini file or URL using :func:`.camb.read_ini`.
+
 Main high-level modules:
 
 .. toctree::

docs/source/index.rst

@@ -617,7 +617,7 @@ SUBROUTINE HMcode(this,State,CAMB_Pk)
                 DO i=1,nk
                     k=exp(CAMB_Pk%log_kh(i))
                     plin=p_lin(k,z,0,cosi)
-                    CALL this%halomod(k,z,p1h,p2h,pfull,plin,lut,cosi)
+                    CALL this%halomod(k,p1h,p2h,pfull,plin,lut,cosi)
                     IF(this%imead==3) THEN
                         CAMB_Pk%nonlin_ratio(i,j)=sqrt(pfull/plin)
                     ELSE IF(this%imead==4) THEN
@@ -641,7 +641,7 @@ SUBROUTINE HMcode(this,State,CAMB_Pk)
             DO i=1,nk
                 k=exp(CAMB_Pk%log_kh(i))
                 plin=p_lin(k,z,0,cosi)
-                CALL this%halomod(k,z,p1h,p2h,pfull,plin,lut,cosi)
+                CALL this%halomod(k,p1h,p2h,pfull,plin,lut,cosi)
                 CAMB_Pk%nonlin_ratio(i,j)=sqrt(pfull/plin)
             END DO
             !$OMP END PARALLEL DO
@@ -844,11 +844,11 @@ FUNCTION r_nl(lut)
 
     END FUNCTION r_nl
 
-    SUBROUTINE halomod(this,k,z,p1h,p2h,pfull,plin,lut,cosm)
+    SUBROUTINE halomod(this,k,p1h,p2h,pfull,plin,lut,cosm)
     class(THalofit) :: this
     !Calcuates 1-halo and 2-halo terms and combines them to form the full halomodel power
     REAL(dl), INTENT(OUT) :: p1h, p2h, pfull
-    REAL(dl), INTENT(IN) :: plin, k, z
+    REAL(dl), INTENT(IN) :: plin, k
     REAL(dl) :: a
     TYPE(HM_cosmology), INTENT(IN) :: cosm
     TYPE(HM_tables), INTENT(IN) :: lut
@@ -859,7 +859,7 @@ SUBROUTINE halomod(this,k,z,p1h,p2h,pfull,plin,lut,cosm)
         p1h=0.
         p2h=0.
     ELSE
-        p1h=this%p_1h(k,z,lut,cosm)
+        p1h=this%p_1h(k,lut,cosm)
         p2h=this%p_2h(k,plin,lut,cosm)
     END IF
 
@@ -1705,22 +1705,22 @@ FUNCTION p_2h(this,k,plin,lut,cosm)
         kdamp=0.05699*lut%sig8z_cold**(-1.089)
         ndamp=2.85
         x=(k/kdamp)**ndamp
-        p_2h=p_dewiggle(k, lut%z, lut%sigv, cosm)*(1.-frac*x/(1.+x))
+        p_2h=p_dewiggle(k, lut%z, plin, lut%sigv, cosm)*(1.-frac*x/(1.+x))
     END IF
 
     !For some strange cosmologies frac>1. so this must be added to prevent p_2h<0.
     IF(p_2h<0.) p_2h=0.
 
     END FUNCTION p_2h
 
-    FUNCTION p_1h(this,k,z,lut,cosm)
+    FUNCTION p_1h(this,k,lut,cosm)
     class(THalofit) :: this
     !Calculates the 1-halo term
     REAL(dl) :: p_1h
-    REAL(dl), INTENT(IN) :: k, z
+    REAL(dl), INTENT(IN) :: k
     TYPE(HM_tables), INTENT(IN) :: lut
     TYPE(HM_cosmology), INTENT(IN) :: cosm
-    REAL(dl) :: Dv, g, fac, et, ks, wk, x, m
+    REAL(dl) :: g, fac, et, ks, wk, x, m
     REAL(dl) :: integrand(lut%n)
     REAL(dl) :: sum
     INTEGER :: i
@@ -1767,35 +1767,30 @@ FUNCTION p_1h(this,k,z,lut,cosm)
 
     END FUNCTION p_1h
 
-    REAL FUNCTION p_dewiggle(k, z, sigv, cosm)
+    REAL FUNCTION p_dewiggle(k, z, p_linear, sigv, cosm)
     ! Call the dewiggled power spectrum, which is linear but with damped wiggles
-    REAL(dl), INTENT(IN) :: k
-    REAL(dl), INTENT(IN) :: z
-    REAL(dl), INTENT(IN) :: sigv
+    REAL(dl), INTENT(IN) :: k, z, p_linear, sigv
     TYPE(HM_cosmology), INTENT(IN) :: cosm
-    REAL(dl) :: p_wiggle, f, p_linear, logk
-    INTEGER, PARAMETER :: itype = 0 ! Matter power here
+    REAL(dl) :: p_wiggle, f, logk
     INTEGER, PARAMETER :: iorder = iorder_wiggle
     INTEGER, PARAMETER :: ifind = ifind_wiggle
     INTEGER, PARAMETER :: imeth = imeth_wiggle
 
