出版社: Academic Pr
出版年: 200111
页数: 664
定价: 605.00元
装帧: HRD
ISBN: 9780122673511
内容简介 · · · · · ·
Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understandin...
Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text.
Since the first edition only five years ago, the simulation world has changed significantly  current techniques have matured and new ones have appeared. This new edition deals with these new developments; in particular, there are sections on:
Â· Transition path sampling and diffusive barrier crossing to simulaterare events
Â· Dissipative particle dynamic as a coursegrained simulation technique
Â· Novel schemes to compute the longranged forces
Â· Hamiltonian and nonHamiltonian dynamics in the context constanttemperature and constantpressure molecular dynamics simulations
Â· Multipletime step algorithms as an alternative for constraints
Â· Defects in solids
Â· The prunedenriched Rosenbluth sampling, recoilgrowth, and concerted rotations for complex molecules
Â· Parallel tempering for glassy Hamiltonians
Examples are included that highlight current applications and the codes of case studies are available on the World Wide Web. Several new examples have been added since the first edition to illustrate recent applications. Questions are included in this new edition. No prior knowledge of computer simulation is assumed.
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Understanding Molecular Simulation的书评 · · · · · · (全部 1 条)
翻译的不是很好，不过国内分子动力学的中译图书很少
> 更多书评1篇

P291 long range interaction (e.g. Coulombic and dipolar potentials) (this chapter deals with the longrange interaction, some algorithm is cutoff ignoring the shortrange's, some considering and also some conduction boundary conditions or real/reciprocal space, Fourier tranformations, etc) P321 After all, molecular dynamics simulations can be used to study the static properties of many body syst...
20150203 14:33
P291 long range interaction (e.g. Coulombic and dipolar potentials)(this chapter deals with the longrange interaction, some algorithm is cutoff ignoring the shortrange's, some considering and also some conduction boundary conditions or real/reciprocal space, Fourier tranformations, etc)P321 After all, molecular dynamics simulations can be used to study the static properties of many body systems and, in addition, md provides information about their dynamcis behavior. Moreover, a standard md simulation is computationally no more expensive than the corresponding mc simulation. Hence, it would seen tempting to conclude that the MC method is an elegant but outdated scheme.As the reader may have guessed, we believe that there are good reasons to us mc rather than md in certain cases. But we stress the phrase in certain cases. All other things being equal, md is clearly the method of choice. Hence, if we use the mc, we should always be prepared to justify your choice. Of course, the reasons may differ from case to case. Sometimes it is simply a mater of ease of programming... Another possible reason is that we are dealing with a system that has no natural dynamics... Usually, the reason to choose the mc technique is that it allow us to perform unphysical trial moves, that is, moves that cannot occur in nature (and, therefore, have no counterpart in molecular dynamics) but are essential for the equilibration of the system.P322 The mc that we discuss here have been developed for situation where either MD cannot be used at all or the natural dynamics of the system are too slow to allow the system to equilibrate on the time scale of a simulation.The reason is that, in the case of large molecules, the probability of acceptance of a random trial insertion in the simulation box is extremely small and hence the number of insertion attempts has to be made prohibitively large. For this reason, the conventional grandcannonical and Gibbs ensemble simulations were limited to the study of adsorption and liquidvapor phase equilibria of small molecules.Clearly, the price we pay for using configurationally biased mc trial moves is a greater complexity of our program. However, the reward is that, with the help of these techniques, we can sometimes speed up a calculation by man orders of magnitude.回应 20150203 14:33 
P225 The great advantage of the Gibbs ensemble method is that we can study coexistence between two phases without creating an interface. This method is also based on the observation that, once the chemical potential of one component in a mixture is fixed, the chemical potential of all other components can be imposed by allowing trial moves that attempt to change the identity of particles (semigra...
