User Guides
Software Introduction
Publications
Literature Citation
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Jaguar | ||||||||||||||||||||||||||||||||||||||||||||
Jaguar can perform high-level quantum chemistry calculations using a range of methods including Hartree-Fock (HF) theory, Generalized Valence Bond (GVB) theory, Density Functional Theory (DFT) and second-order local Möller-Plesset perturbation theory (LMP2). It can also be used to calculate excited states using the configuration interaction singles (CIS) method. In addition, the program can be used to carry out calculations of solvation effects, many different molecular properties, and Weinhold NBO analayses. Jaguar comes with a graphical interface called Maestro, which can be used to set up the system and the calculation. For more information on accessing Maestro, please refer to the man page runmaestro. Please note that Jaguar jobs should not be submitted directly from Maestro. It is recommended that users who are unfamiliar with the package should use Maestro to set up their input files, and then submit the Jaguar jobs using the runscript runjaguar. To use the graphics package, users will need some kind of X-Windows emulator. A fully comprehensive tutorial for using Maestro is available for download from the directory $CHEM/doc/jaguar/maestro8/maestro/tutorial on Magellan. Running Maestro on Magellan: Step 1 Before launching Maestro, users will need to connect to the Magellan. There are two methods to connect to the machine and to set the display environment on their local machine. Method 1: Connect to the machine via ssh: ssh -l userid magellan.rl.ac.uk Users can set the DISPLAY environment variable for their shells using the following commands. csh, tcsh: setenv DISPLAY display-machine-IP:0.0 ksh, bash: export DISPLAY=display-machine-IP:0.0 where display-machine-IP is the IP address of the machine you wish the display to appear on. Method 2: Alternatively, users can log onto Magellan via X-Windows using ssh as follows: ssh -X -l userid magellan.rl.ac.uk There is no need to explicitly set the environment variable if you choose to log onto the machine using this method. Mac users using Tiger (10.4) will need to replace, please replace -X with -Y. Step 2 To launch Maestro, type $CHEM/runmaestro at the prompt. A window with the graphical interface should appear. Below are two tutorials illustrating how to set up Jaguar input files using Maestro. The Jaguar files can then be run in batch on Magellan using the runscript $CHEM/runjaguar . Users should refer to the user guide for full details on the options available. The examples given in this software introduction only provide a brief guide on how to set up a simple calculation. The Jaguar User Guide and the Maestro User Guide are available as PDF files on Magellan in the directories $CHEM/doc/jaguar/jaguar7 and $CHEM/doc/jaguar/maestro8. | ||||||||||||||||||||||||||||||||||||||||||||
Examples | ||||||||||||||||||||||||||||||||||||||||||||
Example 1. DFT Single Point Energy Calculation of Ethene Example 2. Local MP2 Single Point Energy Calculation of Pyrrole Note: All explanations for input/output files are given in red. | ||||||||||||||||||||||||||||||||||||||||||||
| Example 1. DFT Single Point Energy Calculation of Ethene
The following example is a DFT single point energy calculation set up using Maestro. | ||||||||||||||||||||||||||||||||||||||||||||
Input | ||||||||||||||||||||||||||||||||||||||||||||
MAEFILE: run1.mae Section describing molecule & calculation, in this case reading in a Maestro file. &gen General keywords section. basis=6-31G** 6-31G** basis set specified. dftname=B3LYP BLYP used for DFT. iorb2a=9 Molecular orbital number to be saved in a binary file for visualising in Maestro. iorb1a=8 & Each section is delineated by a pair of ampersand (&). entry_name: Scratch &zmat Molecule specification section. Atom labels, followed by Cartesian coordinates. C1 0.7689880000000 1.6759703333333 0.0000000000000 C2 -0.5705120000000 1.6759703333333 0.0000000000000 H3 1.3384880000000 0.7318703333333 0.0000000000000 H4 -1.1400120000000 0.7318703333333 0.0000000000000 H5 -1.1400120000000 2.6199703333333 0.0000000000000 H6 1.3384880000000 2.6199703333333 0.0000000000000 & Input file (gzipped) jagtest1.in can be downloaded here. | ||||||||||||||||||||||||||||||||||||||||||||
Output | ||||||||||||||||||||||||||||||||||||||||||||
The program generates two output files, jagtest1.out and jagtest1.log. The first contains the output from the calculation, and the second contains information about the job including a summary of the results. Several other files will also be produced. The .mae files are specific to Maestro and the .01.in file contains the initial guess that is generated by the preprocessor program pre. In this example, the orbital files (binary files) are also generated - jagtest1_MO_8.vis and jagtest1_MO_9.vis. These molecular orbitals can be visualised in Maestro. jagtest1.out jagtest1.log jagtest1_MO_8.vis
Job jagtest1 started on columbus-lx14 at Tue May 23 10:38:52 2006
jobid: columbus-lx14-0-4472d82b
+--------------------------------------------------------------------+
| Jaguar version 6.0, release 12 |
| |
| Copyright (c) 2005 Schrodinger, LLC. |
| All Rights Reserved. |
| |
| Use of this program should be acknowledged in publications as: |
| Jaguar 6.0, Schrodinger, LLC, Portland, Oregon, 2005. |
+--------------------------------------------------------------------+
Program pre reads and checks input, performs symmetry analysis, and calculates terms dependent on geometry.