-    p_linear = p_lin(k, z, itype, cosm)
     logk = log(k)
     IF (logk < cosm%log_k_wiggle(1) .OR. logk > cosm%log_k_wiggle(nk_wiggle)) THEN
-        p_wiggle = 0.
+        p_wiggle = 0
     ELSE
-        p_wiggle = find(log(k), cosm%log_k_wiggle, cosm%pk_wiggle, nk_wiggle, iorder, ifind, imeth)
+        p_wiggle = find(logk, cosm%log_k_wiggle, cosm%pk_wiggle, nk_wiggle, iorder, ifind, imeth)
     END IF
     f = exp(-(k*sigv)**2)
-    p_dewiggle = p_linear+(f-1.)*p_wiggle*grow(z, cosm)**2
+    p_dewiggle = p_linear+(f-1)*p_wiggle*grow(z, cosm)**2
 
     END FUNCTION p_dewiggle
 
     SUBROUTINE init_wiggle(cosm)
     ! Isolate the power spectrum wiggle
     TYPE(HM_cosmology), INTENT(INOUT) :: cosm
     REAL(dl), ALLOCATABLE :: k(:), Pk(:)
-    REAL(dl), ALLOCATABLE :: logk(:), logPk(:)
     REAL(dl), ALLOCATABLE :: Pk_smooth(:), Pk_wiggle(:)
     INTEGER :: i
     REAL(dl), PARAMETER :: kmin = kmin_wiggle
@@ -1857,7 +1852,6 @@ SUBROUTINE calculate_psmooth(k, z, Pk, Pk_smt, cosm)
     REAL(dl), ALLOCATABLE, INTENT(OUT) :: Pk_smt(:)
     REAL(dl), ALLOCATABLE :: Pk_nw(:)
     TYPE(HM_cosmology), INTENT(IN) :: cosm
-    INTEGER :: ia, na
     REAL(dl), PARAMETER :: sig = wiggle_sigma
 
     ! Reduce dynamic range
@@ -1880,7 +1874,7 @@ SUBROUTINE calculate_nowiggle(k, z, Pk, Pk_nw, cosm)
     REAL(dl), INTENT(IN) :: Pk(:)
     REAL(dl), ALLOCATABLE, INTENT(OUT) :: Pk_nw(:)
     TYPE(HM_cosmology), INTENT(IN) :: cosm
-    INTEGER :: ik, ia, nk
+    INTEGER :: ik, nk
     REAL(dl) :: Pk_norm, Pk_nw_norm
     REAL(dl), PARAMETER :: knorm = knorm_nowiggle
     INTEGER, PARAMETER :: type = 0 ! Matter here
@@ -3329,7 +3323,7 @@ REAL(dl) FUNCTION dc_Mead(z, cosm)
     IMPLICIT NONE
     REAL(dl), INTENT(IN) :: z
     TYPE(HM_cosmology), INTENT(IN) :: cosm
-    REAL(dl) :: lg, bG, Om_m, ai, a
+    REAL(dl) :: lg, bG, Om_m, a
 
     ! See Appendix A of Mead (2017) for naming convention
     REAL(dl), PARAMETER :: p10 = -0.0069

fortran/halofit.f90

@@ -122,8 +122,8 @@ def make_library(cluster=False):
         if not ok:
             print('WARNING: gfortran %s or higher not in path (if you just installed '
                   'you may need to log off and on again).' % _compile.gfortran_min)
-            print('         You can get a Windows gfortran build from https://sourceforge.net/projects/mingw-w64/')
-            print('         - go to Files, and download MinGW-W64 Online Installer.')
+            print('        You can get a Windows gfortran build from https://sourceforge.net/projects/mingw-w64/files/')
+            print('        - go to Files, and download MinGW-W64 Online Installer.')
             if _compile.is_32_bit:
                 raise IOError('No 32bit Windows DLL provided, you need to build or use 64 bit python')
             else:
@@ -192,6 +192,9 @@ def make_library(cluster=False):
             else:
                 print('DLL up to date.')
     else:
+        if not _compile.call_command('make -v'):
+            raise IOError('Build failed - you must have "make" installed. '
+                          'E.g. on ubuntu install with "sudo apt install make" (or use build-essential package).')
         get_forutils()
         print("Compiling source...")
         subprocess.call("make python PYCAMB_OUTPUT_DIR=%s/camb/ CLUSTER_SAFE=%d" %
@@ -303,6 +306,7 @@ def run(self):
               'Programming Language :: Python :: 3.7',
               'Programming Language :: Python :: 3.8',
               'Programming Language :: Python :: 3.9'
+              'Programming Language :: Python :: 3.10'
           ],
           keywords=['cosmology', 'CAMB', 'CMB'],
           install_requires=['scipy>=1.0', 'sympy>=1.0'],