Removed Sqrt function and optimized multiplications
This commit is contained in:
parent
44e386f674
commit
4c27b3c774
SSH key fingerprint:
SHA256:JiuxZNdA5bRWXPMUJChI0AQ75yC+cXY4xM0IaVwEVys
9 changed files with 626 additions and 268 deletions
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@ -3,3 +3,4 @@ IndentWidth: 4
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TabWidth: 4
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UseTab: Always
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BreakBeforeBraces: Attach
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ColumnLimit: 100
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2
Makefile
2
Makefile
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@ -6,7 +6,7 @@ ts := $(shell /usr/bin/date "+%d-%m__%H_%M_%S")
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.DEFAULT_GOAL = MD
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MD: $(SRC)/MD.cpp
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$(CC) $(CFLAGS) $(SRC)MD.cpp -lm -O2 -ftree-vectorize -funroll-loops -pg -o ./out/MD
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$(CC) $(CFLAGS) $(SRC)MD.cpp -lm -O2 -ftree-vectorize -funroll-loops -pg -g -o ./out/MD
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MDorig: $(SRC)/MD-original.cpp
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$(CC) $(CFLAGS) $(SRC)MD-original.cpp -lm -O2 -pg -o ./out/MD-original
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10
analysis/16-10__16_36_40.dot
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10
analysis/16-10__16_36_40.dot
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@ -0,0 +1,10 @@
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digraph {
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graph [fontname=Arial, nodesep=0.125, ranksep=0.25];
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node [fontcolor=white, fontname=Arial, height=0, shape=box, style=filled, width=0];
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edge [fontname=Arial];
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1 [color="#ff0000", fontcolor="#ffffff", fontsize="10.00", label="main\n100.00%\n(0.00%)"];
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1 -> 2 [arrowsize="1.00", color="#ff0000", fontcolor="#ff0000", fontsize="10.00", label="100.00%\n201×", labeldistance="4.00", penwidth="4.00"];
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2 [color="#ff0000", fontcolor="#ffffff", fontsize="10.00", label="VelocityVerlet(double, int, double*, _IO_FILE*)\n100.00%\n(0.00%)\n201×"];
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2 -> 3 [arrowsize="1.00", color="#ff0000", fontcolor="#ff0000", fontsize="10.00", label="100.00%\n201×", labeldistance="4.00", penwidth="4.00"];
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3 [color="#ff0000", fontcolor="#ffffff", fontsize="10.00", label="PotentialAndAcceleration()\n100.00%\n(100.00%)\n201×"];
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}
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177
analysis/16-10__16_36_40.txt
Normal file
177
analysis/16-10__16_36_40.txt
Normal file
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@ -0,0 +1,177 @@
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Flat profile:
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Each sample counts as 0.01 seconds.
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% cumulative self self total
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time seconds seconds calls ms/call ms/call name
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100.06 2.83 2.83 201 14.09 14.09 PotentialAndAcceleration()
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0.00 2.83 0.00 3240 0.00 0.00 _dl_relocate_static_pie
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0.00 2.83 0.00 201 0.00 14.09 VelocityVerlet(double, int, double*, _IO_FILE*)
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0.00 2.83 0.00 201 0.00 0.00 MeanSquaredVelocity()
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0.00 2.83 0.00 1 0.00 0.00 initialize()
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0.00 2.83 0.00 1 0.00 0.00 computeAccelerations()
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0.00 2.83 0.00 1 0.00 0.00 initializeVelocities()
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% the percentage of the total running time of the
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time program used by this function.
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cumulative a running sum of the number of seconds accounted
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seconds for by this function and those listed above it.
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self the number of seconds accounted for by this
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seconds function alone. This is the major sort for this
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listing.
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calls the number of times this function was invoked, if
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this function is profiled, else blank.
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self the average number of milliseconds spent in this
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ms/call function per call, if this function is profiled,
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else blank.
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total the average number of milliseconds spent in this
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ms/call function and its descendents per call, if this
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function is profiled, else blank.
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name the name of the function. This is the minor sort
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for this listing. The index shows the location of
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||||
the function in the gprof listing. If the index is
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||||
in parenthesis it shows where it would appear in
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the gprof listing if it were to be printed.
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Copyright (C) 2012-2023 Free Software Foundation, Inc.
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Copying and distribution of this file, with or without modification,
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||||
are permitted in any medium without royalty provided the copyright
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||||
notice and this notice are preserved.
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||||
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||||
Call graph (explanation follows)
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granularity: each sample hit covers 2 byte(s) for 0.35% of 2.83 seconds
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index % time self children called name
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<spontaneous>
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[1] 100.0 0.00 2.83 main [1]
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0.00 2.83 201/201 VelocityVerlet(double, int, double*, _IO_FILE*) [2]
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0.00 0.00 201/201 MeanSquaredVelocity() [8]
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0.00 0.00 1/1 computeAccelerations() [10]
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0.00 0.00 1/1 initializeVelocities() [11]
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0.00 0.00 1/1 initialize() [9]
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-----------------------------------------------
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0.00 2.83 201/201 main [1]
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[2] 100.0 0.00 2.83 201 VelocityVerlet(double, int, double*, _IO_FILE*) [2]
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2.83 0.00 201/201 PotentialAndAcceleration() [3]
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-----------------------------------------------
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2.83 0.00 201/201 VelocityVerlet(double, int, double*, _IO_FILE*) [2]
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[3] 100.0 2.83 0.00 201 PotentialAndAcceleration() [3]
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-----------------------------------------------
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0.00 0.00 3240/3240 initializeVelocities() [11]
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[7] 0.0 0.00 0.00 3240 _dl_relocate_static_pie [7]
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-----------------------------------------------
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0.00 0.00 201/201 main [1]
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[8] 0.0 0.00 0.00 201 MeanSquaredVelocity() [8]
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-----------------------------------------------
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0.00 0.00 1/1 main [1]
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[9] 0.0 0.00 0.00 1 initialize() [9]
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-----------------------------------------------
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0.00 0.00 1/1 main [1]
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[10] 0.0 0.00 0.00 1 computeAccelerations() [10]
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-----------------------------------------------
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0.00 0.00 1/1 main [1]
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[11] 0.0 0.00 0.00 1 initializeVelocities() [11]
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0.00 0.00 3240/3240 _dl_relocate_static_pie [7]
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-----------------------------------------------
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This table describes the call tree of the program, and was sorted by
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the total amount of time spent in each function and its children.
