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Questions tagged [thermodynamics]

Questions concerned with thermodynamics as related to systems in materials modeling.

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Proof that equilibrium phase fraction(s) is a continuous function of composition

It seems that the equilibrium phase fractions (i.e., relative amounts of phase A1, A2, ..., Aq for a system in which there are q total phases) as a function of composition (for a constant pressure and ...
sgp45's user avatar
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MD simulations of liquid isopropanol predicts wrong thermodynamics proprieties

I am using GROMACS to run molecular dynamics simulations of pure liquids, in the NpT ensemble at room temperature and p = 1 atm. My first test was with isopropanol (also known as 2-propanol). I used ...
AlfredV's user avatar
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How to apply sublattice model for a ternary system?

I already asked a broader version of this question in the physics-SE, but after I got no answer, combined with further understanding of the problem, it was suggested to me to try asking here. I'm ...
asbjos's user avatar
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6 votes
1 answer
94 views

Is it essential to include solvent cage effect in radical reactions?

My question is straightforward and is outlined in the post title: Is it essential to include the solvent cage effect in radical reactions during the computational estimation of Gibbs free energies and ...
farmaceut's user avatar
2 votes
0 answers
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What is the best model to calculate the free energies using ASE thermochemistry?

I am trying to calculate the free energy of adsorption of a small molecule on a 2D material. After adsorption, I am using the thermochemistry module of the Atomic Simulation Environment to calculate ...
ansonthms's user avatar
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6 votes
2 answers
507 views

Effect of temperature on Forcefield parameters in classical molecular dynamics simulations

In classical molecular dynamics simulations of complex molecular systems, the force field (FF) contains information about bonded (bonds, angles, dihedrals and impropers) and non-bonded parameters. It ...
user35952's user avatar
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How do I plot ternary phase diagrams using Flory-Huggins solution theory?

I have three components, $A,B,C$, with 3 Flory-Huggins exchange parameters: $\chi _{AB}, \chi _{BC}, \chi _{AC}$. I want to create a ternary diagram to see how such a mixture behaves and how phase ...
bad_chemist's user avatar
4 votes
0 answers
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Comparing stability of phases under constant pressure [closed]

I have used DFT to calculate the internal energy of a couple of different phases at 0K. As I would also like to compare the relative stability of the phases at finite temperature, I have also computed ...
user2155952's user avatar
4 votes
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76 views

Computation of thermodynamic functions of molecules by molecular parameters [closed]

I want to implement in my program Chemcraft the computation of entropy and Gibbs energy of molecules in approximation "rigid rotor - harmonic oscillator", by the molecular parameters (...
Linkey's user avatar
  • 406
4 votes
1 answer
86 views

How to apply solvent-correction to Gaussian derived Gibbs energies?

I study reaction A + B → C + D in a water using DFT. I think I should apply some kind of correction over RRHO because it is not true in a solvent. I found the given work (https://doi.org/10.1021/...
farmaceut's user avatar
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1 answer
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How may I calculate free energy using PySCF?

I want to calculate the thermodynamic parameters for a single molecule at a certain temperature. How may I do it with PySCF?
greg pits's user avatar
3 votes
1 answer
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How to compute free energy for solvation using gaussian09?

I'm trying to compute the free energy of solvation of a molecule in gaussian09 using the continuum solvation model, but I am haveing difficulties, I don't know how to do it and gaussian manual does ...
AlfredV's user avatar
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How do I define the density of system? [closed]

Lets' say I have a solid nanomaterial made with N atoms in a simulation box with a volume of V as shown below. In this case, the number density of my material is simply $\frac{N}{Volume\; of \; ...
Magic_Number's user avatar
3 votes
1 answer
313 views

Is hexaamminecobalt(III) chloride thermodynamically stable in pure water?

It is often said that "while cobalt(III) per se is strongly oxidising, hexamminecobalt(III) chloride is stable, even in concentrated hydrochloric acid, due to the strong donor properties of the ...
Kanghun Kim's user avatar
2 votes
1 answer
117 views

Relationship between grand potential and free energy?

What is the fundamental relationship between grand potential and free energy? In other words, what assumptions need to be made in order to obtain the free energy equation rather than the grand ...
Manasi Vyas's user avatar
3 votes
1 answer
246 views

Grand potential vs. Gibbs free energy of adsorption for ab initio thermodynamics

I have seen descriptions of ab initio thermodynamics where the phase energy diagram for the oxidation of metal surfaces can be constructed in terms of minimizing the grand potential or the Gibbs free ...
Manasi Vyas's user avatar
4 votes
1 answer
227 views

How to assign a "Boltzmann weight"?

I would like to assign a "Boltzmann weight" i.e. $\exp(-E/kT)$ to interactions between particles based on the relative energies. But wouldn't the largest particle-particle energies have the ...
user avatar
6 votes
2 answers
2k views

How are diffusion coefficients calculated?

