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Parallelized ERI with Domainslib

This commit is contained in:
Anthony Scemama 2023-06-16 18:27:23 +02:00
parent b4211b8d85
commit 3f0dbfc928
21 changed files with 671 additions and 397 deletions
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2
common/README.org
View File

@ -48,6 +48,7 @@ with open(dunetest,'w') as f:
(synopsis "Test for {name} library")
(libraries
alcotest
unix
qcaml.{name}
)
)
@ -61,6 +62,7 @@ with open(dunetest,'w') as f:
str
zarith
getopt
unix
)
#+end_src

5
common/lib/dune
View File

@ -2,7 +2,7 @@
(library
(name common)
(public_name qcaml.common)
(synopsis
(synopsis
"Utility functions used by all the other directories."
)
(libraries
@ -10,8 +10,9 @@
zarith
getopt
camlp-streams
unix
)
(c_names
util
)

15
common/lib/qcaml.ml
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@ -1,7 +1,8 @@
(* | ~root~ | Path to the QCaml source directory |
* | ~name~ | ~"QCaml"~ | *)
(* | ~root~ | Path to the QCaml source directory |
* | ~name~ | ~"QCaml"~ |
* | ~num_domains~ | Number of threads in parallel computations | *)
(* [[file:~/QCaml/common/qcaml.org::*QCaml][QCaml:2]] *)
@ -18,4 +19,14 @@ let root =
|> chop
|> List.rev
|> String.concat Filename.dir_sep
let num_domains =
let result =
try
Unix.getenv "OMP_NUM_THREADS"
|> int_of_string
with Not_found -> 1
in
result - 1
(* QCaml:2 ends here *)

1
common/lib/qcaml.mli
View File

@ -9,4 +9,5 @@
(* [[file:~/QCaml/common/qcaml.org::*QCaml][QCaml:1]] *)
val root : string
val name : string
val num_domains : int
(* QCaml:1 ends here *)

15
common/qcaml.org
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@ -19,10 +19,12 @@
#+begin_src ocaml :tangle (eval mli)
val root : string
val name : string
val num_domains : int
#+end_src
| ~root~ | Path to the QCaml source directory |
| ~name~ | ~"QCaml"~ |
| ~root~ | Path to the QCaml source directory |
| ~name~ | ~"QCaml"~ |
| ~num_domains~ | Number of threads in parallel computations |
#+begin_src ocaml :tangle (eval ml) :exports none
let name = "QCaml"
@ -40,5 +42,14 @@ let root =
|> String.concat Filename.dir_sep
let num_domains =
let result =
try
Unix.getenv "OMP_NUM_THREADS"
|> int_of_string
with Not_found -> 1
in
result - 1
#+end_src

522
docs/common.html
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File diff suppressed because it is too large Load Diff