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Each entry in this table consists of several lines. The line with the
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||||
index number at the left hand margin lists the current function.
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The lines above it list the functions that called this function,
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and the lines below it list the functions this one called.
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||||
This line lists:
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index A unique number given to each element of the table.
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Index numbers are sorted numerically.
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The index number is printed next to every function name so
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it is easier to look up where the function is in the table.
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% time This is the percentage of the `total' time that was spent
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in this function and its children. Note that due to
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different viewpoints, functions excluded by options, etc,
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these numbers will NOT add up to 100%.
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self This is the total amount of time spent in this function.
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children This is the total amount of time propagated into this
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function by its children.
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called This is the number of times the function was called.
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If the function called itself recursively, the number
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only includes non-recursive calls, and is followed by
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a `+' and the number of recursive calls.
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name The name of the current function. The index number is
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printed after it. If the function is a member of a
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cycle, the cycle number is printed between the
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function's name and the index number.
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For the function's parents, the fields have the following meanings:
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self This is the amount of time that was propagated directly
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from the function into this parent.
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children This is the amount of time that was propagated from
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the function's children into this parent.
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called This is the number of times this parent called the
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function `/' the total number of times the function
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was called. Recursive calls to the function are not
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included in the number after the `/'.
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name This is the name of the parent. The parent's index
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number is printed after it. If the parent is a
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member of a cycle, the cycle number is printed between
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the name and the index number.
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If the parents of the function cannot be determined, the word
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`<spontaneous>' is printed in the `name' field, and all the other
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fields are blank.
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For the function's children, the fields have the following meanings:
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self This is the amount of time that was propagated directly
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from the child into the function.
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children This is the amount of time that was propagated from the
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child's children to the function.
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called This is the number of times the function called
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this child `/' the total number of times the child
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was called. Recursive calls by the child are not
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listed in the number after the `/'.
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name This is the name of the child. The child's index
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number is printed after it. If the child is a
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member of a cycle, the cycle number is printed
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between the name and the index number.
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If there are any cycles (circles) in the call graph, there is an
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entry for the cycle-as-a-whole. This entry shows who called the
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cycle (as parents) and the members of the cycle (as children.)
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The `+' recursive calls entry shows the number of function calls that
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were internal to the cycle, and the calls entry for each member shows,
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for that member, how many times it was called from other members of
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the cycle.
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Copyright (C) 2012-2023 Free Software Foundation, Inc.
|
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|
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Copying and distribution of this file, with or without modification,
|
||||
are permitted in any medium without royalty provided the copyright
|
||||
notice and this notice are preserved.
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||||
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Index by function name
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[9] initialize() [10] computeAccelerations() [7] _dl_relocate_static_pie
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[2] VelocityVerlet(double, int, double*, _IO_FILE*) [11] initializeVelocities()
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[8] MeanSquaredVelocity() [3] PotentialAndAcceleration()
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10
analysis/16-10__16_44_31.dot
Normal file
10
analysis/16-10__16_44_31.dot
Normal file
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|
@ -0,0 +1,10 @@
|
|||
digraph {
|
||||
graph [fontname=Arial, nodesep=0.125, ranksep=0.25];
|
||||
node [fontcolor=white, fontname=Arial, height=0, shape=box, style=filled, width=0];
|
||||
edge [fontname=Arial];
|
||||
1 [color="#ff0000", fontcolor="#ffffff", fontsize="10.00", label="main\n100.00%\n(0.00%)"];
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||||
1 -> 2 [arrowsize="1.00", color="#ff0000", fontcolor="#ff0000", fontsize="10.00", label="100.00%\n201×", labeldistance="4.00", penwidth="4.00"];
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||||
2 [color="#ff0000", fontcolor="#ffffff", fontsize="10.00", label="VelocityVerlet(double, int, double*, _IO_FILE*)\n100.00%\n(0.00%)\n201×"];
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||||
2 -> 3 [arrowsize="1.00", color="#ff0000", fontcolor="#ff0000", fontsize="10.00", label="100.00%\n201×", labeldistance="4.00", penwidth="4.00"];
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||||
3 [color="#ff0000", fontcolor="#ffffff", fontsize="10.00", label="PotentialAndAcceleration()\n100.00%\n(100.00%)\n201×"];
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||||
}
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||||
177
analysis/16-10__16_44_31.txt
Normal file
177
analysis/16-10__16_44_31.txt
Normal file
|
|
@ -0,0 +1,177 @@
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|||
Flat profile:
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Each sample counts as 0.01 seconds.
