mirror of
https://github.com/LCPQ/quantum_package
synced 2024-12-22 20:35:19 +01:00
Merge branch 'LCPQ-master'
This commit is contained in:
commit
e2836ee5e0
91
README.md
91
README.md
@ -9,10 +9,11 @@ Quantum package
|
||||
Set of quantum chemistry programs and libraries.
|
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(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)
|
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* Python >= 2.6
|
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@ -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.
|
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- 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)
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||||
|
||||
####Compilation Flags (`<config_file>`)
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|
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`<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 ``$QP_ROOT/config`` : ``ifort.cfg`` and ``gfortran.cfg``. You can edit these files to modify the compiling options.
|
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`<config_file>` is the path to the file which contains all the compilation flags (optimization flags, Lapack libary, etc). There are two example configure files in ``$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
|
||||
* 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
|
||||
`--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) Set environment variable
|
||||
### 2) Load environment variables
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||||
source quantum_package.rc
|
||||
|
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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)
|
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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 :
|
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`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 $QP_ROOT/build.ninja` elsewhere). The compilation will take approximately 3 min.
|
||||
|
||||
If you have set the `--developement` flag in a specific module you can go in
|
||||
the corresponding module directory and run `ninja` to build only this module.
|
||||
You can type `ninja all` in a module for compiling all the submodule
|
||||
If you have set the `--developement` flag you can go in any module directory and run `ninja` to build only this particular module. You can type `ninja all` in a module to compile all the submodules.
|
||||
|
||||
|
||||
### 4) Compiling the OCaml
|
||||
|
||||
cd ocaml ; make ; cd -
|
||||
make -C ocaml
|
||||
|
||||
### 5) Testing if all is ok
|
||||
|
||||
cd testing_no_regression ; ./unit_test.py
|
||||
cd tests ; bats bats/qp.bats
|
||||
|
||||
## Installing behind a firewall !
|
||||
|
||||
1) Download `tsocks`:
|
||||
|
||||
wget http://sourceforge.net/projects/tsocks/files/latest/download
|
||||
mv download tsocks.tar.gz
|
||||
|
||||
2) Tranfer `tsocks.tar.gz` on the remote host
|
||||
|
||||
3) Configure `tsocks` with the proper directory for the `tsocks.conf` file:
|
||||
|
||||
tar -zxvf tsocks.tar.gz
|
||||
cd tsocks-*
|
||||
./configure --with-conf=${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 :
|
||||
- ezfio (if you only whant the ezfiolib)
|
||||
- provider (if you want the provider)
|
||||
- ocaml (if you want the ocaml gestion)
|
||||
interface:<str> The interface is a list of strings sepeared by "," which can contain :
|
||||
- ezfio : to build the EZFIO API
|
||||
- provider : to build the corresponding providers
|
||||
- ocaml : to build the corresponding bindings in OCaml
|
||||
Optional:
|
||||
default: <str> The default value needed,
|
||||
if 'ocaml' is in interface list.
|
||||
default: <str> The default value,
|
||||
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)
|
||||
ATTENTION : The module and the value are separed by a "." not a "_".
|
||||
For exemple (determinants.n_det)
|
||||
ezfio_name: <str> The name for the EZFIO lib
|
||||
Example : 1; =sum(ao_num); (ao_num,3)
|
||||
WARNING : The module and the value are separed by a "." not a "_".
|
||||
For example (determinants.n_det)
|
||||
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 `$QP_ROOT/install/EZFIO/config/`
|
||||
|
||||
#### Fix
|
||||
|
||||
|
||||
@ -4,3 +4,6 @@ Data
|
||||
|
||||
|
||||
This directory contains all the data files needed for the Quantum Package.
|
||||
|
||||
The `basis` directory contains some of the most popular basis sets, and the
|
||||
`pseudo` directory contains pseudopotential data.
|
||||
|
||||
@ -1,36 +0,0 @@
|
||||
1 H Hydrogen
|
||||
2 He Helium
|
||||
3 Li Lithium
|
||||
4 Be Beryllium
|
||||
5 B Boron
|
||||
6 C Carbon
|
||||
7 N Nitrogen
|
||||
8 O Oxygen
|
||||
9 F Fluorine
|
||||
10 Ne Neon
|
||||
11 Na Sodium
|
||||
12 Mg Magnesium
|
||||
13 Al Aluminum
|
||||
14 Si Silicon
|
||||
15 P Phosphorus
|
||||
16 S Sulfur
|
||||
17 Cl Chlorine
|
||||
18 Ar Argon
|
||||
19 K Potassium
|
||||
20 Ca Calcium
|
||||
21 Sc Scandium
|
||||
22 Ti Titanium
|
||||
23 V Vanadium
|
||||
24 Cr Chromium
|
||||
25 Mn Manganese
|
||||
26 Fe Iron
|
||||
27 Co Cobalt
|
||||
28 Ni Nickel
|
||||
29 Cu Copper
|
||||
30 Zn Zinc
|
||||
31 Ga Gallium
|
||||
32 Ge Germanium
|
||||
33 As Arsenic
|
||||
34 Se Selenium
|
||||
35 Br Bromine
|
||||
36 Kr Krypton
|
||||
@ -77,3 +77,4 @@ NCPUs=$(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
|
||||
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
open Core.Std
|
||||
open Qptypes
|
||||
|
||||
let () =
|
||||
let basis ()=
|
||||
let ezfio_filename =
|
||||
Sys.argv.(1)
|
||||
in
|
||||
@ -14,7 +14,26 @@ let () =
|
||||
| _ -> failwith "Error reading basis set"
|
||||
in
|
||||
Input.Ao_basis.to_rst basis
|
||||
|> Rst_string.to_string
|
||||
|> print_endline
|
||||
|
||||
|> Rst_string.to_string
|
||||
|> 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 ();;
|
||||
|
||||
@ -17,11 +17,7 @@ if do_pseudo:
|
||||
else:
|
||||
print "do_pseudo False"
|
||||
|
||||
try:
|
||||
n_det =ezfio.get_determinants_n_det()
|
||||
except IOError:
|
||||
n_det = 1
|
||||
|
||||
n_det =ezfio.get_determinants_n_det()
|
||||
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
|
||||
|
||||
@ -233,4 +229,4 @@ for c, (l_det_bit_alpha, l_det_bit_beta) in zip(psi_coef,psi_det):
|
||||
print bin_det
|
||||
print ""
|
||||
|
||||
print "END_DET"
|
||||
print "END_DET"
|
||||
@ -46,15 +46,4 @@ then
|
||||
exit 1
|
||||
fi
|
||||
|
||||
pseudo="$1"
|
||||
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
|
||||
|
||||
${EMSL_API_ROOT}/EMSL_api.py get_basis_data --treat_l --save --path="${tmpfile}" --basis="${basis}"
|
||||
|
||||
@ -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,
|
||||
"--basis", "BFD-Pseudo"]
|
||||
"--db_dump_path", db_dump_path,
|
||||
"--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)
|
||||
beta = (z_remove / 2)
|
||||
alpha = int(ceil(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 = os.path.expanduser(ezfio_path)
|
||||
ezfio_path = os.path.expandvars(ezfio_path)
|
||||
ezfio_path = os.path.abspath(ezfio_path)
|
||||
|
||||
ezfio_path = full_path(arguments["<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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
Loading…
Reference in New Issue
Block a user