104
docs/gaussian.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-04-24 Mon 19:28 -->
<!-- 2023-06-16 Fri 09:49 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Gaussian</title>
@ -272,41 +272,41 @@ org_html_manager.setup(); // activate after the parameters are set
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org8752877">1. Summary</a></li>
<li><a href="#orgc12310c">2. Atomic shell</a>
<li><a href="#org418bb17">1. Summary</a></li>
<li><a href="#org3107c2d">2. Atomic shell</a>
<ul>
<li><a href="#org3e413df">2.1. Type</a></li>
<li><a href="#orgaa9e5a8">2.2. Access</a></li>
<li><a href="#org40ea971">2.3. Creation</a></li>
<li><a href="#org76ce11e">2.4. Printers</a></li>
<li><a href="#orgd3e8a3d">2.1. Type</a></li>
<li><a href="#org3a79952">2.2. Access</a></li>
<li><a href="#orgf649255">2.3. Creation</a></li>
<li><a href="#orgb538194">2.4. Printers</a></li>
</ul>
</li>
<li><a href="#org20ddf7f">3. Atomic shell pair couple</a>
<li><a href="#org055d620">3. Atomic shell pair couple</a>
<ul>
<li><a href="#org79cc56e">3.1. Type</a></li>
<li><a href="#org2486daa">3.2. Access</a></li>
<li><a href="#org682c85c">3.3. Creation</a></li>
<li><a href="#org6d637d8">3.4. Printers</a></li>
<li><a href="#org85660fe">3.1. Type</a></li>
<li><a href="#orgca1d510">3.2. Access</a></li>
<li><a href="#orgd5c48bb">3.3. Creation</a></li>
<li><a href="#org2949ca5">3.4. Printers</a></li>
</ul>
</li>
<li><a href="#orge37a5fe">4. Atomic shell pair</a>
<li><a href="#orge44bc1a">4. Atomic shell pair</a>
<ul>
<li><a href="#org791264a">4.1. Type</a></li>
<li><a href="#orge08787d">4.2. Access</a></li>
<li><a href="#org49ac790">4.3. Creation</a></li>
<li><a href="#orgb4a074f">4.4. Printers</a></li>
<li><a href="#org8d76a2d">4.1. Type</a></li>
<li><a href="#orgdb75218">4.2. Access</a></li>
<li><a href="#org813d710">4.3. Creation</a></li>
<li><a href="#org864a734">4.4. Printers</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org8752877" class="outline-2">
<h2 id="org8752877"><span class="section-number-2">1</span> Summary</h2>
<div id="outline-container-org418bb17" class="outline-2">
<h2 id="org418bb17"><span class="section-number-2">1</span> Summary</h2>
</div>
<div id="outline-container-orgc12310c" class="outline-2">
<h2 id="orgc12310c"><span class="section-number-2">2</span> Atomic shell</h2>
<div id="outline-container-org3107c2d" class="outline-2">
<h2 id="org3107c2d"><span class="section-number-2">2</span> Atomic shell</h2>
<div class="outline-text-2" id="text-2">
<p>
Set of contracted Gaussians differing only by the powers of \(x\), \(y\) and \(z\), with a
@ -339,8 +339,8 @@ particular powers of \(x,y,z\) (<code>PrimitiveShell.norm_coef_scale</code>)</li
</div>
<div id="outline-container-org3e413df" class="outline-3">
<h3 id="org3e413df"><span class="section-number-3">2.1</span> Type</h3>
<div id="outline-container-orgd3e8a3d" class="outline-3">
<h3 id="orgd3e8a3d"><span class="section-number-3">2.1</span> Type</h3>
<div class="outline-text-3" id="text-2-1">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
@ -351,8 +351,8 @@ particular powers of \(x,y,z\) (<code>PrimitiveShell.norm_coef_scale</code>)</li
</div>
</div>
<div id="outline-container-orgaa9e5a8" class="outline-3">
<h3 id="orgaa9e5a8"><span class="section-number-3">2.2</span> Access</h3>
<div id="outline-container-org3a79952" class="outline-3">
<h3 id="org3a79952"><span class="section-number-3">2.2</span> Access</h3>
<div class="outline-text-3" id="text-2-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">ang_mom</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Angular_momentum.</span>t
@ -429,14 +429,14 @@ particular powers of \(x,y,z\) (<code>PrimitiveShell.norm_coef_scale</code>)</li
</tbody>
</table>
<pre class="example" id="orgd663d82">
<pre class="example" id="org2dea601">
</pre>
</div>
</div>
<div id="outline-container-org40ea971" class="outline-3">
<h3 id="org40ea971"><span class="section-number-3">2.3</span> Creation</h3>
<div id="outline-container-orgf649255" class="outline-3">
<h3 id="orgf649255"><span class="section-number-3">2.3</span> Creation</h3>
<div class="outline-text-3" id="text-2-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">make</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-label">?index</span><span class="org-tuareg-font-lock-operator">:</span>int <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Contracted_shell.</span>t array <span class="org-tuareg-font-lock-operator">-&gt;</span> t
@ -468,8 +468,8 @@ particular powers of \(x,y,z\) (<code>PrimitiveShell.norm_coef_scale</code>)</li
</div>
</div>
<div id="outline-container-org76ce11e" class="outline-3">
<h3 id="org76ce11e"><span class="section-number-3">2.4</span> Printers</h3>
<div id="outline-container-orgb538194" class="outline-3">
<h3 id="orgb538194"><span class="section-number-3">2.4</span> Printers</h3>
<div class="outline-text-3" id="text-2-4">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Format.</span>formatter <span class="org-tuareg-font-lock-operator">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> unit
@ -479,8 +479,8 @@ particular powers of \(x,y,z\) (<code>PrimitiveShell.norm_coef_scale</code>)</li
</div>
</div>
<div id="outline-container-org20ddf7f" class="outline-2">
<h2 id="org20ddf7f"><span class="section-number-2">3</span> Atomic shell pair couple</h2>
<div id="outline-container-org055d620" class="outline-2">
<h2 id="org055d620"><span class="section-number-2">3</span> Atomic shell pair couple</h2>
<div class="outline-text-2" id="text-3">
<p>
An atomic shell pair couple is the cartesian product between two sets of functions, one
