Thom Group Wiki - User contributions [en]

SimpleDMC

2017-04-18T15:47:19Z

Sc2018:

= Theory =

= Compilation of SimpleDMC =

= Examples =

== The Hydrogen Atom ==

=== Gaussian ===
Let's begin by generating a trial wavefunction with Gaussian03. To start with, we need to define an atomic orbital basis, then tell Gaussian03 to use it in conjunction with some ''ab initio'' method. We'll use the STO-6G basis set, where 6 Gaussian primitives are used to represent an atomic orbital. We'll create an input file for Gaussian03, called H.com,

$ cat -n H.com
1 %chk=H.chk
2 #p UHF/STO-6G 6d 10f SCF Test IOP(3/24=10) IOP(3/81=1) Pop=Full
3
4 Hydrogen Atom - UHF STO-6G
5
6 0 2
7 H 0.000 0.000 0.000
8

This may seem cryptic for the moment, but each line (and entry therein) is necessary. Line 1 tells Gaussian03 to put some output in an encrypted file called H.chk. Line 2 is the ``route section": The IOP arguments are ''internal options'', and tell Gaussian03 to spit out data in a certain format. Line 4 contains a title section, and must be included, as must the sandwiching blank lines. Line 6 specifies the charge and multiplicity (number of unpaired electrons + 1). Finally, on line 7, we specify the molecular configuration; atom types and Cartesian position vectors of the constituent atoms are enumerated here.

Now, let's run Gaussian03,

$ g03 H.com

No return value is normally a good sign- you'll typically be greeted with an (unhelpful) SEGFAULT of some kind if the calculation was unsuccessful. It's also worth explicitly checking for errors, since Gaussian is also able to die silently

$ grep "Error" H.log

Gaussian03 writes to two files- H.log and H.chk; the contents of the former are obvious while we've already briefly discussed the contents of the latter. In the output, all we care about is the energy, so invoke

$ grep -n "SCF Done" H.log
219: SCF Done: E(UHF) = -0.471039054196 A.U. after 1 cycles

This is a rather poor value relative to the analytical -0.5 Hartrees, but at least we have something to improve upon. We must now do some conversions to extract information from the checkpoint file

$ formchk H.chk H.fchk
Read checkpoint file H.chk
Write formatted file H.fchk
Rotating derivatives, DoTrsp=T IDiff= 1 LEDeriv= 197 LFDPrp= 0 LDFDPr= 0.

formchk is a Gaussian utility that converts the unreadable H.chk to a formatted checkpoint file, H.fchk. Since this formatted file is more amenable to parsing, it can be used by a number of visualisation/ post-Gaussian tools.

=== qWalk ===
qWalk is a piece of software we can benchmark the simpleDMC software against, possessing both variational
and diffusion Monte Carlo (VMC and DMC, respectively) functionalities. The simpleDMC software also uses
the same input file formats as qWalk, and so we are able to use their file conversion tools to extract data
from a host of ''ab initio'' software suites.

First, we parse the H.fchk file into a number of qWalk input files:

$ ./g032qmc -log H.log -fchk H.fchk
--- read fchk file ---
Number of atoms: 1
Number of basis functions: 1
Number of independant functions: 1
Multiplicity: 2
Number of alpha electrons: 1
Number of beta electrons: 0
Total Energy: -0.471039054195684
Pure/Cartesian d shells: 6D
Pure/Cartesian f shells: 10F
found beta component, scftpe=UHF
--- read log file ---
basis set is from 'AO basis set' section
--- have read files ---
norb=1
spin up end size=1
moCoeff total size=2
writing qwalk input files ...
writing orb file. This could take a few seconds.
output: sample.orb
output: sample.basis
output: sample.slater
output: sample.jast2
output: sample.sys
output: sample.hf
output: sample.opt
Done

Warning: Now the basisset must be the same for the same specie of atoms

We'll try to reproduce the UHF results by use of VMC with qWalk. Let's have a look at sample.hf:

$ cat sample.hf
METHOD { VMC nconfig 1000 }

INCLUDE sample.sys
TRIALFUNC { INCLUDE sample.slater}

Note that we have added "nconfig 1000", which gives us control over how many walkers are to be used
for the VMC. sample.sys contains the system configuration (number of electrons with a given spin,
atomic coordinates, etc.), while sample.slater contains the orbital information for the Slater
determinant (in conjunction with sample.orb and sample.basis). This Slater determinant will be used
to sample the trial wavefunction created by g03. We now run qWalk:

