Merge branch 'LCPQ-master'

README.md

@@ -9,10 +9,11 @@ Quantum package
 Set of quantum chemistry programs and libraries. 
 (under GNU GENERAL PUBLIC LICENSE v2)
 
-For more information, you can visit the [wiki of the project](http://github.com/LCPQ/quantum_package/wiki>), or bellow for the installation instruction.
+For more information, you can visit the [wiki of the project](http://github.com/LCPQ/quantum_package/wiki>), or below for the installation instructions.
 
 # Installation
 
+
 ## Requirements
 * Fortran compiler (`ifort` and `gfortran` are tested)
 * Python >= 2.6
@@ -30,29 +31,30 @@ For more information, you can visit the [wiki of the project](http://github.com/
 
 For example you can type `./configure config/gfortran.cfg --production`
 
-This command have to purpose :
+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).
- - And create the file which contains all the tree dependencies for the binaries.  
+ - 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)
 
 ####Compilation Flags (`<config_file>`)
 
-`<config_file>` is the path to the file who contain all the flags useful for the compilation:  like the optimization flags, the Lapack libary, etc.  We have two default configure file in  ``$QP_ROOT/config`` : ``ifort.cfg`` and ``gfortran.cfg``.  You can edit these files to modify the compiling options. 
+`<config_file>` is the path to the file which contains all the compilation flags (optimization flags, Lapack libary, etc). There are two example configure files in  ``$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` in when calling this script. It's quicker 
+  `--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 for you the `build.ninja` in each module
+* 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) Set environment variable
+### 2) Load environment variables
  
     source quantum_package.rc
+    
 This file contains all the environment variables needed by the quantum package both to compile and run. This should also be done before running calculations.
 
-### Optional) Add some new module
+### Optional) Add some modules
 
       Usage: qp_module.py list (--installed|--avalaible-local|--avalaible-remote)
        qp_module.py install <name>...
@@ -62,61 +64,22 @@ This file contains all the environment variables needed by the quantum package b
  For exemple you can type :
 `qp_module.py install Full_CI`
 
-### 3) Compiling the fortran
+### 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 in a specific module you can go in
+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.
-the corresponding module directory and run `ninja` to build only this module.
-You can type `ninja all` in a module for compiling all the submodule
 
 
 ### 4) Compiling the OCaml
 
-    cd ocaml ; make ; cd -
+    make -C ocaml
 
 ### 5) Testing if all is ok
 
-    cd testing_no_regression ; ./unit_test.py
+    cd tests ; bats bats/qp.bats 
 
-## Installing behind a firewall !
 
-1) Download `tsocks`:
-
-    wget http://sourceforge.net/projects/tsocks/files/latest/download
-    mv download tsocks.tar.gz
-
-2) Tranfer `tsocks.tar.gz` on the remote host
-
-3) Configure `tsocks` with the proper directory for the `tsocks.conf` file:
-
-    tar -zxvf tsocks.tar.gz
-    cd tsocks-*
-    ./configure --with-conf=${PWD}/tsocks.conf
-
-4) Create the `tsocks.conf` file with the following content:
-
-    server = 127.0.0.1
-    server_port = 10000
-
-5) Create the tsocks library:
-
-    make
-
-6) Add the `libtsocks.so` to the `LD_PRELOAD` environment variable:
-
-    export LD_PRELOAD="${PWD}/libtsocks.so.1.8"
-
-7) Create a custom curl command to set the tsocks option: open a file named
-   `curl`, which is accessible from your `PATH` environment variable before the
-   real `curl` command, and fill this file with:
-
-    #!/bin/bash
-    /usr/bin/curl --socks5 127.0.0.1:10000 $@
-
-8) Start a tsocks ssh tunnel:
-
-    ssh -fN -D 10000 user@external-server.com
 