To support my laboratory result, I'm searching for an MD/statistical mechanics approach to predict translational diffusion coefficients in the liquid phase. I'm aiming to describe small peptides and ...
Giuseppe Basile's user avatar
6 votes
0 answers
731 views

How to calculate the Gibbs free energy for a reaction? [closed]

I am trying to learn how to calculate Gibbs free energy for a reaction. Assuming a reaction for two-dimensional TMDCs: MoS2 (solid) + 2Se(gas) ---> MoSe2 (solid)+ 2S (gas) I can calculate the ...
Shahid Sattar's user avatar
5 votes
1 answer
400 views

How to estimate chemical potential at a temperature?

Fermi level is electron chemical potential at 0K and we can obtain it from DFT calculation. However, the chemical potential is dependent on temperature. But I only find the equation for gas or simple ...
Binh Thien's user avatar
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4 votes
1 answer
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COSMO Model and Electric Potential on the Surface of the Cavity Inside Perfect Conductor

I am learning about COSMO model used in chemical engineering for calculating chemical potential and similiar quantites (actitvity coefficients) for solutes in solutions/mixtures. In the model, it is ...
Dario Mirić's user avatar
7 votes
0 answers
149 views

Sigma Profile in COSMO - RS model [closed]

As far as I understand, sigma profile in COSMO - RS is a probability distribution of screening charge density for certain molecular surface segment. In COSMO - RS, molecular surface area is segmented ...
Dario Mirić's user avatar
5 votes
0 answers
55 views

How to derive specific heat of a crystalline material from phonon density of states? [closed]

I have done a simulation of a crystalline material using DFT and have extracted its normal modes and its phonon density of states. Does anyone have an algorithm/code or a detailed resource that can ...
Elie H's user avatar
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3 votes
0 answers
790 views

What input setting in Quantum ESPRESSO will allow me to calculate the free energy of a solid? [closed]

I understand that it's possible to calculate the Gibbs free energy of a system ab initio, see for example: How can we calculate the Gibbs free energy from first principles? I'm wondering how I can do ...
Paulie Bao's user avatar
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8 votes
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256 views

Contribution in action from collisions for a gas?

So if I write the action for a gas: $$ S = \int (T -U) dt \tag{1}$$ where $T$ is the kinetic energy and $U$ is potential energy. I suspect there is a constant term (which does not affect the equations ...
More Anonymous's user avatar
11 votes
1 answer
2k views

How reactivity of a organic molecule depends upon HOMO and LUMO

I am studying the dehydrogenation of an organic molecule. I see the HUMO-LUMO gap remains nearly the same for many dehydrogenated steps (for some steps, it is exactly the same) while the position of ...
astha's user avatar
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5 votes
0 answers
93 views

What is the qualitative meaning of the Nosé thermostat? [closed]

The Nosé thermostat is explained in Chapter 6 of Understanding Molecular Simulation. Perhaps it's because I find it difficult to follow the derivation, but the physical meaning behind the $s$ ...
Connor's user avatar
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8 votes
1 answer
255 views

Functional derivatives in DFT

Crossposted from Physics SE. I am studying density functional theory and I am currently dealing with manipulating the intrinsic free energy, $\mathcal{F}$, which is defined as $$\mathcal{F} = F - \int ...
megamence's user avatar
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18 votes
2 answers
1k views

Flying ice cube effect in molecular dynamics?

I am trying to understand what exactly the flying ice cube effect is, and how it manifests itself in MD simulation. From what I have read about it, I see that as we run certain forms of velocity-...
megamence's user avatar
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7 votes
1 answer
269 views

Can the dehydrogenation energy be negative?

I am studying the dehydrogenation of a cyclohexane ring containing $\ce{B-N}$ on the adjacent position. or simply we can think about $\ce{H3N-BH3}$. If we release one $\ce{H2}$ molecule from it then ...
astha's user avatar
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10 votes
1 answer
169 views

Is it possible to experimentally verify this collision rate formula?

Background Let's say I have the $i$'th gas molecule with velocity $\vec v_i(t)$ at time $t$. To find the net displacement $s_i$ we integrate with respect to $t$: $$ \vec s_i = \int_{0}^{t} \vec v_i(t')...
More Anonymous's user avatar
8 votes
1 answer
151 views

Should I add vdW interaction to estimate chemical potential of metallic elements?

I am considering layered oxides $\ce{LiCoO2}$. Previous papers suggested that vdW interaction should be added to get lattice parameters closer to experimental data. I would like to dope other elements ...
Binh Thien's user avatar
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8 votes
1 answer
424 views

If a molecule's theoretical formation energy is positive, can it still be synthesized?

