Update to MAOOAM v1.3:

Changelog with respect to v1.2
------------------------------

Fortran code:

* Redesign of the aotensor initialization procedure to enable optional storage
of the inner products.
* Inner products are *not* stored by default to avoid excessive memory use.
* Fix Makefile for gfortran > 5.4.0.
* Fix bug where linear/constant terms were not treated correctly in 'read' initial conditions mode.

Lua and Fortran code:

* Add a scale-dependent dissipation process and its associated parameters (nuo and nua) which are zero by default.

fortran/Makefile

@@ -11,8 +11,10 @@ else
   INTEGRATOR = rk2_integrator
   TL_AD_INTEGRATOR = rk2_tl_ad_integrator
 endif
-
-
+ifdef RES
+  ST=_$(RES)
+  $(warning Code will $(RES) the inner products in arrays! It may induce a huge memory usage!)
+endif
 # Define relevant compiler options for debug case and normal case for each compiler
 # Normal Case:
 IFORT_COMPILER_FLAGS = -assume byterecl -O2
@@ -68,7 +70,7 @@ endif
 
 PROGRAMS = maooam test_tl_ad
 
-MODULES = util.mod params.mod inprod_analytic.mod aotensor_def.mod ic_def.mod $(INTEGRATOR).mod stat.mod tensor.mod tl_ad_tensor.mod $(TL_AD_INTEGRATOR).mod $(IFPORT)
+MODULES = util.mod params.mod inprod_analytic$(ST).mod aotensor_def.mod ic_def.mod $(INTEGRATOR).mod stat.mod tensor.mod tl_ad_tensor.mod $(TL_AD_INTEGRATOR).mod $(IFPORT)
 MODULE_OBJECTS = $(MODULES:.mod=.o)
 
 TEST_PROGRAMS = test_inprod_analytic test_aotensor
@@ -92,17 +94,17 @@ test_aotensor.test: test_aotensor
 	./$< |sort  > tests/$<.out
 	diff tests/$<.out tests/$<.ref && echo PASS: $@ || echo FAIL: $@
 
-%.mod: %.f90  
-	$(COMPILER) $(LD_FLAGS) $(COMPILER_FLAGS) -c $<
+%.mod: %.f90
+	$(COMPILER) $(COMPILER_FLAGS) -c $< $(LD_FLAGS) 
 
 %.o: %.f90 $(MODULES)
-	$(COMPILER) $(LD_FLAGS) $(COMPILER_FLAGS) -c $<
+	$(COMPILER) $(COMPILER_FLAGS) -c $< $(LD_FLAGS) 
 
 %: %.o $(MODULE_OBJECTS)
-	$(COMPILER) $(LD_FLAGS) $(COMPILER_FLAGS) $^ -o $@ 
+	$(COMPILER) $(COMPILER_FLAGS) $^ -o $@ $(LD_FLAGS) 
 
-inprod_analytic.mod: params.mod
-aotensor_def.mod: tensor.mod inprod_analytic.mod
+inprod_analytic$(ST).mod: params.mod util.mod
+aotensor_def.mod: tensor.mod inprod_analytic$(ST).mod
 $(INTEGRATOR).mod: aotensor_def.mod
 ic_def.mod: util.mod aotensor_def.mod
 stat.mod: params.mod

fortran/README.md

@@ -27,18 +27,40 @@ resources.
 
 ## Installation ##
 
-The program can be installed with Makefile. We provide configuration files for 
+The program can be installed with Makefile. We provide configuration options for 
 two compilers : gfortran and ifort.
 
