chemshell_qchem / blob
1 <set title="The Q-Chem Interface">
2 <set tag="quantum">
3 <set tag2="q-chem">
5 <file include="head.htp">
8 <h2>Introduction</H2>
10 The interface is designed to access basic functionality of the <A
11 HREF="http://www.q-chem.com/" TARGET="_blank"> Q-Chem program package</A>. Currently the interface is
12 capable of calculating ground state energies and gradients on the restricted
13 closed-shell Hartree-Fock, DFT and RI-MP2 levels of theory.
14 For DFT calculations the functionals BLYP, BP86, B3LYP, B3PW91, BPW91, S-VWN-LDA, PBE0 are available.
16 The interface creates the necessary input files for the Q-Chem run, executes
17 Q-Chem and finally extracts the QM-results.<br><br>
19 In order to use the interface, the environment must be set up as required for a
20 Q-Chem standard run depending on the Q-Chem version. Commonly, at least the
21 shell environment variables<br><br>
23 <TABLE CELLPADDING=3 BORDER="1">
24 <TR>
25 <TD>QC </TD> <TD>Path to Q-Chem main directory </TD>
26 </TR>
27 <TR>
28 <TD>QCAUX </TD> <TD>Path to Q-Chem auxiliary directory </TD>
29 </TR>
30 <TR>
31 <TD>QCSCRATCH </TD> <TD>Path to scratch directory for Q-Chem scratch output</TD>
32 </TR>
33 </TABLE>
34 <br>
36 need to be set and "qchem" needs to be in the path, e.g. by sourcing
37 $QC/bin/qchem.setup.sh
38 (see <A HREF="http://www.q-chem.com/doc_for_web/qchem_manual_3.2.pdf"
39 TARGET="_blank">Q-Chem manual</A>). See also the file "qchemrc" in the
40 example/qchem folder as example file that can be sourced before the
41 ChemShell run.<br><br>
43 Informations on further developments of the Q-Chem interface and how to join the ChemShell-Q-Chem project
44 can be found on <A HREF="http://ccpforge.cse.rl.ac.uk/gf/project/chemshell_qchem/" TARGET="_blank">http://ccpforge.cse.rl.ac.uk/gf/project/chemshell_qchem/</A>.
47 <a name="args"></a>
48 <H2>Command Line Arguments</H2>
49 Currently the following ChemShell command line arguments are available:<br><br>
51 <TABLE CELLPADDING=3 BORDER="1">
52 <TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=$cw1>Argument</TD>
53 <TD ALIGN="LEFT" VALIGN="TOP" WIDTH=$cw2>Argument type</TD>
54 <TD ALIGN="LEFT" VALIGN="TOP" WIDTH=$cw3>Mandatory</TD>
55 <TD ALIGN="LEFT" VALIGN="TOP" WIDTH=$cw4>Default</TD>
56 <TD ALIGN="LEFT" VALIGN="TOP" WIDTH=$cw5>Description</TD>
57 </TR>
59 <TR>
60 <TD ALIGN="LEFT" VALIGN="TOP">basis</TD>
61 <TD ALIGN="LEFT" VALIGN="TOP">keyword</TD>
62 <TD ALIGN="LEFT" VALIGN="TOP">no</TD>
63 <TD ALIGN="LEFT" VALIGN="TOP">STO-3G</TD>
64 <TD ALIGN="LEFT" VALIGN="TOP">Required basis set (Q-Chem library <A HREF="#Notes">[1]</A>)</TD>
65 </TR>
67 <TR>
68 <TD ALIGN="LEFT" VALIGN="TOP">basisspec</TD>
69 <TD ALIGN="LEFT" VALIGN="TOP">ChemShell notation</TD>
