
Database, database()
¶
Code author: Lori A. Burns
Section author: Lori A. Burns
Output¶
At the beginning of a database job is printed a listing of the individual system calculations which will be performed. The output snippet below is from the example job [1] above. It shows each reagent required for the subset of database reactions requested. Note that this is an un-counterpoise-corrected example, and the wrapper is smart enough to compute only once the monomer whose energy will be subtracted from each of the three dimers.
RGC1-HeHe-0.85-dimer
RGC1-He-mono-unCP
RGC1-HeHe-1.0-dimer
RGC1-HeHe-1.5-dimer
At the end of the job, the Requested Energy table is printed that gives the total
energies for the requested model chemistry for each reagent and each reaction, as
well as the stoichoimetric weights by which the reagent energies are transfromed
into the reaction energy. In this case, the dimer is +1 and the monomer is -2,
indicating the the interaction energy is computed from dimer less first monomer
less second (identical) monomer. Error statistics are computed with respect to the reference
energies stored in the database. One of these, the mean absolute deviation, is
returned by the wrapper as an ordinary Python variable. (For databases
without a stored reference energy, e.g., BASIC, large and meaningless numbers are
printed for error.) The other two tables tabulate the PSI variables requested
through keyword tabulate
, in this case the total SCF energy and the number
of atoms in each reagent.
==> Mp2 Total Energy <==
------------------------------------------------------------------------------------------------------
Reaction Reaction Value Reagent 1 Reagent 2
Value Wt Value Wt
------------------------------------------------------------------------------------------------------
RGC1-HeHe-0.85 0.00004802 -5.69430495 1 -2.84717649 -2
RGC1-HeHe-1.0 -0.00000064 -5.69435362 1 -2.84717649 -2
------------------------------------------------------------------------------------------------------
==> Requested Energy <==
------------------------------------------------------------------------------------------------------
Reaction Reaction Energy Reaction Error Reagent 1 Reagent 2
Ref Calc [kcal/mol] [kJ/mol] [Eh] Wt [Eh] Wt
------------------------------------------------------------------------------------------------------
RGC1-HeHe-0.85 0.0376 0.0301 -0.0075 -0.0312 -5.69430495 1 -2.84717649 -2
RGC1-HeHe-1.0 -0.0219 -0.0004 0.0215 0.0899 -5.69435362 1 -2.84717649 -2
------------------------------------------------------------------------------------------------------
Minimal Dev -0.0075 -0.0312
Maximal Dev 0.0215 0.0899
Mean Signed Dev 0.0070 0.0293
Mean Absolute Dev 0.0145 0.0605
RMS Dev 0.0161 0.0673
------------------------------------------------------------------------------------------------------
As well as being printed in the output file, database results from the
tabulate
option are available in the input file as ordinary Python
dictionaries DB_RGT
and DB_RXN
, indexed firstly by reagent or reaction
name and secondly by the requested PSI variable name. See the first
paragraph of Creating a Database for the distinction between
reagents and reactions. For example, an input file like the following
requests a couple variables through tabulate
and then makes use of the
resulting data structures, here, only to print.
set basis 6-31g*
db('mp2','s22',subset='small',tabulate=['CURRENT ENERGY','MP2 CORRELATION ENERGY'])
from pprint import pprint
print_stdout('\nDB_RGT')
pprint(DB_RGT)
print_stdout('\nDB_RXN')
pprint(DB_RXN)
print_stdout('\nmp2 interaction energy of water dimer (S22-2)')
print_stdout(DB_RXN['S22-2']['CURRENT ENERGY'])
The output to the screen is as follows.
