Gromacs
2024.3
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Internal GROMACS namespace.
This namespace is used to contain some implementation-specific functions and classes. These are not meant for direct user access, but typically reside in public headers because of implementation reasons.
Namespaces | |
anonymous_namespace{selection.cpp} | |
Classes | |
class | AnalysisDataHandleImpl |
Private implementation class for AnalysisDataHandle. More... | |
class | AnalysisDataStorageImpl |
Private implementation class for AnalysisDataStorage. More... | |
class | AnalysisDataStorageFrameData |
Internal representation for a single stored frame. More... | |
class | BasicAverageHistogramModule |
Implements average histogram module that averages per-frame histograms. More... | |
class | BasicHistogramImpl |
Base class for private implementation classes for histogram modules. More... | |
class | OptionSectionImpl |
Internal implementation class for storing an option section. More... | |
class | OptionsImpl |
Private implementation class for Options. More... | |
struct | SimdTraits |
Simd traits. More... | |
class | SimdArrayRef |
STL-like container for aligned SIMD type. Used as ArrayRef<SimdReal>. More... | |
class | EnumIndexStore |
Type-specific implementation for IOptionValueStore for an enum option. More... | |
class | SelectionData |
Internal data for a single selection. More... | |
class | IExceptionInfo |
Base class for ExceptionInfo. More... | |
Typedefs | |
typedef std::unique_ptr < AnalysisDataStorageFrame > | AnalysisDataFrameBuilderPointer |
Smart pointer type for managing a storage frame builder. | |
template<typename T > | |
using | SimdTraitsT = typename SimdTraits< T >::type |
template<typename T > | |
using | Simd4TraitsT = typename Simd4Traits< T >::type |
typedef std::vector < std::exception_ptr > | NestedExceptionList |
Internal container type for storing a list of nested exceptions. | |
typedef std::unique_ptr < IExceptionInfo > | ExceptionInfoPointer |
Smart pointer to manage IExceptionInfo ownership. | |
Functions | |
void | disableCudaEventConsumptionCounting () |
Setter for g_useEventConsumptionCounting . | |
AbstractOptionStorage * | createEnumOptionStorage (const AbstractOption &option, const char *const *enumValues, int count, int defaultValue, int defaultValueIfSet, std::unique_ptr< IOptionValueStore< int >> store) |
Helper to create EnumOptionStorage instances. More... | |
void | throwUnlessDerivativeIsConsistentWithFunction (const std::function< double(double)> &function, const std::function< double(double)> &derivative, const std::pair< real, real > &range) |
Ensure analytical derivative is the derivative of analytical function. More... | |
void | throwUnlessDerivativeIsConsistentWithFunction (ArrayRef< const double > function, ArrayRef< const double > derivative, double inputSpacing, const std::pair< real, real > &range) |
Ensure vector of derivative values is the derivative of function vector. More... | |
static double | quotientOfFunctionAndSecondDerivative (double previousPoint, double thisPoint, double nextPoint, double spacing) |
Calculate absolute quotient of function and its second derivative. More... | |
real | findSmallestQuotientOfFunctionAndSecondDerivative (const std::function< double(double)> &f, const std::pair< real, real > &range) |
Find smallest quotient between analytical function and its 2nd derivative. More... | |
real | findSmallestQuotientOfFunctionAndSecondDerivative (ArrayRef< const double > function, double inputSpacing, const std::pair< real, real > &range) |
Find smallest quotient between vector of values and its 2nd derivative. More... | |
static double | quotientOfFunctionAndThirdDerivative (double previousPreviousPoint, double previousPoint, double thisPoint, double nextPoint, double nextNextPoint, double spacing) |
Calculate absolute quotient of function and its third derivative. More... | |
real | findSmallestQuotientOfFunctionAndThirdDerivative (const std::function< double(double)> &f, const std::pair< real, real > &range) |
Find smallest quotient between analytical function and its 3rd derivative. More... | |
real | findSmallestQuotientOfFunctionAndThirdDerivative (ArrayRef< const double > function, double inputSpacing, const std::pair< real, real > &range) |
Find smallest quotient between function and 2nd derivative (vectors) More... | |
std::vector< double > | vectorSecondDerivative (ArrayRef< const double > f, double spacing) |
Calculate second derivative of vector and return vector of same length. More... | |
template<class T , class U > | |
void | fillMultiplexedTableData (const T inputData, U *multiplexedOutputData, std::size_t valuesPerTablePoint, std::size_t numTables, std::size_t thisTableIndex) |