@ -496,8 +496,8 @@ acting on different electrons, since they will be coupled by a two-electron oper
</div>
<div id="outline-container-org79cc56e" class="outline-3">
<h3 id="org79cc56e"><span class="section-number-3">3.1</span> Type</h3>
<div id="outline-container-org85660fe" class="outline-3">
<h3 id="org85660fe"><span class="section-number-3">3.1</span> Type</h3>
<div class="outline-text-3" id="text-3-1">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
@ -508,8 +508,8 @@ acting on different electrons, since they will be coupled by a two-electron oper
</div>
</div>
<div id="outline-container-org2486daa" class="outline-3">
<h3 id="org2486daa"><span class="section-number-3">3.2</span> Access</h3>
<div id="outline-container-orgca1d510" class="outline-3">
<h3 id="orgca1d510"><span class="section-number-3">3.2</span> Access</h3>
<div class="outline-text-3" id="text-3-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">ang_mom</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Angular_momentum.</span>t
@ -594,8 +594,8 @@ acting on different electrons, since they will be coupled by a two-electron oper
</div>
</div>
<div id="outline-container-org682c85c" class="outline-3">
<h3 id="org682c85c"><span class="section-number-3">3.3</span> Creation</h3>
<div id="outline-container-orgd5c48bb" class="outline-3">
<h3 id="orgd5c48bb"><span class="section-number-3">3.3</span> Creation</h3>
<div class="outline-text-3" id="text-3-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">make</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-label">?cutoff</span><span class="org-tuareg-font-lock-operator">:</span>float <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Atomic_shell_pair.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Atomic_shell_pair.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> t option
@ -621,14 +621,14 @@ Default cutoff is \(\epsilon\).
</tbody>
</table>
<pre class="example" id="orgff2a8ea">
<pre class="example" id="org1d1eb7f">
</pre>
</div>
</div>
<div id="outline-container-org6d637d8" class="outline-3">
<h3 id="org6d637d8"><span class="section-number-3">3.4</span> Printers</h3>
<div id="outline-container-org2949ca5" class="outline-3">
<h3 id="org2949ca5"><span class="section-number-3">3.4</span> Printers</h3>
<div class="outline-text-3" id="text-3-4">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Format.</span>formatter <span class="org-tuareg-font-lock-operator">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> unit
@ -638,8 +638,8 @@ Default cutoff is \(\epsilon\).
</div>
</div>
<div id="outline-container-orge37a5fe" class="outline-2">
<h2 id="orge37a5fe"><span class="section-number-2">4</span> Atomic shell pair</h2>
<div id="outline-container-orge44bc1a" class="outline-2">
<h2 id="orge44bc1a"><span class="section-number-2">4</span> Atomic shell pair</h2>
<div class="outline-text-2" id="text-4">
<p>
Data structure to represent pairs of atomic shells. The products of
@ -651,8 +651,8 @@ An atomic shell pair is an array of pairs of contracted shells.
</p>
</div>
<div id="outline-container-org791264a" class="outline-3">
<h3 id="org791264a"><span class="section-number-3">4.1</span> Type</h3>
<div id="outline-container-org8d76a2d" class="outline-3">
<h3 id="org8d76a2d"><span class="section-number-3">4.1</span> Type</h3>
<div class="outline-text-3" id="text-4-1">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
@ -663,8 +663,8 @@ An atomic shell pair is an array of pairs of contracted shells.
</div>
</div>
<div id="outline-container-orge08787d" class="outline-3">
<h3 id="orge08787d"><span class="section-number-3">4.2</span> Access</h3>
<div id="outline-container-orgdb75218" class="outline-3">
<h3 id="orgdb75218"><span class="section-number-3">4.2</span> Access</h3>
<div class="outline-text-3" id="text-4-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">atomic_shell_a</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Atomic_shell.</span>t
@ -731,8 +731,8 @@ An atomic shell pair is an array of pairs of contracted shells.
</div>
</div>
<div id="outline-container-org49ac790" class="outline-3">
<h3 id="org49ac790"><span class="section-number-3">4.3</span> Creation</h3>
<div id="outline-container-org813d710" class="outline-3">
<h3 id="org813d710"><span class="section-number-3">4.3</span> Creation</h3>
<div class="outline-text-3" id="text-4-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">make</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-label">?cutoff</span><span class="org-tuareg-font-lock-operator">:</span>float <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Atomic_shell.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Atomic_shell.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> t option
@ -765,8 +765,8 @@ If an atomic shell pair is not significant, sets the value to <code>None</code>.
</div>
</div>
<div id="outline-container-orgb4a074f" class="outline-3">
<h3 id="orgb4a074f"><span class="section-number-3">4.4</span> Printers</h3>
<div id="outline-container-org864a734" class="outline-3">
<h3 id="org864a734"><span class="section-number-3">4.4</span> Printers</h3>
<div class="outline-text-3" id="text-4-4">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Format.</span>formatter <span class="org-tuareg-font-lock-operator">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> unit
@ -778,7 +778,7 @@ If an atomic shell pair is not significant, sets the value to <code>None</code>.
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2023-04-24 Mon 19:28</p>
<p class="date">Created: 2023-06-16 Fri 09:49</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

