Merge pull request #1476 from uihsnv/log_spacing (6536399f) · Commits · 郑智淋 / lammps

doc/src/variable.txt

+13 −3

Original line number	Diff line number	Diff line
		@@ -52,7 +52,7 @@ style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {st
		sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
		random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x)
		ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),
		stride(x,y,z), stride2(x,y,z,a,b,c),
		logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c),
		vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
		group functions = count(group), mass(group), charge(group),
		xcm(group,dim), vcm(group,dim), fcm(group,dim),
		@@ -459,8 +459,8 @@ Math functions: sqrt(x), exp(x), ln(x), log(x), abs(x), \
		sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), \
		random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), \
		ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), \
		stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), \
		swiggle(x,y,z), cwiggle(x,y,z)
		logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), \
		vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
		Group functions: count(ID), mass(ID), charge(ID), xcm(ID,dim), \
		vcm(ID,dim), fcm(ID,dim), bound(ID,dir), \
		gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), \
		@@ -670,6 +670,16 @@ sequence of output timesteps:

		100,150,200,...950,1000,1500,2000,...9500,10000,15000,etc :pre

		The logfreq3(x,y,z) function generates y points between x and z (inclusive),
		that are separated by a multiplicative ratio: (z/x)^(1/(y-1)). Constraints
		are: x,z > 0, y > 1, z-x >= y-1. For eg., if logfreq3(10,25,1000) is used in
		a variable by the "fix print"_fix_print.html command, then the interval
		between 10 and 1000 is divided into 24 parts with a multiplicative
		separation of ~1.21, and it will generate the following sequence of output
		timesteps:

		10, 13, 15, 18, 22, 27, 32,...384, 465, 563, 682, 826, 1000 :pre

		The stride(x,y,z) function uses the current timestep to generate a new
		timestep. X,y >= 0 and z > 0 and x <= y are required. The generated
		timesteps increase in increments of z, from x to y, i.e. it generates

src/variable.cpp

+71 −11

Original line number	Diff line number	Diff line
		@@ -64,8 +64,8 @@ enum{DONE,ADD,SUBTRACT,MULTIPLY,DIVIDE,CARAT,MODULO,UNARY,
		NOT,EQ,NE,LT,LE,GT,GE,AND,OR,XOR,
		SQRT,EXP,LN,LOG,ABS,SIN,COS,TAN,ASIN,ACOS,ATAN,ATAN2,
		RANDOM,NORMAL,CEIL,FLOOR,ROUND,RAMP,STAGGER,LOGFREQ,LOGFREQ2,
		STRIDE,STRIDE2,VDISPLACE,SWIGGLE,CWIGGLE,GMASK,RMASK,GRMASK,
		IS_ACTIVE,IS_DEFINED,IS_AVAILABLE,
		LOGFREQ3,STRIDE,STRIDE2,VDISPLACE,SWIGGLE,CWIGGLE,GMASK,RMASK,
		GRMASK,IS_ACTIVE,IS_DEFINED,IS_AVAILABLE,
		VALUE,ATOMARRAY,TYPEARRAY,INTARRAY,BIGINTARRAY,VECTORARRAY};

		// customize by adding a special function
		@@ -2297,8 +2297,8 @@ double Variable::evaluate(char str, Tree *tree, int ivar)
		sqrt(),exp(),ln(),log(),abs(),sin(),cos(),tan(),asin(),acos(),atan(),
		atan2(y,x),random(x,y,z),normal(x,y,z),ceil(),floor(),round(),
		ramp(x,y),stagger(x,y),logfreq(x,y,z),logfreq2(x,y,z),
		stride(x,y,z),vdisplace(x,y),swiggle(x,y,z),cwiggle(x,y,z),
		gmask(x),rmask(x),grmask(x,y)
		logfreq3(x,y,z),stride(x,y,z),vdisplace(x,y),swiggle(x,y,z),
		cwiggle(x,y,z),gmask(x),rmask(x),grmask(x,y)
		---------------------------------------------------------------------- */

		double Variable::collapse_tree(Tree *tree)
		@@ -2705,6 +2705,35 @@ double Variable::collapse_tree(Tree *tree)
		return tree->value;
		}

		if (tree->type == LOGFREQ3) {
		int ivalue1 = static_cast<int> (collapse_tree(tree->first));
		int ivalue2 = static_cast<int> (collapse_tree(tree->second));
		int ivalue3 = static_cast<int> (collapse_tree(tree->extra[0]));
		if (tree->first->type != VALUE \|\| tree->second->type != VALUE \|\|
		tree->extra[0]->type != VALUE) return 0.0;
		tree->type = VALUE;
		if (ivalue1 <= 0 \|\| ivalue2 <= 1 \|\| ivalue3 <= 0 \|\|
		ivalue3-ivalue1+1 < ivalue2 )
		error->all(FLERR,"Invalid math function in variable formula");
		if (update->ntimestep < ivalue1) tree->value = ivalue1;
		//else if (update->ntimestep <= ivalue3){
		else {
		tree->value = ivalue1;
		double logsp = ivalue1;
		double factor = pow(((double)ivalue3)/ivalue1, 1.0/(ivalue2-1));
		int linsp = ivalue1;
		while (update->ntimestep >= (tree->value)) {
		logsp *= factor;
		linsp++;
		if (linsp > logsp) tree->value = linsp;
		else tree->value = ceil(logsp)-(((int)ceil(logsp)-1)/ivalue3);
		}
		}
		if (update->ntimestep > ivalue3)
		error->all(FLERR,"Calls to variable exceeded limit");
		return tree->value;
		}