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% cumulative self self total
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time seconds seconds calls ms/call ms/call name
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100.06 2.87 2.87 201 14.29 14.29 PotentialAndAcceleration()
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0.00 2.87 0.00 3240 0.00 0.00 _dl_relocate_static_pie
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0.00 2.87 0.00 201 0.00 14.29 VelocityVerlet(double, int, double*, _IO_FILE*)
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0.00 2.87 0.00 201 0.00 0.00 MeanSquaredVelocity()
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0.00 2.87 0.00 1 0.00 0.00 initialize()
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0.00 2.87 0.00 1 0.00 0.00 computeAccelerations()
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0.00 2.87 0.00 1 0.00 0.00 initializeVelocities()
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% the percentage of the total running time of the
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time program used by this function.
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|
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cumulative a running sum of the number of seconds accounted
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seconds for by this function and those listed above it.
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|
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self the number of seconds accounted for by this
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seconds function alone. This is the major sort for this
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listing.
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||||
|
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calls the number of times this function was invoked, if
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this function is profiled, else blank.
|
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self the average number of milliseconds spent in this
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ms/call function per call, if this function is profiled,
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else blank.
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total the average number of milliseconds spent in this
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ms/call function and its descendents per call, if this
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function is profiled, else blank.
|
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|
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name the name of the function. This is the minor sort
|
||||
for this listing. The index shows the location of
|
||||
the function in the gprof listing. If the index is
|
||||
in parenthesis it shows where it would appear in
|
||||
the gprof listing if it were to be printed.
|
||||
|
||||
Copyright (C) 2012-2023 Free Software Foundation, Inc.
|
||||
|
||||
Copying and distribution of this file, with or without modification,
|
||||
are permitted in any medium without royalty provided the copyright
|
||||
notice and this notice are preserved.
|
||||
|
||||
Call graph (explanation follows)
|
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|
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|
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granularity: each sample hit covers 2 byte(s) for 0.35% of 2.87 seconds
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index % time self children called name
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<spontaneous>
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[1] 100.0 0.00 2.87 main [1]
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0.00 2.87 201/201 VelocityVerlet(double, int, double*, _IO_FILE*) [2]
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0.00 0.00 201/201 MeanSquaredVelocity() [8]
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0.00 0.00 1/1 computeAccelerations() [10]
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0.00 0.00 1/1 initializeVelocities() [11]
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0.00 0.00 1/1 initialize() [9]
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-----------------------------------------------
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0.00 2.87 201/201 main [1]
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[2] 100.0 0.00 2.87 201 VelocityVerlet(double, int, double*, _IO_FILE*) [2]
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2.87 0.00 201/201 PotentialAndAcceleration() [3]
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-----------------------------------------------
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2.87 0.00 201/201 VelocityVerlet(double, int, double*, _IO_FILE*) [2]
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[3] 100.0 2.87 0.00 201 PotentialAndAcceleration() [3]
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-----------------------------------------------
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0.00 0.00 3240/3240 initializeVelocities() [11]
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[7] 0.0 0.00 0.00 3240 _dl_relocate_static_pie [7]
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-----------------------------------------------
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0.00 0.00 201/201 main [1]
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[8] 0.0 0.00 0.00 201 MeanSquaredVelocity() [8]
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-----------------------------------------------
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0.00 0.00 1/1 main [1]
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[9] 0.0 0.00 0.00 1 initialize() [9]
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-----------------------------------------------
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0.00 0.00 1/1 main [1]
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[10] 0.0 0.00 0.00 1 computeAccelerations() [10]
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-----------------------------------------------
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0.00 0.00 1/1 main [1]
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[11] 0.0 0.00 0.00 1 initializeVelocities() [11]
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0.00 0.00 3240/3240 _dl_relocate_static_pie [7]
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-----------------------------------------------
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|
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This table describes the call tree of the program, and was sorted by
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the total amount of time spent in each function and its children.
|
||||
|
||||
Each entry in this table consists of several lines. The line with the
|
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index number at the left hand margin lists the current function.
|
||||
The lines above it list the functions that called this function,
|
||||
and the lines below it list the functions this one called.
|
||||
This line lists:
|
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index A unique number given to each element of the table.
|
||||
Index numbers are sorted numerically.
|
||||
The index number is printed next to every function name so
|
||||
it is easier to look up where the function is in the table.
|
||||
|
||||
% time This is the percentage of the `total' time that was spent
|
||||
in this function and its children. Note that due to
|
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different viewpoints, functions excluded by options, etc,
|
||||
these numbers will NOT add up to 100%.
|
||||
|
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self This is the total amount of time spent in this function.
|
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|
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children This is the total amount of time propagated into this
|
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function by its children.
|
||||
|
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called This is the number of times the function was called.
|
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If the function called itself recursively, the number
|
||||
only includes non-recursive calls, and is followed by
|
||||
a `+' and the number of recursive calls.
|
||||
|
||||
name The name of the current function. The index number is
|
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printed after it. If the function is a member of a
|
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cycle, the cycle number is printed between the
|
||||
function's name and the index number.
|
||||
|
||||
|
||||
For the function's parents, the fields have the following meanings:
|
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|
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self This is the amount of time that was propagated directly
|
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from the function into this parent.
|
||||
|
||||
children This is the amount of time that was propagated from
|
||||
the function's children into this parent.
|
||||
|
||||
called This is the number of times this parent called the
|
||||
function `/' the total number of times the function
|
||||
was called. Recursive calls to the function are not
|
||||
included in the number after the `/'.