-By default, gfortran is selected. To select one or the other, simply modify the 
-Makefile accordingly. If gfortran is selected, the code should be compiled 
-with gfortran 4.7+ (allows for allocatable arrays in namelists). 
-If ifort is selected, the code has been tested with the version 14.0.2 and we 
-do not guarantee compatibility with older compiler version.
+By default, gfortran is selected. To select one or the other, simply modify the
+Makefile accordingly or pass the COMPILER flag to `make`. If gfortran is
+selected, the code should be compiled with gfortran 4.7+ (allows for
+allocatable arrays in namelists).  If ifort is selected, the code has been
+tested with the version 14.0.2 and we do not guarantee compatibility with older
+compiler version.
+
+To install, unpack the archive in a folder or clone with git:
+
+```bash     
+git clone https://github.com/Climdyn/MAOOAM.git
+cd MAOOAM
+```
+     
+and run:
+
+```bash
+make
+```   
+By default, the inner products of the basis functions, used to compute the
+coefficients of the ODEs, are not stored in memory. If you want to enable the
+storage in memory of these inner products, run make with the following flag:
+
+```bash
+make RES=store
+```
+
+Depending on the chosen resolution, storing the inner products may result in a
+huge memory usage and is not recommended unless you need them for a specific
+purpose.
 
-To install, unpack the archive in a folder, and run:
-     make
-
  Remark: The command "make clean" removes the compiled files.
 
 For Windows users, a minimalistic GNU development environment
@@ -59,8 +81,6 @@ initialization.
 * rk2_integrator.f90 : A module which contains the Heun integrator for the model equations.
 * rk4_integrator.f90 : A module which contains the RK4 integrator for the model equations.
 * Makefile : The Makefile.
-* gfortran.mk : Gfortran compiler options file.
-* ifort.mk : Ifort compiler options file.
 * params.f90 : The model parameters module.
 * tl_ad_tensor.f90 : Tangent Linear (TL) and Adjoint (AD) model tensors definition module
 * rk2_tl_ad_integrator.f90 : Heun Tangent Linear (TL) and Adjoint (AD) model integrators module
@@ -97,6 +117,9 @@ The modeselection.nml namelist can then be filled :
 * Note that the variables of the model are numbered according to the chosen
   order of the blocks.
 
+The Makefile allows to change the integrator being used for the time evolution.
+The user should modify it according to its need.
+By default a RK2 scheme is selected.
 
 Finally, the IC.nml file specifying the initial condition should be defined. To
 obtain an example of this configuration file corresponding to the model you
@@ -116,7 +139,7 @@ It will generate two files :
 
 The tangent linear and adjoint models of MAOOAM are provided in the
 tl_ad_tensor, rk2_tl_ad_integrator and rk4_tl_ad_integrator modules. It is
-documented [here](./doc/html/md_tl_ad_doc.html).
+documented [here](./doc/html/md_doc_tl_ad_doc.html).
 
 
 ------------------------------------------------------------------------

fortran/aotensor_def.f90

@@ -140,7 +140,8 @@ END SUBROUTINE func
     CALL func(theta(1),0,0,(Cpa / (1 - atmos%a(1,1) * sig0)))
     DO i = 1, natm
        DO j = 1, natm
-          CALL func(psi(i),psi(j),0,-(((atmos%c(i,j) * betp) / atmos%a(i,i))) - (kd * kdelta(i,j)) / 2)
+          CALL func(psi(i),psi(j),0,-(((atmos%c(i,j) * betp) / atmos%a(i,i))) -&
+               &(kd * kdelta(i,j)) / 2 + atmos%a(i,j)*nuap)
           CALL func(theta(i),psi(j),0,(atmos%a(i,j) * kd * sig0) / (-2 + 2 * atmos%a(i,i) * sig0))
           CALL func(psi(i),theta(j),0,(kd * kdelta(i,j)) / 2)
           CALL func(theta(i),theta(j),0,(-((sig0 * (2. * atmos%c(i,j) * betp +&
@@ -167,8 +168,8 @@ END SUBROUTINE func
           CALL func(A(i),theta(j),0,-(ocean%K(i,j)) * dp / (ocean%M(i,i) + G))
        END DO
        DO j = 1, noc
-          CALL func(A(i),A(j),0,-((ocean%N(i,j) * betp + ocean%M(i&
-               &,i) * (rp + dp) * kdelta(i,j))) / (ocean%M(i,i) + G))
+          CALL func(A(i),A(j),0,-((ocean%N(i,j) * betp + ocean%M(i,i) * (rp + dp) * kdelta(i,j)&
+               & - ocean%M(i,j)**2*nuop)) / (ocean%M(i,i) + G))
           DO k = 1, noc
              CALL func(A(i),A(j),A(k),-(ocean%C(i,j,k)) / (ocean%M(i,i) + G))
           END DO
@@ -224,8 +225,6 @@ SUBROUTINE init_aotensor
 
     CALL simplify(aotensor)
 
-    CALL deallocate_inprod ! Clean the inner product tensors
-
   END SUBROUTINE init_aotensor
 END MODULE aotensor_def
 

fortran/doc/gen_doc.md

@@ -33,13 +33,35 @@ The program can be installed with Makefile. We provide configuration files for
 two compilers : gfortran and ifort.
 
