io.g96.in
Class InCorG96

java.lang.Object
  io.g96.in.InBlock
      io.g96.in.InCorG96

public class InCorG96

extends InBlock

Read blocks from a final coordinate (POSITION) or a trajectory (POSITIONRED) file until all requirements are fulfilled. In general (with exceptions, see below), this means, that the following blocks are read: TIMESTEP, POSITION(RED), BOX. The TIMESTEP block in G96 is sort broken for trajectories longer than 100 ns. The box block is not available for vacuum simulations, so attempt to handle that gracefully.

Author:

vincent

Field Summary

private boolean	attemptTimeStepRead
private boolean	foundBadTimestep
private static boolean	foundZeroBox
boolean	readFrameSuccessful

Fields inherited from class io.g96.in.InBlock

endPattern, fileName, startPattern, stream, tok

Constructor Summary

InCorG96()

InCorG96(java.lang.String fileName)

Method Summary

static void	assertNonDuplicateBlock(java.lang.String blockName, java.util.Set frameKeys) If we want to read a block type that we have already read for this frame, it's likely an error.
java.util.HashMap	getFrame(boolean isVacuum) Read all the blocks we need to have a valid frame.
double[]	parseBoxBlock(java.util.ArrayList block) Parse the (BOX) block and put the stuff into box.
double[]	parseGenBoxBlock(java.util.ArrayList block) Parse the (GENBOX) block and put the stuff into box.
static double[][]	parsePositionBlock(java.util.ArrayList block)
static double[][]	parsePositionredBlock(java.util.ArrayList block)
java.util.HashMap	parseTimeStepBlock(java.util.ArrayList block) Parse a Gromos96 TIMESTEP block.
G96Frame	readFrame() Read and parse a Gromos96 frame from file.
G96Frame	readFrame(boolean isVacuum)
static boolean	skipBlock(java.lang.String blockName) We don't care about any blocks except the TIMESTEP, POSITION(RED) and the BOX block.

Methods inherited from class io.g96.in.InBlock

assertBlockName, assertBlockSize, close, getBlocks, getNextBlock, open, parseDoubleArray, parseDoubleArray, parseDoubleArray, parseDoubleMatrix, readTitle, skipLine, slurp

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

foundBadTimestep

private boolean foundBadTimestep

attemptTimeStepRead

private boolean attemptTimeStepRead

foundZeroBox

private static boolean foundZeroBox

readFrameSuccessful

public boolean readFrameSuccessful

Constructor Detail

InCorG96

public InCorG96()
         throws java.io.IOException

Throws:

java.io.IOException

InCorG96

public InCorG96(java.lang.String fileName)
         throws java.io.IOException

Throws:

java.io.IOException

Method Detail

skipBlock

public static boolean skipBlock(java.lang.String blockName)

We don't care about any blocks except the TIMESTEP, POSITION(RED) and the BOX block. This function is a shorthand to check for that.

Parameters:

blockName -

Returns:

whether we want to skip that block.

assertNonDuplicateBlock

public static void assertNonDuplicateBlock(java.lang.String blockName,
                                           java.util.Set frameKeys)
                                    throws java.io.IOException

If we want to read a block type that we have already read for this frame, it's likely an error. This function throws an IOException if that's the case.

Parameters:

blockName -

frameKeys -

Throws:

java.io.IOException

parseBoxBlock

public double[] parseBoxBlock(java.util.ArrayList block)
                       throws java.io.IOException

Parse the (BOX) block and put the stuff into box. That's it, doodz.

Parameters:

block -

Throws:

java.io.IOException

parseGenBoxBlock

public double[] parseGenBoxBlock(java.util.ArrayList block)
                          throws java.io.IOException

Parse the (GENBOX) block and put the stuff into box. That's it, doodz.

Parameters:

block -

Throws:

java.io.IOException

parsePositionredBlock

public static double[][] parsePositionredBlock(java.util.ArrayList block)
                                        throws java.io.IOException

Parameters:

block -

Returns:

the positions

Throws:

java.io.IOException

parsePositionBlock

public static double[][] parsePositionBlock(java.util.ArrayList block)
                                     throws java.io.IOException

Parameters:

block -

Returns:

the positions

Throws:

java.io.IOException

parseTimeStepBlock

public java.util.HashMap parseTimeStepBlock(java.util.ArrayList block)
                                     throws java.io.IOException

Parse a Gromos96 TIMESTEP block. Watch out for the formatting bug.

Parameters:

block -

Returns:

the time and step values

Throws:

java.io.IOException

getFrame

public java.util.HashMap getFrame(boolean isVacuum)
                           throws java.io.IOException

Read all the blocks we need to have a valid frame. Assumes the following order of blocks TITLE (optional) TIMESTEP (optional) POSITION | POSITIONRED BOX (optional, see isVaccum)

Parameters:

isVacuum - determines whether we should attempt to read a box block (we don't in vacuum)

Returns:

HashMap of (blockNames, blocks)

Throws:

java.io.IOException

readFrame

public G96Frame readFrame()
                   throws java.io.IOException

Read and parse a Gromos96 frame from file.

Returns:

the next frame

Throws:

java.io.IOException

readFrame

public G96Frame readFrame(boolean isVacuum)
                   throws java.io.IOException

Throws:

java.io.IOException