|
||||
|
||||
name This is the name of the parent. The parent's index
|
||||
number is printed after it. If the parent is a
|
||||
member of a cycle, the cycle number is printed between
|
||||
the name and the index number.
|
||||
|
||||
If the parents of the function cannot be determined, the word
|
||||
`<spontaneous>' is printed in the `name' field, and all the other
|
||||
fields are blank.
|
||||
|
||||
For the function's children, the fields have the following meanings:
|
||||
|
||||
self This is the amount of time that was propagated directly
|
||||
from the child into the function.
|
||||
|
||||
children This is the amount of time that was propagated from the
|
||||
child's children to the function.
|
||||
|
||||
called This is the number of times the function called
|
||||
this child `/' the total number of times the child
|
||||
was called. Recursive calls by the child are not
|
||||
listed in the number after the `/'.
|
||||
|
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name This is the name of the child. The child's index
|
||||
number is printed after it. If the child is a
|
||||
member of a cycle, the cycle number is printed
|
||||
between the name and the index number.
|
||||
|
||||
If there are any cycles (circles) in the call graph, there is an
|
||||
entry for the cycle-as-a-whole. This entry shows who called the
|
||||
cycle (as parents) and the members of the cycle (as children.)
|
||||
The `+' recursive calls entry shows the number of function calls that
|
||||
were internal to the cycle, and the calls entry for each member shows,
|
||||
for that member, how many times it was called from other members of
|
||||
the cycle.
|
||||
|
||||
Copyright (C) 2012-2023 Free Software Foundation, Inc.
|
||||
|
||||
Copying and distribution of this file, with or without modification,
|
||||
are permitted in any medium without royalty provided the copyright
|
||||
notice and this notice are preserved.
|
||||
|
||||
Index by function name
|
||||
|
||||
[9] initialize() [10] computeAccelerations() [7] _dl_relocate_static_pie
|
||||
[2] VelocityVerlet(double, int, double*, _IO_FILE*) [11] initializeVelocities()
|
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[8] MeanSquaredVelocity() [3] PotentialAndAcceleration()
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350
cp_output.txt
350
cp_output.txt
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@ -1,202 +1,202 @@
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time (s) T(t) (K) P(t) (Pa) Kinetic En. (n.u.) Potential En. (n.u.) Total En. (n.u.)
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0.0000e+00 99.823046157131 0.000000000000 2276.129839537671 -21170.987155723738 -18894.857316186066
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0.0000e+00 99.823046157131 0.000000000000 2276.129839537671 -21170.987155723738 -18894.857316186070
|
||||
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|
||||
6.4000e-13 100.830134370164 137291796.435539186001 2299.093109253177 -21216.254315185190 -18917.161205932014
|
||||
6.4500e-13 100.769333836480 76790530.791780740023 2297.706756959738 -21213.478762451316 -18915.772005491577
|
||||
6.5000e-13 100.718706329717 0.000000000000 2296.552366432895 -21211.168192827798 -18914.615826394904
|
||||
6.5500e-13 100.677880214588 174120187.506460100412 2295.621463776105 -21209.305675427080 -18913.684211650976
|
||||
6.6000e-13 100.653356339579 55952001.336968310177 2295.062279040331 -21208.187730950503 -18913.125451910171
|
||||
6.6500e-13 100.640958226726 0.000000000000 2294.779581650246 -21207.623870046969 -18912.844288396722
|
||||
6.7000e-13 100.639446819821 0.000000000000 2294.745119083861 -21207.557431716308 -18912.812312632446
|
||||
6.7500e-13 100.648448314501 184333714.889515161514 2294.950367986076 -21207.971234640954 -18913.020866654879
|
||||
6.8000e-13 100.672529346630 54293960.884311541915 2295.499455174934 -21209.073530805072 -18913.574075630138
|
||||
6.8500e-13 100.707723185659 0.000000000000 2296.301932661492 -21210.683117522782 -18914.381184861290
|
||||
6.9000e-13 100.750217435514 138303134.855293035507 2297.270871537115 -21212.625957837834 -18915.355086300719
|
||||
6.9500e-13 100.801028078367 0.000000000000 2298.429437868405 -21214.948521267317 -18916.519083398911
|
||||
7.0000e-13 100.855620721515 0.000000000000 2299.674240034537 -21217.443694229241 -18917.769454194706
|
||||
7.0500e-13 100.912322255911 0.000000000000 2300.967128394045 -21220.035131608522 -18919.068003214477
|
||||
7.1000e-13 100.969409215777 93534525.905966445804 2302.268805088978 -21222.644218472913 -18920.375413383936
|
||||
7.1500e-13 101.027596522277 44072793.526799157262 2303.595571499188 -21225.303672369249 -18921.708100870062
|
||||
7.2000e-13 101.083913384717 136421853.714707911015 2304.879688704619 -21227.877902503333 -18922.998213798714
|
||||
