Merge branch 'LCPQ-master'
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README.md
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README.md
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@ -32,27 +32,21 @@ Demo
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### 1) Configure
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$ ./configure <config_file> (--production | --development)
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For example you can type `./configure config/gfortran.cfg --production`
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$ ./configure <config_file>
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For example you can type `./configure config/gfortran.cfg`
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This command has two purposes :
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- Download and install all the requirements.
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Installing OCaml and the Core library may take some time (up to 20min on an old machine).
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- Create the file which contains all the dependencies for the binaries.
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It's not a Makefile, but a Ninja file (so don't type `make` is hopeless, type `ninja` instead)
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It's not a Makefile, but a Ninja file (so don't type `make` it's hopeless, type `ninja` instead)
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####Compilation Flags (`<config_file>`)
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#### Compilation Flags (`<config_file>`)
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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 ``$QP_ROOT/config`` : ``ifort.cfg`` and ``gfortran.cfg``. You can copy these files to create a new file adapted to your architecture.
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#### What utilization of the code will you do?
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* If you only want the binaries (for production workflow) use the flag
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`--production`. It compiles faster.
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* Else if you are a developer and you want to be able to compile specific modules use: `--development`. It will create the `build.ninja` in each module.
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### 2) Load environment variables
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source quantum_package.rc
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@ -75,24 +69,16 @@ Usage:
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### 3) Compiling the Fortran
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Just type `ninja` if you are in `$QP_ROOT` (or `ninja -f $QP_ROOT/build.ninja` elsewhere). The compilation will take approximately 3 min.
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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.
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### 4) Compiling the OCaml
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make -C $QP_ROOT/ocaml
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Just type `ninja` if you are in `$QP_ROOT`. The compilation will take approximately 3 min.
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### 5) Testing if all is ok
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cd tests ; ./run_tests.sh
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# Note on EZFIO.cfg
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##Format specification :
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## Format specification:
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```
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Required:
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@ -119,7 +105,7 @@ Optional:
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(by default is <module_lower>)
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```
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##Example of EZFIO.cfg:
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## Example of EZFIO.cfg:
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```
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[thresh_SCF]
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@ -135,19 +121,23 @@ doc: Calculated HF energy
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interface: ezfio
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```
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#FAQ
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# FAQ
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### My hartree-Fock segfault !
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A old version of Lapack have a bug. Just relax your convergence criterium
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### Error: ezfio_* is already defined.
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#### Why ?
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You have two or more ezfio configuration files for the same variable. Check files in `$QP_ROOT/install/EZFIO/config/`
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You have two or more ezfio configuration files for the same variable. Check files in `$QP_ROOT/install/EZFIO/config/` and the all the `EZFIO.cfg`.
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#### Fix
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- rm $QP_ROOT/install/EZFIO/config/*
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- ninja
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### Error: Seg Fault (139)
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@ -160,7 +150,7 @@ Program exited with code 139.
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It's caused when we call the DGEMM routine of LAPACK.
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##### Fix
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#### Fix
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Set `ulimit -s unlimited`, before runing `qp_run`. It seems to fix the problem.
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@ -10,6 +10,7 @@ type t =
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|Na|Mg |Al|Si|P |S |Cl|Ar
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|K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
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|Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe
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|Pt
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with sexp
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let of_string x =
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@ -69,6 +70,7 @@ let of_string x =
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| "Te" | "Tellurium" -> Te
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| "I" | "Iodine" -> I
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| "Xe" | "Xenon" -> Xe
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| "Pt" | "Platinum" -> Pt
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| x -> raise (ElementError ("Element "^x^" unknown"))
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@ -128,6 +130,7 @@ let to_string = function
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| Te -> "Te"
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| I -> "I"
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| Xe -> "Xe"
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| Pt -> "Pt"
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let to_long_string = function
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@ -186,6 +189,7 @@ let to_long_string = function
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| Te -> "Tellurium"
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| I -> "Iodine"
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| Xe -> "Xenon"
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| Pt -> "Platinum"
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let to_charge c =
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@ -245,6 +249,7 @@ let to_charge c =
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| Te -> 52
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| I -> 53
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| Xe -> 54
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| Pt -> 78
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in Charge.of_int result
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@ -304,6 +309,7 @@ let of_charge c = match (Charge.to_int c) with
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| 52 -> Te
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| 53 -> I
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| 54 -> Xe
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| 78 -> Pt
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| x -> raise (ElementError ("Element of charge "^(string_of_int x)^" unknown"))
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@ -364,6 +370,7 @@ let covalent_radius x =
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| Te -> 1.38
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| I -> 1.39
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| Xe -> 1.40
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| Pt -> 1.30
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in
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Units.angstrom_to_bohr *. (result x)
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|> Positive_float.of_float
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@ -425,6 +432,7 @@ let vdw_radius x =
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| Te -> 2.06
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| I -> 1.98
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| Xe -> 2.16
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| Pt -> 1.75
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in
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Units.angstrom_to_bohr *. (result x)
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|> Positive_float.of_float
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@ -486,6 +494,7 @@ let mass x =
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| Te -> 127.60
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| I -> 126.90447
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| Xe -> 131.293
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| Pt -> 195.084
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in
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result x
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|> Positive_float.of_float
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@ -7,6 +7,7 @@ type t =
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|Na|Mg |Al|Si|P |S |Cl|Ar
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|K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
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|Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe
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|Pt
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with sexp
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(** String conversion functions *)
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