IMP  2.1.0
The Integrative Modeling Platform
Simulator.h
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1 /**
2  * \file IMP/atom/Simulator.h
3  * \brief Simple molecular dynamics optimizer.
4  *
5  * Copyright 2007-2013 IMP Inventors. All rights reserved.
6  *
7  */
8 
9 #ifndef IMPATOM_SIMULATOR_H
10 #define IMPATOM_SIMULATOR_H
11 
12 #include <IMP/atom/atom_config.h>
13 
14 #include <IMP/kernel/Particle.h>
15 #include <IMP/Optimizer.h>
16 #include <IMP/kernel/internal/units.h>
17 #include <IMP/algebra/Vector3D.h>
18 
19 IMPATOM_BEGIN_NAMESPACE
20 
21 // for swig
22 class SimulationParameters;
23 
24 //! The base class for simulators.
25 /**
26  A simulator is an optimizer with dynamic tracking of time,
27  such that each frame is associated with a (possibly variable size)
28  time step.
29 
30  The simulation can be invoked directly by calling simulate(fs) for
31  a given time in femtoseconds, or by calling Optimizer::optimize(nf)
32  for a give number of frames.
33  */
34 class IMPATOMEXPORT Simulator : public Optimizer {
35  public:
36  /**
37  @param m model associated with simulater
38  @param name simulater name where %1% is a joker
39  @param wave_factor if >=1.001, use wave time step size with larger maximal
40  time step, using simulate_wave() when calling optimize()
41 
42  @note wave_factor is an advanced feature - if you're not sure, just use its
43  default, see also simulate_wave()
44  @note wave_factor is experimental and liable to change at any time.
45 
46  \see simulate()
47  */
48  Simulator(kernel::Model *m, std::string name = "Simulator %1%",
49  double wave_factor = 1.0);
50 
51  //! Simulate for a given time in fs
52  /**
53  simulate for a given time, by calling the protected
54  method do_step() iteratively.
55 
56  @param time_in_fs time in femtoseconds
57  */
58  double simulate(double time_in_fs);
59 
60  //! Simulate for a given time in fs using a wave step function
61  //! with maximal time step increased by up to max_time_step_factor
62  /**
63  simulate for a given time, by calling the protected
64  method do_step() iteratively, and using a self adjusting time
65  step that can grow up to max_time_step_factor times than
66  the default time step returned by get_maximum_time_step()
67 
68  @param time_in_fs time_in_fs in femtoseconds
69  @param max_time_step_factor the maximal factor by which the
70  maximum time step is exceeded
71  @param base base by which time step increases or decreases
72  during the wave
73 
74  @note This function is experimental and liable to change at any
75  time.
76  */
77  double simulate_wave(double time_in_fs, double max_time_step_factor = 10.0,
78  double base = 1.5);
79 
80  double get_temperature() const { return temperature_; }
81  void set_temperature(double d) { temperature_ = d; }
82  /** \name Time steps
83  The simulator has a maximum allowed time step. It can take
84  shorter ones if needed due to stability concerns.
85 
86  As with all times in \imp, the time step is in fs.
87  @{
88  */
89  void set_maximum_time_step(double ts) { max_time_step_ = ts; }
90  double get_maximum_time_step() const { return max_time_step_; }
91  double get_last_time_step() const {
92  if (last_time_step_ < 0)
93  return get_maximum_time_step();
94  else
95  return last_time_step_;
96  }
97 /** @} */
98 #ifndef IMP_DOXYGEN
99  void set_time_step(double ts) { set_maximum_time_step(ts); }
100 #endif
101 
102  double get_kt() const;
103 
104  /**
105  returns the simulation time in femtoseconds that was performed
106  by this simulator since it was constructed
107  @note this time can be tweaked using set_current_time() )
108  */
109  double get_current_time() const { return current_time_; }
110 
111  /**
112  Sets the current simulation time in femtoseconds to ct.
113  */
114  void set_current_time(double ct) { current_time_ = ct; }
115 
116  /** Get the set of particles used in the simulation.
117  This may be different then the stored set, eg if
118  no particles are stored, the kernel::Model is searched for
119  appropriate particles.
120  */
121  kernel::ParticlesTemp get_simulation_particles() const;
122 
123  kernel::ParticleIndexes get_simulation_particle_indexes() const;
124 
125  /** \name Explicitly specifying particles
126 
127  One can explicitly specify which particles should be used for
128  molecular dynamics. Each particle must be a Mass and
129  core::XYZ particle. If none are specified, the model
130  is searched for appropriate particles.
131  @{
132  */
133  IMP_LIST(public, Particle, particle, kernel::Particle *, kernel::Particles);
134 
135  protected:
136  /** @} */
137  virtual Float do_optimize(unsigned int max_steps) IMP_OVERRIDE IMP_FINAL;
138 
139  /** A Simulator class can perform setup operations before a series
140  of simulation steps is taken. */
141  virtual void setup(const kernel::ParticleIndexes &) {};
142 
143  /** Perform a single time step and return the amount that time
144  should be advanced. A maximum time step value is passed.
145  */
146  virtual double do_step(const kernel::ParticleIndexes &sc, double dt) = 0;
147 
148  /** Return true if the passed particle is appropriate for
149  the simulation.
150  */
151  virtual bool get_is_simulation_particle(kernel::ParticleIndex p) const = 0;
152 
153  private:
154  // see simulate() documentation
155  double do_simulate(double time);
156  // see simulate_wave() documentation
157  double do_simulate_wave(double time_in_fs, double max_time_step_factor = 10.0,
158  double base = 1.5);
159  double temperature_;
160  double max_time_step_;
161  double current_time_;
162  double last_time_step_;
163  double wave_factor_; // if >1.0, use simulate_wave() from do_optimize()
164 };
165 
167 
168 /**\name Energy conversions
169 
170  The native energy units in \imp are difficult to do any sort of math with.
171  One can convert the quantities into more useful ones.
172  @{
173 */
174 IMPATOMEXPORT double get_energy_in_femto_joules(double energy_in_kcal_per_mol);
175 IMPATOMEXPORT double get_force_in_femto_newtons(
176  double force_in_kcal_per_mol_per_angstrom);
177 
178 IMPATOMEXPORT double get_spring_constant_in_femto_newtons_per_angstrom(
179  double k_in_kcal_per_mol_per_angstrom_square);
180 
181 /** @} */
182 
183 IMPATOM_END_NAMESPACE
184 
185 #endif /* IMPATOM_SIMULATOR_H */
double get_kt(double T)
The base class for simulators.
Definition: Simulator.h:34
double get_current_time() const
Definition: Simulator.h:109
Import IMP/kernel/Optimizer.h in the namespace.
void set_current_time(double ct)
Definition: Simulator.h:114
Class to handle individual model particles.
Base class for all optimizers.
Classes to handle individual model particles.
#define IMP_OBJECTS(Name, PluralName)
Define the types for storing sets of objects.
virtual void setup(const kernel::ParticleIndexes &)
Definition: Simulator.h:141
double Float
Basic floating-point value (could be float, double...)
Definition: base/types.h:20
Simple 3D vector class.
#define IMP_LIST(protection, Ucname, lcname, Data, PluralData)
A macro to provide a uniform interface for storing lists of objects.
virtual double do_optimize(unsigned int ns)=0
override this function to do actual optimization
Class for storing model, its restraints, constraints, and particles.