10
docs/gaussian_integrals.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-04-24 Mon 13:50 -->
<!-- 2023-06-16 Fri 18:25 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Gaussian integrals</title>
@ -250,18 +250,18 @@ org_html_manager.setup(); // activate after the parameters are set
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgdc976ae">1. Summary</a></li>
<li><a href="#org78d032d">1. Summary</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgdc976ae" class="outline-2">
<h2 id="orgdc976ae"><span class="section-number-2">1</span> Summary</h2>
<div id="outline-container-org78d032d" class="outline-2">
<h2 id="org78d032d"><span class="section-number-2">1</span> Summary</h2>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2023-04-24 Mon 13:50</p>
<p class="date">Created: 2023-06-16 Fri 18:25</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

10
docs/linear_algebra.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-12-13 Tue 10:55 -->
<!-- 2023-05-26 Fri 15:34 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Linear Algebra</title>
@ -250,18 +250,18 @@ org_html_manager.setup(); // activate after the parameters are set
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgb899d84">1. Summary</a></li>
<li><a href="#orgdf211e4">1. Summary</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgb899d84" class="outline-2">
<h2 id="orgb899d84"><span class="section-number-2">1</span> Summary</h2>
<div id="outline-container-orgdf211e4" class="outline-2">
<h2 id="orgdf211e4"><span class="section-number-2">1</span> Summary</h2>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2022-12-13 Tue 10:55</p>
<p class="date">Created: 2023-05-26 Fri 15:34</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

10
docs/top.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-04-24 Mon 19:28 -->
<!-- 2023-06-16 Fri 18:25 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Top-level</title>
@ -250,18 +250,18 @@ org_html_manager.setup(); // activate after the parameters are set
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgab35359">1. Summary</a></li>
<li><a href="#orga2f9258">1. Summary</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgab35359" class="outline-2">
<h2 id="orgab35359"><span class="section-number-2">1</span> Summary</h2>
<div id="outline-container-orga2f9258" class="outline-2">
<h2 id="orga2f9258"><span class="section-number-2">1</span> Summary</h2>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2023-04-24 Mon 19:28</p>
<p class="date">Created: 2023-06-16 Fri 18:25</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

3
dune-project
View File

@ -25,7 +25,7 @@
QCaml provides a programming framewrok work wave function methods
in quantum chemistry.")
(depends
(ocaml (>= 4.10))
(ocaml (>= 5.0))
(dune (>= 1.10))
(camlp-streams (>= 5.0))
trexio
@ -33,6 +33,7 @@ in quantum chemistry.")
getopt
zarith
alcotest
domainslib
)
)

18
examples/ex_hartree_fock.ml
View File

@ -1,11 +1,11 @@
(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Header][Header:1]] *)
(* [[file:ex_hartree_fock.org::*Header][Header:1]] *)
module Command_line = Qcaml.Common.Command_line
module Util = Qcaml.Common.Util
let () =
(* Header:1 ends here *)
(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Definition][Definition:1]] *)
(* [[file:ex_hartree_fock.org::*Definition][Definition:1]] *)
let open Command_line in
begin
set_header_doc (Sys.argv.(0));
@ -31,7 +31,7 @@ begin
end;
(* Definition:1 ends here *)
(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Interpretation][Interpretation:1]] *)
(* [[file:ex_hartree_fock.org::*Interpretation][Interpretation:1]] *)
let basis_file = Util.of_some @@ Command_line.get "basis" in
let nuclei_file = Util.of_some @@ Command_line.get "xyz" in
@ -51,26 +51,26 @@ let multiplicity =
in
(* Interpretation:1 ends here *)
(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Computation][Computation:1]] *)
(* [[file:ex_hartree_fock.org::*Computation][Computation:1]] *)
let nuclei =
Qcaml.Particles.Nuclei.of_xyz_file nuclei_file
in
(* Computation:1 ends here *)
(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Computation][Computation:2]] *)
(* [[file:ex_hartree_fock.org::*Computation][Computation:2]] *)
let ao_basis =
Qcaml.Ao.Basis.of_nuclei_and_basis_filename ~nuclei basis_file
in
(* Computation:2 ends here *)
(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Computation][Computation:3]] *)
let simulation = Qcaml.Simulation.make ~charge ~multiplicity ~nuclei ao_basis in
(* [[file:ex_hartree_fock.org::*Computation][Computation:3]] *)
let simulation = Qcaml.Simulation.make ~multiplicity ~charge ~nuclei ao_basis in
(* Computation:3 ends here *)
(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Computation][Computation:4]] *)
(* [[file:ex_hartree_fock.org::*Computation][Computation:4]] *)
let hf = Qcaml.Mo.Hartree_fock.make ~guess:`Huckel simulation in
(* Computation:4 ends here *)
(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Output][Output:1]] *)
(* [[file:ex_hartree_fock.org::*Output][Output:1]] *)
Format.printf "@[%a@]" (Mo.Hartree_fock.pp) hf
(* Output:1 ends here *)