20150203 10:00
P225 The great advantage of the Gibbs ensemble method is that we can study coexistence between two phases without creating an interface.This method is also based on the observation that, once the chemical potential of one component in a mixture is fixed, the chemical potential of all other components can be imposed by allowing trial moves that attempt to change the identity of particles (semigrandcanonical ensembe simulations)P226 Naively, we might try to measure this quantity by using the particle insertion method to obtain...(the word 'Naively' used here, so cute)P233 ClausiusClapeyron equationP235 In the same spirit, P241 The introduction of a particle into the solid phase requires the presence of a vacancy in the lattice. Such defects do occur in real solids, but their concentration is so low (for example, in the case of a hardsphere crystal near melting, there is on average one defect in a system of 8000 particles) that one would need a very large crystal to observe a reasonable number of holes in a simulation. Hence, the Gibbs ensemble technique, although still valid in principle, would not be very practical for the study of solidliquid or solidsolid coexistence.P243 The equation of state of the singleoccupancy cell model appears to develop a cusp or possibly even a weak firstorder phase transition. (cusp)P245 Although we can still use an Einstein crystal as reference system, it is often nontrivial to find a path to this reference system that is free of phase transitions and not plagued by divergences of the intergrand of equation (plagued by)P248 Atomic solids with continuous potentials, to use a linear coupling scheme that simultaneously switches on the Einstein spring constants and switches off the hardcore interactions. An alternative in discontinuous is to consider a system where we can switch on the spring constants, while leaving the hardcore interactions between the particles unaffected.P263 Thus far, we have described crystals as if they were free of imperfections. However, any real crystal will contain point defects, such as vacancies and interstitials. In addition, one may find extended defects such as dislocations and grain boundaries. In equilibrium, point defects are the most common. Clearly, to have a realistic description of a crystal, it is important to have an expression for the equilibrium concentration of vacancies and interstitials, and their contribution to the free energy. This is not completely trivial, as the concept of a point defect is inextricably linked to that of a lattice site. (inextricably)回应 20150203 10:00 
P201 In many respects, computer simulations resemble experiments. Yet, in the study of firstorder phase transitions, there seems to be a difference. In experiments, a firstorder phase transition is easy to locate: at the right density and temperature, we will observed that an initially homogeneous system will separate into two distinct phases, divided by an interface. Measurement of the properti...
20150202 21:18
P201 In many respects, computer simulations resemble experiments. Yet, in the study of firstorder phase transitions, there seems to be a difference. In experiments, a firstorder phase transition is easy to locate: at the right density and temperature, we will observed that an initially homogeneous system will separate into two distinct phases, divided by an interface. Measurement of the properties of the coexisting phases is then quite straightforward. In contrast, in a simulation we often locate a firstorder phase transition by computing the thermodynamic properties of the individual phases, then finding the point where the temperature, pressure, and chemical potentials of two bulk phases are equal.P203 The great advantage of the Gibbs method over the conventional techniques for studying phase coexistence is that, in the Gibbs method, the system spontaneously finds the densities and compositions of the coexisting phases. Hence, there is no need to compute the relevant chemical potentials as a function of pressure at a number of different composition and then construct the coexistence line.P206 Monte Carlo steps in the Gibbs ensemble method, particle displacement, volume change and exchange of particles.P214 Assuming that we have a working algorithm to perform a simulation in the Gibbs ensemble, we must now address the question whether the number generated in a simulation are reliable. First of all, the equilibrium conditions should be fulfilled: The pressure in bout subsystems must be equal, the chemical potential must be equal in both phases (within the statistical error)回应 20150202 21:18 
P111 The principal idea of importance sampling is to use a Monte Carlo procedure to generate a random walk in those regions of phase space that have an important contribution to the ensemble average. P125 Often we are interested in the transformation of a crystal from one structure to another or even in the change of the shape of the crystalline unit cell with temperature or with applied stress. ...