7.2500e-13 101.138079781396 0.000000000000 2306.114771749349 -21230.354134606740 -18924.239362857392
|
||||
7.3000e-13 101.185173168893 0.000000000000 2307.188578536978 -21232.507853406780 -18925.319274869802
|
||||
7.3500e-13 101.223380989136 146989078.742990165949 2308.059779758620 -21234.256387747701 -18926.196607989081
|
||||
7.4000e-13 101.253330191092 0.000000000000 2308.742670883125 -21235.628428886586 -18926.885758003460
|
||||
7.4500e-13 101.270582567130 0.000000000000 2309.136053467772 -21236.421442171089 -18927.285388703316
|
||||
7.5000e-13 101.273396455537 52543282.456574238837 2309.200214757313 -21236.555933864642 -18927.355719107327
|
||||
7.5500e-13 101.260786312900 50478875.563574224710 2308.912682738989 -21235.986832501607 -18927.074149762619
|
||||
7.6000e-13 101.233044644123 114192522.871038958430 2308.280127006295 -21234.727285010249 -18926.447158003954
|
||||
7.6500e-13 101.189872317893 184462270.039994239807 2307.295726872682 -21232.763457390120 -18925.467730517437
|
||||
7.7000e-13 101.132587047742 57767040.799043327570 2305.989528376672 -21230.155248726005 -18924.165720349334
|
||||
7.7500e-13 101.055898509856 172816247.226023346186 2304.240903423289 -21226.661093183924 -18922.420189760636
|
||||
7.8000e-13 100.959467989391 199581971.051283359528 2302.042128756307 -21222.265466617799 -18920.223337861491
|
||||
7.8500e-13 100.844822900482 0.000000000000 2299.428031933284 -21217.037854075639 -18917.609822142356
|
||||
7.9000e-13 100.708132571311 0.000000000000 2296.311267328539 -21210.803457083985 -18914.492189755445
|
||||
7.9500e-13 100.550485537268 82852587.335772410035 2292.716655341487 -21203.611955150660 -18910.895299809174
|
||||
8.0000e-13 100.376412827676 64663370.565698914230 2288.747510902349 -21195.670061385939 -18906.922550483589
|
||||
8.0500e-13 100.186766131912 62818096.025483205914 2284.423253931498 -21187.016783314251 -18902.593529382753
|
||||
8.1000e-13 99.984661803613 40673745.137080766261 2279.814942423770 -21177.794440305268 -18897.979497881497
|
||||
8.1500e-13 99.771608746194 145899561.290219128132 2274.956981861916 -21168.072042023734 -18893.115060161817
|
||||
8.2000e-13 99.536365488773 52575189.963680595160 2269.593048197502 -21157.335923320457 -18887.742875122956
|
||||
8.2500e-13 99.296347675291 26785077.410323355347 2264.120246792247 -21146.381777252624 -18882.261530460375
|
||||
8.3000e-13 99.053958371976 44394650.135883234441 2258.593371513431 -21135.319572248671 -18876.726200735240
|
||||
8.3500e-13 98.814387873513 48920596.857503794134 2253.130769627244 -21124.386318174595 -18871.255548547349
|
||||
8.4000e-13 98.580425959226 99841331.509202137589 2247.796052696377 -21113.709426046964 -18865.913373350588
|
||||
8.4500e-13 98.359247104798 47265490.834025457501 2242.752810581264 -21103.616095547739 -18860.863284966475
|
||||
8.5000e-13 98.150778120109 0.000000000000 2237.999374426633 -21094.102841060951 -18856.103466634318
|
||||
8.5500e-13 97.956110742763 0.000000000000 2233.560637647702 -21085.219160019216 -18851.658522371516
|
||||
8.6000e-13 97.778084686544 0.000000000000 2229.501350395175 -21077.094264684652 -18847.592914289478
|
||||
8.6500e-13 97.619512630961 0.000000000000 2225.885646393703 -21069.856257654676 -18843.970611260971
|
||||
8.7000e-13 97.483219554591 0.000000000000 2222.777939807006 -21063.634066039929 -18840.856126232924
|
||||
8.7500e-13 97.371998065401 26645073.594592589885 2220.241906695506 -21058.555489846447 -18838.313583150943
|
||||
8.8000e-13 97.289063475627 0.000000000000 2218.350861473178 -21054.767939119294 -18836.417077646118
|
||||
8.8500e-13 97.235933357948 0.000000000000 2217.139407296186 -21052.341552060258 -18835.202144764073
|
||||
8.9000e-13 97.214039677538 50761698.241924010217 2216.640195328641 -21051.342483409026 -18834.702288080385
|
||||
8.9500e-13 97.223115878022 0.000000000000 2216.847147646244 -21051.759012974377 -18834.911865328133
|
||||
9.0000e-13 97.263060663199 0.000000000000 2217.757954528770 -21053.586579172108 -18835.828624643338
|
||||
9.0500e-13 97.332007238955 31399035.525223702192 2219.330049996223 -21056.739562300841 -18837.409512304617
|
||||
9.1000e-13 97.427574349810 134108345.848324850202 2221.509137502272 -21061.108561615412 -18839.599424113141
|
||||
9.1500e-13 97.543947992142 46993105.597973980010 2224.162648189872 -21066.427494868138 -18842.264846678267
|
||||
9.2000e-13 97.680103711247 0.000000000000 2227.267222804752 -21072.649039091615 -18845.381816286863
|
||||
9.2500e-13 97.830104234863 0.000000000000 2230.687481761891 -21079.501925474477 -18848.814443712585
|
||||
9.3000e-13 97.989644951229 42377817.226953580976 2234.325272824404 -21086.789585493065 -18852.464312668661
|
||||
9.3500e-13 98.156013360592 46175612.273578442633 2238.118746530958 -21094.388188631252 -18856.269442100296
|
||||
9.4000e-13 98.324581727232 56844353.038441985846 2241.962382886327 -21102.086544355116 -18860.124161468790
|
||||