6
examples/ex_hartree_fock.org
View File

@ -75,14 +75,16 @@ in
#+END_SRC
* Computation
We first read the =xyz= file to create a molecule:
#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml
let nuclei =
Qcaml.Particles.Nuclei.of_xyz_file nuclei_file
in
#+END_SRC
Then we create an Gaussian AO basis using the atomic coordinates:
Then we create a Gaussian AO basis using the atomic coordinates:
#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml
let ao_basis =
Qcaml.Ao.Basis.of_nuclei_and_basis_filename ~nuclei basis_file
@ -91,7 +93,7 @@ in
We create a simulation from the nuclei and the basis set:
#+BEGIN_SRC ocaml :comments link :exports code :tangle ex_hartree_fock.ml
let simulation = Qcaml.Simulation.make ~nuclei ao_basis in
let simulation = Qcaml.Simulation.make ~multiplicity ~charge ~nuclei ao_basis in
#+END_SRC
and we can make the Hartree-Fock computation:

28
gaussian/lib/basis.ml
View File

@ -107,13 +107,6 @@ let of_nuclei_and_basis_filenames ~nuclei filenames =
let of_trexio f =
let nuclei = Particles.Nuclei.of_trexio f in
(*
let nucl_num = Array.length nuclei in
let prim_num = Trexio.read_basis_prim_num f in
let shell_num = Trexio.read_basis_shell_num f in
let shell_factor = Trexio.read_basis_shell_factor f in
let prim_factor = Trexio.read_basis_prim_factor f in
*)
let shell_ang_mom = Trexio.read_basis_shell_ang_mom f
|> Array.map Common.Angular_momentum.of_int
in
@ -137,7 +130,7 @@ let of_trexio f =
| Some x -> x
| None -> assert false)
in
let index_ = ref 0 in
let contracted_shells =
Array.mapi (fun i (_,center) ->
@ -180,9 +173,24 @@ let of_trexio f =
{ contracted_shells ; atomic_shells ; size = !index_;
general_basis = [];
}
let to_trexio _ _ =
let to_trexio _f _t =
failwith "Not implemented"
(*
Trexio.write_basis_type f "Gaussian" ;
Trexio.write_basis_shell_num f t.size;
let prim_num =
Array.fold_left (fun accu i -> accu + Array.length i) 0 t.contracted_shells
in
Trexio.read_basis_prim_num f prim_num;
let nucleus_index =
Array.map
in
let shell_factor = Trexio.read_basis_shell_factor f in
let prim_factor =
Trexio.read_basis_prim_factor f in
()
*)
let pp ppf t =
Format.fprintf ppf "@[%s@]" (to_string t)

1
gaussian_integrals/README.org
View File

@ -50,6 +50,7 @@ with open(dunetest,'w') as f:
alcotest
unix
trexio
domainslib
qcaml.{name}
)
)

5
gaussian_integrals/lib/dune
View File

@ -2,7 +2,7 @@
(library
(name gaussian_integrals)
(public_name qcaml.gaussian_integrals)
(synopsis
(synopsis
"Integrals on the Gaussian basis sets"
)
(libraries
@ -11,8 +11,9 @@
qcaml.gaussian
qcaml.operators
unix
domainslib
)
(modules_without_implementation matrix_on_basis)
)