 By default, gfortran is selected. To select one or the other, simply modify the 
-Makefile accordingly. If gfortran is selected, the code should be compiled 
-with gfortran 4.7+ (allows for allocatable arrays in namelists). 
-If ifort is selected, the code has been tested with the version 14.0.2 and we 
-do not guarantee compatibility with older compiler version.
-
-To install, unpack the archive in a folder, and run:
-     make
+Makefile accordingly or pass the COMPILER flag to `make`. If gfortran is
+selected, the code should be compiled with gfortran 4.7+ (allows for
+allocatable arrays in namelists).  If ifort is selected, the code has been
+tested with the version 14.0.2 and we do not guarantee compatibility with older
+compiler version.
+
+To install, unpack the archive in a folder or clone with git:
+
+```bash     
+git clone https://github.com/Climdyn/MAOOAM.git
+cd MAOOAM
+```
+     
+and run:
+
+```bash     
+make
+```     
+By default, the inner products of the basis functions, used to compute the
+coefficients of the ODEs, are not stored in memory. If you want to enable the
+storage in memory of these inner products, run make with the following flag:
+
+```bash
+make RES=store
+```
+
+Depending on the chosen resolution, storing the inner products may result in a
+huge memory usage and is not recommended unless you need them for a specific
+purpose.
 
  Remark: The command "make clean" removes the compiled files.
 
@@ -61,8 +83,6 @@ initialization.
 * rk2_integrator.f90 : A module which contains the Heun integrator for the model equations.
 * rk4_integrator.f90 : A module which contains the RK4 integrator for the model equations.
 * Makefile : The Makefile.
-* gfortran.mk : Gfortran compiler options file.
-* ifort.mk : Ifort compiler options file.
 * params.f90 : The model parameters module.
 * tl_ad_tensor.f90 : Tangent Linear (TL) and Adjoint (AD) model tensors definition module
 * rk2_tl_ad_integrator.f90 : Heun Tangent Linear (TL) and Adjoint (AD) model integrators module
@@ -98,6 +118,9 @@ The modeselection.nml namelist can then be filled :
 * Note that the variables of the model are numbered according to the chosen
   order of the blocks.
 
+The Makefile allows to change the integrator being used for the time evolution.
+The user should modify it according to its need.
+By default a RK2 scheme is selected.
 
 Finally, the IC.nml file specifying the initial condition should be defined. To
 obtain an example of this configuration file corresponding to the model you
@@ -117,7 +140,7 @@ It will generate two files :
 
 The tangent linear and adjoint models of MAOOAM are provided in the
 tl_ad_tensor, rk2_tl_ad_integrator and rk4_tl_ad_integrator modules. It is
-documented [here](./md_tl_ad_doc.html).
+documented [here](./md_doc_tl_ad_doc.html).
 
 
 ------------------------------------------------------------------------

fortran/doc/html/LICENSE_8txt.html

@@ -463,7 +463,7 @@ <h2 class="groupheader">Variable Documentation</h2>
 </div><!-- contents -->
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>
-Generated on Thu Jan 5 2017 15:58:39 by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Mon Feb 19 2018 16:12:31 by &#160;<a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/>
 </a> 1.8.11
 </small></address>

fortran/doc/html/annotated.html

@@ -107,7 +107,7 @@
 </div><!-- contents -->
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>
-Generated on Thu Jan 5 2017 15:58:41 by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Mon Feb 19 2018 16:12:32 by &#160;<a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/>
 </a> 1.8.11
 </small></address>