Copy (temporary) table data into aligned multiplexed vector. More... | |
void | printFatalErrorHeader (FILE *fp, const char *title, const char *func, const char *file, int line) |
Formats a common header for fatal error messages. More... | |
void | printFatalErrorMessageLine (FILE *fp, const char *text, int indent) |
Formats a line of fatal error message text. More... | |
void | printFatalErrorFooter (FILE *fp) |
Formats a common footer for fatal error messages. More... | |
void | assertHandler (const char *condition, const char *msg, const char *func, const char *file, int line) |
Called when an assert fails. More... | |
template<typename T > | |
static void | ignoreValueHelper (const T &) |
Helper for ignoring values in macros. More... | |
void | current_function_helper () |
Helper for defining GMX_CURRENT_FUNCTION. | |
void gmx::internal::fillMultiplexedTableData | ( | const T | inputData, |
U * | multiplexedOutputData, | ||
std::size_t | valuesPerTablePoint, | ||
std::size_t | numTables, | ||
std::size_t | thisTableIndex | ||
) |
Copy (temporary) table data into aligned multiplexed vector.
This routine takes the temporary data generated for a single table and writes multiplexed output into a multiple-table-data vector. If the output vector is empty we will resize it to fit the data, and otherwise we assert the size is correct to add out input data.
T | Type of container for input data |
U | Type of container for output data |
[in] | inputData | Input data for single table |
[in,out] | multiplexedOutputData | Multiplexed output vector, many tables. |
[in] | valuesPerTablePoint | Number of real values for each table point, for instance 4 in DDFZ tables. |
[in] | numTables | Number of tables mixed into multiplexed output |
[in] | thisTableIndex | Index of this table in multiplexed output |
real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative | ( | const std::function< double(double)> & | f, |
const std::pair< real, real > & | range | ||
) |
Find smallest quotient between analytical function and its 2nd derivative.
Used to calculate spacing for quadratic spline tables. This function divides the function value by the second derivative (or a very small number when that is zero), and returns the smallest such quotient found in the range.
Our quadratic tables corresponds to linear interpolation of the derivative, which means the derivative will typically have larger error than the value when interpolating. The spacing required to reach a particular relative tolerance in the derivative depends on the quotient between the first derivative and the third derivative of the function itself.
You should call this routine with the analytical derivative as the "function" parameter, and the quotient between "function and second derivative" will then correspond to the quotient bewteen the derivative and the third derivative of the actual function we want to tabulate.
Since all functions that can be tabulated efficiently are reasonably smooth, we simply check 1,000 points in the interval rather than bother about implementing any complicated global optimization scheme.
f | Analytical function |
range | Interval |
real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative | ( | ArrayRef< const double > | function, |
double | inputSpacing, | ||
const std::pair< real, real > & | range | ||
) |
Find smallest quotient between vector of values and its 2nd derivative.
Used to calculate spacing for quadratic spline tables. This function divides the function value by the second derivative (or a very small number when that is zero), and returns the smallest such quotient found in the range.
Our quadratic tables corresponds to linear interpolation of the derivative, which means the derivative will typically have larger error than the value when interpolating. The spacing required to reach a particular relative tolerance in the derivative depends on the quotient between the first derivative and the third derivative of the function itself.
You should call this routine with the analytical derivative as the "function" parameter, and the quotient between "function and second derivative" will then correspond to the quotient bewteen the derivative and the third derivative of the actual function we want to tabulate.
function | Vector with function values |
inputSpacing | Spacing between function values |
range | Interval to check |
real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative | ( | const std::function< double(double)> & | f, |
const std::pair< real, real > & | range | ||
) |
Find smallest quotient between analytical function and its 3rd derivative.