61
gaussian_integrals/lib/two_electron_integrals.ml
View File

@ -1,6 +1,7 @@
(** Two electron integrals
*)
open Common
open Linear_algebra
open Gaussian
@ -9,11 +10,12 @@ open Operators
open Constants
let cutoff = integrals_cutoff
module Bs = Basis
module Cs = Contracted_shell
module Csp = Contracted_shell_pair
module Bs = Basis
module Cs = Contracted_shell
module Csp = Contracted_shell_pair
module Cspc = Contracted_shell_pair_couple
module Fis = Four_idx_storage
module Fis = Four_idx_storage
module type Two_ei_structure =
sig
@ -23,15 +25,16 @@ module type Two_ei_structure =
end
module Make(T : Two_ei_structure) = struct
include Four_idx_storage
type t = Basis.t Four_idx_storage.t
let class_of_contracted_shell_pair_couple = T.class_of_contracted_shell_pair_couple
let class_of_contracted_shell_pair_couple = T.class_of_contracted_shell_pair_couple
let store_class ?(cutoff=integrals_cutoff) data contracted_shell_pair_couple cls =
let to_powers x =
let store_class ?(cutoff=integrals_cutoff) data contracted_shell_pair_couple cls =
let to_powers x =
let open Zkey in
match to_powers x with
| Three x -> x
@ -49,7 +52,7 @@ module Make(T : Two_ei_structure) = struct
let j_c = Cs.index (Csp.shell_b shell_p) + j_c + 1 in
let xj = to_powers powers_j in
Array.iteri (fun k_c powers_k ->
let k_c = Cs.index (Csp.shell_a shell_q) + k_c + 1 in
let k_c = Cs.index (Csp.shell_a shell_q) + k_c + 1 in
let xk = to_powers powers_k in
Array.iteri (fun l_c powers_l ->
let l_c = Cs.index (Csp.shell_b shell_q) + l_c + 1 in
@ -69,13 +72,13 @@ module Make(T : Two_ei_structure) = struct
let of_basis ?operator basis =
let of_basis ?operator basis =
let n = Bs.size basis
and shell = Bs.contracted_shells basis
in
let eri_array =
let eri_array =
Fis.create ~size:n `Dense
(*
Fis.create ~size:n `Sparse
@ -92,19 +95,11 @@ module Make(T : Two_ei_structure) = struct
Printf.printf "%d significant shell pairs computed in %f seconds\n"
(List.length shell_pairs) (Unix.gettimeofday () -. t0);
let ishell = ref max_int in
let t0 = Unix.gettimeofday () in
let f shell_p =
let () =
(*
if Parallel.rank < 2 && Cs.index (Csp.shell_a shell_p) < !ishell then
*)
if Cs.index (Csp.shell_a shell_p) < !ishell then
(ishell := Cs.index (Csp.shell_a shell_p) ; print_int !ishell ; print_newline ())
let () =
Printf.printf "%3d %3d\n%!" (Cs.index (Csp.shell_a shell_p)) (Cs.index (Csp.shell_b shell_p))
in
let sp =
@ -113,13 +108,13 @@ module Make(T : Two_ei_structure) = struct
try
List.iter (fun shell_q ->
let () =
let () =
if Cs.index (Csp.shell_a shell_q) >
Cs.index (Csp.shell_a shell_p) then
raise Exit
in
let sq = Csp.shell_pairs shell_q in
let cspc =
let cspc =
if Array.length sp < Array.length sq then
Cspc.make ~cutoff shell_p shell_q
else
@ -137,15 +132,19 @@ module Make(T : Two_ei_structure) = struct
with Exit -> ()
in
(*
List.rev shell_pairs
*)
shell_pairs
(*
|> Parallel.list_iter f ;
*)
|> List.iter f;
Printf.printf "Computed %s Integrals in parallel in %f seconds\n%!"
let pool = Domainslib.Task.setup_pool ~num_domains:Qcaml.num_domains () in
let _ =
Domainslib.Task.run pool (fun _ ->
shell_pairs
|> List.map (fun sp ->
Domainslib.Task.async pool (fun _ -> f sp) )
|> List.iter (fun task -> ignore (Domainslib.Task.await pool task) ) ;
)
in
Domainslib.Task.teardown_pool pool;
Printf.printf "Computed %s Integrals in %f seconds\n%!"
T.name (Unix.gettimeofday () -. t0);
eri_array