9.4500e-13 98.492884883650 131755971.208583459258 2245.799972011855 -21109.772051806522 -18863.972079794668
|
||||
9.5000e-13 98.651587182847 61568287.064323358238 2249.418645782224 -21117.018743873188 -18867.600098090963
|
||||
9.5500e-13 98.801142011416 41643130.795075871050 2252.828742158335 -21123.846914048911 -18871.018171890577
|
||||
9.6000e-13 98.938967520086 73259641.783949539065 2255.971390725065 -21130.138592788975 -18874.167202063909
|
||||
9.6500e-13 99.054039784001 0.000000000000 2258.595227841667 -21135.390897197209 -18876.795669355542
|
||||
9.7000e-13 99.152235518797 59873855.602763965726 2260.834252302347 -21139.871903597585 -18879.037651295239
|
||||
9.7500e-13 99.228184578056 65545500.698350228369 2262.566015925288 -21143.336738616123 -18880.770722690835
|
||||
9.8000e-13 99.287298173864 133043291.212442725897 2263.913903257108 -21146.032356642452 -18882.118453385345
|
||||
9.8500e-13 99.332676848904 67949306.321874767542 2264.948611776982 -21148.100272307907 -18883.151660530926
|
||||
9.9000e-13 99.358256017024 0.000000000000 2265.531858933527 -21149.264149767259 -18883.732290833734
|
||||
9.9500e-13 99.365437590893 118461652.350641697645 2265.695610644240 -21149.587715831000 -18883.892105186758
|
||||
1.0000e-12 99.359604739027 0.000000000000 2265.562612016248 -21149.316492673417 -18883.753880657168
|
||||
|
|
|
|||
BIN
out/MD
BIN
out/MD
Binary file not shown.
137
src/MD.cpp
137
src/MD.cpp
|
|
@ -38,6 +38,7 @@ double sigma = 1.;
|
|||
double epsilon = 1.;
|
||||
double m = 1.;
|
||||
double kB = 1.;
|
||||
double epsilon_8 = epsilon * 8.;
|
||||
|
||||
double NA = 6.022140857e23;
|
||||
double kBSI = 1.38064852e-23; // m^2*kg/(s^2*K)
|
||||
|
|
@ -95,11 +96,9 @@ main () {
|
|||
char trash[10000], prefix[1000], tfn[1000], ofn[1000], afn[1000];
|
||||
FILE *infp, *tfp, *ofp, *afp;
|
||||
|
||||
printf (
|
||||
"\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
printf ("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
printf (" WELCOME TO WILLY P CHEM MD!\n");
|
||||
printf (
|
||||
" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
printf (" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
printf ("\n ENTER A TITLE FOR YOUR CALCULATION!\n");
|
||||
scanf ("%s", prefix);
|
||||
strcpy (tfn, prefix);
|
||||
|
|
@ -109,11 +108,9 @@ main () {
|
|||
strcpy (afn, prefix);
|
||||
strcat (afn, "_average.txt");
|
||||
|
||||
printf (
|
||||
"\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
printf ("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
printf (" TITLE ENTERED AS '%s'\n", prefix);
|
||||
printf (
|
||||
" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
printf (" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
|
||||
/* Table of values for Argon relating natural units to SI units:
|
||||
* These are derived from Lennard-Jones parameters from the article
|
||||
|
|
@ -134,17 +131,14 @@ main () {
|
|||
// Edit these factors to be computed in terms of basic properties in
|
||||
// natural units of the gas being simulated
|
||||
|
||||
printf (
|
||||
"\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
printf (
|
||||
" WHICH NOBLE GAS WOULD YOU LIKE TO SIMULATE? (DEFAULT IS ARGON)\n");
|
||||
printf ("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
printf (" WHICH NOBLE GAS WOULD YOU LIKE TO SIMULATE? (DEFAULT IS ARGON)\n");
|
||||
printf ("\n FOR HELIUM, TYPE 'He' THEN PRESS 'return' TO CONTINUE\n");
|
||||
printf (" FOR NEON, TYPE 'Ne' THEN PRESS 'return' TO CONTINUE\n");
|
||||
printf (" FOR ARGON, TYPE 'Ar' THEN PRESS 'return' TO CONTINUE\n");
|
||||
printf (" FOR KRYPTON, TYPE 'Kr' THEN PRESS 'return' TO CONTINUE\n");
|
||||
printf (" FOR XENON, TYPE 'Xe' THEN PRESS 'return' TO CONTINUE\n");
|
||||
printf (
|
||||
" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
printf (" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
scanf ("%s", atype);
|
||||
|
||||
if (strcmp (atype, "He") == 0) {
|
||||
|
|
@ -186,17 +180,13 @@ main () {
|
|||
timefac = 2.09618e-12;
|
||||
strcpy (atype, "Ar");
|
||||
}
|
||||
printf (
|
||||
"\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
printf ("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
printf ("\n YOU ARE SIMULATING %s GAS! \n", atype);
|
||||
printf (
|
||||
"\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
printf ("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
|
||||
printf (
|
||||
"\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
printf ("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
printf ("\n YOU WILL NOW ENTER A FEW SIMULATION PARAMETERS\n");
|
||||
printf (
|
||||
" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
printf (" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
|
||||
printf ("\n\n ENTER THE INTIAL TEMPERATURE OF YOUR GAS IN KELVIN\n");
|
||||
scanf ("%lf", &Tinit);
|
||||
// Make sure temperature is a positive number!