Used to calculate table spacing. This function divides the function value by the second derivative (or a very small number when that is zero), and returns the smallest such quotient found in the range.
Our quadratic tables corresponds to linear interpolation of the derivative, which means the derivative will typically have larger error than the value when interpolating. The spacing required to reach a particular relative tolerance in the derivative depends on the quotient between the first derivative and the third derivative of the function itself.
You should call this routine with the analytical derivative as the "function" parameter, and the quotient between "function and second derivative" will then correspond to the quotient bewteen the derivative and the third derivative of the actual function we want to tabulate.
Since all functions that can be tabulated efficiently are reasonably smooth, we simply check 1,000 points in the interval rather than bother about implementing any complicated global optimization scheme.
f | Analytical function |
range | Interval |
real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative | ( | ArrayRef< const double > | function, |
double | inputSpacing, | ||
const std::pair< real, real > & | range | ||
) |
Find smallest quotient between function and 2nd derivative (vectors)
Used to calculate table spacing. This function divides the function value by the second derivative (or a very small number when that is zero), and returns the smallest such quotient found in the range.
Our quadratic tables corresponds to linear interpolation of the derivative, which means the derivative will typically have larger error than the value when interpolating. The spacing required to reach a particular relative tolerance in the derivative depends on the quotient between the first derivative and the third derivative of the function itself.
You should call this routine with the analytical derivative as the "function" parameter, and the quotient between "function and second derivative" will then correspond to the quotient bewteen the derivative and the third derivative of the actual function we want to tabulate.
function | Vector with function values |
inputSpacing | Spacing between function values |
range | Interval to check |
|
static |
Calculate absolute quotient of function and its second derivative.
This is a utility function used in the functions to find the smallest quotient in a range.
[in] | previousPoint | Value of function at x-h. |
[in] | thisPoint | Value of function at x. |
[in] | nextPoint | Value of function at x+h. |
[in] | spacing | Value of h. |
|
static |
Calculate absolute quotient of function and its third derivative.
This is a utility function used in the functions to find the smallest quotient in a range.
[in] | previousPreviousPoint | Value of function at x-2h. |
[in] | previousPoint | Value of function at x-h. |
[in] | thisPoint | Value of function at x. |
[in] | nextPoint | Value of function at x+h. |
[in] | nextNextPoint | Value of function at x+2h. |
[in] | spacing | Value of h. |
void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction | ( | const std::function< double(double)> & | function, |
const std::function< double(double)> & | derivative, | ||
const std::pair< real, real > & | range | ||
) |
Ensure analytical derivative is the derivative of analytical function.
This routine evaluates the numerical derivative of the function for a few (1000) points in the interval and checks that the relative difference between numerical and analytical derivative is within the expected error for the numerical derivative approximation we use.
The main point of this routine is to make sure the user has not made a mistake or sign error when defining the functions.
function | Analytical function to differentiate |
derivative | Analytical derivative to compare with |
range | Range to test |
If | the provided derivative does not seem to match the function. |
void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction | ( | ArrayRef< const double > | function, |
ArrayRef< const double > | derivative, | ||
double | inputSpacing, | ||
const std::pair< real, real > & | range | ||
) |
Ensure vector of derivative values is the derivative of function vector.
This routine differentiates a vector of numerical values and checks that the relative difference to a provided vector of numerical derivatives is smaller than the expected error from the numerical differentiation.
The main point of this routine is to make sure the user has not made a mistake or sign error when defining the functions.
To avoid problems if the vectors change from zero to finite values at the start/end of the interval, we only check inside the range requested.
function | Numerical function value vector to differentiate |
derivative | Numerical derivative vector to compare with |
inputSpacing | Distance between input points |
range | Range to test |
If | the provided derivative does not seem to match the function. |
std::vector< double > gmx::internal::vectorSecondDerivative | ( | ArrayRef< const double > | f, |
double | spacing | ||
) |
Calculate second derivative of vector and return vector of same length.
5-point approximations are used, with endpoints using non-center interpolation.
f | Vector (function) for which to calculate second derivative |
spacing | Spacing of input data. |
If | the input vector has fewer than five data points. |