70 <TD ALIGN="LEFT" VALIGN="TOP">no</TD>
71 <TD ALIGN="LEFT" VALIGN="TOP">sto-3g all</TD>
72 <TD ALIGN="LEFT" VALIGN="TOP">Required basis set (ChemShell library <A HREF="#Notes">[2]</A>)</TD>
73 </TR>
75 <TR>
76 <TD ALIGN="LEFT" VALIGN="TOP">charge</TD>
77 <TD ALIGN="LEFT" VALIGN="TOP">integer</TD>
78 <TD ALIGN="LEFT" VALIGN="TOP">no</TD>
79 <TD ALIGN="LEFT" VALIGN="TOP">0</TD>
80 <TD ALIGN="LEFT" VALIGN="TOP">Total charge</TD>
81 </TR>
83 <TR>
84 <TD ALIGN="LEFT" VALIGN="TOP">accuracy</TD>
85 <TD ALIGN="LEFT" VALIGN="TOP">keyword</TD>
86 <TD ALIGN="LEFT" VALIGN="TOP">no</TD>
87 <TD ALIGN="LEFT" VALIGN="TOP">medium</TD>
88 <TD ALIGN="LEFT" VALIGN="TOP">Determines accuracy of SCF calculation <A HREF="#Notes">[3]</A>: debug, lowest, low, medium, high, highest </TD>
89 </TR>
91 <TR>
92 <TD ALIGN="LEFT" VALIGN="TOP">grid</TD>
93 <TD ALIGN="LEFT" VALIGN="TOP">integer</TD>
94 <TD ALIGN="LEFT" VALIGN="TOP">no</TD>
95 <TD ALIGN="LEFT" VALIGN="TOP">undefined</TD>
96 <TD ALIGN="LEFT" VALIGN="TOP">Determines size and type of DFT grid in Q-Chem notation <A HREF="#Notes">[4]</A>.</TD>
97 </TR>
99 <TR>
100 <TD ALIGN="LEFT" VALIGN="TOP">jobname</TD>
101 <TD ALIGN="LEFT" VALIGN="TOP">string</TD>
102 <TD ALIGN="LEFT" VALIGN="TOP">no</TD>
103 <TD ALIGN="LEFT" VALIGN="TOP">qchem</TD>
104 <TD ALIGN="LEFT" VALIGN="TOP">Determines the name of Q-chem input (jobname.com), output (jobname.log) and scratch (jobname.scr <A HREF="#Notes">[5]</A>).</TD>
105 </TR>
106 <TR>
107 <TD ALIGN="LEFT" VALIGN="TOP">hamiltonian</TD>
108 <TD ALIGN="LEFT" VALIGN="TOP">keyword</TD>
109 <TD ALIGN="LEFT" VALIGN="TOP">no</TD>
110 <TD ALIGN="LEFT" VALIGN="TOP">hf</TD>
111 <TD ALIGN="LEFT" VALIGN="TOP">Choice of QM Hamiltonian: hf, blyp, bp86, b3lyp <A HREF="#Notes">[6]</A>, b3lyp5 <A HREF="#Notes">[6]</A>, b3pw91, bpw91, s-vwn-lda, pbe0, rimp2, rimp2_svp <A HREF="#Notes">[7]</A></TD>
112 </TR>
113 <TR>
114 <TD ALIGN="LEFT" VALIGN="TOP">mem_total</TD>
115 <TD ALIGN="LEFT" VALIGN="TOP">integer</TD>
116 <TD ALIGN="LEFT" VALIGN="TOP">no</TD>
117 <TD ALIGN="LEFT" VALIGN="TOP">2000</TD>
118 <TD ALIGN="LEFT" VALIGN="TOP">Sets the total memory available to Q-Chem, in megabytes <A HREF="#Notes">[8]</A>.</TD>
119 </TR>
120 <TR>
121 <TD ALIGN="LEFT" VALIGN="TOP">mem_static</TD>
122 <TD ALIGN="LEFT" VALIGN="TOP">integer</TD>
123 <TD ALIGN="LEFT" VALIGN="TOP">no</TD>
124 <TD ALIGN="LEFT" VALIGN="TOP">100</TD>
125 <TD ALIGN="LEFT" VALIGN="TOP">Sets the memory for individual Q-Chem program modules, in megabytes <A HREF="#Notes">[9]</A>.</TD>
126 </TR>
127 <TR>
128 <TD ALIGN="LEFT" VALIGN="TOP">harmonic</TD>
129 <TD ALIGN="LEFT" VALIGN="TOP">bool</TD>
130 <TD ALIGN="LEFT" VALIGN="TOP">no</TD>
131 <TD ALIGN="LEFT" VALIGN="TOP">undefined</TD>
