# Questions tagged [thermodynamics]

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

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### 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 ...
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### 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-...
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### 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 ...
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### How to calculate t-zero temperature using Thermo-Calc- Python (TCPython) for multiple alloys?

T-zero temperature is the temperature at which the Gibbs energies of two phases are equal. Here, I wish to find the temperature at which FCC and BCC have same Gibbs energy. Thermo-Calc console mode ...
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232 views

### What thermodynamic data is collected in order to build a CALPHAD model?

To build a model using the CALPHAD approach, i.e. Gibbs free energy as a function of composition and temperature, typically taking the form of a Redlich-Kister polynomial, what kind of thermodynamic ...
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### 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 ...
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### 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 ...
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### What are the methods for calculating solvation effects in free energies and how do they compare?

I've just found this paper (J. Chem. Phys. 141, 174106 (2014)) that deals with the translational and rotational entropies in solution. The method is promising but, unfortunately, requires a ...
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### 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 ...
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569 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 ...
439 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 ...
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### 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 ...
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 ...
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### 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 ...
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### 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 ...
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### 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 ...
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### 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 ...
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### 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 ...
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### 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 ...
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### 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 ...
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### 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 ...
741 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 ...
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### 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 ...
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407 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 ...
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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 ...
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### 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 ...
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### What is the qualitative meaning of the Nosé thermostat? [closed]

The NosĆ© 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 $s$ ...
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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 ...
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### 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 ...
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### How to apply solvent-correction to Gaussian derived Gibbs energies?

I study reaction A + B ā 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/...
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### CASSCF and thermochemistryā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 ...
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### 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 ...
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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 ...
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### Doubt regarding Ehull (energy above convex hull) and formation energy

I am creating a ML model for predicting thermodynamic-stability of 2-d materials, for predicting stability formation energy and Ehull (Energy above convex hull) is used and this is how it is also ...
43 views

### 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 ...
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### 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 (...
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