From 33637e1ed45295bd9759451666c6e3f188081506 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 18 Dec 2015 22:12:04 +0100 Subject: [PATCH] Improved README.md --- README.md | 203 +++++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 202 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 955138a..f39e0d9 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,203 @@ -# qmcchem QMC=Chem : Quantum Monte Carlo for Chemistry +============================================ + + +QMC=Chem is the quantum Monte Carlo program of the +[Toulouse group](http://qmcchem.ups-tlse.fr). +It is meant to be used in the *post-Full-CI* context : a quasi-Full-CI +calculation is done with the +[quantum package](https://github.com/LCPQ/quantum_package), +and this wave function is used as a trial wave function for the fixed-node +diffusion Monte Carlo algorithm. + + +* Parallel efficiency of 98.3% on 16_000 cores +* The load balancing is optimal: the workers always work 100% of the time, + independently of their respective CPU speeds +* Efficient: 0.96 Pflops/s on 76_800 cores of Curie in 2011 +* All network communications are non-blocking, + with the [ZeroMQ](http://zeromq.org) library +* All the implemented algorithms are CPU-bound : the only limit + is the available CPU time +* The number of simultaneous worker nodes can be variable during a calculation +* Fully fault-tolerant (crashing nodes don't stop the running calculation) +* QMC=Chem has been used in grid environments (EGI european grid) and + in Cloud environments (rance Grilles) coupled to supercomputers + + +*Warning*: QMC=Chem is under the GPLv2 license. Any modifications to or +software including (via compiler) GPL-licensed code must also be made available +under the GPL along with build & install instructions. + +Example of a QMC=Chem calculation +--------------------------------- + +Calculation with the quantum package +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +1) Create the ``xyz`` file containing the nuclear coordinates of the system + +```bash +$ cat > h2o.xyz << EOF +3 +Water molecule +O 0. 0. 0. +H 0.9572 0. 0. +H -0.239987 0.926627 0. +EOF +``` + +2) Choose a suitable basis set and create the [EZFIO database](https://github.com/LCPQ/ezfio) + +```bash +$ qp_create_ezfio_from_xyz -b cc-pvdz h2o.xyz -o h2o +``` + +3) Run the SCF calculation + +```bash +$ qp_run SCF h2o +``` +4) Run the CIPSI calculation + +```bash +$ qp_run full_ci h2o +``` + +5) Transform the input for use in QMC=Chem + +```bash +$ qp_run save_for_qmcchem h2o +``` + +FN-DMC calculation with QMC=Chem +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Before using QMC=Chem, you need to load the environment variables: + +```bash +$ source qmcchem.rc +``` + +In QMC=Chem, everything goes through the use of the ``qmcchem`` command. +When a command is run with no arguments, it prints a help message. +This is mainly the manual of QMC=Chem. For example: + +```bash +$ qmcchem +QMC=Chem command + + qmcchem SUBCOMMAND + +=== subcommands === + + debug Debug ZeroMQ communications + edit Edit input data + md5 Manipulate input MD5 keys + result Displays the results computed in an EZFIO directory. + run Run a calculation + stop Stop a running calculation + version print version information + help explain a given subcommand (perhaps recursively) + +missing subcommand for command qmcchem + +$ qmcchem edit +Run a calculation + + qmcchem run EZFIO_FILE + + +Run QMC=Chem + + +=== flags === + + [-a] Add more resources to a running calculation. + [-d] Start a dataserver process on the local host. + [-q ] Start a qmc process on the local host. + [-s ] Start a qmc process on . + [-help] print this help text and exit + (alias: -?) + +missing anonymous argument: EZFIO_FILE +``` + +1) Set the parameters for a VMC calculation to create initial walker positions + +```bash +$ qmcchem edit -h +Edit input data + + qmcchem edit EZFIO_FILE [INPUT] + + +Edit input data + + +=== flags === + + [-c] Clear blocks + [-e energy] Fixed reference energy to normalize DMC weights + [-f 0|1] Correct wave function to verify electron-nucleus cusp + condition + [-j jastrow_type] Type of Jastrow factor [ None | Core | Simple ] + [-l seconds] Length (seconds) of a block + [-m method] QMC Method : [ VMC | DMC ] + [-n norm] Truncation t of the wave function : Remove determinants + with a + contribution to the norm less than t + [-s sampling] Sampling algorithm : [ Langevin | Brownian ] + [-t seconds] Requested simulation time (seconds) + [-ts time_step] Simulation time step + [-w walk_num] Number of walkers per CPU core + [-wt walk_num_tot] Total number of stored walkers for restart + [-help] print this help text and exit + (alias: -?) + +$ qmcchem edit h2o -f 1 -m VMC -n 1.e-5 -s Langevin -t 300 -l 10 +``` + +3) Get info on the wave function + +```bash +$ qmcchem info h2o +``` + +4) Run the VMC calculation + +```bash +$ qmcchem run h2o +``` + +5) Set the correct parameters for FN-DMC + +```bash +$ qmcchem edit h2o -e -76.438 -m DMC -s Brownian -ts 3.e-4 -t 3600 -l 30 +``` + +6) Run the FN-DMC calculation + +```bash +$ qmcchem run h2o +``` + +7) Print the result + +```bash +$ qmcchem result h2o + +``` + + + + +References +---------- + +[Quantum Monte Carlo for large chemical systems: Implementing efficient strategies for petascale platforms and beyond](http://dx.doi.org/10.1002/jcc.23216) +> Anthony Scemama , Michel Caffarel , Emmanuel Oseret and William Jalby (2013), in: Journal of Computational Chemistry, 34:11(938--951) + +[Quantum Monte Carlo with very large multideterminant wavefunctions](http://arxiv.org/abs/1509.03114) +> Anthony Scemama , Thomas Applencourt , Emmanuel Giner and Michel Caffarel (2015), in: ArXiv ePrints:arXiv:1510.00730 [physics.chem-ph] +