I have designed a molecule using hydrocarbons A and B. I am getting the formation energy slightly positive (~0.04 eV). As per my experience, any positive formation energy means that the designed ...
astha's user avatar
  • 1,673
6 votes
1 answer
129 views

Is it possible to analytically solve for a particular phase region of a CALPHAD database? (instead of guessing and checking)

As I understand it, a given CALPHAD database is essentially just a set of equations that model the Gibbs free energy of each phase within a given alloy system (set of elements). Typically, the main ...
sgp45's user avatar
  • 632
4 votes
2 answers
104 views

CASSCF and thermochemistry—effect of excited determinants on rotational and vibrational modes

So this question is linked to the other question I asked about the electronic patition function and CASSCF. When calculating thermochemical data (e.g. Gibbs Free energy) the partition functions are ...
S R Maiti's user avatar
  • 7,001
4 votes
1 answer
210 views

Excited determinants, electronic partition function and thermochemistry calculation

While studying statistical thermodynamics I came across the partition functions, which connect the quantum world to the macroscopic world. I understand that partition functions are used to calculate ...
S R Maiti's user avatar
  • 7,001
6 votes
1 answer
428 views

Thermo-calc: Calculate precipitation driving force by parallel tangent construction

I want to calculate the difference in Gibbs free energies between a Zr-Cu-Al liquid (composition - Zr 65 Cu 27.5 Al 7.5 at%) and the CuZr2 solid phase as a function of temperature (300 - 1000 K). In ...
Sachin Muley's user avatar
12 votes
1 answer
2k views

Selection of appropriate Langevin damping parameter for MD of solid metal

I am performing an MD simulation involving solid metal. The system is in the NVT ensemble, and I am using the Langevin thermostat (fix Langevin in LAMMPS) to enforce this. I have previously used the ...
anneb101's user avatar
  • 995
3 votes
0 answers
69 views

Doubt in Raoultian and Henrian Standard State [closed]

$Si(liq)=Si_\text{(1 wt% Fe)}$ Can you describe what is going on here?All that they ask for is change in Gibbs free energy for the process.I am completely unable to figure why this particular model is ...
user586228's user avatar
7 votes
1 answer
97 views

High accuracy energy methods, are they worth it?

I'm trying to figure out for myself the necessity of high-accuracy compound methods for energy like W1 or Gn families. I'm learning computational chemistry by myself and sometimes lack systematical ...
Roman's user avatar
  • 2,373
9 votes
1 answer
575 views

Why is specific heat not zero at absolute zero?

In this old paper on Monte Carlo simulations of Lennard-Jones solid, specific heat behaviour (both $c_p$ and $c_v$) have been reported. As you can see from the picture below, both $c_p$ and $c_v$ goes ...
Magic_Number's user avatar
11 votes
1 answer
434 views

How to get order constitution data for single equilibrium calculation in Thermo-Calc's TC Python module?

I know that it is possible to get order constitution data for phases when using Thermo-Calc's GUI (e.g. to get "BCC_B2 DISORD" instead of just "BCC_B2") for a single equilibrium ...
sgp45's user avatar
  • 632
7 votes
1 answer
184 views

For ergodicity, what is the significance of the R value and slope?

I am calculating MSDs for the first time and have been struggling to find newbie-level resources on understanding them. If anyone could please suggest any resources or provide guidance on how to ...
NTS's user avatar
  • 759
6 votes
0 answers
297 views

Why does Thermo-Calc one axis equilibrium calculation get stuck in never ending loop? [closed]

I've been trying to run a Thermo-Calc one axis equilibrium calculation on some quaternary alloys in the TCHEA4 database. Most of the calculations work fine, but for some alloys it gets stuck in a loop ...
sgp45's user avatar
  • 632
9 votes
1 answer
464 views

For a Thermo-Calc database, is it possible to view the equation/parameters of the Gibbs free energy models?

I want to get the equations that model free energy for a given phase in a given alloy system (see attached image). I do not just want to get values of free energy for specific compositions. Is it ...
sgp45's user avatar
  • 632
10 votes
1 answer
177 views

Correcting thermodynamic data for concentration, what concentration is best to use?

In computational chemistry when using transition state theory we often use standard states for all involved structures. However, sometimes people argue that it should be corrected for concentration (...
DSVA's user avatar
  • 363
11 votes
1 answer
557 views

How does one compute the boiling point of a liquid made of a particular molecule?

This question is in relation to Anomalous boiling point of "iso-" alkanes on Chemistry SE. I want to compute the boiling point of the different isomers of an n-carbon alkane to check what ...
Safdar Faisal's user avatar
19 votes
1 answer
614 views

Is there any reason not to sum the kinetic and potential energy from an NPT simulation to get internal energy?

I would be very grateful for some newbie-level advice from a thermodynamics guru. I ran NPT simulations on a particular system (in CP2K software) to get fluid densities for use in fluid dynamics ...
NTS's user avatar
  • 759
12 votes
1 answer
418 views

Are there any MD packages that do proper free energy sampling in the NPT ensemble?

Statistical Mechanics is the basis of molecular level calculations of properties and averages. Nowadays free energy calculations are fairly "turn-the-crank", which is not necessarily a good ...
B. Kelly's user avatar
  • 4,366
18 votes
1 answer
1k views

What are the ways to ensure thermodynamic stability of a DFT modelled new structure?

One way of predicting the thermodynamic stability of a DFT modelled structure is to calculate the energy above convex hull, which was used as the criterion in The Materials Project database. For ...
Achintha Ihalage's user avatar