fortran/doc/html/aotensor__def_8f90.html

@@ -150,7 +150,7 @@
 </div><!-- contents -->
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>
-Generated on Thu Jan 5 2017 15:58:39 by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Mon Feb 19 2018 16:12:31 by &#160;<a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/>
 </a> 1.8.11
 </small></address>

fortran/doc/html/classes.html

@@ -107,7 +107,7 @@
 </div><!-- contents -->
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>
-Generated on Thu Jan 5 2017 15:58:41 by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Mon Feb 19 2018 16:12:32 by &#160;<a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/>
 </a> 1.8.11
 </small></address>

fortran/doc/html/files.html

@@ -115,7 +115,7 @@
 </div><!-- contents -->
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>
-Generated on Thu Jan 5 2017 15:58:42 by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Mon Feb 19 2018 16:12:32 by &#160;<a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/>
 </a> 1.8.11
 </small></address>

fortran/doc/html/functions.html

@@ -96,23 +96,23 @@
 <div class="contents">
 <div class="textblock">Here is a list of all data types members with links to the data types they belong to:</div><ul>
 <li>a
-: <a class="el" href="structinprod__analytic_1_1atm__tensors.html#af50962da7a48c98d8b118dee9cc16dcd">inprod_analytic::atm_tensors</a>
+: <a class="el" href="structinprod__analytic_1_1atm__tensors.html#abb8c2b843f31f85eadf4c183b9bbfc35">inprod_analytic::atm_tensors</a>
 </li>
 <li>b
-: <a class="el" href="structinprod__analytic_1_1atm__tensors.html#aa6b446e5bd3e7ea7278f1c1cad7f46cf">inprod_analytic::atm_tensors</a>
+: <a class="el" href="structinprod__analytic_1_1atm__tensors.html#a427a3462d211c39009bb85e0cfe4a59b">inprod_analytic::atm_tensors</a>
 </li>
 <li>c
-: <a class="el" href="structinprod__analytic_1_1atm__tensors.html#a6f560bb68ce7081409034cb755e7a164">inprod_analytic::atm_tensors</a>
-, <a class="el" href="structinprod__analytic_1_1ocean__tensors.html#a146670849488f50eff7b1937077a67ff">inprod_analytic::ocean_tensors</a>
+: <a class="el" href="structinprod__analytic_1_1atm__tensors.html#a1fcb71de592cf7d87e8c7e13e445832c">inprod_analytic::atm_tensors</a>
+, <a class="el" href="structinprod__analytic_1_1ocean__tensors.html#a0601d4c16c2f7d9e8789619ac9e25311">inprod_analytic::ocean_tensors</a>
 </li>
 <li>d
-: <a class="el" href="structinprod__analytic_1_1atm__tensors.html#a00e06ac193f03e4dcd337439cc489f78">inprod_analytic::atm_tensors</a>
+: <a class="el" href="structinprod__analytic_1_1atm__tensors.html#a0641c2984e3cf9eff629771519162b05">inprod_analytic::atm_tensors</a>
 </li>
 <li>elems
 : <a class="el" href="structtensor_1_1coolist.html#a49ece7bfa6e6e37b4223a1c63b5c7839">tensor::coolist</a>
 </li>
 <li>g
-: <a class="el" href="structinprod__analytic_1_1atm__tensors.html#a9b4ecfbc139ac739d5ec82b087e421a5">inprod_analytic::atm_tensors</a>
+: <a class="el" href="structinprod__analytic_1_1atm__tensors.html#a4543ab64bfdcdb2aac1f2d9b1af2ee36">inprod_analytic::atm_tensors</a>
 </li>
 <li>h
 : <a class="el" href="structinprod__analytic_1_1atm__wavenum.html#aa7df1690e97e43365ca0c2b1222924b5">inprod_analytic::atm_wavenum</a>
@@ -122,15 +122,15 @@