 # Note on EZFIO.cfg
 
@@ -126,24 +89,24 @@ You can type `ninja all` in a module for compiling all the submodule
 Required:
     [<provider_name>]   The name of the provider in irp.f90 and in the EZFIO lib
     doc:<str>           The plain text documentation
-    type:<str>          A Fancy_type supported by the ocaml.
+    type:<str>          A type supported by the OCaml.
                             type `ei_handler.py get_supported_type` for a list
-    interface:<str>     The interface is list of string sepeared by ","  who can containt :
+    interface:<str>     The interface is a list of strings sepeared by ","  which can contain :
-                          - ezfio (if you only whant the ezfiolib)
+                          - ezfio : to build the EZFIO API
-                          - provider (if you want the provider)
+                          - provider : to build the corresponding providers 
-                          - ocaml (if you want the ocaml gestion)
+                          - ocaml : to build the corresponding bindings in OCaml
 Optional:
-    default: <str>      The default value needed,
+    default: <str>      The default value,
-                            if 'ocaml' is in interface list.
+                            needed if 'ocaml' is in interface list.
                            ! No list is allowed for now !
     size: <str>         The size information.
                             (by default is one)
-                            Example : 1, =sum(ao_num); (ao_num,3)
+                            Example : 1; =sum(ao_num); (ao_num,3)
-                            ATTENTION : The module and the value are separed by a "." not a "_".
+                            WARNING : The module and the value are separed by a "." not a "_".
-                            For exemple (determinants.n_det)
+                            For example (determinants.n_det)
-    ezfio_name: <str>   The name for the EZFIO lib
+    ezfio_name: <str>   The name in the EZFIO API
                              (by default is <provider_name>)
-    ezfio_dir: <str>    Will be the folder of EZFIO.
+    ezfio_dir: <str>    Will be the directory of EZFIO.
                               (by default is <module_lower>)
 ```
 
@@ -169,7 +132,7 @@ interface: ezfio
 
 #### Why ?
 
-You have two or more ezfio configuration file for the same variable. Check in `$QP_ROOT/install/config/`
+You have two or more ezfio configuration files for the same variable. Check files in `$QP_ROOT/install/EZFIO/config/`
 
 #### Fix
 

data/README.rst

@@ -4,3 +4,6 @@ Data
 
 
 This directory contains all the data files needed for the Quantum Package.
+
+The `basis` directory contains some of the most popular basis sets, and the
+`pseudo` directory contains pseudopotential data.

data/periodic-table

@@ -1,36 +0,0 @@
-  1 H   Hydrogen
-  2 He  Helium
-  3 Li  Lithium
-  4 Be  Beryllium
-  5 B   Boron
-  6 C   Carbon
-  7 N   Nitrogen
-  8 O   Oxygen
-  9 F   Fluorine