start of program pre
Job name: jagtest1
Executables used: /usr/local/Chem-Apps/schrodinger/jaguar-v60012/bin/Linux-x86
Temporary files : /scratch/ht3/jagtest1
Maestro file (input): run1.mae
Maestro file (output): jagtest1.01.mae
basis set: 6-31g**
net molecular charge: 0
multiplicity: 1
number of basis functions.... 50
Input geometry:
angstroms
atom x y z
C1 0.7689880000 1.6759703333 0.0000000000
C2 -0.5705120000 1.6759703333 0.0000000000
H3 1.3384880000 0.7318703333 0.0000000000
H4 -1.1400120000 0.7318703333 0.0000000000
H5 -1.1400120000 2.6199703333 0.0000000000
H6 1.3384880000 2.6199703333 0.0000000000
principal moments of inertia:
amu*angstrom^2: 3.59282 16.95659 20.54941
g*cm^2: 5.96601747E-40 2.81571037E-39 3.41231212E-39
rotational constants:
cm^(-1): 4.69203696 0.99416384 0.82034625
GHz: 140.66372929 29.80428223 24.59336183
Molecular weight: 28.03 amu
Stoichiometry: C2H4
Molecular Point Group: D2h
Molecule translated to center of mass
Molecule reoriented along symmetry axes
Point Group used: D2h Symmetry deduced.
Symmetrized geometry:
angstroms
atom x y z
C1 0.0000000000 0.0000000000 0.6697500000
C2 0.0000000000 0.0000000000 -0.6697500000
H3 0.0000000000 0.9440500000 1.2392500000
H4 0.0000000000 0.9440500000 -1.2392500000
H5 0.0000000000 -0.9440500000 -1.2392500000
H6 0.0000000000 -0.9440500000 1.2392500000
nuclear repulsion energy....... 33.031961813 hartrees
Plot box parameters (in Angstoms):
x min,max: -1.949150 2.072597
y min,max: -2.541550 2.750222
z min,max: -2.836750 2.878364
plot resolution: 4.724315
points: 19 25 27
DFT specification.
Non-default options chosen:
SCF calculation type: DFT
DFT=Becke_3_Parameter/HF+Slater+Becke88+VWN+LYP (B3LYP)
Electron density computed on grid number -7
end of program pre
Program onne calculates one-electron integrals and ECP contribution if applicable.
start of program onee
smallest eigenvalue of S: 7.092E-03
number of canonical orbitals..... 50
end of program onee
Program hfig calculates Hartree-Fock initial guess.
start of program hfig
initial wavefunction generated automatically from atomic wavefunctions
Orbitals occupation.
Irreducible Total no No of occupied orbitals
representation orbitals Shell_1 Shell_2 ...