DB_RGT
{'S22-16-dimer': {'CURRENT ENERGY': -155.37373581838636,
'DF-MP2 CORRELATION ENERGY': -0.523870772178089},
'S22-16-monoA-unCP': {'CURRENT ENERGY': -78.29412053242164,
'DF-MP2 CORRELATION ENERGY': -0.2629759351596186},
'S22-16-monoB-unCP': {'CURRENT ENERGY': -77.07606823017188,
'DF-MP2 CORRELATION ENERGY': -0.2594122526144091},
'S22-2-dimer': {'CURRENT ENERGY': -152.40958884746667,
'DF-MP2 CORRELATION ENERGY': -0.3797598812113561},
'S22-2-monoA-unCP': {'CURRENT ENERGY': -76.19905879745446,
'DF-MP2 CORRELATION ENERGY': -0.1887118848315123},
'S22-2-monoB-unCP': {'CURRENT ENERGY': -76.19902978067739,
'DF-MP2 CORRELATION ENERGY': -0.18857384937354635},
'S22-8-dimer': {'CURRENT ENERGY': -80.67416758080654,
'DF-MP2 CORRELATION ENERGY': -0.2844102558783027},
'S22-8-monoA-unCP': {'CURRENT ENERGY': -40.336952636980364,
'DF-MP2 CORRELATION ENERGY': -0.14185962536715307},
'S22-8-monoB-unCP': {'CURRENT ENERGY': -40.336952636980506,
'DF-MP2 CORRELATION ENERGY': -0.14185962536715097}}
DB_RXN
{'S22-16': {'CURRENT ENERGY': -0.0035470557928363178,
'DF-MP2 CORRELATION ENERGY': -0.0014825844040612934},
'S22-2': {'CURRENT ENERGY': -0.011500269334817403,
'DF-MP2 CORRELATION ENERGY': -0.0024741470062974724},
'S22-8': {'CURRENT ENERGY': -0.0002623068456699684,
'DF-MP2 CORRELATION ENERGY': -0.0006910051439986686}}
mp2 interaction energy of water dimer (S22-2)
-0.0115002693348
Available Databases¶
Below are documented for particular databases the availibility of the generic database function options cp, rlxd, benchmark, and the string options for subset. The full reagent member list, which can also be used in conjunction with subset, is not included here for consideration of space and may be found in the database file. The database Python files are very readable and should be consulted for more particular questions.
S66by8¶
- cp
'off'
||'on'
- rlxd
'off'
- subset
'small'
'large'
'equilibrium'
'HB'
eight-point (0.9, 0.95, 1.0, 1.05, 1.1, 1.25, 1.5, 2.0)dissociation curve hydrogen-bonded systems
'MX'
eight-point (0.9, 0.95, 1.0, 1.05, 1.1, 1.25, 1.5, 2.0)dissociation curve mixed-influence systems
'DD'
eight-point (0.9, 0.95, 1.0, 1.05, 1.1, 1.25, 1.5, 2.0)dissociation curve dispersion-dominated systems
S66¶
- cp
'off'
||'on'
- rlxd
'off'
- subset
'small'
'large'
'HB'
hydrogen-bonded systems'MX'
mixed-influence systems'DD'
dispersion-dominated systems
S22by5¶
- cp
'off'
||'on'
- rlxd
'off'
- subset
'small'
'large'
'equilibrium'
'mol1'
five-point (0.9, 1.0, 1.2, 1.5, 2.0)dissociation curve for molecule 1
- ...
'mol22'
five-point (0.9, 1.0, 1.2, 1.5, 2.0)dissociation curve for molecule 22
S22¶
- cp
'off'
||'on'
- rlxd
'off'
- benchmark
'S220'
Jurecka et al. PCCP 8 1985 (2006).'S22A'
Takatani et al. JCP 132 144104 (2010).'S22B'
Marshall et al. JCP 135 194102 (2011).
- subset
'small'
water dimer, methane dimer, ethene-ethine'large'
adenine-thymine'HB'
hydrogen-bonded systems'MX'
mixed-influence systems'DD'
dispersion-dominated systems'S11'
smaller systems in S22'WATER'
water dimer
RSE42¶
- benchmark
'RSE42'
[E. Soydas and U. Bozkaya, JCTC, 9, 1452-1460 (2013)].'RSE42'
[E. Soydas and U. Bozkaya, JCTC, 9, 1452-1460 (2013)].
- subset
'small'
<members_description>'large'
<members_description>'RSE30'
smaller systems in RSE42'<subset>'
<members_description>
RGC10¶
- cp
'off'
||'on'
- rlxd
'off'
- subset
'small'
'large'
'equilibrium'
'HeHe'
18-point dissociation curve for helium dimer'HeNe'
18-point dissociation curve for helium-neon complex'HeAr'
18-point dissociation curve for helium-argon complex'HeKr'
18-point dissociation curve for helium-krypton complex'NeNe'
18-point dissociation curve for neon dimer'NeAr'
18-point dissociation curve for neon-argon complex'NeKr'
18-point dissociation curve for neon-krypton complex'ArAr'
18-point dissociation curve for argon dimer'ArKr'
18-point dissociation curve for argon-krypton complex'KrKr'
18-point dissociation curve for krypton dimer
NHTBH¶
- cp
'off'
- rlxd
'off'
- subset
'small'
'large'
NCB31¶
- cp
'off'
||'on'
- rlxd
'off'
||'on'
- benchmark
'<benchmark_name>'
<Reference>.'<default_benchmark_name>'
<Reference>.