132 <TD ALIGN="LEFT" VALIGN="TOP">Specifies if either cartesian GTOs (1) or pure spherical harmonics (0) are used.</TD>
133 </TR>
134 <TR>
135 <TD ALIGN="LEFT" VALIGN="TOP">purecart</TD>
136 <TD ALIGN="LEFT" VALIGN="TOP">integer</TD>
137 <TD ALIGN="LEFT" VALIGN="TOP">no</TD>
138 <TD ALIGN="LEFT" VALIGN="TOP">undefined</TD>
139 <TD ALIGN="LEFT" VALIGN="TOP">Allows for specification of cartesian GTOs vs. pure sherical harmonics by Q-Chem nomenclature <A HREF="#Notes">[10]</A>.</TD>
140 </TR>
142 <TR>
143 <TD ALIGN="LEFT" VALIGN="TOP">guess</TD>
144 <TD ALIGN="LEFT" VALIGN="TOP">keyword</TD>
145 <TD ALIGN="LEFT" VALIGN="TOP">no</TD>
146 <TD ALIGN="LEFT" VALIGN="TOP">sad</TD>
147 <TD ALIGN="LEFT" VALIGN="TOP">Initial guess for the one-particle density matrix: SAD, CORE, GWH or READ <A HREF="#Notes">[11]</A>.</TD>
148 </TR>
150 <TR>
151 <TD ALIGN="LEFT" VALIGN="TOP">separate_jk</TD>
152 <TD ALIGN="LEFT" VALIGN="TOP">bool</TD>
153 <TD ALIGN="LEFT" VALIGN="TOP">no</TD>
154 <TD ALIGN="LEFT" VALIGN="TOP">1</TD>
155 <TD ALIGN="LEFT" VALIGN="TOP">Switch on/off the separate formation of Coulomb and exchange part <A HREF="#Notes">[12]</A>.</TD>
156 </TR>
158 <TR>
159 <TD ALIGN="LEFT" VALIGN="TOP">grain</TD>
160 <TD ALIGN="LEFT" VALIGN="TOP">integer</TD>
161 <TD ALIGN="LEFT" VALIGN="TOP">no</TD>
162 <TD ALIGN="LEFT" VALIGN="TOP">-1</TD>
163 <TD ALIGN="LEFT" VALIGN="TOP">Controls the number of lowest-level boxes in one dimension for CFMM <A HREF="#Notes">[13]</A>: -1, 1 , >=8 <A HREF="#Notes">[14]</A>.
164 </TD>
165 </TR>
167 <TR>
168 <TD ALIGN="LEFT" VALIGN="TOP">lin_k</TD>
169 <TD ALIGN="LEFT" VALIGN="TOP">bool</TD>
170 <TD ALIGN="LEFT" VALIGN="TOP">no</TD>
171 <TD ALIGN="LEFT" VALIGN="TOP">0</TD>
172 <TD ALIGN="LEFT" VALIGN="TOP">Switch on/off linear scaling screening for the exchange part (LinK <A HREF="#Notes">[15]</A>) <A HREF="#Notes">[16]</A>.</TD>
173 </TR>
175 <TR>
176 <TD ALIGN="LEFT" VALIGN="TOP">dft_d</TD>
177 <TD ALIGN="LEFT" VALIGN="TOP">keyword</TD>
178 <TD ALIGN="LEFT" VALIGN="TOP">no</TD>
179 <TD ALIGN="LEFT" VALIGN="TOP">undefined</TD>
180 <TD ALIGN="LEFT" VALIGN="TOP">Switch on Grimme's dispersion type correction: EMPIRICAL_GRIMME <A HREF="#Notes">[17]</A>.</TD>
181 </TR>
183 <TR>
184 <TD ALIGN="LEFT" VALIGN="TOP">add</TD>
185 <TD ALIGN="LEFT" VALIGN="TOP">Q-Chem notation</TD>
186 <TD ALIGN="LEFT" VALIGN="TOP">no</TD>
187 <TD ALIGN="LEFT" VALIGN="TOP">undefined</TD>
188 <TD ALIGN="LEFT" VALIGN="TOP">Set additional Q-Chem input. Use with care <A HREF="#Notes">[18]</A> !</TD>
189 </TR>
191 </TABLE>
195 <H3>
196 <A NAME="Notes">Notes and references </A></H3>
198 <OL>
199 <LI>
200 Using the argument "basis" the basis set needs to be specified in Q-Chem nomenclature. In particular note that the basis set Ahlrichs SVP is denoted as VDZ** in Q-Chem.