Ag 12 3
B1g 2 0
B2g 4 0
B3g 7 1
Au 2 0
B1u 12 2
B2u 7 1
B3u 4 1
------------------------
Orbital occupation/shell 1.000
end of program hfig
Program probe insures orthogonalization.
start of program probe
end of program probe
Program grid generates grids.
start of program grid
number of gridpoints:
atom C1 C2 H3 H4 H5 H6 total
grid # 1 29 0 42 0 0 0 71
grid # 2 31 0 69 0 0 0 100
grid # 3 61 0 133 0 0 0 194
grid # 4 110 0 268 0 0 0 378
grid # 5 1395 0 2430 0 0 0 3825
grid # 6 480 0 756 0 0 0 1236
grid # 7 1733 0 3001 0 0 0 4734
grid # 8 2087 0 3033 0 0 0 5120
grid # 9 263 0 464 0 0 0 727
grid #10 798 646 3040 2888 2641 2812 12825
end of program grid
Program rwr generates Q operators.
start of program rwr
end of program rwr
Program scf performs SCF calculation.
start of program scf
number of electrons.......... 16
number of alpha electrons.... 8
number of beta electrons..... 8
number of orbitals, total.... 50
number of doubly-occ'd orbs.. 8
number of open shell orbs.... 0
number of occupied orbitals.. 8
number of virtual orbitals... 42
number of hamiltonians....... 1
number of shells............. 1
SCF type: DFT=Becke_3_Parameter/HF+Slater+Becke88+VWN+LYP (B3LYP)
i u d i g
t p i c r RMS maximum
e d i u i energy density DIIS
r t s t d total energy change change error
etot 1 N N 5 M -78.30088172199 7.1E-03 1.6E-01
etot 2 Y Y 6 M -78.55941504826 2.6E-01 3.9E-03 5.7E-02
etot 3 N Y 2 U -78.58726801911 2.8E-02 1.1E-03 2.1E-02
etot 4 Y Y 6 M -78.59281597938 5.5E-03 2.1E-04 3.3E-03
etot 5 N Y 2 U -78.59292742491 1.1E-04 2.5E-05 6.0E-04
etot 6 Y N 6 M -78.59292909009 1.7E-06 0.0E+00 0.0E+00
Energy components, in hartrees:
(A) Nuclear repulsion............ 33.03196181346
(E) Total one-electron terms..... -169.72339527299
(I) Total two-electron terms..... 58.09850436944
(J) Coulomb.................... 70.36905361061
(K) Exchange+Correlation....... -12.27054924117
(L) Electronic energy............ -111.62489090355 (E+I)
(N) Total energy................. -78.59292909009 (A+L)
DFT energy.
SCFE: SCF energy: DFT(b3lyp) -78.59292909009 hartrees iterations: 6
HOMO energy: -0.26614
LUMO energy: 0.01570
Orbital energies/symmetry label:
-10.18876 Ag -10.18792 B1u -0.75191 Ag -0.57132 B1u
-0.46209 B2u -0.41060 Ag -0.35146 B3g -0.26614 B3u
0.01570 B2g 0.11616 Ag 0.13617 B2u 0.15253 B1u
0.24070 B3g 0.32563 B1u 0.47473 Ag 0.54877 B3u
0.57047 B2u 0.63595 B2g
end of program scf
start of program elden
Calculating orbital amplitude...
Files written:
jagtest1_MO_8.vis
jagtest1_MO_9.vis
end of program elden
Summary of CPU time used.
Total cpu seconds user: 1.310 user+sys: 1.580
Total elapsed time: 7 seconds
Job jagtest1 completed on columbus-lx14 at Tue May 23 10:38:59 2006
Checkout succeeded: JAGUAR_MAIN/1E96 5BDC 9400 AEA2
License file: /usr/local/Chem-Apps/schrodinger/license
License Server: @columbus-lxfs
Checkout succeeded: JAGUAR_MAIN/1E96 5BDC 9400 AEA2
License file: /usr/local/Chem-Apps/schrodinger/license
License Server: @columbus-lxfs
Job jagtest1 started on columbus-lx14 at Tue May 23 10:38:52 2006
jobid: columbus-lx14-0-4472d82b
Jaguar version 6.0, release 12
Molecular Point Group: D2h
Point Group used: D2h
pre (input checking) done.