|
||||
|
|
@ -210,11 +200,9 @@ main () {
|
|||
Tinit /= TempFac;
|
||||
|
||||
printf ("\n\n ENTER THE NUMBER DENSITY IN moles/m^3\n");
|
||||
printf (
|
||||
" FOR REFERENCE, NUMBER DENSITY OF AN IDEAL GAS AT STP IS ABOUT 40 "
|
||||
printf (" FOR REFERENCE, NUMBER DENSITY OF AN IDEAL GAS AT STP IS ABOUT 40 "
|
||||
"moles/m^3\n");
|
||||
printf (
|
||||
" NUMBER DENSITY OF LIQUID ARGON AT 1 ATM AND 87 K IS ABOUT 35000 "
|
||||
printf (" NUMBER DENSITY OF LIQUID ARGON AT 1 ATM AND 87 K IS ABOUT 35000 "
|
||||
"moles/m^3\n");
|
||||
|
||||
scanf ("%lf", &rho);
|
||||
|
|
@ -258,8 +246,7 @@ main () {
|
|||
// Files that we can write different quantities to
|
||||
tfp = fopen (tfn, "w"); // The MD trajectory, coordinates of every
|
||||
// particle at each timestep
|
||||
ofp = fopen (
|
||||
ofn,
|
||||
ofp = fopen (ofn,
|
||||
"w"); // Output of other quantities (T, P, gc, etc) at every timestep
|
||||
afp = fopen (afn, "w"); // Average T, P, gc, etc from the simulation
|
||||
|
||||
|
|
@ -299,9 +286,7 @@ main () {
|
|||
Tavg = 0;
|
||||
|
||||
int tenp = floor (NumTime / 10);
|
||||
fprintf (
|
||||
ofp,
|
||||
" time (s) T(t) (K) P(t) (Pa) "
|
||||
fprintf (ofp, " time (s) T(t) (K) P(t) (Pa) "
|
||||
"Kinetic En. (n.u.) Potential En. (n.u.) Total En. (n.u.)\n");
|
||||
printf (" PERCENTAGE OF CALCULATION COMPLETE:\n [");
|
||||
for (i = 0; i < NumTime + 1; i++) {
|
||||
|
|
@ -359,8 +344,8 @@ main () {
|
|||
Tavg += Temp;
|
||||
Pavg += Press;
|
||||
|
||||
fprintf (ofp, " %8.4e %20.12f %20.12f %20.12f %20.12f %20.12f \n",
|
||||
i * dt * timefac, Temp, Press, KE, PE, KE + PE);
|
||||
fprintf (ofp, " %8.4e %20.12f %20.12f %20.12f %20.12f %20.12f \n", i * dt * timefac,
|
||||
Temp, Press, KE, PE, KE + PE);
|
||||
}
|
||||
|
||||
// Because we have calculated the instantaneous temperature and pressure,
|
||||
|
|
@ -369,15 +354,11 @@ main () {
|
|||
Tavg /= NumTime;
|
||||
Z = Pavg * (Vol * VolFac) / (N * kBSI * Tavg);
|
||||
gc = NA * Pavg * (Vol * VolFac) / (N * Tavg);
|
||||
fprintf (afp,
|
||||
" Total Time (s) T (K) P (Pa) PV/nT "
|
||||
fprintf (afp, " Total Time (s) T (K) P (Pa) PV/nT "
|
||||
"(J/(mol K)) Z V (m^3) N\n");
|
||||
fprintf (
|
||||
afp,
|
||||
" -------------- ----------- --------------- "
|
||||
fprintf (afp, " -------------- ----------- --------------- "
|
||||
"-------------- --------------- ------------ -----------\n");
|
||||
fprintf (
|
||||
afp,
|
||||
fprintf (afp,
|
||||
" %8.4e %15.5f %15.5f %10.5f %10.5f %10.5e "
|
||||
" %i\n",
|
||||
i * dt * timefac, Tavg, Pavg, gc, Z, Vol * VolFac, N);
|
||||
|
|
@ -385,8 +366,7 @@ main () {
|
|||
printf ("\n TO ANIMATE YOUR SIMULATION, OPEN THE FILE \n '%s' WITH VMD "
|
||||
"AFTER THE SIMULATION COMPLETES\n",
|
||||
tfn);
|
||||
printf (
|
||||
"\n TO ANALYZE INSTANTANEOUS DATA ABOUT YOUR MOLECULE, OPEN THE FILE "
|
||||
printf ("\n TO ANALYZE INSTANTANEOUS DATA ABOUT YOUR MOLECULE, OPEN THE FILE "
|
||||
"\n "
|
||||
" '%s' WITH YOUR FAVORITE TEXT EDITOR OR IMPORT THE DATA INTO EXCEL\n",
|
||||
ofn);
|
||||
|
|
@ -399,8 +379,7 @@ main () {
|
|||
printf ("\n PERCENT ERROR of pV/nT AND GAS CONSTANT: %15.5f\n",
|
||||
100 * fabs (gc - 8.3144598) / 8.3144598);
|
||||
printf ("\n THE COMPRESSIBILITY (unitless): %15.5f \n", Z);
|
||||
printf ("\n TOTAL VOLUME (m^3): %10.5e \n",
|
||||
Vol * VolFac);
|
||||
printf ("\n TOTAL VOLUME (m^3): %10.5e \n", Vol * VolFac);
|
||||
printf ("\n NUMBER OF PARTICLES (unitless): %i \n", N);
|
||||
|
||||
fclose (tfp);
|
||||
|
|
@ -495,50 +474,57 @@ Kinetic () { // Write Function here!