202 <LI>
203 If a basis set is taken from the ChemShell library the basis set is explicitly included in the Q-Chem input within a $basis-section and the Q-Chem $rem-variable
204 basis is set to "gen" (see <A HREF="http://www.q-chem.com/doc_for_web/qchem_manual_3.2.pdf" TARGET="_blank">Q-Chem manual</A>). As for an explicit basis set the default guess
205 (Superposition of atomic densities, SAD) is not available, the guess is created by basis set projection based on an initial STO-3G calculation.
208 <LI>
209 The different levels determine the SCF accuracy concerning three aspects: (A) The SCF convergence, (B) the threshold for density based Schwarz screening
210 of electron repulsion integrals and (C) the DFT grid size.
211 <TABLE CELLPADDING=3 BORDER="1" >
212 <TR><TD> keyword</TD><TD ALIGN="CENTER"> (A) </TD><TD ALIGN="CENTER"> (B) </TD><TD ALIGN="CENTER"> (C) </TD></TR>
213 <TR><TD> debug </TD><TD ALIGN="CENTER"> 10<sup>-3</sup></TD><TD ALIGN="CENTER"> 10<sup>-6</sup></TD><TD ALIGN="CENTER">"Low quality" grid </TD></TR>
214 <TR><TD> lowest </TD><TD ALIGN="CENTER"> 10<sup>-4</sup></TD><TD ALIGN="CENTER"> 10<sup>-7</sup></TD><TD ALIGN="CENTER"> SG-0 </TD></TR>
215 <TR><TD> low </TD><TD ALIGN="CENTER"> 10<sup>-5</sup></TD><TD ALIGN="CENTER"> 10<sup>-8</sup></TD><TD ALIGN="CENTER"> SG-0 </TD></TR>
216 <TR><TD> medium </TD><TD ALIGN="CENTER"> 10<sup>-6</sup></TD><TD ALIGN="CENTER"> 10<sup>-9</sup></TD><TD ALIGN="CENTER"> SG-1 </TD></TR>
217 <TR><TD> high </TD><TD ALIGN="CENTER"> 10<sup>-7</sup></TD><TD ALIGN="CENTER"> 10<sup>-10</sup></TD><TD ALIGN="CENTER"> 75/302 </TD></TR>
218 <TR><TD> highest</TD><TD ALIGN="CENTER"> 10<sup>-8</sup></TD><TD ALIGN="CENTER"> 10<sup>-11</sup></TD><TD ALIGN="CENTER"> 110/590 </TD></TR>
219 </TABLE>
220 Use the largest affordable accuracy. Typically "medium" is sufficient
221 for standard SCF energetics but you might need to choose "high" for RI-MP2,
222 gradients or also for large QM regions! For details concerning the grid abbreviations see <A HREF="http://www.q-chem.com/doc_for_web/qchem_manual_3.2.pdf" TARGET="_blank">Q-Chem manual</A>.
224 <LI>
225 If not specified the DFT grid is chosen according to the argument "accuracy".
227 <LI>
228 The Q-Chem scratch is written to $QCSCRATCH/jobname.scr/
230 <LI>
231 B3LYP and B3LYP5 differ in the correlation functional:
232 <TABLE BORDER=0>
233 <TR><TD>B3LYP </TD><TD>(correlation: 0.8100 LYP + 0.1900 VWN1RPA)</TD></TR>
234 <TR><TD>B3LYP5</TD><TD>(correlation: 0.8100 LYP + 0.1900 VWN )</TD></TR>
235 </TABLE>
236 For example, Q-Chem-B3LYP corresponds to Turbomole-B3LYP_GAUSSIAN (and Gaussian-B3LYP), while Q-CHEM-B3LYP5 corresponds to Turbomole-B3LYP (and original parameters).
237 Possible remaining differences are due to different DFT grids (see argument "accuracy" or "grid").
239 <LI>
240 Use this Hamiltonian for RI-MP2 calculations with SVP auxiliary basis set. In addition specify the "basis" argument as usual <A HREF="#Notes">[1]</A>.</TD>.