20150201 17:37
P111 The principal idea of importance sampling is to use a Monte Carlo procedure to generate a random walk in those regions of phase space that have an important contribution to the ensemble average.P125 Often we are interested in the transformation of a crystal from one structure to another or even in the change of the shape of the crystalline unit cell with temperature or with applied stress. In such cases it is essential that the shape of the simulation box has enough freedom to allow for such changes in crystal structure without creating grain boundaries or other highly stressed configurations.P139 The molecular dynamics technique is a scheme for studying the natural time evolution of a classical system of N particles in volume V. In such simulations, the total energy is a constant of motion.The method is used in the ParrinelloRahman scheme to simulate crystalline solids under conditions of constant stress [102, 103]. In this approach, both the volume and the shape of the crystal unit cell are allowed to fluctuate. As a consequence, the ParrinelloRahman scheme is particularly useful for studying displacive phase transitions in solids.P147 In the andersen approach to isothermal molecular dynamics simulation, constant temperature is achieved by stochastic collisions with a heat bath. Extendlagrangian formulation.P152 the thermodynamic friction coefficientP189 In science, as in life, there is no such thing as a free lunch. ..This was the reason why, for the measurement of chemical potentials, the particleremoval method was not a viable alternative to the particleinsertion scheme. For instance, we could consider a change in the Hamiltonian of a system that does not change the free energy of the system.回应 20150201 17:37

P12 the bath are weakly coupled, so that we may ignore their interaction energy. Boltzmann distribution for a system at temperature T P13 The relation between the Helmholtz free energy and the partition function is often more convenient to use than the relation between lnQ and the entropy. P17 We can either compute that quantity by time averaging (the MD approach) or by ensemble averaging (the ...
20150131 10:35
P12 the bath are weakly coupled, so that we may ignore their interaction energy.Boltzmann distribution for a system at temperature TP13 The relation between the Helmholtz free energy and the partition function is often more convenient to use than the relation between lnQ and the entropy.P17 We can either compute that quantity by time averaging (the MD approach) or by ensemble averaging (the MC approach).P25 Clearly, it would be much preferable to sample many points in the region where the region where the Boltzmann factor is large and few elsewhere. This is the basic idea behind importance sampling.P31 We focus on Monte Carlo methods to models phenomena that do not depend on time. Dynamic Monte Carlo schemes are used to generate a numerical solution of the the master equation that is supposed to describe the time evolution of the system under study.The prime purpose of the kind of Monte Carlo or Molecular Dynamics program that we shall be discussing is to compute equilibrium properties of classical manybody systems.The Metropolis method was introduced as a Markov process in which a random walk is constructed in such a way that the probability of visiting a particular point is proportional to the Boltzmann factor.P32 The boundary conditions, e.g. free or hard or periodic.P33 Although the use of periodic boundary condition proves to be surprisingly effective method for simulating homogeneous bulk systems, one should always be aware that the use of such boundary conditions may lead to spurious correlations not present in a truly macroscopic bulk system. (not exactly isotropic)Shortranged means that the total potential energy of a given particle is dominated by interactions with neighboring particles that are closer than some cutoff distance.P37 Truncate potentials: simple truncation (not for dynamics), truncation and shift (Dynamics, no discontinuities and no impulsive corrections to the pressure), minimum image convention.P39 One should be extremely careful when applying truncated and shifted potential in models with anisotropic interactions. In that case, truncation should not be carried out at a fixed value of the distance between the molecular centers of mass but at a point where the pair potential has a fixed value, because otherwise the potential cannot be shifted to 0 at the point where it is truncated. For Monte Carlo simulations, this is not serious, but for Molecular Dynamics simulations this would be quite disastrous, as the system would no longer conserve energy, unless the impulsive forces due to the truncating and shifting are taken into account explicitly.Minimum image convention not for dynamic.P43 We should distinguish between trial moves that involve only the molecular centers of mass and those that change the orientation or possibly even the conformation of a molecule.回应 20150131 10:35 
P63 Molecular Dynamics simulation is a technique for computing the equilibrium and transport properties of a classical manybody system. First, we prepare a sample: we select a model system consisting of N particles and we solve Newton's equations of motion for this system until the properties of the system no longer change with time (we equilibrate the system. After equilibration, we perform the...