- 10 Ne  Neon
- 11 Na  Sodium
- 12 Mg  Magnesium
- 13 Al  Aluminum
- 14 Si  Silicon
- 15 P   Phosphorus
- 16 S   Sulfur
- 17 Cl  Chlorine
- 18 Ar  Argon
- 19 K   Potassium
- 20 Ca  Calcium
- 21 Sc  Scandium
- 22 Ti  Titanium
- 23 V   Vanadium
- 24 Cr  Chromium
- 25 Mn  Manganese
- 26 Fe  Iron
- 27 Co  Cobalt
- 28 Ni  Nickel
- 29 Cu  Copper
- 30 Zn  Zinc
- 31 Ga  Gallium
- 32 Ge  Germanium
- 33 As  Arsenic
- 34 Se  Selenium
- 35 Br  Bromine
- 36 Kr  Krypton

install/scripts/install_ocaml.sh

@@ -77,3 +77,4 @@ NCPUs=$(cat /proc/cpuinfo  | grep -i  MHz | wc -l)
 ${QP_ROOT}/bin/opam install -j ${NCPUs} ${PACKAGES} -y -q || exit 1
 
 rm -f ../_build/ocaml.log
+

ocaml/qp_print_basis.ml

@@ -1,7 +1,7 @@
 open Core.Std
 open Qptypes
 
-let () =
+let basis ()=
   let ezfio_filename =
     Sys.argv.(1)
   in
@@ -18,3 +18,22 @@ let () =
   |> print_endline
 
 
+let mo ()=
+  let ezfio_filename =
+    Sys.argv.(1)
+  in
+  if (not (Sys.file_exists_exn ezfio_filename)) then
+    failwith "Error reading EZFIO file";
+  Ezfio.set_file ezfio_filename;
+  let mo_coef =
+    match Input.Mo_basis.read () with
+    | Some mo_coef -> mo_coef
+    | _ -> failwith "Error reading the mo set"
+  in
+  Input.Mo_basis.to_rst mo_coef 
+  |> Rst_string.to_string
+  |> print_endline
+
+
+basis ();;
+mo ();;

plugins/qmcpack/qp_convert_qmcpack_from_ezfio.py

@@ -17,11 +17,7 @@ if do_pseudo:
 else:
 	print "do_pseudo False"
 
-try:
+n_det =ezfio.get_determinants_n_det()
-        n_det =ezfio.get_determinants_n_det()
-except IOError:
-        n_det = 1
-
 if n_det == 1:
 	print "multi_det False"
 else:
@@ -52,7 +48,7 @@ print "Atomic coord in Bohr"
 
 for i,t in enumerate(zip(l_label,l_charge,l_coord_str)):
 	try :
-		l = (t[0],t[1]+zcore[i],t[2])
+		l = (t[0],t[1]+zcore[i],t[1])
 	except NameError:
 		l = t
 	print " ".join(map(str,l))
@@ -197,11 +193,11 @@ if do_pseudo:
 				l_str.append(l_dump)
 	
 		str_ = "PARAMETERS FOR {0} ON ATOM {1} WITH ZCORE {2} AND LMAX {3} ARE"
-		print str_.format(a,i+1,int(zcore[i]),int(len(l_str)-1))
+		print str_.format(a,i+1,zcore[i],len(l_str))
 	
 		for i, l in enumerate(l_str):
 			str_ = "FOR L= {0} COEFF N ZETA"
-			print str_.format(int(len(l_str)-i-1))
+			print str_.format(len(l_str)-i-1)
 			for ii, ll in enumerate(l):
 				print " ",ii+1, ll
 	

scripts/get_basis.sh

@@ -46,15 +46,4 @@ then
   exit 1
 fi
 
-pseudo="$1"
+${EMSL_API_ROOT}/EMSL_api.py get_basis_data --treat_l --save --path="${tmpfile}" --basis="${basis}"
-shift
-
-if [[ -z $pseudo ]]
-then
-    ${EMSL_API_ROOT}/EMSL_api.py get_basis_data --treat_l --save --path="${tmpfile}" --basis="${basis}"
-else
-    ${EMSL_API_ROOT}/EMSL_api.py get_basis_data --save --path="${tmpfile}" --basis="${basis}" --db_path="${EMSL_API_ROOT}/db/Pseudo.db"
-#    echo ${EMSL_API_ROOT}/EMSL_api.py get_basis_data --save --path="${tmpfile}" --basis="${basis}" --db_path="${EMSL_API_ROOT}/db/Pseudo.db" 1>&2
-#    echo $PWD/BASIS
-fi
-

scripts/pseudo/put_pseudo_in_ezfio.py

@@ -4,7 +4,7 @@