- subset
'small'
3: HF-HF, He-Ne, HCCH-HCCH'large'
1: BzBz_PD'HB6'
hydrogen-bonded'CT7'
charge-transfer'DI6'
dipole-interacting'WI7'
weakly interacting'PPS5'
pi-pi stacking
NBC10¶
- cp
'off'
||'on'
- rlxd
'off'
- benchmark
'NBC100'
Burns et al. JCP 134 084107 (2011).'NBC10A'
Marshall et al. JCP 135 194102 (2011).
- subset
'small'
'large'
'equilibrium'
'BzBz_S'
dissociation curve for benzene dimer, sandwich'BzBz_T'
dissociation curve for benzene dimer, t-shaped'BzBz_PD34'
dissociation curve for benzene dimer, parallel displaced by 3.4A'BzH2S'
dissociation curve for benzene-H2S'BzMe'
dissociation curve for benzene-methane'MeMe'
dissociation curve for methane dimer'PyPy_S2'
dissociation curve for pyridine dimer, sandwich'PyPy_T3'
dissociation curve for pyridine dimer, t-shaped'BzBz_PD32'
dissociation curve for benzene dimer, parallel displaced by 3.2A'BzBz_PD36'
dissociation curve for benzene dimer, parallel displaced by 3.6A
JSCH¶
- cp
'off'
||'on'
- rlxd
'off'
- subset
'small'
'large'
'HB'
hydrogen-bonded systems (coplanar base-pairs)'MX'
interstrand systems (adjacent base-pairs on different strands)'DD'
stacked systems (adjacent base-pairs on same strand)
HTR40¶
- benchmark
'<benchmark_name>'
<Reference>.'<default_benchmark_name>'
<Reference>.
- subset
'small'
<members_description>'large'
<members_description>'<subset>'
<members_description>
HTBH¶
- cp
'off'
- rlxd
'off'
- subset
'small'
'large'
HSG¶
- cp
'off'
||'on'
- rlxd
'off'
- benchmark
'HSG0'
Faver et al. JCTC 7 790 (2011).'HSGA'
Marshall et al. JCP 135 194102 (2011).
- subset
'small'
'large'
HBC6¶
- cp
'off'
||'on'
- rlxd
'off'
||'on'
- benchmark
'HBC60'
Thanthiriwatte et al. JCTC 7 88 (2011).'HBC6A'
Marshall et al. JCP 135 194102 (2011).
'HBC6ARLX'
Sherrill group, unpublished.
- subset
'small'
'large'
'equilibrium'
equilibrium points for the six systems'FaOOFaOO'
dissociation curve for formic acid dimer'FaONFaON'
dissociation curve for formamide dimer'FaNNFaNN'
dissociation curve for formamidine dimer'FaOOFaON'
dissociation curve for formic acid- formamide complex'FaONFaNN'
dissociation curve for formamide- formamidine complex'FaOOFaNN'
dissociation curve for formic acid- formamidine complex
BENCH12¶
- benchmark
'<benchmark_name>'
<Reference>.'<default_benchmark_name>'
<Reference>.
- subset
'small'
'large'
'alkenes'
'alkanes'
'acenes'
'thiophenes'
'h2o_size'
'h2o_shape'
'atoms'
'S22_HB'
'S22_MX'
'S22_DD'
BASIC¶
- cp
'off'
- rlxd
'off'
- subset [
'h2o'
,'nh3'
,'ch4'
]
BAKERJCC96¶
- cp
'off'
- rlxd
'off'
BAKERJCC93¶
- cp
'off'
- rlxd
'off'
- subset
'small'
'large'
ACENES¶
- cp
'off'
||'on'
- rlxd
'off'
- subset
'small'
'large'
'FIRST3'
benzene, napthalene, and anthracene dimers'FIRST5'
benzene - pentacene dimers'FIRST10'
benzene - decacene dimers
A24alt¶
- cp
'off'
<erase this comment and after unless on is a valid option> ||'on'
- rlxd
'off'
<erase this comment and after unless on is valid option> ||'on'
- benchmark
'<benchmark_name>'
<Reference>.'<default_benchmark_name>'
<Reference>.
- subset
'small'
<members_description>'large'
<members_description>'<subset>'
<members_description>
A24¶
- cp
'off'
<erase this comment and after unless on is a valid option> ||'on'
- rlxd
'off'
<erase this comment and after unless on is valid option> ||'on'
- benchmark
'<benchmark_name>'
<Reference>.'<default_benchmark_name>'
<Reference>.
- subset
'small'
<members_description>'large'
<members_description>'<subset>'
<members_description>