20150201 14:10
P63 Molecular Dynamics simulation is a technique for computing the equilibrium and transport properties of a classical manybody system.First, we prepare a sample: we select a model system consisting of N particles and we solve Newton's equations of motion for this system until the properties of the system no longer change with time (we equilibrate the system. After equilibration, we perform the actual measurement. P65 A program: 1) we read in the parameters that specify the conditions of the run ( initial temperature, number of particles, density, time step); 2) we initialize the system (we select initial positions and velocities); 3) we compute the forces on all particles; 4) we integrate Newton's equations of motion. 5) compute and print the averages of measured quantities. (similar to the FEM, I think)P66 First, we put each particle on its lattice site and then we attribute to each velocity component of every particle a value that is drawn from a uniform distribution in the interval [0.5, 0.5]. This initial velocity distribution is Maxwellian neither in shape nor even in width. Subsequently, we shift all velocities, such that the total momentum is zero and we scale the resulting velocities to adjust the mean kinetic energy to the desired value.P67 We use the position of all particles at the present and previous time steps, combined with our knowledge of the force acting on the particles, to predict the positions at the next time step.The calculation of the force acting on every particle, P69 integrating the equations of motion, (verlet algorithm)P71 It is obvious that a good molecular dynamics program requires a good algorithm to integrate Newton's equation of motion.P72 energy conservation is an important criterion, but actually we should distinguish two kind of energy conservation, namely, short time and long time.The sophisticated higherorder algorithms tend to have a very good energy conservation for short times (e.g. during a few time steps). However, they often have the undesirable feature that the overall energy drifts for long times. In contrast, Verletstyle algorithms tend to have only moderate shortterm energy conservation but little longterm drift.Lyapunov instability(For writing response letter) Clearly, this statement requires some clarification. First of all, one should realize that the aim of an MD simulation is not to predict precisely what will happen to a system that has been prepared in a precisely known initial condiction: we are always interested in statistical predictions. We wish to predict the average behavior of a system that was prepared in an initial state about which we know something (e.g. total energy) but by no means everything. In this respect, MD simulations differ fundamentally from numerical schemes for predicting the trajectory of satellites through space: in the latter case, we really wish to predict the true trajectory. We cannot afford to launch an ensemble of satellites and make statistical predictions about their destination. However, in MD simulations, statistical predictions are are good enough. Still, this would not justify the use of inaccurate trajectories unless the trajectories obtained numerically, in some sense, are close to true trajectories.P73 A shadow orbit is a true trajectory of a manybody system that closely follows the numerical trajectory for a time that is long compared to the time it takes the Lyapunov instability to develop.Hence, our trust in MD as a tool to study the time evolution of manybody systems is based largely on belief. To conclude this discussion, let us say that there is clearly still a corpse in the closet. We believe this corpse will not haunt us, and we quickly close the closet.True Hamiltonian dynamics leaves the magnitude of any volume element in phase space unchanged, but many numerical schemes, in particular those not are not time reversible, do not reproduce this areapreserving property.It is plausible that nonreversible algorithms will have serious longterm energy drift problems. Reversible, areapreserving algorithms will not change the magnitude of the volume in phase space.P74 Other algorithms is based simply on a truncated Taylor expansion of the particle coordinated. (Euler algorithm (X), Leap Frog algorithm (at halfinteger time step), Beeman algorithm (same trajectories and estimates of the velocity), Velocitycorrected Verlet algorithm.P77 Liouville approach: Liouville operator, trotter identity.P81 The liouville formalism allows us to derive the Verlet algorithm as a special case of the Trotter expansion of the timeevolution operator.The extreme sensitivity of the trajectories to small differences in initial conditions.P87 (For Lan) Diffusion is the process whereby an initially nonuniform concentration profile is smoothed in the absence of flow. Diffusion is caused by the molecular motion of the particles in the fluid. The macroscopic law that describes diffusion is known as Fick's law, which states that the flux of the diffusing species is proportional to the negative gradient in the concentration of that species.P90 D is a macroscopic transport coefficient, whereas, the time dependence of its second moment has a microscopic interpretation: it is the meansquared distance over which the labeled molecules have move in a time interval t. The diffusion coefficient to the integral of the velocity autocorrelation function. Such a relation between a transport coefficient and an integral over a timecorrelation function called GreenKubo relation.回应 20150201 14:10 
P111 The principal idea of importance sampling is to use a Monte Carlo procedure to generate a random walk in those regions of phase space that have an important contribution to the ensemble average. P125 Often we are interested in the transformation of a crystal from one structure to another or even in the change of the shape of the crystalline unit cell with temperature or with applied stress. ...