$ ./qwalk sample.hf
output to sample.hf.o
System
Wave function
Pseudopotential
Could not open sample.hf.config. Generating configurations from scratch

and upon completion, are left with three files,

{| class="wikitable"
|sample.hf.o
|Information about the run.
|-
|sample.hf.log
|Log for statistical analysis.
|-
|sample.hf.config
|Checkfile for the run.
|}

We can extract averages from the VMC by invoking

$ ./gosling sample.hf.log
#####################
vmc: 100 total blocks reblocked into 100
#####################
Threw out the first 0 blocks in the averaging.
total_energy0 -0.4702684082 +/- 0.000922386677 (sigma 0.425114576 )
kinetic0 0.7706545412 +/- 0.003605881864 (sigma 1.448514687 )
potential0 -1.240922949 +/- 0.003148015019 (sigma 1.21325133 )
nonlocal0 0 +/- 0 (sigma 0 )
weight0 1 +/- 6.661338148e-17 (sigma 0 )

--------Properties differences-------------
approximate number of independent points: 212415.3753

We see that the VMC estimate of the energy of the trial wavefunction (-0.470(2)) matches
relatively well with the UHF energy (-0.471039054195684). We have also obtained the
sample.hf.config file, containing the distribution of walkers sampling the
trial wavefunction.

$ head -8 sample.hf.config
walker {
nElec 1 ndim 3
-0.731706383078456 0.620589802605041 -0.092157439050284
}
walker {
nElec 1 ndim 3
0.366970593352899 0.216757302067973 -0.48313699793852
}

=== simpleDMC ===

We can use this distribution of walkers as a starting point for our DMC calculations with
simpleDMC. We require an input file to run simpleDMC, sample.simple:

$ cat sample.simple
simple {
nWalkers 1000 # Number of walkers
nSteps 10000 # Maximum number of steps
dTau 0.001 # Timestep
dETrial -0.5 # Trial energy should start (> FCI energy but close to it)
dWeightInit 1.0 # Initial weight
bConstWalkerNum false # Are we enforcing a constant number of walkers? (Currently not working)
nWalkersSpace 20480 # Walker growth space (Maximum number of walkers permitted)
dWeightTarget 10000.0 # Total weight above which we undertake population control
dWeightMin 1500.0 # Total weight below which we undertake population control
dLowThresh 1.0 # If walker has weight below this, try to either kill or recombine it
dWeightBranch 1.5 # If walker has weight above this, we branch the walker
nShiftSteps 1 # Vary the shift every nShiftSteps steps.
dShiftDamp 1.0 # Larger shift damping is more radical damping
dOldWeight 0.0 # The total weight at the previous cycle for calculating the shift
bUpdateShift false # Are we updating the shift every nShiftSteps cycles?
}

simpleDMC reuses the input files of qWalk, and can be invoked by listing the files as command line
arguments (in any order)

$ ./simpleDMC.x sample.{sys,slater,orb,basis,simple,hf.config,hf.log} >> sample.log

We pass all of the output to sample.log since the majority of information concerning the simulation is
streamed straight to STDOUT. We are primarily concerned with the final nSteps lines, since these give
the various energetic quantities associated with the system of walkers at each timestep. In fact, with
a little foresight, the fifth column corresponds to the total energy averaged over all walkers at that
timestep. Averaging over this column, we obtain the DMC energy:

$ export nsteps=10000
$ tail -n $nsteps sample.log | awk '{ sum += $5; n++ } END { if (n > 0) print sum / n; }'
-0.498772

This quantity is in very good agreement with the exact energy of -0.5 Hartrees.

<math>V = \frac{\epsilon}{2} \sum_{i<j} \left[ \left(\frac{r_{ij}}{\sigma}\right)^2+\left(\frac{\sigma}{r_{ij}}\right)^2 \right]</math>

SimpleDMC

2016-11-22T01:17:46Z

Sc2018:

Main Page

2016-11-22T01:16:26Z

Sc2018: /* Useful Software */

Good Evening, Guten Abend, and Willkommen to ze new Thom Group Wiki
= Contents =
== [[Calendar | Calendar]] ==
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

== Group Meetings ==

===Research Period===
{|
|+
|'''Date''' || '''Mini-talk'''
|-
|15th August 2016 || Jonathan
|-
|30th August 2016 || Charlie
|-
|12th September 2016 || James
|-
|26th September 2016 || CANCELLED
|}

===Michaelmas Term===
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|10th October 2016 || Charlie || Hugh
|-
|24th October 2016 || Verena || Sav
|-
|7th November 2016 || Choi || Alex
|-
|21st November 2016 || Ruth || Verena
|-
|5th December 2016 || [AJWT away]
|}