 Create the pseudo potential for a given atom
 
 Usage:
-    put_pseudo_in_ezfio.py <ezfio_path>
+    put_pseudo_in_ezfio.py <ezfio_path> <pseudo_name>  [<db_dump_path>]
 
 Help:
     atom is the Abreviation of the atom
@@ -28,7 +28,7 @@ import re
 p = re.compile(ur'\|(\d+)><\d+\|')
 
 
-def get_pseudo_str(l_atom):
+def get_pseudo_str(db_dump_path,pseudo_name,l_atom):
     """
     Run EMSL_local for getting the str of the pseudo potential
 
@@ -53,7 +53,6 @@ def get_pseudo_str(l_atom):
 
     EMSL_root = "{0}/install/emsl/".format(qpackage_root)
     EMSL_path = "{0}/EMSL_api.py".format(EMSL_root)
-    db_path = "{0}/db/Pseudo.db".format(EMSL_root)
 
     str_ = ""
 
@@ -63,8 +62,8 @@ def get_pseudo_str(l_atom):
             l_cmd_atom = ["--atom", a]
 
             l_cmd_head = [EMSL_path, "get_basis_data",
-                          "--db_path", db_path,
+                          "--db_dump_path", db_dump_path,
-                          "--basis", "BFD-Pseudo"]
+                          "--basis", pseudo_name]
 
             process = Popen(l_cmd_head + l_cmd_atom, stdout=PIPE, stderr=PIPE)
 
@@ -180,19 +179,22 @@ def get_zeff_alpha_beta(str_ele):
     #
 
     from elts_num_ele import name_to_elec
+    from math import ceil, floor
     z = name_to_elec[name]
 
     z_eff = z - z_remove
 
-    alpha = (z_remove / 2)
+    alpha = int(ceil(z_remove / 2.))
-    beta = (z_remove / 2)
+    beta = int(floor(z_remove / 2.))
+
+    # Remove more alpha, than beta
 
     #  _
     # |_)  _ _|_     ._ ._
     # | \ (/_ |_ |_| |  | |
     #
 
-    return [z_eff, alpha, beta]
+    return [z_remove, z_eff, alpha, beta]
 
 
 def add_zero(array, size, type):
@@ -224,6 +226,12 @@ def make_it_square(matrix, dim, type=float):
 
     return matrix
 
+def full_path(path):
+    path = os.path.expanduser(path)
+    path = os.path.expandvars(path)
+    path = os.path.abspath(path)
+    return path
+
 if __name__ == "__main__":
     arguments = docopt(__doc__)
     # ___
@@ -235,19 +243,22 @@ if __name__ == "__main__":
     # E Z F I O #
     # ~#~#~#~#~ #
 
-    ezfio_path = arguments["<ezfio_path>"]
+    ezfio_path = full_path(arguments["<ezfio_path>"])
-    ezfio_path = os.path.expanduser(ezfio_path)
-    ezfio_path = os.path.expandvars(ezfio_path)
-    ezfio_path = os.path.abspath(ezfio_path)
-
     ezfio.set_file("{0}".format(ezfio_path))
 
     # ~#~#~#~#~#~#~#~#~#~#~ #
     # P s e u d o _ d a t a #
     # ~#~#~#~#~#~#~#~#~#~#~ #
 
+    if arguments["<db_dump_path>"]:
+        db_dump_path = full_path(arguments["<db_dump_path>"])
+    else:
+        db_dump_path= full_path("{0}/data/BFD-Pseudo.dump".format(qpackage_root))
+
+    pseudo_name = arguments["<pseudo_name>"]
     l_ele = ezfio.get_nuclei_nucl_label()
-    str_ = get_pseudo_str(l_ele)
+
+    str_ = get_pseudo_str(db_dump_path,pseudo_name,l_ele)
 
     #  _
     # |_) _. ._ _  _
@@ -257,7 +268,7 @@ if __name__ == "__main__":
     l_str_ele = [str_ele for str_ele in str_.split("Element Symbol: ")