|
|||
// printf(" Total Kinetic Energy is %f\n",N*mvs*m/2.);
|
||||
return kin;
|
||||
}
|
||||
|
||||
double
|
||||
getF (double dist) {}
|
||||
|
||||
double
|
||||
getLocalPot (double dist) {}
|
||||
|
||||
// void
|
||||
// transposeMatrix (double mat[MAXPART][3], double matT[3][MAXPART]) {
|
||||
// for (int i = 0; i < 3; i++) {
|
||||
// for (int j = 0; j < MAXPART; j++) {
|
||||
// matT[i][j] = mat[j][i];
|
||||
// }
|
||||
// }
|
||||
// }
|
||||
|
||||
double
|
||||
PotentialAndAcceleration () {
|
||||
double quot, rnorm, term1, term2, Pot;
|
||||
int i, j, k;
|
||||
double f, dist, tmp = 0.;
|
||||
double distTmp = 0;
|
||||
double posItoJ[3]; // position of i relative to j
|
||||
double epsilon_8 = 8. * epsilon;
|
||||
|
||||
memset (a, 0, sizeof (a));
|
||||
double Pot = 0.;
|
||||
// double rT[3][MAXPART];
|
||||
// transposeMatrix (r, rT);
|
||||
|
||||
Pot = 0.;
|
||||
|
||||
for (i = 0; i < N - 1; i++) {
|
||||
for (j = i + 1; j < N; j++) {
|
||||
for (int i = 0; i < N - 1; i++) {
|
||||
for (int j = i + 1; j < N; j++) {
|
||||
double quot, rnorm, term1, term2;
|
||||
// CALCULATE POTENTIAL ENERGY
|
||||
dist = 0.;
|
||||
distTmp = 0;
|
||||
double dist = 0.;
|
||||
double posItoJ[3]; // position of i relative to j
|
||||
|
||||
for (int k = 0; k < 3; k++) {
|
||||
// POT
|
||||
distTmp = r[i][k] - r[j][k];
|
||||
double distTmp = r[i][k] - r[j][k];
|
||||
dist += distTmp * distTmp;
|
||||
// ACCEL
|
||||
posItoJ[k] = distTmp;
|
||||
}
|
||||
|
||||
quot = sigma / sqrt (dist);
|
||||
term2 = quot * quot;
|
||||
term2 = term2 * term2 * term2;
|
||||
term1 = term2 * term2;
|
||||
|
||||
Pot += 8 * epsilon * (term1 - term2);
|
||||
quot = sigma * sigma / dist;
|
||||
term2 = quot * quot * quot;
|
||||
Pot += epsilon_8 * term2 * (term2 - 1);
|
||||
|
||||
// From derivative of Lennard-Jones with sigma and epsilon
|
||||
// set equal to 1 in natural units!
|
||||
double rSqd_inv7
|
||||
= 1.0 / (dist * dist * dist * dist * dist * dist * dist);
|
||||
double rSqd_inv4 = rSqd_inv7 * dist * dist * dist;
|
||||
f = 24 * (2 * rSqd_inv7 - rSqd_inv4);
|
||||
|
||||
double distSqd = dist * dist;
|
||||
double rSqd_inv4 = 1.0 / (distSqd * distSqd);
|
||||
double rSqd_inv7 = rSqd_inv4 / (distSqd * dist);
|
||||
double f = 24.0 * (2.0 * rSqd_inv7 - rSqd_inv4);
|
||||
// from F = ma, where m = 1 in natural units!
|
||||
for (k = 0; k < 3; k++) {
|
||||
tmp = posItoJ[k] * f;
|
||||
for (int k = 0; k < 3; k++) {
|
||||
double tmp = posItoJ[k] * f;
|
||||
a[i][k] += tmp;
|
||||
a[j][k] -= tmp;
|
||||
}
|
||||
|
|
@ -599,8 +585,7 @@ computeAccelerations () {
|
|||
}
|
||||
// From derivative of Lennard-Jones with sigma and epsilon
|
||||
// set equal to 1 in natural units!
|
||||
double rSqd_inv7
|
||||
= 1.0 / (rSqd * rSqd * rSqd * rSqd * rSqd * rSqd * rSqd);
|
||||
double rSqd_inv7 = 1.0 / (rSqd * rSqd * rSqd * rSqd * rSqd * rSqd * rSqd);
|
||||
double rSqd_inv4 = rSqd_inv7 * rSqd * rSqd * rSqd;
|
||||
f = 24 * (2 * rSqd_inv7 - rSqd_inv4);
|
||||
|
||||
|
|
@ -649,14 +634,12 @@ VelocityVerlet (double dt, int iter, double *PE, FILE *fp) {
|
|||
for (j = 0; j < 3; j++) {
|
||||
if (r[i][j] < 0.) {
|
||||
v[i][j] *= -1.; //- elastic walls
|
||||
psum
|
||||
+= 2 * m * fabs (v[i][j]) / dt; // contribution to pressure
|
||||
psum += 2 * m * fabs (v[i][j]) / dt; // contribution to pressure
|
||||
// from "left" walls
|
||||
}
|
||||
if (r[i][j] >= L) {
|
||||
v[i][j] *= -1.; //- elastic walls
|
||||
psum
|
||||
+= 2 * m * fabs (v[i][j]) / dt; // contribution to pressure
|
||||
psum += 2 * m * fabs (v[i][j]) / dt; // contribution to pressure
|
||||
// from "right" walls
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in a new issue