===Lent Term 2017===
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|9th January || ||
|-
|23rd January || ||
|-
|6th February || ||
|-
|20th February || ||
|-
|6th March || ||
|}

== [[Group_List | Group List]] ==
(see also http://www.ch.cam.ac.uk/group/thom)
- An up to date list of group members

== [[Computer_List | Computer List]] ==
- Group computers available.
== [[Introduction | Introduction to basic shell commands]] ==
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up ssh keys and general bash commands what are helpful
# using [[GIT]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

== Useful Software ==
# Using QChem
# Using [[QCMagic]]
# [[SimpleDMC]]

== Useful Information ==
# Guidelines on [[Code Review]]

== [[Archiving_data | Archiving data for the university repository]] ==
== [[Website_to_do | To-do list for the Thom Group Website]] ==

= To Do List =
--A category containing all those affiliated with the group

-a pretty picture

-their research interests

-current location and contact deets

-publication history

--A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

--A "How to:" page on using qchem

--A Pretty picture for the $wgLogo

--A job opportunities page with method of contact for Monsieur Docteur Thom

--A list of drinkable clarets from the past 5 years

"A watched QCHEM calculation never converges"

SimpleDMC

2016-11-22T01:14:21Z

Sc2018: Created page with "= Examples = == The Hydrogen Atom == === Gaussian === Let's begin by generating a trial wavefunction with Gaussian03. To start with, we need to define an atomic orbital basi..."

= Examples =

== The Hydrogen Atom ==

=== Gaussian ===
Let's begin by generating a trial wavefunction with Gaussian03. To start with, we need to define an atomic orbital basis, then tell Gaussian03 to use it in conjunction with some ''ab initio'' method. We'll use the STO-6G basis set, where 6 Gaussian primitives are used to represent an atomic orbital. We'll create an input file for Gaussian03, called H.com,

$ cat -n H.com
1 %chk=H.chk
2 #p UHF/STO-6G 6d 10f SCF Test IOP(3/24=10) IOP(3/81=1) Pop=Full
3
4 Hydrogen Atom - UHF STO-6G
5
6 0 2
7 H 0.000 0.000 0.000
8

This may seem cryptic for the moment, but each line (and entry therein) is necessary. Line 1 tells Gaussian03 to put some output in an encrypted file called H.chk. Line 2 is the ``route section": The IOP arguments are ''internal options'', and tell Gaussian03 to spit out data in a certain format. Line 4 contains a title section, and must be included, as must the sandwiching blank lines. Line 6 specifies the charge and multiplicity (number of unpaired electrons + 1). Finally, on line 7, we specify the molecular configuration; atom types and Cartesian position vectors of the constituent atoms are enumerated here.

Now, let's run Gaussian03,

$ g03 H.com

No return value is normally a good sign- you'll typically be greeted with an (unhelpful) SEGFAULT of some kind if the calculation was unsuccessful. It's also worth explicitly checking for errors, since Gaussian is also able to die silently

$ grep "Error" H.log

Gaussian03 writes to two files- H.log and H.chk; the contents of the former are obvious while we've already briefly discussed the contents of the latter. In the output, all we care about is the energy, so invoke

$ grep -n "SCF Done" H.log
219: SCF Done: E(UHF) = -0.471039054196 A.U. after 1 cycles

This is a rather poor value relative to the analytical -0.5 Hartrees, but at least we have something to improve upon. We must now do some conversions to extract information from the checkpoint file

$ formchk H.chk H.fchk
Read checkpoint file H.chk
Write formatted file H.fchk
Rotating derivatives, DoTrsp=T IDiff= 1 LEDeriv= 197 LFDPrp= 0 LDFDPr= 0.

formchk is a Gaussian utility that converts the unreadable H.chk to a formatted checkpoint file, H.fchk. Since this formatted file is more amenable to parsing, it can be used by a number of visualisation/ post-Gaussian tools.

=== qWalk ===
qWalk is a piece of software we can benchmark the simpleDMC software against, possessing both variational
and diffusion Monte Carlo (VMC and DMC, respectively) functionalities. The simpleDMC software also uses
the same input file formats as qWalk, and so we are able to use their file conversion tools to extract data
from a host of ''ab initio'' software suites.