                  if str_ele]
 
-    for i in "l_zeff v_k n_k dz_k v_kl n_kl dz_kl".split():
+    for i in "l_zeff l_remove v_k n_k dz_k v_kl n_kl dz_kl".split():
         exec("{0} = []".format(i))
 
     alpha_tot = 0
@@ -296,11 +307,13 @@ if __name__ == "__main__":
         # Z _ e f f , a l p h a / b e t a _ e l e c #
         # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
 
-        zeff, alpha, beta = get_zeff_alpha_beta(str_ele)
+        zremove, zeff, alpha, beta = get_zeff_alpha_beta(str_ele)
 
         alpha_tot += alpha
         beta_tot += beta
         l_zeff.append(zeff)
+        l_remove.append(zremove)
+
     #                                  _
     #  /\   _|  _|   _|_  _     _  _ _|_ o  _
     # /--\ (_| (_|    |_ (_)   (/_ /_ |  | (_)
@@ -311,6 +324,7 @@ if __name__ == "__main__":
     # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
 
     ezfio.nuclei_nucl_charge = l_zeff
+    ezfio.pseudo_nucl_charge_remove = l_remove
 
     alpha_tot = ezfio.get_electrons_elec_alpha_num() - alpha_tot
     beta_tot = ezfio.get_electrons_elec_beta_num() - beta_tot

src/Pseudo/EZFIO.cfg

@@ -1,3 +1,10 @@
+[nucl_charge_remove]
+doc: Nuclear charges removed
+type:double precision
+size: (nuclei.nucl_num)
+interface: ezfio, provider
+
+
 [pseudo_klocmax]
 doc: test
 type:integer

tests/bats/qp.bats

@@ -1,5 +1,9 @@
 #!/usr/bin/env bats
 
+#                
+#   |\/| o  _  _ 
+#   |  | | _> (_ 
+#                
 # floating point number comparison
 # Compare two numbers ($1, $2) with a given precision ($3)
 # If the numbers are not equal, the exit code is 1 else it is 0
@@ -19,8 +23,13 @@ function eq() {
     fi
 }
 
-#: "${QP_ROOT?Please source your quantum_package.rc}"
 
+
+
+#   ___           
+#    |  ._  o _|_ 
+#   _|_ | | |  |_ 
+#                 
 source ${QP_ROOT}/install/EZFIO/Bash/ezfio.sh
 TEST_DIR=${QP_ROOT}/tests/work/
 
@@ -45,8 +54,6 @@ function test_exe() {
   fi
 }
 
-
-
 function run_HF() {
   thresh=1.e-8
   test_exe SCF || skip
@@ -72,8 +79,12 @@ function run_FCI() {
   eq $energy_pt2 $4 $thresh
 }
 
-# ================== TESTS =======================
+#   ___             
+#    |  _   _ _|_   
+#    | (/_ _>  |_   
+#                   
 
+#=== HBO
 @test "init HBO STO-3G" {
   run_init HBO.xyz "-b STO-3G" hbo.ezfio
 }
@@ -83,9 +94,7 @@ function run_FCI() {
 }
 
 
-
+#=== H2O
-
-
 @test "init H2O cc-pVDZ" {
   run_init h2o.xyz "-b cc-pvdz" h2o.ezfio
 }
@@ -123,9 +132,7 @@ function run_FCI() {
 }
 
 
-
+#=== H2O Pseudo
-
-
 @test "init H2O VDZ pseudo" {
   run_init h2o.xyz "-p bfd -b vdz-bfd" h2o_pseudo.ezfio
 }
@@ -138,10 +145,7 @@ function run_FCI() {
   run_FCI h2o_pseudo.ezfio 2000    -17.1593409053142  -17.1699581090466
 }
 
-
+#=== Convert
-
-
-
 @test "gamess convert HBO.out" {
   cp ${QP_ROOT}/tests/input/HBO.out .
   qp_convert_output_to_ezfio.py HBO.out
@@ -163,8 +167,6 @@ function run_FCI() {
 }
 
 
-
-
 # TODO N_int = 1,2,3,4,5
 # TODO mod(64) MOs
 # TODO All G2 SCF energies