Merge branch 'master' of github.com:LCPQ/quantum_package into LCPQ-master

README.md

@@ -32,27 +32,21 @@ Demo
 
 ### 1) Configure
 
-    $ ./configure <config_file> (--production | --development)
-
-For example you can type `./configure config/gfortran.cfg --production`
+    $ ./configure <config_file> 
+    
+For example you can type `./configure config/gfortran.cfg`
 
 This command has two purposes :
 
  - Download and install all the requirements.
    Installing OCaml and the Core library may take some time (up to 20min on an old machine).
  - Create the file which contains all the dependencies for the binaries.  
-   It's not a Makefile, but a Ninja file (so don't type `make` is hopeless, type `ninja` instead)
+   It's not a Makefile, but a Ninja file (so don't type `make` it's hopeless, type `ninja` instead)
 
-####Compilation Flags (`<config_file>`)
+#### Compilation Flags (`<config_file>`)
 
 `<config_file>` is the path to the file which contains all the compilation flags (optimization flags, Lapack libary, etc). There are two example configure files in  ``$QP_ROOT/config`` : ``ifort.cfg`` and ``gfortran.cfg``.  You can copy these files to create a new file adapted to your architecture. 
 
-#### What utilization of the code will you do?
-
-* If you only want the binaries (for production workflow) use the flag
-  `--production`. It compiles faster. 
-* Else if you are a developer and you want to be able to compile specific modules use: `--development`. It will create the `build.ninja` in each module.
-
 ### 2) Load environment variables
  
     source quantum_package.rc
@@ -75,24 +69,16 @@ Usage:
 
 ### 3) Compiling the Fortran
 
-Just type `ninja` if you are in `$QP_ROOT` (or `ninja -f $QP_ROOT/build.ninja` elsewhere). The compilation will take approximately 3 min.
-
-If you have set the `--developement` flag you can go in any module directory and run `ninja` to build only this particular module. You can type `ninja all` in a module to compile all the submodules.
-
-
-### 4) Compiling the OCaml
-
-    make -C $QP_ROOT/ocaml
+Just type `ninja` if you are in `$QP_ROOT`. The compilation will take approximately 3 min.
 
 ### 5) Testing if all is ok
 
     cd tests ; ./run_tests.sh
 
 
-
 # Note on EZFIO.cfg
 
-##Format specification :
+## Format specification:
 
 ```
 Required:
@@ -119,7 +105,7 @@ Optional:
                               (by default is <module_lower>)
 ```
 
-##Example of EZFIO.cfg:
+## Example of EZFIO.cfg:
 
 ```
 [thresh_SCF]
@@ -135,19 +121,23 @@ doc: Calculated HF energy
 interface: ezfio
 ```
 
-#FAQ
+# FAQ
+
+### My hartree-Fock segfault !
+
+A old version of Lapack have a bug. Just relax your convergence criterium
+
 
 ### Error: ezfio_* is already defined.
 
 #### Why ?
 
-You have two or more ezfio configuration files for the same variable. Check files in `$QP_ROOT/install/EZFIO/config/`
+You have two or more ezfio configuration files for the same variable. Check files in `$QP_ROOT/install/EZFIO/config/` and the all the `EZFIO.cfg`.
 
 #### Fix
 
     - rm $QP_ROOT/install/EZFIO/config/*
     - ninja 
-    
 
 ### Error: Seg Fault (139)
 
@@ -160,7 +150,7 @@ Program exited with code 139.
 
 It's caused when we call the DGEMM routine of LAPACK. 
 
-##### Fix
+#### Fix
 
 Set `ulimit -s unlimited`, before runing `qp_run`. It seems to fix the problem.
 

ocaml/Element.ml

@@ -10,6 +10,7 @@ type t =
 |Na|Mg                              |Al|Si|P |S |Cl|Ar
 |K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
 |Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe
+                           |Pt          
 with sexp
 
 let of_string x = 
@@ -69,6 +70,7 @@ let of_string x =
 |  "Te"  |  "Tellurium"   ->  Te
 |  "I"   |  "Iodine"      ->  I
 |  "Xe"  |  "Xenon"       ->  Xe
+|  "Pt"  |  "Platinum"    ->  Pt
 | x -> raise (ElementError ("Element "^x^" unknown"))
 
 
@@ -128,6 +130,7 @@ let to_string = function
 | Te  -> "Te"
 | I   -> "I"
 | Xe  -> "Xe"
+| Pt  -> "Pt"
 
 
 let to_long_string = function
@@ -186,6 +189,7 @@ let to_long_string = function
 | Te  ->  "Tellurium"
 | I   ->  "Iodine"
 | Xe  ->  "Xenon"
+| Pt  ->  "Platinum"
 
 
 let to_charge c = 
@@ -245,6 +249,7 @@ let to_charge c =
   | Te  -> 52
   | I   -> 53
   | Xe  -> 54
+  | Pt  -> 78
   in Charge.of_int result
 
 
@@ -304,6 +309,7 @@ let of_charge c = match (Charge.to_int c) with
 |  52  -> Te
 |  53  -> I
 |  54  -> Xe
+|  78  -> Pt
 | x -> raise (ElementError ("Element of charge "^(string_of_int x)^" unknown"))
 
 
@@ -364,6 +370,7 @@ let covalent_radius x =
   | Te  -> 1.38
   | I   -> 1.39
   | Xe  -> 1.40
+  | Pt  -> 1.30
   in
   Units.angstrom_to_bohr *. (result x)
   |> Positive_float.of_float
@@ -425,6 +432,7 @@ let vdw_radius x =
   | Te  -> 2.06
   | I   -> 1.98
   | Xe  -> 2.16
+  | Pt  -> 1.75
   in
   Units.angstrom_to_bohr *. (result x)
   |> Positive_float.of_float
@@ -486,6 +494,7 @@ let mass x =
   | Te  -> 127.60
   | I   -> 126.90447
   | Xe  -> 131.293
+  | Pt  -> 195.084
   in
   result x
   |> Positive_float.of_float

ocaml/Element.mli

@@ -7,6 +7,7 @@ type t =
 |Na|Mg                              |Al|Si|P |S |Cl|Ar
 |K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
 |Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe
+                           |Pt
 with sexp
 
 (** String conversion functions *)