20150201 17:37
P111 The principal idea of importance sampling is to use a Monte Carlo procedure to generate a random walk in those regions of phase space that have an important contribution to the ensemble average.P125 Often we are interested in the transformation of a crystal from one structure to another or even in the change of the shape of the crystalline unit cell with temperature or with applied stress. In such cases it is essential that the shape of the simulation box has enough freedom to allow for such changes in crystal structure without creating grain boundaries or other highly stressed configurations.P139 The molecular dynamics technique is a scheme for studying the natural time evolution of a classical system of N particles in volume V. In such simulations, the total energy is a constant of motion.The method is used in the ParrinelloRahman scheme to simulate crystalline solids under conditions of constant stress [102, 103]. In this approach, both the volume and the shape of the crystal unit cell are allowed to fluctuate. As a consequence, the ParrinelloRahman scheme is particularly useful for studying displacive phase transitions in solids.P147 In the andersen approach to isothermal molecular dynamics simulation, constant temperature is achieved by stochastic collisions with a heat bath. Extendlagrangian formulation.P152 the thermodynamic friction coefficientP189 In science, as in life, there is no such thing as a free lunch. ..This was the reason why, for the measurement of chemical potentials, the particleremoval method was not a viable alternative to the particleinsertion scheme. For instance, we could consider a change in the Hamiltonian of a system that does not change the free energy of the system.回应 20150201 17:37 
P201 In many respects, computer simulations resemble experiments. Yet, in the study of firstorder phase transitions, there seems to be a difference. In experiments, a firstorder phase transition is easy to locate: at the right density and temperature, we will observed that an initially homogeneous system will separate into two distinct phases, divided by an interface. Measurement of the properti...
20150202 21:18
P201 In many respects, computer simulations resemble experiments. Yet, in the study of firstorder phase transitions, there seems to be a difference. In experiments, a firstorder phase transition is easy to locate: at the right density and temperature, we will observed that an initially homogeneous system will separate into two distinct phases, divided by an interface. Measurement of the properties of the coexisting phases is then quite straightforward. In contrast, in a simulation we often locate a firstorder phase transition by computing the thermodynamic properties of the individual phases, then finding the point where the temperature, pressure, and chemical potentials of two bulk phases are equal.P203 The great advantage of the Gibbs method over the conventional techniques for studying phase coexistence is that, in the Gibbs method, the system spontaneously finds the densities and compositions of the coexisting phases. Hence, there is no need to compute the relevant chemical potentials as a function of pressure at a number of different composition and then construct the coexistence line.P206 Monte Carlo steps in the Gibbs ensemble method, particle displacement, volume change and exchange of particles.P214 Assuming that we have a working algorithm to perform a simulation in the Gibbs ensemble, we must now address the question whether the number generated in a simulation are reliable. First of all, the equilibrium conditions should be fulfilled: The pressure in bout subsystems must be equal, the chemical potential must be equal in both phases (within the statistical error)回应 20150202 21:18

P291 long range interaction (e.g. Coulombic and dipolar potentials) (this chapter deals with the longrange interaction, some algorithm is cutoff ignoring the shortrange's, some considering and also some conduction boundary conditions or real/reciprocal space, Fourier tranformations, etc) P321 After all, molecular dynamics simulations can be used to study the static properties of many body syst...