onee (1-electron integrals) done.
hfig (HF initial guess) done.
probe (project orbitals) done.
grid (grid generation) done.
rwr (Q operators) done.
scf type: DFT=Becke_3_Parameter/HF+Slater+Becke88+VWN+LYP (B3LYP)
i u d i g
t p i c r RMS maximum
e d i u i energy density DIIS
r t s t d total energy change change error
etot 1 N N 5 M -78.30088172199 7.1E-03 1.6E-01
etot 2 Y Y 6 M -78.55941504826 2.6E-01 3.9E-03 5.7E-02
etot 3 N Y 2 U -78.58726801911 2.8E-02 1.1E-03 2.1E-02
etot 4 Y Y 6 M -78.59281597938 5.5E-03 2.1E-04 3.3E-03
etot 5 N Y 2 U -78.59292742491 1.1E-04 2.5E-05 6.0E-04
etot 6 Y N 6 M -78.59292909009 1.7E-06 0.0E+00 0.0E+00
scf (DFT) done.
elden (electron density) done.
Job jagtest1 completed on columbus-lx14 at Tue May 23 10:38:59 2006
jagtest1_MO_8.vis visualised in Maestro.
Output file (gzipped) jagtest1.out can be downloaded here. Output file (gzipped) jagtest1.log can be downloaded here. | ||||||||||||||||||||||||||||||||||||||||||||
| Example 2. Local MP2 Single Point Energy Calculation of Pyrrole
The following example is a Local MP2 single point energy calculation set up using Maestro using similar steps as in Example 1. | ||||||||||||||||||||||||||||||||||||||||||||
Input | ||||||||||||||||||||||||||||||||||||||||||||
Select New Project from the main menu and this time save the project as jagtest2.prj. Follow the steps given in Example 1, selecting pyrrole from the fragment list instead of ethene. Select Applications => Jaguar => Single Point Energy from the Menu bar in the Main window. Next select the Theory tab and changed the level of theory to Local MP2 with all pairs correlated. Save it as a Jaguar input file with the name jagtest2.in, and exit the graphical interface using the Quit option from the Maestro drop down menu. jagtest2.inMAEFILE: jagtest2.mae &gen basis=6-31G** mp2=3 Value 3 for running a LMP2 calculation (for valence electrons only). & entry_name: Scratch &zmat C1 -1.4852182000000 1.9972441000000 0.0049511000000 C2 -2.9006322000000 1.9894531000000 -0.0037639000000 C3 -3.3182642000000 3.3016751000000 -0.0020229000000 N4 -2.2045662000000 4.1004491000000 0.0074351000000 C5 -1.0821102000000 3.3139851000000 0.0117461000000 H6 -2.2101572000000 5.1123531000000 0.0107201000000 H7 -3.5454852000000 1.1202571000000 -0.0105749000000 H8 -4.3095992000000 3.7344141000000 -0.0066899000000 H9 -0.8308012000000 1.1352001000000 0.0061411000000 H10 -0.0956162000000 3.7576091000000 0.0192581000000 & Input file (gzipped) jagtest2.in can be downloaded here. | ||||||||||||||||||||||||||||||||||||||||||||
Output | ||||||||||||||||||||||||||||||||||||||||||||
After the calculation has completed, jagtest2.out and jagtest2.log will be written to the working directory.