242 <LI>
243 Make sure you physically provide the specified RAM. For large QM regions the default (2GB) needs to be increased. See <A HREF="http://www.q-chem.com/doc_for_web/qchem_manual_3.2.pdf" TARGET="_blank">Q-Chem manual</A> for details.
245 <LI>
246 Make sure you physically provide the specified RAM. For large QM regions the default (100MB) needs to be increased. See <A HREF="http://www.q-chem.com/doc_for_web/qchem_manual_3.2.pdf" TARGET="_blank">Q-Chem manual for details</A>.
248 <LI>
249 If the "purecart" argument is used, the specifications by "harmonic" are overwritten. See <A HREF="http://www.q-chem.com/doc_for_web/qchem_manual_3.2.pdf" TARGET="_blank">Q-Chem manual</A> for the purecart variable.
251 <LI>
252 Q-Chem provides the core hamiltonian guess (CORE), the superposition of atomic densities (SAD, default), and
253 the generalized Wolfsberg-Helmholtz guess (GWH). Additionally by the keyword "READ" an adequate guess can be read in from file. For this purpose, the file containing the guess
254 needs to be located in the scratch directory, i.e. $QCSCRATCH/jobname.scr/. See <A HREF="http://www.q-chem.com/doc_for_web/qchem_manual_3.2.pdf" TARGET="_blank">Q-Chem manual</A> for details.
256 <LI>
257 Switch on for large QM systems as "separate_jk" is required to make use of
258 CFMM <A HREF="#Notes">[13]</A> and LinK <A HREF="#Notes">[15]</A>.
260 <LI>
261 C. A. White, B. G. Johnson, P. M.W. Gill and M. Head-Gordon, The Continuous Fast Multipole Method, <em>Chem. Phys. Letters</em>, <strong>230</strong>, 8 (1994).
263 <LI>Use the default (-1) unless you really want to change the CFMM behavior (-1: Program decides best value turning on CFMM when useful, 1: Do not use CFMM, n >=8: Use CFMM with n lowest-level boxes in one dimension).
265 <LI>
266 C. Ochsenfeld, C. A. White, and M. Head-Gordon, Linear and sublinear scaling of Hartree-Fock-type exchange matrices, <em>J. Chem. Phys.</em>, <strong>109</strong>, 1663 (1998).
268 <LI>
269 Switch on for large QM systems (several hundreds of atoms).
271 <LI>
272 For further information (D2 or D3, damping function etc.) and other options see <A HREF="http://www.q-chem.com/doc_for_web/qchem_manual_3.2.pdf" TARGET="_blank">Q-Chem manual</A>.
274 <LI>
275 Set any additional input designated for the $rem-section of Q-Chem (see <A HREF="http://www.q-chem.com/doc_for_web/qchem_manual_3.2.pdf" TARGET="_blank">Q-Chem manual</A>) by specifying<br>
276 <TABLE BORDER=0 style="font-size:12">
277 <TR><TD>add =</TD><TD>{</TD><TD>[rem_name1]</TD><TD>[rem_value1]</TD></TR>
278 <TR><TD> </TD><TD> </TD><TD>[rem_name2]</TD><TD>[rem_value2]</TD></TR>
279 <TR><TD> </TD><TD> </TD><TD>. </TD><TD> </TD></TR>
280 <TR><TD> </TD><TD> </TD><TD>. </TD><TD> </TD></TR>
281 <TR><TD> </TD><TD> </TD><TD>. </TD><TD> </TD></TR>
282 <TR><TD> </TD><TD>}</TD><TD> </TD><TD> </TD></TR>
283 </TABLE>
284 Use with care and be aware, of course, that by this the Q-Chem output may be modified in such a way that the proper extraction of QM results may fail!
286 </OL>
288 <H3>
289 Examples</H3>
290 Some basic examples are provided in the example/qchem folder along with an example for setting the Q-Chem environment (qchemrc).
291 The names of example inputs (.chm) and corresponding outputs (.log) are structured as follows:<br>
293 [system]_[e(nergy)/g(radient)]_[QM/QMMM]_[Hamiltonian]_[basis/(basis)spec]_[basisname] <br>
295 For the DNA-Enzyme complex also the required Amber prmtop and inpcrd are provided.
297 <file include="tail.htp">