229
linear_algebra/lib/cholesky.ml Normal file
View File

@ -0,0 +1,229 @@
open Lacaml.D
let full_ldl m_A =
let n = Mat.dim1 m_A in
assert (Mat.dim2 m_A = n);
let v_D = Vec.make0 n in
let m_Lt = Mat.identity n in
let v_D_inv = Vec.make0 n in
let compute_d j =
let l_jk =
Mat.col m_Lt j
in
let l_jk__d_k =
Vec.mul ~n:(j-1) l_jk v_D
in
m_A.{j,j} -. dot ~n:(j-1) l_jk l_jk__d_k
in
let compute_l i =
let l_ik__d_k =
Mat.col m_Lt i
|> Vec.mul ~n:(i-1) v_D
in
fun j ->
assert (i > j);
let l_jk =
Mat.col m_Lt j
in
v_D_inv.{j} *. ( m_A.{j,i} -. dot ~n:(j-1) l_ik__d_k l_jk )
in
for i=1 to n do
for j=1 to (i-1) do
m_Lt.{j,i} <- compute_l i j;
done;
let d_i = compute_d i in
v_D.{i} <- d_i;
v_D_inv.{i} <- 1. /. d_i;
done;
m_Lt, v_D
let pivoted_ldl threshold m_A =
(* {% $P A P^\dagger = L D L^\dagger$. %}
Input : Matrix $A$
Output : Matrices $L, D, P$.
*)
let n = Mat.dim1 m_A in
assert (Mat.dim2 m_A = n);
let pi = Array.init (n+1) (fun i -> i) in
let v_D = Vec.init n (fun i -> abs_float m_A.{i,i}) in
let m_Lt = Mat.identity n in
let v_D_inv = Vec.make0 n in
let compute_d i =
let l_ik =
Mat.col m_Lt i
in
let l_ik__d_k =
Vec.mul ~n:(i-1) l_ik v_D
in
m_A.{pi.(i),pi.(i)} -. dot ~n:(i-1) l_ik l_ik__d_k
in
let compute_l i =
let l_ik__d_k =
Mat.col m_Lt i
|> Vec.mul ~n:(i-1) v_D
in
fun j ->
assert (i > j);
let l_jk =
Mat.col m_Lt j
in
v_D_inv.{j} *. ( m_A.{pi.(j),pi.(i)} -. dot ~n:(j-1) l_ik__d_k l_jk )
in
let maxloc v i =
let rec aux pos value i =
if i > n then
pos
else if v_D.{i} > value then
aux i v_D.{i} (i+1)
else
aux pos value (i+1)
in
aux i v.{i} (i+1)
in
let pivot i =
let j = maxloc v_D i in
let p_i, p_j = pi.(i), pi.(j) in
pi.(i) <- p_j;
pi.(j) <- p_i;
in
let () =
try
for i=1 to n do
pivot i;
for j=1 to (i-1) do
m_Lt.{j,i} <- compute_l i j;
done;
let d_i = compute_d i in
if abs_float d_i < threshold then
raise Exit;
v_D.{i} <- d_i;
v_D_inv.{i} <- 1. /. d_i;
done
with Exit -> ()
in
m_Lt, v_D, pi
(*
let test_case () =
let matrix_diff m_A m_B =
Mat.syrk_trace (Mat.sub m_A m_B)
in
let vector_diff v_A v_B =
let v = Vec.sub v_A v_B in
dot v v
in
let m_A = Mat.random 1000 1000 in
let m_A = Mat.add m_A (Mat.transpose_copy m_A) in
let test_full_small () =
let m_A =
Mat.of_array [| [| 4. ; 12. ; -16. |] ;
[| 12. ; 37. ; -43. |] ;
[| -16. ; -43. ; 98. |] |]
in
let m_L_ref =
Mat.of_array [| [| 1. ; 0. ; 0. |] ;
[| 3. ; 1. ; 0. |] ;
[| -4. ; 5. ; 1. |] |]
in
let m_Lt_ref =
Mat.transpose_copy m_L_ref
in
let v_D_ref =
Vec.of_array [| 4. ; 1. ; 9. |]
in
let m_Lt, v_D = full_ldl m_A in
Alcotest.(check (float 1.e-15)) "full L" 0. (matrix_diff m_Lt m_Lt_ref);
Alcotest.(check (float 1.e-15)) "full D" 0. (vector_diff v_D v_D_ref);
let m_D = Mat.of_diag v_D in
let m_B = gemm ~transa:`T m_Lt @@ gemm m_D m_Lt in
Alcotest.(check (float 1.e-15)) "full L" 0. (matrix_diff m_A m_B);
()
in
let test_full () =
let m_Lt, v_D = full_ldl m_A in
let m_D = Mat.of_diag v_D in
let m_B = gemm ~transa:`T m_Lt @@ gemm m_D m_Lt in
Alcotest.(check (float 1.e-15)) "full D" 0. (matrix_diff m_A m_B);
()
in
let test_pivoted () =
let m_Lt, v_D, pi = pivoted_ldl 0. m_A in
let n = Mat.dim1 m_A in
let m_P = Mat.make0 n n in
for i=1 to n do
m_P.{i,pi.(i)} <- 1.
done;
let m_D = Mat.of_diag v_D in
let m_B =
gemm ~transa:`T m_P @@
gemm ~transa:`T m_Lt @@
gemm m_D @@
gemm m_Lt m_P
in
Alcotest.(check (float 1.e-14)) "pivoted D" 0. (matrix_diff m_A m_B);
()
in
let test_truncated () =
let m_Lt, v_D, pi = pivoted_ldl 0.001 m_A in
let n = Mat.dim1 m_Lt in
let m_P = Mat.make0 n n in
for i=1 to n do
m_P.{i,pi.(i)} <- 1.
done;
let m_D = Mat.of_diag v_D in
let m_B =
gemm ~transa:`T m_P @@
gemm ~transa:`T m_Lt @@
gemm m_D @@
gemm m_Lt m_P
in
Alcotest.(check (float 1.e-3)) "full D" 0. (matrix_diff m_A m_B);
()
in
[
"Small", `Quick, test_full_small;
"Full", `Quick, test_full;
"Pivoted", `Quick, test_pivoted ;
"Truncated", `Quick, test_truncated ;
]
*)