20150203 14:33
P291 long range interaction (e.g. Coulombic and dipolar potentials)(this chapter deals with the longrange interaction, some algorithm is cutoff ignoring the shortrange's, some considering and also some conduction boundary conditions or real/reciprocal space, Fourier tranformations, etc)P321 After all, molecular dynamics simulations can be used to study the static properties of many body systems and, in addition, md provides information about their dynamcis behavior. Moreover, a standard md simulation is computationally no more expensive than the corresponding mc simulation. Hence, it would seen tempting to conclude that the MC method is an elegant but outdated scheme.As the reader may have guessed, we believe that there are good reasons to us mc rather than md in certain cases. But we stress the phrase in certain cases. All other things being equal, md is clearly the method of choice. Hence, if we use the mc, we should always be prepared to justify your choice. Of course, the reasons may differ from case to case. Sometimes it is simply a mater of ease of programming... Another possible reason is that we are dealing with a system that has no natural dynamics... Usually, the reason to choose the mc technique is that it allow us to perform unphysical trial moves, that is, moves that cannot occur in nature (and, therefore, have no counterpart in molecular dynamics) but are essential for the equilibration of the system.P322 The mc that we discuss here have been developed for situation where either MD cannot be used at all or the natural dynamics of the system are too slow to allow the system to equilibrate on the time scale of a simulation.The reason is that, in the case of large molecules, the probability of acceptance of a random trial insertion in the simulation box is extremely small and hence the number of insertion attempts has to be made prohibitively large. For this reason, the conventional grandcannonical and Gibbs ensemble simulations were limited to the study of adsorption and liquidvapor phase equilibria of small molecules.Clearly, the price we pay for using configurationally biased mc trial moves is a greater complexity of our program. However, the reward is that, with the help of these techniques, we can sometimes speed up a calculation by man orders of magnitude.回应 20150203 14:33 
P225 The great advantage of the Gibbs ensemble method is that we can study coexistence between two phases without creating an interface. This method is also based on the observation that, once the chemical potential of one component in a mixture is fixed, the chemical potential of all other components can be imposed by allowing trial moves that attempt to change the identity of particles (semigra...
20150203 10:00
P225 The great advantage of the Gibbs ensemble method is that we can study coexistence between two phases without creating an interface.This method is also based on the observation that, once the chemical potential of one component in a mixture is fixed, the chemical potential of all other components can be imposed by allowing trial moves that attempt to change the identity of particles (semigrandcanonical ensembe simulations)P226 Naively, we might try to measure this quantity by using the particle insertion method to obtain...(the word 'Naively' used here, so cute)P233 ClausiusClapeyron equationP235 In the same spirit, P241 The introduction of a particle into the solid phase requires the presence of a vacancy in the lattice. Such defects do occur in real solids, but their concentration is so low (for example, in the case of a hardsphere crystal near melting, there is on average one defect in a system of 8000 particles) that one would need a very large crystal to observe a reasonable number of holes in a simulation. Hence, the Gibbs ensemble technique, although still valid in principle, would not be very practical for the study of solidliquid or solidsolid coexistence.P243 The equation of state of the singleoccupancy cell model appears to develop a cusp or possibly even a weak firstorder phase transition. (cusp)P245 Although we can still use an Einstein crystal as reference system, it is often nontrivial to find a path to this reference system that is free of phase transitions and not plagued by divergences of the intergrand of equation (plagued by)P248 Atomic solids with continuous potentials, to use a linear coupling scheme that simultaneously switches on the Einstein spring constants and switches off the hardcore interactions. An alternative in discontinuous is to consider a system where we can switch on the spring constants, while leaving the hardcore interactions between the particles unaffected.P263 Thus far, we have described crystals as if they were free of imperfections. However, any real crystal will contain point defects, such as vacancies and interstitials. In addition, one may find extended defects such as dislocations and grain boundaries. In equilibrium, point defects are the most common. Clearly, to have a realistic description of a crystal, it is important to have an expression for the equilibrium concentration of vacancies and interstitials, and their contribution to the free energy. This is not completely trivial, as the concept of a point defect is inextricably linked to that of a lattice site. (inextricably)回应 20150203 10:00 
P201 In many respects, computer simulations resemble experiments. Yet, in the study of firstorder phase transitions, there seems to be a difference. In experiments, a firstorder phase transition is easy to locate: at the right density and temperature, we will observed that an initially homogeneous system will separate into two distinct phases, divided by an interface. Measurement of the properti...