First, we parse the H.fchk file into a number of qWalk input files:

$ ./g032qmc -log H.log -fchk H.fchk
--- read fchk file ---
Number of atoms: 1
Number of basis functions: 1
Number of independant functions: 1
Multiplicity: 2
Number of alpha electrons: 1
Number of beta electrons: 0
Total Energy: -0.471039054195684
Pure/Cartesian d shells: 6D
Pure/Cartesian f shells: 10F
found beta component, scftpe=UHF
--- read log file ---
basis set is from 'AO basis set' section
--- have read files ---
norb=1
spin up end size=1
moCoeff total size=2
writing qwalk input files ...
writing orb file. This could take a few seconds.
output: sample.orb
output: sample.basis
output: sample.slater
output: sample.jast2
output: sample.sys
output: sample.hf
output: sample.opt
Done

Warning: Now the basisset must be the same for the same specie of atoms

We'll try to reproduce the UHF results by use of VMC with qWalk. Let's have a look at sample.hf:

$ cat sample.hf
METHOD { VMC nconfig 1000 }

INCLUDE sample.sys
TRIALFUNC { INCLUDE sample.slater}

Note that we have added "nconfig 1000", which gives us control over how many walkers are to be used
for the VMC. sample.sys contains the system configuration (number of electrons with a given spin,
atomic coordinates, etc.), while sample.slater contains the orbital information for the Slater
determinant (in conjunction with sample.orb and sample.basis). This Slater determinant will be used
to sample the trial wavefunction created by g03. We now run qWalk:

$ ./qwalk sample.hf
output to sample.hf.o
System
Wave function
Pseudopotential
Could not open sample.hf.config. Generating configurations from scratch

and upon completion, are left with three files,

{| class="wikitable"
|sample.hf.o
|Information about the run.
|-
|sample.hf.log
|Log for statistical analysis.
|-
|sample.hf.config
|Checkfile for the run.
|}

We can extract averages from the VMC by invoking

$ ./gosling sample.hf.log
#####################
vmc: 100 total blocks reblocked into 100
#####################
Threw out the first 0 blocks in the averaging.
total_energy0 -0.4702684082 +/- 0.000922386677 (sigma 0.425114576 )
kinetic0 0.7706545412 +/- 0.003605881864 (sigma 1.448514687 )
potential0 -1.240922949 +/- 0.003148015019 (sigma 1.21325133 )
nonlocal0 0 +/- 0 (sigma 0 )
weight0 1 +/- 6.661338148e-17 (sigma 0 )

--------Properties differences-------------
approximate number of independent points: 212415.3753

We see that the VMC estimate of the energy of the trial wavefunction (-0.470(2)) matches
relatively well with the UHF energy (-0.471039054195684). We have also obtained the
sample.hf.config file, containing the distribution of walkers sampling the
trial wavefunction.

$ head -8 sample.hf.config
walker {
nElec 1 ndim 3
-0.731706383078456 0.620589802605041 -0.092157439050284
}
walker {
nElec 1 ndim 3
0.366970593352899 0.216757302067973 -0.48313699793852
}

=== simpleDMC ===

We can use this distribution of walkers as a starting point for our DMC calculations with
simpleDMC. We require an input file to run simpleDMC, sample.simple:

$ cat sample.simple
simple {
nWalkers 1000 # Number of walkers
nSteps 10000 # Maximum number of steps
dTau 0.001 # Timestep
dETrial -0.5 # Trial energy should start (> FCI energy but close to it)
dWeightInit 1.0 # Initial weight
bConstWalkerNum false # Are we enforcing a constant number of walkers? (Currently not working)
nWalkersSpace 20480 # Walker growth space (Maximum number of walkers permitted)
dWeightTarget 10000.0 # Total weight above which we undertake population control
dWeightMin 1500.0 # Total weight below which we undertake population control
dLowThresh 1.0 # If walker has weight below this, try to either kill or recombine it
dWeightBranch 1.5 # If walker has weight above this, we branch the walker
nShiftSteps 1 # Vary the shift every nShiftSteps steps.
dShiftDamp 1.0 # Larger shift damping is more radical damping
dOldWeight 0.0 # The total weight at the previous cycle for calculating the shift
bUpdateShift false # Are we updating the shift every nShiftSteps cycles?
}

simpleDMC reuses the input files of qWalk, and can be invoked by listing the files as command line
arguments (in any order)

$ ./simpleDMC.x sample.{sys,slater,orb,basis,simple,hf.config,hf.log} >> sample.log

We pass all of the output to sample.log since the majority of information concerning the simulation is
streamed straight to STDOUT. We are primarily concerned with the final nSteps lines, since these give
the various energetic quantities associated with the system of walkers at each timestep. In fact, with
a little foresight, the fifth column corresponds to the total energy averaged over all walkers at that
timestep. Averaging over this column, we obtain the DMC energy:

$ export nsteps=10000
$ tail -n $nsteps sample.log | awk '{ sum += $5; n++ } END { if (n > 0) print sum / n; }'
-0.498772

This quantity is in very good agreement with the exact energy of -0.5 Hartrees.