 : <a class="el" href="structtensor_1_1coolist__elem.html#a0ed51fd9ddc1c2168d8c138eb5da5f66">tensor::coolist_elem</a>
 </li>
 <li>k
-: <a class="el" href="structinprod__analytic_1_1ocean__tensors.html#a1ab0d8f229b274e954a53cc1ce40cac1">inprod_analytic::ocean_tensors</a>
+: <a class="el" href="structinprod__analytic_1_1ocean__tensors.html#a9715c83158697198ef484b0bc549bcc3">inprod_analytic::ocean_tensors</a>
 , <a class="el" href="structtensor_1_1coolist__elem.html#a368c80ca537d7c5d6e1fbba8a85dec38">tensor::coolist_elem</a>
 </li>
 <li>m
 : <a class="el" href="structinprod__analytic_1_1atm__wavenum.html#a72be0a86c5f5801b88ebf78506523bd2">inprod_analytic::atm_wavenum</a>
-, <a class="el" href="structinprod__analytic_1_1ocean__tensors.html#a6f8f8b2b4ef239db0a9f751d7e8452e8">inprod_analytic::ocean_tensors</a>
+, <a class="el" href="structinprod__analytic_1_1ocean__tensors.html#a9f72e3b14a98a50209f86b01626f6c53">inprod_analytic::ocean_tensors</a>
 </li>
 <li>n
-: <a class="el" href="structinprod__analytic_1_1ocean__tensors.html#a5087e225a596aee2d668f6282dd6a019">inprod_analytic::ocean_tensors</a>
+: <a class="el" href="structinprod__analytic_1_1ocean__tensors.html#a2ccccfae8fb93871f6d7d81d90676b19">inprod_analytic::ocean_tensors</a>
 </li>
 <li>nelems
 : <a class="el" href="structtensor_1_1coolist.html#aac72e7727f1b161da2b9d54e25eb7aae">tensor::coolist</a>
@@ -144,14 +144,14 @@
 , <a class="el" href="structinprod__analytic_1_1ocean__wavenum.html#a0738c305f503d7864a9073c5cea352ab">inprod_analytic::ocean_wavenum</a>
 </li>
 <li>o
-: <a class="el" href="structinprod__analytic_1_1ocean__tensors.html#abab4899297820e7a92cc8d363a91ed13">inprod_analytic::ocean_tensors</a>
+: <a class="el" href="structinprod__analytic_1_1ocean__tensors.html#a1002c698464fe4761ac8f0c53908c796">inprod_analytic::ocean_tensors</a>
 </li>
 <li>p
 : <a class="el" href="structinprod__analytic_1_1atm__wavenum.html#a5a938641d8939931bc4eb71499298a6a">inprod_analytic::atm_wavenum</a>
 , <a class="el" href="structinprod__analytic_1_1ocean__wavenum.html#a3170ff1b2a81b58ae81527a964682c06">inprod_analytic::ocean_wavenum</a>
 </li>
 <li>s
-: <a class="el" href="structinprod__analytic_1_1atm__tensors.html#ad95a5329b72aae59807e7cdf043ab52c">inprod_analytic::atm_tensors</a>
+: <a class="el" href="structinprod__analytic_1_1atm__tensors.html#a27edca850b0482aea4aac985ec64124d">inprod_analytic::atm_tensors</a>
 </li>
 <li>typ
 : <a class="el" href="structinprod__analytic_1_1atm__wavenum.html#a1c12be211e96c5a773aae4c2146a3792">inprod_analytic::atm_wavenum</a>
@@ -160,13 +160,13 @@
 : <a class="el" href="structtensor_1_1coolist__elem.html#ac569057f08f5f8ea171b87aa7b9dd428">tensor::coolist_elem</a>
 </li>
 <li>w
-: <a class="el" href="structinprod__analytic_1_1ocean__tensors.html#ae4875d9d3ea854b3b7b57e0c07a07ede">inprod_analytic::ocean_tensors</a>
+: <a class="el" href="structinprod__analytic_1_1ocean__tensors.html#ad14f4b5bea84f71ecb4f6665b15e78f1">inprod_analytic::ocean_tensors</a>
 </li>
 </ul>
 </div><!-- contents -->
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>
-Generated on Thu Jan 5 2017 15:58:42 by &#160;<a href="http://www.doxygen.org/index.html">
+Generated on Mon Feb 19 2018 16:12:32 by &#160;<a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/>
 </a> 1.8.11
 </small></address>