mirror of https://gitlab.com/QEF/q-e.git
70 lines
3.6 KiB
Plaintext
70 lines
3.6 KiB
Plaintext
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This example shows how to use the 3-Dimensional Reference Interaction
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Site Model (3D-RISM) in pw.x. 3D-RISM calculates the integral equation
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of the solvent theory, to provide solvent distributions:
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A.Kovalenko, F.Hirata, Chem. Phys. Lett. 1998, 290, 237-244.
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Solvent molecules have explicit internal structures, and interactions
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are defined as classical molecular force fields (written in MOL-format).
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The correlation among solvents are decomposed into correlations between
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two atoms in solvetns, which are calculated by 1D-RISM. In pw.x, 1D-RISM
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is performed at first, and the result allows to calculate 3D-RISM.
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Solute is treated by qunatum mechanical DFT, that is the system with
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the ion-cores and the electrons means the solute in pw.x.
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3D-RISM calculates distributions around solute for all solvent atoms,
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while correlations between solvent atoms are involved.
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One can perform 3D-RISM coupled with SCF (i.e. 3D-RISM-SCF).
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And pprism.x allows to plot solvent distributions.
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If ESM method is applied for DFT calculation, Laue-RISM is performed
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instead of 3D-RISM. The coupling method of ESM and Laue-RISM is called
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as ESM-RISM, which is able to simulate solvated slab system. Here,
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boundary condition of ESM must be `BC1', and boundary condition of
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ESM-RISM becomes Vacuum/Slab/Solvent. ESM-RISM works even if slab is
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`charged', because solvent with opposite charge screens slab naturally.
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The details of the example calculation:
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1) A H2O molecule in NaCl(aq)
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Performing 3D-RISM-SCF calculation for a H2O molecule, to optimize
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the charge density and the solvent distributions simultaneously.
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The solvent system is aqueous solution of sodium chloride (0.1M).
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Molecular force field for water is Simple Point Charge (SPC) model.
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Also, the atomic positions are relaxed under solvent environment.
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2) A HCHO molecule in water
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Performing 3D-RISM-SCF calculation for a HCHO molecule, to optimize
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the charge density and the solvent distributions simultaneously.
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The solvent system is water (SPC). The Lennard-Jones force field
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of HCHO is OPLS-AA. After 3D-RISM-SCF, pprism.x plots distributions
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of the oxygen and the hydrogen atom in solvent water.
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3) A Li(100) slab with ethanol
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Performing ESM-RISM calculation for a Li(100) slab with solvent
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ethanol, to optimize the charge density and the solvent distributions
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simultaneously. The system is defined as Vacuum/Li(100)/EtOH, where
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ESM is applied for the Li(100) slab and Laue-RISM is applied for the
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solvent ethanol (OPLS-UA). The Lennard-Jones force field of Li is UFF.
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After ESM-RISM, pprism.x plots distributions of the solvent atoms.
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4) A charged Al(111) slab with NaCl(aq)
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Performing ESM-RISM calculation for an Al(111) slab with aqueous
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solution of sodium chloride (5.0M), to optimize the charge density,
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the solvent distributions and the atomic positions of the Al(111)
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simultaneously. The system is defined as Vacuum/Al(111)/NaCl(aq),
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where ESM for the Al(111) and Laue-RISM for NaCl(aq). The Al(111)
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slab has +0.1 charge, which is defined by "tot_charge". If ESM-RISM
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calculation is converged, the Na+ ions will decrease and the Cl- ions
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will increase to cause -0.1 charge for the solvent system.
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5) A Cl- ion in NaCl(aq)
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Performing ESM-RISM calculation for an Cl- ion with aqueous solution
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of sodium chloride (1.0M), to obtain the solvation free energy of
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Cl- ion in bulk solution. By defining 'laue_expand_right' and
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'laue_expand_left' in input file, one can calculate the situation
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that an isolated atom/molecule/ion is in bulk solution. Using this
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model one can calculate the salvation free energy with 'explicitly'
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controlled the chemical potential of atoms.
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