Job jagtest2 started on columbus-lx01 at Tue May 23 11:05:00 2006
jobid: columbus-lx01-0-4472de4c
+--------------------------------------------------------------------+
| Jaguar version 6.0, release 12 |
| |
| Copyright (c) 2005 Schrodinger, LLC. |
| All Rights Reserved. |
| |
| Use of this program should be acknowledged in publications as: |
| Jaguar 6.0, Schrodinger, LLC, Portland, Oregon, 2005. |
+--------------------------------------------------------------------+
start of program pre
Job name: jagtest2
Executables used: /usr/local/Chem-Apps/schrodinger/jaguar-v60012/bin/Linux-x86
Temporary files : /scratch/ht3/jagtest2
Maestro file (input): jagtest2.mae
Maestro file (output): jagtest2.01.mae
basis set: 6-31g**
net molecular charge: 0
multiplicity: 1
number of basis functions.... 100
Input geometry:
angstroms
atom x y z
C1 -1.4852182000 1.9972441000 0.0049511000
C2 -2.9006322000 1.9894531000 -0.0037639000
C3 -3.3182642000 3.3016751000 -0.0020229000
N4 -2.2045662000 4.1004491000 0.0074351000
C5 -1.0821102000 3.3139851000 0.0117461000
H6 -2.2101572000 5.1123531000 0.0107201000
H7 -3.5454852000 1.1202571000 -0.0105749000
H8 -4.3095992000 3.7344141000 -0.0066899000
H9 -0.8308012000 1.1352001000 0.0061411000
H10 -0.0956162000 3.7576091000 0.0192581000
principal moments of inertia:
amu*angstrom^2: 54.68831 56.20510 110.89341
g*cm^2: 9.08121385E-39 9.33308250E-39 1.84142964E-38
rotational constants:
cm^(-1): 0.30824926 0.29993064 0.15201653
GHz: 9.24108032 8.99169450 4.55734094
Molecular weight: 67.04 amu
Stoichiometry: C4NH5
Molecular Point Group: C2v
Point Group used: C1 (symmetry turned off)
nuclear repulsion energy....... 161.099415926 hartrees
Non-default options chosen:
Post-SCF correlation type: LMP2 Post-SCF calculation to be performed.
LMP2 energy will be computed with 2e frozen core for Li-Ne
and 10e frozen core for Na-Ar
end of program pre
start of program onee
smallest eigenvalue of S: 1.262E-03
number of canonical orbitals..... 100
end of program onee
start of program hfig
initial wavefunction generated automatically from atomic wavefunctions
Irreducible Total no No of occupied orbitals
representation orbitals Shell_1 Shell_2 ...
No Symm 100 18
------------------------
Orbital occupation/shell 1.000
end of program hfig
start of program probe
end of program probe
start of program grid
number of gridpoints:
atom C1 C2 C3 N4 C5 H6 H7 H8
grid # 1 87 87 87 91 87 73 73 73
grid # 2 95 95 95 99 95 118 118 118
grid # 3 181 181 182 186 182 224 224 224
grid # 4 336 336 330 332 330 459 461 462
number of gridpoints:
atom H9 H10 total
grid # 1 73 73 804
grid # 2 118 118 1069
grid # 3 224 224 2032
grid # 4 461 462 3969
end of program grid
start of program rwr
end of program rwr
start of program scf
number of electrons.......... 36
number of alpha electrons.... 18
number of beta electrons..... 18
number of orbitals, total.... 100
number of doubly-occ'd orbs.. 18
number of open shell orbs.... 0
number of occupied orbitals.. 18
number of virtual orbitals... 82
number of hamiltonians....... 1
number of shells............. 1
SCF type: HF
i u d i g
t p i c r RMS maximum
e d i u i energy density DIIS
r t s t d total energy change change error
etot 1 N N 5 M -208.15579961112 7.6E-03 1.5E-01
etot 2 Y Y 6 M -208.73894368191 5.8E-01 2.8E-03 8.2E-02
etot 3 Y Y 6 M -208.80759959028 6.9E-02 1.2E-03 2.2E-02
etot 4 N Y 2 U -208.81560501285 8.0E-03 6.5E-04 1.4E-02
etot 5 Y Y 6 M -208.81712970966 1.5E-03 1.0E-03 8.0E-03
etot 6 N Y 2 U -208.81795230472 8.2E-04 1.1E-04 1.6E-03
etot 7 Y Y 6 M -208.81802696528 7.5E-05 2.8E-05 2.1E-04
etot 8 Y N 6 M -208.81803106643 4.1E-06 0.0E+00 0.0E+00
Energy components, in hartrees:
(A) Nuclear repulsion............ 161.09941592608
(E) Total one-electron terms..... -600.92743143963
(I) Total two-electron terms..... 231.00998444711
(J) Coulomb.................... 260.15937246091
(K) Exchange................... -29.14938801380
(L) Electronic energy............ -369.91744699251 (E+I)
(N) Total energy................. -208.81803106643 (A+L)
SCF energy.