		if (tree->type == STRIDE) {
		int ivalue1 = static_cast<int> (collapse_tree(tree->first));
		int ivalue2 = static_cast<int> (collapse_tree(tree->second));
		@@ -2820,8 +2849,8 @@ double Variable::collapse_tree(Tree *tree)
		sqrt(),exp(),ln(),log(),sin(),cos(),tan(),asin(),acos(),atan(),
		atan2(y,x),random(x,y,z),normal(x,y,z),ceil(),floor(),round(),
		ramp(x,y),stagger(x,y),logfreq(x,y,z),logfreq2(x,y,z),
		stride(x,y,z),stride2(x,y,z),vdisplace(x,y),swiggle(x,y,z),
		cwiggle(x,y,z),gmask(x),rmask(x),grmask(x,y)
		logfreq3(x,y,z),stride(x,y,z),stride2(x,y,z),vdisplace(x,y),
		swiggle(x,y,z),cwiggle(x,y,z),gmask(x),rmask(x),grmask(x,y)
		---------------------------------------------------------------------- */

		double Variable::eval_tree(Tree *tree, int i)
		@@ -3300,8 +3329,8 @@ tagint Variable::int_between_brackets(char *&ptr, int varallow)
		sqrt(),exp(),ln(),log(),abs(),sin(),cos(),tan(),asin(),acos(),atan(),
		atan2(y,x),random(x,y,z),normal(x,y,z),ceil(),floor(),round(),
		ramp(x,y),stagger(x,y),logfreq(x,y,z),logfreq2(x,y,z),
		stride(x,y,z),stride2(x,y,z,a,b,c),vdisplace(x,y),swiggle(x,y,z),
		cwiggle(x,y,z)
		logfreq3(x,y,z),stride(x,y,z),stride2(x,y,z,a,b,c),vdisplace(x,y),
		swiggle(x,y,z),cwiggle(x,y,z)
		------------------------------------------------------------------------- */

		int Variable::math_function(char word, char contents, Tree **tree,
		@@ -3321,9 +3350,9 @@ int Variable::math_function(char word, char contents, Tree **tree,
		strcmp(word,"floor") && strcmp(word,"round") &&
		strcmp(word,"ramp") && strcmp(word,"stagger") &&
		strcmp(word,"logfreq") && strcmp(word,"logfreq2") &&
		strcmp(word,"stride") && strcmp(word,"stride2") &&
		strcmp(word,"vdisplace") && strcmp(word,"swiggle") &&
		strcmp(word,"cwiggle"))
		strcmp(word,"logfreq3") && strcmp(word,"stride") &&
		strcmp(word,"stride2") && strcmp(word,"vdisplace") &&
		strcmp(word,"swiggle") && strcmp(word,"cwiggle"))
		return 0;

		// parse contents for comma-separated args
		@@ -3583,6 +3612,37 @@ int Variable::math_function(char word, char contents, Tree **tree,
		argstack[nargstack++] = ceil(value);
		}

		} else if (strcmp(word,"logfreq3") == 0) {
		if (narg != 3)
		print_var_error(FLERR,"Invalid math function in variable formula",ivar);
		if (tree) newtree->type = LOGFREQ3;
		else {
		int ivalue1 = static_cast<int> (value1);
		int ivalue2 = static_cast<int> (value2);
		int ivalue3 = static_cast<int> (values[0]);
		if (ivalue1 <= 0 \|\| ivalue2 <= 1 \|\| ivalue3 <= 0 \|\|
		ivalue3-ivalue1+1 < ivalue2 )
		print_var_error(FLERR,"Invalid math function in variable formula",ivar);
		double value;
		if (update->ntimestep < ivalue1) value = ivalue1;
		//else if (update->ntimestep <= ivalue3){
		else {
		value = ivalue1;
		double logsp = ivalue1;
		double factor = pow(((double)ivalue3)/ivalue1, 1.0/(ivalue2-1));
		int linsp = ivalue1;
		while (update->ntimestep >= value) {
		logsp *= factor;
		linsp++;
		if (linsp > logsp) value = linsp;
		else value = ceil(logsp)-(((int)ceil(logsp)-1)/ivalue3);
		}
		}
		if (update->ntimestep > ivalue3)
		error->all(FLERR,"Calls to variable exceeded limit");
		argstack[nargstack++] = value;
		}

		} else if (strcmp(word,"stride") == 0) {
		if (narg != 3)
		print_var_error(FLERR,"Invalid math function in variable formula",ivar);

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