20150202 21:18
P201 In many respects, computer simulations resemble experiments. Yet, in the study of firstorder phase transitions, there seems to be a difference. In experiments, a firstorder phase transition is easy to locate: at the right density and temperature, we will observed that an initially homogeneous system will separate into two distinct phases, divided by an interface. Measurement of the properties of the coexisting phases is then quite straightforward. In contrast, in a simulation we often locate a firstorder phase transition by computing the thermodynamic properties of the individual phases, then finding the point where the temperature, pressure, and chemical potentials of two bulk phases are equal.P203 The great advantage of the Gibbs method over the conventional techniques for studying phase coexistence is that, in the Gibbs method, the system spontaneously finds the densities and compositions of the coexisting phases. Hence, there is no need to compute the relevant chemical potentials as a function of pressure at a number of different composition and then construct the coexistence line.P206 Monte Carlo steps in the Gibbs ensemble method, particle displacement, volume change and exchange of particles.P214 Assuming that we have a working algorithm to perform a simulation in the Gibbs ensemble, we must now address the question whether the number generated in a simulation are reliable. First of all, the equilibrium conditions should be fulfilled: The pressure in bout subsystems must be equal, the chemical potential must be equal in both phases (within the statistical error)回应 20150202 21:18 
P111 The principal idea of importance sampling is to use a Monte Carlo procedure to generate a random walk in those regions of phase space that have an important contribution to the ensemble average. P125 Often we are interested in the transformation of a crystal from one structure to another or even in the change of the shape of the crystalline unit cell with temperature or with applied stress. ...
20150201 17:37
P111 The principal idea of importance sampling is to use a Monte Carlo procedure to generate a random walk in those regions of phase space that have an important contribution to the ensemble average.P125 Often we are interested in the transformation of a crystal from one structure to another or even in the change of the shape of the crystalline unit cell with temperature or with applied stress. In such cases it is essential that the shape of the simulation box has enough freedom to allow for such changes in crystal structure without creating grain boundaries or other highly stressed configurations.P139 The molecular dynamics technique is a scheme for studying the natural time evolution of a classical system of N particles in volume V. In such simulations, the total energy is a constant of motion.The method is used in the ParrinelloRahman scheme to simulate crystalline solids under conditions of constant stress [102, 103]. In this approach, both the volume and the shape of the crystal unit cell are allowed to fluctuate. As a consequence, the ParrinelloRahman scheme is particularly useful for studying displacive phase transitions in solids.P147 In the andersen approach to isothermal molecular dynamics simulation, constant temperature is achieved by stochastic collisions with a heat bath. Extendlagrangian formulation.P152 the thermodynamic friction coefficientP189 In science, as in life, there is no such thing as a free lunch. ..This was the reason why, for the measurement of chemical potentials, the particleremoval method was not a viable alternative to the particleinsertion scheme. For instance, we could consider a change in the Hamiltonian of a system that does not change the free energy of the system.回应 20150201 17:37
这本书的其他版本 · · · · · · ( 全部4 )
 世界图书出版公司版 20108 / 10人读过 / 有售
 化学工业出版社版 20043 / 18人读过
 Academic Press版 199608 / 4人读过
以下豆列推荐 · · · · · · ( 全部 )
 Book in DIFFER (Lokidrift)
 ~/books/CompChem (edotia)
 分子模拟 (炼金术士)
 赴美书单20110809 (zzyy)
 80340162 Computer Simulation and Its Advances in Fluids (器識為先)
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订阅关于Understanding Molecular Simulation的评论:
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1 有用 iphyer 20131201
其实1980s剑桥的那本液体动力学模拟依然值得借鉴，但是这本书比较方便的到而且价格合理，推荐这个网站：http://www.pages.drexel.edu/~cfa22/msim/ 基本的重点网页都有讲解，非常画龙点睛。最棒的是提供C代码可以动手实践，比干讲理论好太多了。
2 有用 予秋 20150205
正如作者所言，此书讲的是分子模拟背后的理论，not a cookbook, it is physics that behind the recipes of molar simulation, nice one. 写作学习亦可用，尤其Discussion section is elegant.
1 有用 Mathematica 20130505
做分子模拟很好的入门 需要统力基础
1 有用 iphyer 20131201
其实1980s剑桥的那本液体动力学模拟依然值得借鉴，但是这本书比较方便的到而且价格合理，推荐这个网站：http://www.pages.drexel.edu/~cfa22/msim/ 基本的重点网页都有讲解，非常画龙点睛。最棒的是提供C代码可以动手实践，比干讲理论好太多了。
1 有用 Mathematica 20130505
做分子模拟很好的入门 需要统力基础
2 有用 予秋 20150205
正如作者所言，此书讲的是分子模拟背后的理论，not a cookbook, it is physics that behind the recipes of molar simulation, nice one. 写作学习亦可用，尤其Discussion section is elegant.