SCFE: SCF energy: HF -208.81803106643 hartrees iterations: 8
HOMO energy: -0.28780
LUMO energy: 0.20103
Orbital energies:
-15.60608 -11.24637 -11.24633 -11.20352 -11.20249 -1.28260
-1.03374 -0.96711 -0.78456 -0.75785 -0.72630 -0.58475
-0.57170 -0.55815 -0.53736 -0.51888 -0.33813 -0.28780
0.20103 0.22323 0.26082 0.28912 0.31065 0.32009
0.32934 0.41664 0.41976 0.50213
end of program scf
start of program local
Localized doubly occupied orbitals
orbitals 6 through 18
using Mulliken Atomic Population Localization
end of program local
start of program lmp2
number of orbitals, total....... 100
number of frozen core orbitals.. 5
number of valence mp2 orbitals.. 13
number of occupied orbitals..... 18
number of virtual orbitals...... 82
number of exchange hamiltonians. 169
Iteration LMP2 Energy Correction Delta C
1 -0.74147112281
2 -0.68071646698 0.01896510599
3 -0.68683353797 0.00318822536
4 -0.68697083314 0.00054496799
5 -0.68697413742 0.00004756318
----------- LMP2 Converged ---------
Hartree-Fock energy..... -208.81803106643
LMP2 Energy Correction.. -0.68697413742
Total LMP2 Energy....... -209.50500520386
Total energy = HF energy + LMP2 energy correction.
end of program lmp2
Total cpu seconds user: 28.180 user+sys: 29.280
Total elapsed time: 42 seconds
Job jagtest2 completed on columbus-lx01 at Tue May 23 11:05:42 2006
Checkout succeeded: JAGUAR_MAIN/1E96 5BDC 9400 AEA2
License file: /usr/local/Chem-Apps/schrodinger/license
License Server: @columbus-lxfs
Checkout succeeded: JAGUAR_MAIN/1E96 5BDC 9400 AEA2
License file: /usr/local/Chem-Apps/schrodinger/license
License Server: @columbus-lxfs
Job jagtest2 started on columbus-lx01 at Tue May 23 11:05:00 2006
jobid: columbus-lx01-0-4472de4c
Jaguar version 6.0, release 12
Molecular Point Group: C2v
Point Group used: C1 (symmetry turned off)
pre (input checking) done.
onee (1-electron integrals) done.
hfig (HF initial guess) done.
probe (project orbitals) done.
grid (grid generation) done.
rwr (Q operators) done.
scf type: HF
i u d i g
t p i c r RMS maximum
e d i u i energy density DIIS
r t s t d total energy change change error
etot 1 N N 5 M -208.15579961112 7.6E-03 1.5E-01
etot 2 Y Y 6 M -208.73894368191 5.8E-01 2.8E-03 8.2E-02
etot 3 Y Y 6 M -208.80759959028 6.9E-02 1.2E-03 2.2E-02
etot 4 N Y 2 U -208.81560501285 8.0E-03 6.5E-04 1.4E-02
etot 5 Y Y 6 M -208.81712970966 1.5E-03 1.0E-03 8.0E-03
etot 6 N Y 2 U -208.81795230472 8.2E-04 1.1E-04 1.6E-03
etot 7 Y Y 6 M -208.81802696528 7.5E-05 2.8E-05 2.1E-04
etot 8 Y N 6 M -208.81803106643 4.1E-06 0.0E+00 0.0E+00
scf (HF) done.
local (localization) done.
Iter LMP2 Energy Delta C
elmp2 1 -209.55950218924
elmp2 2 -209.49874753341 1.9E-02
elmp2 3 -209.50486460440 3.2E-03
elmp2 4 -209.50500189958 5.4E-04
elmp2 5 -209.50500520386 4.8E-05
lmp2 done.
Job jagtest2 completed on columbus-lx01 at Tue May 23 11:05:42 2006
Output file (gzipped) jagtest2.out can be downloaded here. Output file (gzipped) jagtest2.log can be downloaded here. |