3
qcaml.opam
View File

@ -18,7 +18,7 @@ description: """
QCaml provides a programming framewrok work wave function methods
in quantum chemistry."""
depends: [
"ocaml" {>= "4.10"}
"ocaml" {>= "5.0"}
"dune" {>= "1.10"}
"camlp-streams" {>= "5.0"}
"trexio"
@ -26,4 +26,5 @@ depends: [
"getopt"
"zarith"
"alcotest"
"domainslib"
]

10
simulation/lib/simulation.ml
View File

@ -1,10 +1,10 @@
(* [[file:~/QCaml/simulation/simulation.org::*Simulation][Simulation:2]] *)
(* [[file:../simulation.org::*Simulation][Simulation:2]] *)
open Common
open Particles
open Operators
(* Simulation:2 ends here *)
(* [[file:~/QCaml/simulation/simulation.org::*Type][Type:2]] *)
(* [[file:../simulation.org::*Type][Type:2]] *)
type t = {
charge : Charge.t;
electrons : Electrons.t;
@ -24,7 +24,7 @@ type t = {
* | ~operators~ | List of extra operators (range-separation, f12, etc) | *)
(* [[file:~/QCaml/simulation/simulation.org::*Access][Access:2]] *)
(* [[file:../simulation.org::*Access][Access:2]] *)
let nuclei t = t.nuclei
let charge t = t.charge
let electrons t = t.electrons
@ -41,7 +41,7 @@ let operators t = t.operators
* - operators : ~[]~ *)
(* [[file:~/QCaml/simulation/simulation.org::*Creation][Creation:2]] *)
(* [[file:../simulation.org::*Creation][Creation:2]] *)
let make
?(multiplicity=1)
?(charge=0)
@ -65,7 +65,7 @@ let make
{ charge ; nuclei ; electrons ; ao_basis ; operators}
(* Creation:2 ends here *)
(* [[file:~/QCaml/simulation/simulation.org::*Printers][Printers:2]] *)
(* [[file:../simulation.org::*Printers][Printers:2]] *)
let pp ppf t =
let formula = Nuclei.formula t.nuclei in
let n_aos = Ao.Basis.size t.ao_basis in

10
simulation/lib/simulation.mli
View File

@ -7,7 +7,7 @@
*
* #+NAME: open *)
(* [[file:~/QCaml/simulation/simulation.org::open][open]] *)
(* [[file:../simulation.org::open][open]] *)
open Common
open Particles
open Operators
@ -17,14 +17,14 @@ open Operators
*
* #+NAME: types *)
(* [[file:~/QCaml/simulation/simulation.org::types][types]] *)
(* [[file:../simulation.org::types][types]] *)
type t
(* types ends here *)
(* Access *)
(* [[file:~/QCaml/simulation/simulation.org::*Access][Access:1]] *)
(* [[file:../simulation.org::*Access][Access:1]] *)
val nuclei : t -> Nuclei.t
val charge : t -> Charge.t
val electrons : t -> Electrons.t
@ -36,7 +36,7 @@ val operators : t -> Operator.t list
(* Creation *)
(* [[file:~/QCaml/simulation/simulation.org::*Creation][Creation:1]] *)
(* [[file:../simulation.org::*Creation][Creation:1]] *)
val make : ?multiplicity:int -> ?charge:int ->
?operators:Operator.t list-> nuclei:Nuclei.t ->
Ao.Basis.t -> t
@ -45,6 +45,6 @@ val make : ?multiplicity:int -> ?charge:int ->
(* Printers *)
(* [[file:~/QCaml/simulation/simulation.org::*Printers][Printers:1]] *)
(* [[file:../simulation.org::*Printers][Printers:1]] *)
val pp : Format.formatter -> t -> unit
(* Printers:1 ends here *)